BUILDING AND RESTORING LIVING
Walter H. Adey
National Museum of Natural History
AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW YORK • OXFORD
PARIS • SAN DIEGO • SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO
Academic Press is an imprint of Elsevier
Acknowledgments and Dedication xv
C H A P T E R
C H A P T E R
The Origin of Life: Microcosm Earth 2
Microcosms and Mesocosms of Aquatic Substrate: The Active Role of Rock, Mud,
Ecosystems 5 and Sand
Restoration of Damaged Ecological
Systems 8 The Solid Earth and Life 44
Summary 8 Chemical Relationships Between Rocks,
Taxonomic Notes 8 Sea Water, and Organisms 48
References 9 The Solid Earth, Rock, and Model
Sediments and Model Ecosystems 51
P A R T Geological Storage 59
PHYSICAL ENVIRONMENT C H A P T E R
C H A P T E R
Water Composition: Management of
2 Salinity, Hardness, and Evaporation
The Envelope: Physical Parameters and Water Structure and Characteristics 62
Energy State Ocean Salinity 63
Hardness of Fresh Waters 67
Temperature 17 Water and Model Ecosystems 71
Water Motion 23 Algal Scrubbing and Water Composition 71
Tides: Simulating the Effects of Sun Marine Microcosms and Aquaria 72
and Moon 35 Quality of Top-up Water 73
References 41 References 73
C H A P T E R C H A P T E R
The Input of Solar Energy: Organisms and Gas Exchange: Oxygen,
Lighting Requirements Carbon Dioxide, pH, and Alkalinity
Photosynthesis and Its Origin 75 Oxygen Exchange 118
Solar Radiation and Water 79 Oxygen, Model Ecosystems, and Ecosystem
Light Absorption by Water Plants 82 Restoration 120
Light Intensity and Plants 82 Carbon Dioxide Exchange 121
Photorespiration 88 Carbon Dioxide and Global Aquatic
Light and Model Ecosystems 89 Restoration 122
Light and Physiological Considerations 91 Managing Carbon Dioxide and pH in Microcosms
Summary 91 and Mesocosms 124
References 92 Gas Exchange and Selected Model
C H A P T E R References 128
6 C H A P T E R
The Input of Organic Energy:
Particulates and Feeding 9
Particulates, Energy Supply, and Aquatic The Primary Nutrients – Nitrogen,
Ecosystems 93 Phosphorus, and Silica: Limitation and
Inorganic Particulates 95 Eutrophication
Organic Particulates 95
Humic Substance 97 Nutrients in Natural Waters 131
Particulates and Aquatic Models 97 Eutrophication and Hypereutrophication of
Biofilms 98 Natural Waters 134
Particulate Import in Aquatic Models 100 Nutrients and Model Ecosystems 136
Aquatic Ecosystem Restoration 100 Summary 139
References 100 References 140
P A R T C H A P T E R
BIOCHEMICAL ENVIRONMENT Biomineralization and Calcification: A Key to
Biosphere and Ecosystem Function
C H A P T E R
The Process of Biomineralization 143
7 The Carbonate System and the Formation
of Calcite and Aragonite 143
Metabolism: Respiration, Photosynthesis, Halimeda: Photosynthesis-Induced
and Biological Loading Calcification 145
Calcification in Stony Corals 146
Metabolism 105 Calcification, Stony Corals, Coral Reefs, and
Respiration 106 Global Warming 148
Bacterial Metabolism 110 Calcification in Mesocosms and Aquaria 150
Photosynthesis 112 Coral Reef Aquaria and Stony Coral
Biological Loading 114 Calcification 151
References 115 References 154
C H A P T E R Food Webs in Model Ecosystems 195
Establishment of Food Webs 196
11 Trophic Structure in Aquaria 201
The Organisms 202
Control of the Biochemical Environment: References 202
Filters, Bacteria, and the Algal Turf Scrubber
Sterilization Methods 156
C H A P T E R
Bacteriological Filtration 156
Reef Systems 157 14
Foam Fractionation (Protein Skimming) 158 Primary Producers: Plants That
Photosynthetic Methods 158
Grow on the Bottom
Algal Turfs 159
The Algal Turf Scrubber (ATS™) 161
Benthic Algae 203
Algal Scrubbers and the Modeling of
Algae in Model Ecosystems 219
Submerged Aquatic Vegetation 222
Marine SAV and Model Ecosystems 229
Freshwater SAV and Model Ecosystems 231
Emergent Aquatic Vegetation 234
P A R T
EAV and Model Ecosystems 242
Plant Communities and the Restoration of
III Wild Ecosystems 250
C H A P T E R C H A P T E R
Community Structure: Biodiversity Herbivores: Predators of Plants and
in Model Ecosystems Omnivores, Predators of Plants and Animals
The Framework of Biodiversity 173
Types of Herbivores 254
The Community 175
Plant Defenses 256
The Biome 175
Modifications of Marine and Freshwater
Features of Communities 181
The Magnitude of Biodiversity 183
Herbivores and Model Ecosystems 263
Community Structure and Ecological Models 186
Scaling and Reproduction 186
Model Diversity 187
References 189 C H A P T E R
C H A P T E R
Carnivores: Predators of Animals
The Carnivore Predator 267
Trophic Structure: Ecosystems and the The Prey 268
Dynamics of Food Chains The Dynamics of Predation 269
Marine and Freshwater Predators 269
Energy Capture and Flow 192 Predators and Synthetic Ecosystems 275
Food Webs 193 References 279
C H A P T E R P A R T
Plankton and Planktivores: Floating Plants ECOLOGICAL SYSTEMS IN
and Animals and Their Predators MICROCOSMS, MESOCOSMS,
Plankton Size and Composition 282
The Bacteria 282
Phytoplankton 282 C H A P T E R
The Planktonic Food Web 286
Mechanisms of Filter Feeding 288 20
Plankton, Particulates, and Model Ecosystems 293
Wild Ecosystem Restoration 300 Models of Coral Reef Ecosystems
Modeling Coral Reef Ecosystems 344
Caribbean Coral Reef Microcosm at the
C H A P T E R Museum of Natural History 345
Coral Reef Microcosm at the Smithsonian
18 Marine Station 353
Great Barrier Reef Mesocosm 353
Detritus and Detritivores: The Dynamics of A 130-Gallon Reef Microcosm 356
Muddy Bottoms Summary 368
The Deep Ocean 307
Fungi 307 C H A P T E R
Meiobenthos: Protozoans 309 21
Meiofauna: The Multicellular Invertebrates 311
Macrobenthos 313 A Subarctic/Boreal Microcosm: Test of a
Deposit Feeding in Saltwater Soft Bottoms 317 Biogeographic Model
Deposit Feeding in Freshwater Soft Bottoms 319
Carnivores and the Detritivore Community 321 The Rocky, Embayed Coast of the Northwestern
Detritus and Its Role in Model Ecosystems 321 Atlantic Geological History 371
References 327 The Gulf of Maine 376
The Core Subarctic 387
Core Subarctic vs Mixed Subarctic/Boreal 393
C H A P T E R
A Maine Shore Microcosm 395
An Opportunity to Test Biogeographic Theory 403
19 References 404
Symbionts and Other Feeders
C H A P T E R
Zooxanthellae and Their Animal Hosts 329
Biology and Ecology of Corals 332 22
The Positive Feedback Loop between
Photosynthesis and Calcification 334 Estuaries: Ecosystem Modeling and
Anthozoans and Microcosms, Mesocosms, and Restoration
Parasitism 336 Where Fresh and Salt Waters Interact 405
Environment, General Health, and Disease 337 Chesapeake Bay in Mesocosm 406
Biodiversity 337 A Florida Estuary in Mesocosm 416
Quarantine (Prevention of Transmission) 337 Nutrient Dynamics in Estuarine Models 439
Disease Treatment in Model Ecosystems 338 Estuarine Restoration 439
References 339 References 441
C H A P T E R Nutrient Removal from Agricultural Wastewaters
(Nonpoint Source) 474
23 Nutrient Removal from Rivers 479
Bioenergy and Solar Energy Recovery Using ATS
Freshwater Ecosystem Models Systems 480
Aquacultural Wastewaters 481
A Florida Everglades Stream and Wetland 443 Industrial Wastewaters and ATS Systems 484
A Blackwater Home Aquarium 450 References 489
Restoration of Freshwater Ecosystems 452
P A R T
P A R T VI
THE ENVIRONMENT AND
ECOLOGICAL ENGINEERING C H A P T E R
C H A P T E R
Microcosms, Mesocosms, and Macrocosms:
24 Building and Restoring Ecosystems, a
Organisms and Natural Products:
Commercial Ecosystem Culture Principles of Ecological Modeling 494
Ecosystems in Home Aquaria 498
The Aquarium World 458 Applied Model Ecosystems 499
Pharmaceutical Culture 462 References 499
C H A P T E R
Large Scale: Water Quality Management
with Solar Energy Capture
The Quality of US Surface and Ground
Nutrient Removal from Domestic
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By the mid-20th century, widespread concerns were being top priority of all human society. It seems highly
expressed for the way in which modern human popula- unlikely, no matter what our scientific and technical
tions and their industrial endeavors and products were prowess, that humans can survive on this planet, with
affecting both the environment in which they lived and our few domesticated species, in the midst of a radi-
the planet’s wild populations and their ecosystems. Some cally altered atmosphere and hydrosphere and a dys-
predictions for the future were dire, and enough environ- functional biosphere. It is most discomforting to hear
mental activism developed so that some of the more of new plans to purposefully inject pollutants into the
conspicuous problems (e.g. raw sewage, oil spills, DDT, stratosphere, to act like a volcanic eruption, or to spray
PCBs, chlorofluorocarbons, and atomic power radioac- iron dust on the oceans, hopefully to increase photo-
tive materials) were subsequently ameliorated or at least synthesis, and thereby, at least temporarily, reduce
subject to management (though never fully corrected). global warming effects. Why is it that so much of our
However, the larger, more widespread, and chronic efflu- educated humanity cannot conceive of working with
ent problems of human society (e.g. nutrients, CO2, and our biosphere, using processes that we know well, to
moderately toxic hydrocarbons) have continued to expand solve multiple environmental problems?
their reach into every corner of the biosphere, atmosphere, Ranging from the domestication of a few wild
and hydrosphere. The ever-growing global human popu- species by chance beginning 10 000 years or more ago
lation, the continuing process of habitat destruction, and to that by design in the last few centuries, human
the ever-expanding desire of that population for a western efforts to extend utilization of our biosphere beyond
lifestyle, rich in fossil energy use and synthesized products, hunter-gathering have almost always been at the level
using abundant raw materials, suggest that these prob- of an individual species. Limited polyculture, as farm
lems, already built up over a century or more, and now ponds, is practiced in some countries, and in the latter
growing geometrically with population expansion, are not half of the 20th century “permaculture,” following
going to be so easily ameliorated. some ancient practices on land, advocated polyculture;
Atmospheric CO2 increase, with its concomitant however, by and large, our domesticates remain mono-
global warming, already seems beyond correction to a cultures. Compared to the global biodiversity (even the
large percentage of scientists, engineers, and educated already greatly reduced biodiversity of today), the
public. Yet, the degradation of our natural waters, and numbers of domesticated species remain vanishingly
especially our oceans, the latter being of considerably small. The intensive management of farms and aqua-
greater mass than the atmosphere, is slower to be rec- cultures provides one of the most extensive elements
ognized; and orders of magnitude more difficult to cor- of coastal and oceanic pollution and wild ecosystem
rect. In many coastal waters, decades of environmental loss. Unfortunately, especially in western cultures, it
effort backed by large financial expenditures have remains deeply ingrained that only by optimizing all
failed to prevent a continuing and serious reduction in aspects of single species culture, often at great environ-
water quality. Although, in many countries, regula- mental cost, can we hope to support current human
tions to contain the widespread pollution of the atmos- populations. It also does not help that most economic
phere and natural waters have been initiated, habitat models call for ever-continuing growth, when this is
destruction continues and increasing population and clearly the root of our failure to meet environmental
advancing prosperity have overcome most efforts to problems.
stem the tide of environmental degradation. As some This book focuses on efforts to interact with and
writers have so succinctly stated, we are slowly begin- effectively “domesticate” at the ecosystem level, to
ning to stew in our own toxic brew. build experimental ecosystems to learn, and to under-
We are hardly alone in expressing our grave concern take ecological engineering, as interaction with “wild”
for the future of the human race if the full understand- ecosystems. Ultimately, we propose to optimize bio-
ing and correction of these issues does not become the geochemical function and biodiversity, and to reform
our relationship to our biosphere. As we explain in this degradation, and the waters of the Baltic Sea and
book, symbiosis has been a critical part of organic evolu- Chesapeake Bay are considerably more altered than
tion. Likewise, humans have formed a number of sym- those around Tierra Del Fuego. However, as we shall
bioses with plant and animal domesticates. Some very point out in our following text, numerous studies and
influential and critical scientists have recognized that reports declare a global scale alteration of species
the human symbioses collectively called farming have and community function that is likely to continue and
been a mixed blessing for the human race. Nevertheless, deepen. We have written this 3rd edition on the basic
current human populations are demanding an ever- premise that most aquatic ecosystems are no longer
expanding intensive global scale farming that typically “wild,” being subject to significant and negative
uses monocultures to optimize a single return; usually unplanned and uncontrolled human effects. We now
this return is biomass for food, materials, and, more must treat wild ecosystems as controlled systems that
recently, energy. However, the human race also requires must be managed, and human effects ameliorated, just
ecosystem/biosphere level atmospheric and hydros- as in our “captive” ecosystems. We have expanded our
pheric cleaning, soil structuring services, and general earlier treatment of “Building Living Ecosystems” to
biogeochemical stabilization that our farming sym- “Building and Restoring Living Ecosystems,” applying
bioses do not and probably cannot provide. Global much of the original methodology, where appropriate,
warming is only one example of human overpowering to “wild” systems management. We show that large-
of those global ecosystem services. As we describe in scale ecosystem cleaning of human pollution, using
depth in this book, the experimental study of living solar/algal techniques, can also provide considerable
ecosystems can lead to “domesticated” ecosystems that usable energy to replace the fossil fuel use that is
are far more efficient at solar energy capture than farm responsible for much of the global environmental
monocultures, without providing the inevitable envi- degradation. Just as we have organized in the past to
ronmental degradation of those monocultures. We industrialize, we must now re-organize to more fully
demonstrate that use of such systems can clean up much integrate with the Earth’s biosphere while switching to
of the damage already visited on our planet. renewable energy sources.
Significantly increased energy and materials conser- It has been 15 years since the 1st edition of Dynamic
vation is essential to current and future generations. Aquaria was completed; it has gone through several
While this has been locally necessary in the past, as printings, and the response, especially in the academic
many communities and even civilizations have found and professional world, has been quite favorable.
out to their detriment, our great numbers and increasing Some of the model or controlled ecosystems described
individual requirements have now expanded the con- in the 1st edition are still in operation. One system,
servation requirement to a global level. Unfortunately, with its mechanical–electrical systems re-built, has
we are unlikely to achieve the level of conservation now been in operation for over 25 years. A few have
needed to stop the global warming “steamroller,” and been extensively researched, and we can now report
ultimately coastal and oceanic depletion, unless we in depth on their function. Those long-term systems
expand the scale and depth of our photosynthetic sym- that have been carefully studied have shown complex
bioses to both the landscape and the ecosystem level. community and trophic structuring and extraordinary
Some environmentalists will find the thought of domes- biotic diversities based on reproductively maintained
ticating high-diversity, high-efficiency ecosystems as populations.
undesirable, perhaps even encouraging human society The scientific context in which our approach to living
to neglect conservation and population reduction. systems modeling has developed has changed signifi-
Indeed, this is a potential dilemma. However, even if a cantly. In the year Dynamic Aquaria was first published
broad spectrum of human society could be brought into (1991), the journal Ecological Engineering also appeared.
an extensive conservation mode, the inertia of global It has now completed its 15th year and has published
population and degradation provides environmental over 500 articles. Several scientific studies describing the
problems that are realistically beyond a simple conser- approaches of other scientists to living systems model-
vation solution. ing have also appeared during the same time frame, and
In the earlier editions of this book, we presented a more peripherally, but of considerable interest, the
methodology for re-creating functioning wild aquatic Society and journal Restoration Ecology have matured.
ecosystems for research and education. The underlying In the public display/education arena, the
philosophy centered on the notion that many of those Smithsonian exhibit conveying the principles of
ecosystems remained in the “wild state” and that it ecosystem operation to the public at large has now
was possible to re-create or model them experimen- moved to and become the “Smithsonian Marine
tally. Clearly, there is a broad gradient of ecosystem Ecosystems Exhibit” at Fort Pierce, Florida. However,
very few large public aquaria built during the past 20 the many millions of species in the world, most have
years, unless adjacent to a good and abundant source evolved chemical/ mechanical systems that are of
of high-quality water, have chosen to take an ecological potential use to the human race. Yet, we are forcing
route – for most, the graphic design and artistic back- them into extinction at ever-increasing rates, every day
drop may be ecologically oriented, but the organisms losing forever invaluable information.
displayed are specimens isolated from a real ecology. Maybe one day we will know so much about genetic
This is most unfortunate, because it is only with codes and cellular and organism development that we
broader public understanding that the massive loss of can create de novo any organic possibility; and, on the
diversity, so characteristic of today’s biosphere, can be other hand, maybe that day will be as far away as
halted. This must be accomplished through steward- atomic fusion and artificial photosynthesis. In the
ship of the environment and the ecosystems in which meantime, it behoves the human race to develop as
organisms live by most of our population. The concept many symbioses with species and their ecosystems as
that species can be saved one by one at best applies we can manage. We are an integral part of organic evo-
only to mammals and a few birds and fish, if at all. lution and organic complexity. If we try to escape that
Finally, the hobby world of aquaria remains in fer- fact, a fact as deeply and broadly based as any of our
ment with ideas that still exceed the funding capability scientific and engineering knowledge, and a narrow
of scientific and information systems to test and convey parasitism of a few species, the rest be damned, we
reality. Unquestionably, many new “hobby” techniques, are likely to commit ourselves to early extinction.
both those tested in the garage and those provided by Multimillions of species in the past have failed to adapt
enterprising businesses, are increasingly capable of and traveled that well-worn route. Sooner or later, an
culturing many species under optimum conditions of astronomical event may well cause our extinction.
growth and sometimes reproduction. The recent Reef However, we will just as likely survive a few more mil-
Aquarium “bible” by Delbeek and Sprung is a shining lion years if we will use our intellect to adapt to the
example of progress in the hobby. However, hobby sys- reality of our base in organic evolution.
tems mostly remain polycultures, and real ecosystems, This edition is divided into five broad sections,
consisting of diverse communities of organisms in an each containing two to seven chapters. Most chapters
environment approaching that of a wild analog and begin with a review of the subject matter relative to the
processing energy and nutrients through food webs, larger picture of ecology, ecosystems, and the Earth’s
are rare. biosphere as a whole. Part of our appreciation of
In this edition, we greatly expand on the use of the complexities of smaller ecosystems comes from
ecosystem modeling techniques to clean natural waters understanding the more universal context in which all
and the atmosphere. We also show how large rivers, ecosystems operate. Where appropriate, the remainder
bays, and even the ocean and atmosphere can be man- of each chapter deals with the building of microcosms
aged in a far healthier state, and kept that way, if and mesocosms of ecosystems for research and also
we will only adapt a more conservation-minded and gives examples of the unique aspects of small home
ecosystem-centered approach to the human future. aquarium systems. Finally, where appropriate, we dis-
We briefly discuss a critical area of aquatic ecosys- cuss how the information presented relates to the
tem modeling that is especially ripe and far overdue larger concern of environmental restoration.
for development, namely systems for identification Part I discusses the physical environment, elements
and extraction of pharmaceutical drugs already devel- of which at the ecosystem level have often been mis-
oped by a host of wild species. In our anthropocentric understood by environmental scientists and ignored
arrogance, humans tend to conclude that with our by aquarists and hobbyists. We discuss our further
brains, tool use, and language we are far beyond other understanding of the shapes, material, and construc-
organisms. Humans have long thought of harnessing a tion of the envelope that will hold various size aquaria;
few animal species to “work” for us, and have tried to the temperature, water composition, and motion; solar
co-opt the energy storage of a number of plant species; energy; and the substrate, or rock, mud, and sand, that
however, for many, most life is thought of as useful makes up the floor of the system and in part provides
only to “tree-huggers” and in the way of our for all critical geological storage. We also examine the
“progress.” We tend to forget the story of penicillin, critical role of suspended particulates, inorganic and
and the parallel stories of many lesser known drugs. organic, in aquatic ecosystems. Since it is based in the
Up to a half century ago, serious bacterial infections physical factors discussed in this section, we also pres-
often meant death or dismemberment. Then we ent a biogeographic model for the world’s ocean
learned of and eventually co-opted the chemical coasts. Much ecosystem modeling is likely to be carried
“invention” of penicillin by the fungus Penicillium. Of out within the framework of this model.
In Part II, on the biochemical environment, we dis- commensurate with the many years of extensive moni-
cuss the mechanisms of gas and nutrient exchange, as toring data now available. Calcification and biodiver-
well as the management of animal wastes in small sity investigations of the latter, 130-gallon coral reef
models. We particularly examine “ecosystem metabo- system, are covered in Chapter 20.
lism” contrasting the interlocking functions of plants Efforts are now under way to apply the concepts pre-
with animals needed for the successful operation of sented in this book to commercial-scale culture of organ-
these dynamic ecosystems. We continue to describe our isms and the production of human food. Both concepts
primary means of controlling the biochemical environ- will assist in protecting endangered wild communities
ment by using managed communities of algae, and to by greatly reducing wild harvest. Both concepts will cir-
thereby achieve the simulation of larger volumes of cumvent the increasing tendency for wild harvests to
open water and where appropriate export to other com- lose their economic viability. Equally important, the
munities or geological storage. Because biomineraliza- basic water quality control methodologies described in
tion, especially calcification, represents an internal sink this book are applicable to relatively inexpensive and
and needs special treatment in semi-closed ecosystem high-quality treatment of a broad spectrum of both
models, we provide a chapter reviewing what is known human wastewaters and the streams, rivers and bays, as
about this complex subject, and we relate this to the well as coastal waters that are impacted by those waste-
management of controlled ecologies. One of our longer- waters. In Part V, we describe some of the ongoing
lived coral reef models was used to extensively research efforts to make these endeavors commercially viable
this subject. Much of this has been published in scientific and environmentally successful at large scale.
journals, and the basics are presented in Chapter 10. HydroMentia, Inc. of Ocala, Florida, provides the princi-
The ecosystem concept remains a subject of ani- pal commercial effort to expand these methodologies to
mated scientific debate. However, most scientists landscape scale. Some of HydroMentia’s engineering
would accept for a definition something approaching processes are proprietary, including the use of ATS™ for
“diverse communities of organisms, supported and phosphorus and heavy metal removal. Commercial
constrained by a given physical–chemical environment, endeavors should examine the HydroMentia organiza-
interacting to capture and process energy and nutrients tion website and contact their representatives for further
in food webs.” In Part III, we deal with the organisms, information.
their diverse communities, and their food webs. It has Finally, in Part VI, we present a series of principles
been clearly and repeatedly demonstrated that given a for establishing and operating living ecosystems. This
reasonable facsimile of the wild environment, with is where the real scientific learning process begins, in
appropriate imports and exports, and a diverse mix of reducing our endeavors to core concepts, each of which
introduced species of the wild biota, the species of we strive to better understand in the framework of the
ecosystem models will self-organize communities and ecological function of the natural world. Most impor-
food webs to process energy and nutrients. Finally, in tant, we come to understand that the key element to
Chapter 19 of Part III, we introduce symbiosis, and dis- success lies in boundaries, the open end of the defini-
cuss the considerable role that this process has played tion of an ecosystem. No ecosystem stands alone.
in organic evolution. As humans continue to push other Understanding the conditions at the boundaries, the
species “out of our way” and drive ever more of them imports and exports, knowing which species must be
into extinction, it is essential to remember that a sym- simulated by human action because scaling factors
biosis or joining together of organisms has often pro- effectively place them across the boundaries, and,
vided a highly successful evolutionary strategy. finally knowing where to draw the boundaries to make
In Part IV, we present case studies of numerous the modeling effort practical, will determine the mag-
microcosms, mesocosms, and aquaria. Treatment of nitude of success. Restoration of human-impacted wild
the Florida Everglades Mesocosm and the authors’ ecosystems differs primarily in scale; the concepts are
14-year-old 130-gallon coral reef is greatly expanded quite similar.
Acknowledgments and Dedication
It has been nearly 30 years since we initiated the develop- have been many and their wisdom and effects are
ment of the concepts presented in this book and began always helpful, Pat Kangas has been ever behind the
the long process of R&D that produced the very promis- principles and broader goals. And among our long
ing array of ideas and working systems now in motion. time friends, Susan Bradley has always been ready to
For those who will open their eyes and minds, we speak come to our rescue, whether for a creative design or
of the methods of a new rapprochement with nature. A technical computer problems, while Addie Moray and
generation ago, neither the method of experimenting Mary Ellen McCaffrey gave unselfishly of their time for
with captured ecosystems nor the concept of learning some of the administrative tasks. We say again, a book
from, and then “domesticating” ecosystem processes must teach, and while text is paramount, a picture is
was widely accepted either in the aquarium hobby ever “worth a thousand words.” Again in this edition,
world or in the science and ecological engineering com- photographers Nick Caloyianis and Clarita Berger
munities. As exhilarating as these years have been for us, worked their superb magic to provide what only
they have not been without physical, emotional, and photography can convey.
financial struggles, especially for our far-flung families, The erratic path to knowledge in natural history sci-
students, colleagues, business associates, and financiers. ence is, in the end, ever exciting, and because of the
So many people have helped us, we are losing count, and “ivory tower” environment in which it is carried out,
here we can single out only those who were strikingly we would not wish to lose a moment of it. The applied
important in more recent years. We apologize to the far world, and finding the funding to make it happen, can
more numerous helpers and facilitators that we do not be more brutal. To those engineering colleagues and
specifically mention but without whose assistance the financial and business associates who have not only
accomplishments we present would be far more lim- traveled with us in our efforts to bring the solar energy-
ited. The contributions of many of these individuals are capturing and water and atmosphere cleansing process
mentioned in the earlier editions. of ATS to a very needy world, but also have picked up
To all the members of our families, who have the ball and run up-the-mountain when we have tired,
inevitably lived with Dynamic Aquaria and its precedent we feel a gratitude and comradeship that is inexpress-
research for decades, we thank each of you for your ible. At a time when algae was still a bad word, a cousin
patience (and guidance). Special tribute goes to Nathene to red tide and the failed food promise of the 1950s,
Loveland, Karen’s mother for her encouragement in ini- Don Panoz and Richard Purgason started the ball rolling
tiating the R&D endeavor, and for her enthusiasm and with Aquatic BioEnhancement Systems. We are espe-
multifaceted support, and to Walter Adey Sr., Walter’s cially indebted to the HydroMentia crew, especially
father, for a guide to life that lives on. Whitcomb and Margaret Palmer on the business and
Science and engineering is meant to be questioned, financial side, and Allen Stuart and Mark Zivojnovich
tested and re-tested, but the road of true progress can on the engineering side. The engineering innovations
be long, convoluted and tiresome. To our numerous and managerial devotion of the HydroMentia staff
students and assistants, the energy of youth always to solving these serious environmental problems is
made up for whatever we lacked, and we are deeply extraordinary by any measure; HydroMentia picked
conscious of the gratitude we owe you. We are espe- up the ball when it was slowing and we are now
cially indebted to our longtime friend, colleague, and approaching the goal posts, at least the ones most visi-
student, Sue Lutz; she came to our rescue, to help us ble in the fog of time. Whit especially had the vision,
meet the various deadlines, while we needed to be on interest, and resources to take the chance on this jour-
our research vessel in the Canadian Maritimes; without ney, even when the walls in the fog soared out of sight.
her multifaceted talents we could not have completed We are particularly grateful to both Mark and Allen
this edition. In recent years, Allegra Small and Don who provided their consistent support in supplying
Spoon additionally provided the dedicated support that editing, current data and information for this edition.
was a requirement for success, and while our colleagues Above all, we thank all of you for your friendship and
xvi Acknowledgments and Dedication
ongoing, stimulating interchanges and discussions. especially Melissa Read, Project Manager, of Elsevier
HydroMentia, this edition of Dynamic Aquaria, is dedi- Book Productions in Oxford, England, Gregory Harris,
cated to you. the Designer for Elsevier, who stuck with us to create a
Organism culture, by sustainable and non-polluting new cover design, and Pat Gonzalez of Academic Press
means, is essential to our future use of organisms from in San Diego, who helped guide us in the initial process
our hydrosphere. However, the “tragedy of the com- of this endeavor.
mons” haunts us, and as long as there are “fish in the The global environment is under siege by an explod-
sea”, the ability to make this shift will be illusory. On ing human populace driven by pre-historic genes.
the ornamental culture side, we have to take our hats However, we can think and reason; we are not the deer,
off to Morgan Lidster for his “green thumb.” However, rabbits, and lemmings who cannot know they are
the financial mountain was overpowering, and we destroying the environment that they depend on and
now put our hopes in SeaQuest of Utah for further are heading for population collapse. We can learn and
motion in this very challenging arena. respond to the challenges. We surely must try, because,
Finally, we thank our publisher Dr. Andy Richford, with our technical prowess and global influence,
Senior Acquisition Editor, Life Sciences Books of humans will hardly be alone in this collapse. We salute
Elsevier and Academic Press in London, for providing all of those who have helped us, and often carried
us the opportunity to expand and broaden our scope in us on our way; we think the ideas expressed herein
this edition, and for the unending enthusiasm and will help in our “coming to terms” with the realities of
encouragement of the Elsevier/Academic Press staff, nature.
C H A P T E R
This book presents the process of building, managing, in these endeavors and concepts (e.g. Osmond et al.,
and restoring living aquatic ecosystems (in microcosms, 2004). However, critically important at this juncture,
mesocosms, and macrocosms) and its background, Petersen et al. (2003) have had the resources to demon-
rationale, status, and future. We argue that there is no strate a scaling rationale that demonstrates veracity
qualitative difference between a rationally constructed thresholds. In general, as might be expected, larger
ecosystem in microcosm and mesocosm and that in a models can more accurately depict the function of their
macrocosm. In this book, we use the term macrocosm for analog. However, as Petersen et al. (2003) demonstrate,
a wild ecosystem that has been altered or constrained by large microcosms and moderate-sized mesocosms
human endeavor. Human constraints are largely degrad- have already begun to pass those thresholds; and we
ing in effect because they have mostly been performed expand that concept by greatly increasing the biodiver-
with little concern for the continued function of the sity and ecosystem linkage of these models.
ecosystem. However, they can be constructive, such as a In our view, no longer are there aquatic ecosystems
scientific or restorationist effort at repair, revitalization, (including the oceans) on planet Earth that have not
and even optimization. been significantly altered directly or indirectly by
There has been a tendency on the part of some sci- human activities. Many species have been driven to
entists to regard the modeling of living ecosystems as extinction, some as large as the Steller sea cow, and
impossibly complex; that is, they view true ecosystems many more have had their ecological role greatly
as beyond human construction. The tendency in meso- reduced and whole ecosystems altered (e.g. the North
cosm research today is to restrict efforts to a few Atlantic codfish). Many fresh and coastal waters have
species interactions, to keep control and limit the vari- been radically altered, some to a nearly “dead” state
ables, but producing a result that most ecologists (e.g. upper Chesapeake Bay); even the open oceans
would hardly accept as an ecosystem. In the aquarium have been degraded by food-chain concentrated toxic
world, the feeling is widespread that total control over compounds that have rendered some organisms infer-
very limited diversity (gardening rather than ecology) tile and others subject to organ malfunction and can-
is necessary to achieve anything but an explosion of cers. Finally, simply to encompass what would be a
weeds and parasites. Yet, as we shall discuss in this very long list, a global girding biome, coral reefs, are
book, since the first edition was published, it has been facing drastic reduction, if not practical extinction. It
possible for many years to operate in “aquaria” the has long been accepted by ecologists that ecosystem
most complex ecosystems in the sea, coral reefs; these supports are critically important to the survival of
microcosms of a few cubic meters, behave chemically human societies; the advent of concern for the effects
as wild reefs, and have a biotic diversity per square of global warming, and the clearly impending collapse
meter exceeding that known for the wild. Similarly, we of our access to clean water has spread the ecosystem
demonstrate the ability to produce whole estuaries, for support concern far more widely. We feel that much of
periods of up to a decade, with much of their biotic the ecosystem damage can be corrected, and our basic
complexity intact. These estuaries were first attempts standard of living maintained if we greatly increase
and the future bodes well for those willing to move on our efforts now. We have the tools, but time is running
to larger, more sophisticated, systems. We are not alone out for their application.
2 1. Introduction
We start our discussion by demonstrating that the In addition to the millions of stars in our galaxy,
development and evolution of life is very likely an composed mostly of hydrogen and helium, there are
inevitable part of the chemistry of the universe. We enormous masses of interstellar gas and dust. This inter-
demonstrate that the definition of an ecosystem becomes stellar gas and dust is enriched in the heavier elements
a functional reality given the right physical/chemical (i.e. formed in the cooling, nuclear furnaces of dying stars
ecologically engineered) framework, and an appropri- and then blown into space in supernovae. The prevailing
ately inserted, food web-based collection of species. In chemistry in these interstellar regions has been called
this scenario, inserted organisms self-organize into a com- an “organic cosmochemistry” (Oró, 1994). It has been
munity of species interacting to process energy and nutrients shown that the numerous hydrogen, carbon, nitrogen,
through a complex of food webs (i.e. an ecosystem). Since no and oxygen compounds, identified both in interstellar
ecosystem stands alone, the key element becomes under- space and in the comets and meteorites that arrive
standing and re-creating the boundary conditions, the on Earth, can be abiotically combined in the laboratory
imports, and the exports. The ecosystem is the most to provide water and a number of critical pre-biotic
complex end-point of biotic evolution, and when the compounds (Table 1.1). A large proportion of cometary
experimental method is applied, and disassembly and material is frozen water and some scientists have
reassembly utilized, progress in understanding is most demonstrated that the volume of incoming comets has
rapid. Scaling becomes our primary difficulty in model- been more than sufficient to provide the Earth’s oceans
ing, because almost by definition, some species are too (Frank and Huyghe, 1990). “Furthermore, a large array
big or wide ranging for microcosms and mesocosms of proteinic and nonproteinic amino acids, carboxylic
and others have been fished out or otherwise damaged acids, purines, pyrimidines, hydrocarbons, and other
in macrocosms. We need to know enough about these molecules has been found in the relatively primitive car-
ecosystems to interact with them to replace or provide bonaceous chondritic meteorites” that have landed on
the effects (e.g. grazing or predation) of the missing Earth (Oró, 1994).
species; the process is continuously heuristic. Most theories of the origin of the solar system (e.g.
Because we are inextricably enmeshed in our bio- Brown et al., 1992) start with condensation out of a solar
sphere and its ecosystems, and because we process nebula. In these models, the inner planets (including
global-scale quantities of energy and nutrients, human Earth) had all of their volatiles (including the principal
endeavors must seriously consider the effects those elements and molecules of life) blasted out of them by
endeavors will have on our ecosystems and how they the sun as they formed. Newer concepts of the forma-
can be ameliorated. Microcosms and mesocosms are tion of the Earth–Moon system (e.g. Redfern, 2001),
ideally suited for this task (see also Osmond et al., 2004). mostly evolve around the impact of a Mars-sized
object with the early Earth, resulting in the Moon being
ejected with many of the planetary dynamic characteris-
THE ORIGIN OF LIFE: MICROCOSM EARTH tics (orbit, spin, and wobble) formed or altered by the
impact. In either case, the Earth started as a rocky “cin-
The four most abundant chemical elements (99%) of der” (like the planet Mercury today). It became revital-
most living organisms, by number of atoms, are hydro- ized with oceans and gases, most likely, from cometary
gen, oxygen, carbon, and nitrogen. The elemental com- and meteorite introduction. We now know that at the
position of the universe (Figure 1.1) compared to that of outer margins of the solar system, there are a large num-
the crust of the Earth (Figure 3.6) suggests that living ber of ice objects that form the Oort Cloud. These pro-
organisms have more in common with the universe as a vide the comets that are sometimes perturbed into the
whole than with the Earth alone. Even the relative pro- inner solar system, where they can impact the planets
portions of these elements are about the same in living bringing water and organic compounds (Redfern, 2001).
organisms as they are in the universe (although hydro- The key to the next step was a planetary mass and tem-
gen is lower), but very different from that in the Earth’s perature environment in which the already omnipresent
crust. Including the oceans (which are one-sixteenth the water components could be present in their liquid phase.
mass of the crust) with the crust, in this elemental analy- While this may have happened on Mars and Venus as
sis, has very little effect on the relationship. In the Earth’s well as on planet Earth, it is only on Earth that the con-
crust, by weight, oxygen, silica, aluminum, and iron, fol- ditions for life have remained for 4 billion years. Later
lowed by sodium, magnesium, potassium, and calcium, cometary and asteroid impacts snuffed out some of that
are far above the very small percentages of hydrogen, life when they impacted, but so far none have reset the
carbon, nitrogen, and phosphorus. If the whole Earth is life clock.
considered (as an estimate), the big four, at 93%, are iron, Chemically, water is a most unusual material.
oxygen, silica, and magnesium. By accepted physical/chemical rules, under normal
The Origin of Life: Microcosm Earth 3
FIGURE 1.1 Relative abundances of the chemical elements in the universe (based on silicon as 104). Note that
except for the very unreactive helium, the three most abundant elements of life are the same as those in the universe
with the critical nutrient nitrogen next in line. From The Biological Chemistry of the Elements by Fraústo da Silva and
Williams (1993). Reprinted by permission of John Wiley & Sons, Inc.
pressures, one would expect this ubiquitous compound compound to form a “semicrystalline” liquid at mod-
to exist only as a solid or as a gas, depending on tem- erate temperatures, water appears in its most familiar
perature. However, due largely to the polarization of liquid form over a relatively wide temperature range.
individual water molecules and the tendency of this At the same time, it becomes a “universal” solvent.
4 1. Introduction
TABLE 1.1 Biomonomers, Biopolymers, and Chemical Properties That Can Be Derived
from Interstellar and Cometary Molecules
Molecule Formula Biomolecules and chemical properties
Hydrogen H2 Reducing agent
Water H2O Universal solvent
Ammonia NH3 Catalysis and amination
Carbon monoxide CO ( H2) Fatty acids
(Linear nitriles) H(C)nCN (Fatty acids)
Formaldehyde CH2O Ribose and glycerol
Acetaldehyde CH3CHO ( CH2O) Deoxyribose
Aldehydes RCHO ( HCN NH3) Amino acids
Hydrogen sulfide H2S ( as above) Cysteine and methionine
Hydrogen cyanide HCN Purines (e.g. adenine)
Cyanacetylene HC3N ( cyanate) Pyrimidines
Phosphate* (PN) PO3 ( nucleosides)
4 Mononucleotides (e.g. ATP)
Cyanamide H2NCN (condensation) Biopolymers: peptides and oligonucleotides
* Detected in interplanetary dust particles of possible cometary origin and in meteorites. From Oró (1994). Reprinted by
permission of Cambridge University Press.
Almost every chemical element that occurs in the Thus, while it seems that cellular structures with
Earth’s crust dissolves in water, ultimately finding its simple organic compounds would be just “everyday”
way into the sea. Water also has one of the highest chemistry in a pre-biotic world, is there an “external”
capacities of any compound for storing and exchanging information component required to kick-start life from
heat, and it has great surface tension. Thus, this almost there? Very long polymers, strings of smaller organic
miraculous material is a basic stabilizing element, resist- molecules, are the everyday “magic” of organic chemists
ing temperature variations. and industrial plants today, but they are also part of the
Most of the above are debated only in the details by critical stuff of life. Some scientists would have it that
scientists today. The critical step, from simple organic the ordered, endlessly replicating structure of inor-
molecules, abundant in the colder parts of the uni- ganic clay minerals could provide a template against
verse, to life is where the debate lies. Indeed, this may which many simple organic compounds could become
have not been a step, but rather a flickering, on-and-off polymers. This can be done in the laboratory, and it
process, happening millions of times before taking is an intriguing idea that in the pre-biotic world this
hold. Was it enough that physical energy inputs, is where carbon and silicon chemistry come together.
whether from lighting at the surface of the sea or Carbon and silicon are chemically similar, as elements:
hydrothermal energy at ocean spreading centers (van they form multiple bonds with themselves and many
Dover, 2000), into the primitive ocean soup (water plus other elements – silicon, one step up on the periodic
simple inorganic compounds) created the next level of table, is roughly twice as heavy as carbon.
complexity of organic compounds? This has been Could it be that silicon, the key chemical element in
repeatedly accomplished in the laboratory. It may be the crust of cinder Earth, and carbon, coming with
that anywhere in the universe, except near stars, when water from the cold outer solar system to bring poten-
the temperature is right and water is liquid, then the tial life to a later, temperature-moderated Earth, pro-
organic soup is ready to brew. vided the next step up the ladder to full-blown life? In
Water has a tendency, because of its surface tension, the contact between the primordial water, rich in a wide
to create membranes and “bubble” structures. Lipids, variety of simple organics and cellular bubbles, and
present among the universal, simple, organic com- abundant clay minerals formed from erosion of rocks,
pounds, spontaneously accumulate on these “bubbles” polymers could have formed from all the types of sim-
to form membranes and cellular structures. This can be pler organics, including nucleic acids. Possibly formed
abiotically accomplished in the laboratory (Hanczyc in much the same way, RNA is the basic message carrier
and Szostak, 2004). Membranes can isolate, structure, of life today, and could well have preceded DNA. This
and locate organic reactions making them more effi- is the so-called RNA world that some researchers see as
cient than they would be in the greater “soup.” an essential phase (Orgel, 2004).
Microcosms and Mesocosms of Aquatic Ecosystems 5
Such RNA in the ammonia, carbon dioxide rich and over the last 3 billion years. Photosynthesis “invented”
anaerobic early world, could theoretically exist and repli- by early life has kept the Earth from the fate of Venus –
cate itself, becoming more complex, based on natural a boiling, runaway greenhouse – by continually lock-
selection. Eventually, the RNA molecules would have ing a large part of this carbon into semi-permanent
found themselves inside developing cellular bubbles, storage. By releasing carbon from geological burial to
where they could have co-opted those structures, to the atmosphere, we are courting both human and bio-
spontaneously produce what one would have to call life. sphere disasters every bit as much as we were (and are)
This very basic life probably began “soaking up” the with our nuclear arsenals. Many scientists are more
organic chemicals of the soup. However, until regular immediately concerned with a global warming that
energy sources and a means of synthesizing carbon and will disrupt many human societies creating global fric-
nitrogen compounds from CO2 and NH3 (and eventually tion. Photosynthesis may be somewhat more effective
N2) were tapped to bring reproduction and growth with higher levels of CO2 (there is still much debate on
together, the future of this “life” had to be uncertain, and this point). However, most scientists have concluded
perhaps frequently snuffed out. Eventually, several path- that this natural increase of photosynthesis cannot
ways for fixation of carbon and nitrogen evolved in what keep up with our destruction of forests and tundra and
could be called primitive bacteria, leading to the highly the release of fossil fuels carbon. Desertification and
successful Calvin cycle of cyanobacteria (Raymond, the reduction of more efficient land photosynthesis by
2005). Tied to solar energy capture by the early photo- rising sea level, with human societies putting more and
synthetic bacteria, some 3.5 billion years ago, life became more CO2 into the atmosphere in a struggle to obtain
firmly established on Earth. From there, with occasional energy to survive the harsher conditions, could push
disruptions, as large comets and asteroids continued to us to the high temperatures and sea levels of the
arrive, life was on its way to creating the modern, com- Cretaceous with far less land area. Perhaps then mod-
plex Earth, so fully integrated, at least from its crust to ern human societies would collapse (Diamond, 2005)
the atmosphere, with life. and save the biosphere from a runaway greenhouse
Today, the overwhelming geochemical evidence is tumble.
that cellular life formed very quickly in the pre-biotic Today, all the Earth is a microcosm, or at least the con-
soup (at 3.6–3.8 billion years ago) within at most a few cepts of microcosm, mesocosm, macrocosm, and bio-
hundred million years of the formation of a liquid ocean sphere lie a spectrum of overlapping scale. No one
on Earth (Gedulin and Arrhenius, 1994). Furthermore, doubts any longer that we can affect our Earth on a
it is difficult not to conclude that life will form quickly global scale. The principles that we describe in this book
(on a geological scale) anywhere in the universe where for microcosms and mesocosms are very much the same
the physical conditions for liquid water develop as what we would use for macrocosms and the oceans.
(National Research Council, 1990). We cannot return to a more simple state where the bio-
The Gaia concept was popular several decades ago sphere can be counted on to “cover up” for us. We must
and has now faded. The basic premise of Gaia, that quickly learn to properly manage the biosphere.
some life made more life easier, even possible for more
advanced life, is certainly correct. The primordial soup
was necessary for the development of cellular systems MICROCOSMS AND MESOCOSMS OF
and the earliest molecular complexes that could be AQUATIC ECOSYSTEMS
called life. The early bacteria that survived on the soup
were a necessary condition for photosynthesis and Over the last third of the 20th century, scientists in a
eventually the symbiotic incorporation of photosyn- variety of laboratories around the world have been mak-
thetic bacteria into early protists to greatly expand the ing significant advances in keeping marine, estuarine,
process of pulling CO2 out of the atmosphere and and freshwater organisms in aquaria-like simulations
replacing it with oxygen. And so on it went to life on of wild environments; they have generally been referred
land, eventually to primates and humans. to as model ecosystems or microcosms. Some of these
Whatever is to be made of these arguments about the become quite large, and when they exceed a few thou-
development and expansion of early life, one thing sand gallons in water volume, they are sometimes called
is very clear: photosynthesis eventually came to be mesocosms. There is no sharp line between the micro-
the key to most life on Earth. Also, it is likely that the cosm and the aquarium. Perhaps it is best to draw the
Earth’s crust, biosphere, oceans, and atmosphere line at the point where the desire for strict ecosystem
together hold more carbon than ever before because of simulation is relaxed because of size, cost, or interest.
continual outgassing of CO2 from the Earth’s mantle The older literature on “ecological microcosms” or
6 1. Introduction
“controlled ecologies” was reviewed by Adey (1987; universal waste products urea and highly toxic ammo-
1995), Adey and Loveland (1998), and Kangas and Adey nia to the less toxic nitrite and thence to the least toxic
(1996). Petersen et al. (2003) point out that mesocosms nitrate; and more recently (3) either in special anaero-
have become as numerous as field studies and they pro- bic chambers, or in open-aerated trickle systems, the
vide citations that would allow an extensive review of denitrification of nitrate nitrogen to atmospheric gas
recent literature. Osmond et al. (2004) discuss the use of nitrogen. Either separately or in conjunction with the
a very large mesocosm (Biosphere II) in the context of above systems, oxygen input into the aquarium and car-
global climate change, and argue for the much wider use bon dioxide release from the aquarium are maximized
of mesocosms to understand and solve our global to support not only the organisms being maintained,
change problems. but also the essential respiration activity of the bacteria.
In the Earth’s biosphere no ecosystem stands alone. The respiration of the bacteria in these filters releases
Indeed, as we noted above, the primary energy source considerable carbon dioxide, which can significantly
for the biosphere itself is derived externally from the acidify the culture. Thus, buffering with calcium car-
sun; the remainder internally, from the Earth’s heat. bonate in a wide variety of forms is often used. Hendal
Most of the original biotic materials came from outside (2006) and Delbeek and Sprung (2005) provide recent
the Earth and, to some extent, are still arriving; the reviews of these methods for aquaria. In most cases,
remainder derive by erosion from the Earth’s crust. these methods are sufficient to maintain many organ-
External solar and lunar cycles are also important isms. However, they rarely achieve the quality of unpol-
sources of information. The boundaries of an ecosystem luted wild waters.
are entirely arbitrary. However, whether carrying out The basic principles of bacteriological filtration (and
pure field research or drawing boundaries for modeling sewage treatment) lie in the assumption that microbes
purposes, drawing those boundaries so that cross- have been the dominant force controlling water quality
boundary interchanges can be known and measured or in the wild. However, this is likely to be incorrect, since
estimated is a key to success. All ecosystems have cross- far more organic material is stored in soils and geologi-
boundary interchanges, and the microcosm builder cal sediments than exists in the biosphere. In addition,
must know what those interchanges are and simulate the Earth’s atmosphere is rich in oxygen and, prior to
them accordingly or the model ecosystem will have little human involvement, was very poor in carbon dioxide.
relationship with the wild analog. Higher plants and algae have created far more organic
When modeling boundaries are established for most matter than microbes have degraded, with a concomi-
aquatic ecosystems, water inflow and outflow are impor- tant production of oxygen and removal of carbon diox-
tant parameters. In many cases (e.g. coral reefs and rocky ide from the biosphere. Thus, plants have been and
shores), where local biomass exceeds diurnal recycling (until humans started burning coal and oil and using
capabilities, incoming water quality is crucial to ecosys- rivers to dump their wastes) remain the dominant force
tem function, and when it is not possible to provide that controlling Earth’s water and atmospheric chemistry
flow from an undamaged wild source ecosystem, a and particularly the needs of higher animals. Humans
water quality management system is established. There assume that lack of raw materials to maximize produc-
are three basic approaches to the management of water tion is a basic need that must be managed; thus, the pri-
quality in aquatic models (i.e. to match the lack of high- mary requirement is rapid breakdown of all organics to
quality incoming water). One approach is abiological, in basic mineral elements (carbon, nitrogen, phosphorus,
which chemical methods such as ozonation and physical sulfur, silica, etc.). We disagree with this concept.
methods such as physical filtration, protein skimming, Primary productivity in the wild is sometimes limited
and ultraviolet radiation are used to offset the effects of a by the lack of “nutrients.” On the other hand, excess
poor water quality. These methods are almost always nutrients usually result in unstable (bloom) conditions.
used with the second, more generalized, approach of Farming and aquaculture almost invariably add nutri-
bacteriological filtration, which is employed in various ents to drive productivity of a single organism. How-
forms and has been used in virtually all aquarium sys- ever, the result is either unstable or semistable, requiring
tems (and sewage systems) of the past 50 years. continuous careful management to avoid a variety of
The bacteriological (or biological) filter is a device of “crash” scenarios. Biospheric, and ultimately ecosys-
almost infinite variety used to maximize surfaces with tem, stability lies not in the rapid breakdown of organ-
bacterial cultures (i.e. bacterial films) in close contact ics but rather in emphasis on their storage as either
with flowing water of the system being managed. The plant biomass or geological materials. Stability in the
purpose is threefold: (1) the trapping and breakdown biosphere, in most wild ecosystems, and in microcosms
of organic particulates; (2) the degradation of the and mesocosms must lie in competition for scarce
Microcosms and Mesocosms of Aquatic Ecosystems 7
resources including carbon and nutrients. In aquacul- of organisms in the commercial aquarium trade. The
ture systems designed to produce food, these require- suffering of the animals is deplorable, and there exists
ments are reduced locally to maximize growth, but the very real possibility that intensive collection will
must be managed in a broader context, or they will deplete the environment and upset the balance of
be passed onto wild ecosystems where degradation is natural communities. While large numbers of plants
inevitable. It is probably best to recycle all human and animals may die in the wild during environmental
organic wastes, but the next best approach would be to extremes, in general, human impacts are becoming
pump them into sealed oil wells or deep mines (geolog- severe enough to shift the delicate survival balance
ical storage). Had that been done for the last century, we negatively for many species and even for ecosystems.
would be faced with neither global warming nor pol- For recreation and education purposes, we cannot
luted rivers and coasts and could perhaps tap the accept subjecting organisms to stressful conditions
resulting methane gas for energy. We have not taken beyond their normal environmental range. Even for
that approach and, at this stage, we need to quickly research purposes, it is crucial that scientists be sensi-
organize to emphasize the locking up of nutrients, tive to the health of the organisms involved and to the
including carbon in plant (including algal) biomass. potential negative impacts of collecting.
The third approach, which we describe in this vol- Open water culture can help in some situations, and
ume, is to match an undegraded analog wild ecosys- are increasingly important in coral reef culture. How-
tem as closely as possible with the microcosm or ever, through the use of ecosystem techniques, culture
mesocosm of interest, in terms of physical and chemi- systems can produce most of the organisms (and live
cal characteristics, cross-boundary exchanges, and as rock) used in the aquarium trade, and distributors, deal-
many organisms, with their food webs, as possible. In ers, and hobbyists can maintain functioning systems
some cases, especially for smaller systems, human and reduce losses dramatically. Indeed, experimental
manipulation must account for the cross-boundary ecosystems and their organisms can be maintained sep-
exchanges of organisms that have a significantly larger arately from wild ecosystems and endangered organ-
territory in the wild than is available in the model. isms can be nurtured for return to the wild. Zoological
Water quality control of high biomass of benthic sys- parks have made a strong entrance into this arena in
tems usually involves open water exchange with recent decades, and now public aquaria, with sufficient
phytoplankton-dominated communities in the wild. We financial and scientific expertise, can do likewise. Many
simulate this process with algal photosynthetic sys- freshwater fish have been bred in aquaria, and in the
tems, allowing production and export or recycling of past decade increasing numbers of marine species of
biomass (and nutrients) as appropriate. Foam fraction- fish have been also. Because of our success in breeding
ation, filtration, and engineered bacterial systems are hundreds of species of marine invertebrates and plants
not generally employed because they remove plankton in our ecosystem tanks, the prognosis for greatly reduc-
and swimming or floating larvae on the one hand and ing wild collecting is encouraging, and we describe sys-
unbalance water chemistry on the other. tems for accomplishing this objective. We also describe
In Chapter 25, we describe several large-scale systems culture systems that can be used for identifying organ-
for the closed or semi-closed aquaculture of food fish. isms that have potential for the production of pharma-
These systems use the same Algal Turf Scrubber (ATS™) ceutical drugs and for initial harvest culture until the
systems described in this book for controlling water synthetic equivalents can be produced.
quality in microcosms and mesocosms. Technically these As we have pointed out, there is already a large
aquaculture operations are quite successful, and indeed applied world that uses microcosms as tools for testing
one system is still operating as a commercial endeavor the fates of pollutants in wild ecosystems and hopefully
after 10 years. However, until truly sustainable wild fish- developing standards for lessening pollutant loads as a
eries, without habitat degradation, can become the rule, result. These testing procedures use either highly simpli-
and a cost is levied on nutrient release from aquaculture, fied ecosystems or a few species without a real ecology.
it will be difficult for these sustainable methods to be However, the results derived would be more applicable
truly cost competitive. to the real world if the models used were the more com-
The hobby aquarium industry, in its public educa- plex systems that we describe in this book. Of equal
tion effects, can have an incalculable positive effect on interest, it has long been known that up to a certain level,
the need for public understanding of biology and ecol- ecosystems have a considerable capability for accepting
ogy. Since it is “hands on” per unit effort it is probably polluting elements and degrading or detoxifying and
far more effective than text book/lecture education. storing them. We have much to learn from ecosystems in
However, as practiced today, there are enormous losses this respect, as we detail in Part V. However, what is most
8 1. Introduction
relevant in the real world, where efficiency counts, is that (microalgae). The ATS™ was derived from mesocosm
knowledge gained, through models, of ecosystem R&D, and is itself a biodiverse ecosystem that provides
processes can lead to more economic means of handling multi-solutions. It demonstrates the great potential of
large quantities of pollutants and keeping those pollu- microcosm and mesocosm research, but in the solution
tants from degrading wild ecosystems. of grave problems of mankind.
RESTORATION OF DAMAGED
ECOLOGICAL SYSTEMS It is quite reasonable that we wish to understand in
depth the complex ecosystem processes in which we
We have used the term macrocosm for wild ecosys- are enmeshed. It may well be essential to our contin-
tems that have come under the significant influence of ued existence as a species. To develop ecosystems in
human activities and are in need of restoration to pre- microcosms, mesocosms, and aquaria, and to control
vent loss of biodiversity and the degraded provision of their relationship to the rest of the world is simply the
“ecological services” to human society. It may be that experimental method of science at the most complex
most ecosystems on Earth are now macrocosms, but scale of biology. The ecosystem is the exquisite poten-
there is certainly a broad gradient between those in tial of the universe, and we can capture it and look at it
great need of repair and those minimally affected. logically for understanding or for its intrinsic beauty.
There is no lack of understanding of the current, seri- To build and control ecosystem models and to use the
ous nature of our loss of ecosystem function and sup- knowledge and techniques gained to restore damaged
port. We cite two recent authors: Jared Diamond (2005) ecosystems is an essential endeavor.
calling notice to the global level of ecosystem degrada-
tion that can lead to social collapse, and Robert
Livingston (2006) calling notice specifically to serious TAXONOMIC NOTES
aquatic ecosystem degradation. There is considerable
scientific consensus that human society, in its alteration As we have noted, the biological world is far more
of the biosphere, is approaching a number of thresholds complex than the chemical world. While the core chemi-
beyond which ecosystem supports will begin to fail and cal elements and compounds have a standard terminol-
potentially cause social collapse. There are many ogy that has long existed for chemistry, the biological
dimensions to the loss of ecosystem supports: for exam- world remains in flux. The Linnean system has been
ple Diamond (2005) lists 12 key problems. As we dis- backed up by a formal, international system for the stan-
cuss in Chapter 25, a number of these relate to a need to dardization and stabilization of nomenclature, but the
restrict human population growth and human demand result is hardly stable. Some of these changes are
for continued resources as well as the increasing num- reflected in advances in our understanding of organis-
ber of invasive species caused by globalization (see also mic evolution, prodded on by a rapidly advancing
Ruiz and Carlton, 2003). However, better than half of knowledge of what is called “molecular biology,” the
the basic problems relate to water and atmospheric documentation of genetic coding. Unfortunately, some
quality control and to fisheries. We describe in Chapter change also comes from nomenclatural wrestling. For
25 how in working with numerous microcosms and basic reference we provide a modern “tree of life” (Figure
mesocosms, we have identified a practical methodol- 1.2) from Knoll (2003); the volumes of Parker (1982) can
ogy for solving these problems using large-scale solar continue to fill in that framework down to family and
energy capture through algal photosynthesis. These genus. In our descriptions of microcosms and meso-
ATS™ systems have already been scaled up to a mod- cosms, as one part of the demonstration of “success” or
ule size of up to 5 acres and 40 Mgpd by HydroMentia, veracity of modeling of an analog wild ecosystem, we
Inc. of Ocala, Florida. HydroMentia offers nutrient, tox- provide species lists. Since these lists were accomplished,
ics, and atmospheric carbon removal with water oxy- some genus and species names have changed. In this edi-
genation and bioenergy supply as by-products at the tion, we have not “updated” these changes because it
scale of large rivers (formal designs for ATS™ systems would have meant returning to the specialists that iden-
up to 1500 acres, processing billions of gallons per day, tified the flora and fauna in the first place, or in some
have been developed). There are numerous other cases finding new specialists, and this would have
approaches to bioenergy, which are also carbon neutral, changed the basic function of the volume very little. In
but they either add to nutrient problems (e.g. corn, soy, most situations, field guides will provide the older
and switchgrass) or are monocultural in their solution names along with their newer versions.
FIGURE 1.2 Family tree of eukaryotes and ancestral bacteria (there are other, more distantly related bacteria,
such as the Archaea, that are minimally shown). All of the major lines of eukaryotes, including the five major
groups, had already formed well back in the pre-Cambrian, probably before the major animal groups evolved.
After Knoll (2003).
Diamond, J. (2005) Collapse: How Societies Choose to Fail or Succeed.
Viking Penguin, New York.
Adey, W. (1987) Marine microcosms. In: Restoration Ecology. Frank, L. and Huyghe, P. (1990) The Big Splash. Birch Lane Press,
W. Jordan, M. Gilpin, and J. Aber (Eds). Cambridge University Secaucus, New York.
Press, Cambridge. Fraústo da Silva, J. and Williams, R. W. (1993) The Biological Chemistry
Adey, W. (1995) Controlled ecologies. In: Encyclopedia of Environmental of the Elements. Clarendon Press, Oxford.
Biology. W. A. Nierenberg (Ed.). Academic Press, San Diego. Gedulin, B. and Arrhenius, G. (1994) Sources and geochemical evo-
Adey, W. and Loveland, K. (1998) Dynamic Aquaria: Building Living lution of RNA precursor molecules: the role of phosphate. In:
Ecosystems, 2nd edn. Academic Press, San Diego. Early Life on Earth. S. Bengston (Ed.). Columbia University Press,
Brown, G., Hawkesworth, C., and Wilson, R. (1992) Understanding the New York.
Earth. Cambridge University Press, Cambridge. Hanczyc, M. and Szostak, J. (2004) Replicating vesicles as models of
Delbeek, C. and Sprung, J. (2005). The Reef Aquarium, Science, Art and primitive cell growth and division. Curr. Opin. Chem. Biol. 8:
Technology, Vol. III. Ricordea Publishing, Coconut Grove, Florida. 660–664.
10 1. Introduction
Hendal, J. (2006) Advanced Marine Aquarium Techniques. TFH research: scaling up in experimental ecosystem science. Glob.
Publications, Neptune City. Change Biol. 10: 393–407.
Kangas, P. and Adey, W. (1996) Mesocosms and ecological engineer- Parker, S. (1982) Synopsis and Classification of Living Organisms. Vols 1
ing. Ecol. Eng. 6(1–3): 1–224. and 2 McGraw-Hill, New York.
Knoll, A. (2003) Biomineralization and evolutionary history. Rev. Petersen, J., Kemp, W. M., Bartleson, R., Boynton, W., Chung-chi Chen,
Mineral. Geochem. 54: 329–356. Cornwell, J., Gardner, R., Hinkle, D., Houde, E., Malone, T. H.,
Livingston, R. (2006) Restoration of Aquatic Systems. Taylor and Mowitt, W., Murray, L., Sanford, L., Stevenson, J. C., Sundberg, K.,
Francis, Boca Raton, Florida. and Suttles, S. (2003) Multiscale experiments in coastal ecology:
National Research Council (1990) The Search for Life’s Origins: Progress improvising realism and advancing theory. Bioscience 53: 1181–1197.
and Future Directions in Planetary Biology and Chemical Evolution. Raymond, J. (2005) The evolution of biological carbon and nitrogen
National Academy Press, Washington, DC. cycling – a genemic perspective. Rev. Mineral. Geochem. 59: 211–231.
Orgel, L. (2004) Prebiotic chemistry and the origin of the RNA world. Redfern, R. (2001) Origins: The Evolution of Continents, Oceans and Life.
Crit. Rev. Biochem. Mol. 39: 99–123. The University of Oklahoma Press, Norman.
Oró, J. (1994) Early chemical stages in the origin of life. In: Early Life on Ruiz, G. and Carlton, J. (2003) Invasive Species. Island Press,
Earth. S. Bengtson (Ed.). Columbia University Press, New York. Washington, DC.
Osmond, B., Ananyev, G., Berry, J., Langdon, C., Kolber, Z., Gunghai, L., van Dover, C.-L. (2000) The Ecology of Deep-Sea Hydrothermal Vents.
Monson, R., Nichol, C., Rascher, U., Schurr, U., Smith S., and Princeton University Press, Princeton, New Jersey.
Yakir, D. (2004) Changing the way we think about global change
P A R T
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C H A P T E R
Physical Parameters and Energy State
The shape and size of an aquatic ecosystem relative 1–2 meters. The construction of molded fiberglass
to its controlling physical and energy parameters can tanks or poured concrete or concrete block tanks sealed
determine the basic character of the system. This is with a wide variety of commercially available sealants
especially true of the thickness of the water mass and its has considerable advantages for systems larger than
relationship to the bottom. A 100-meter-deep lake of about a thousand liters. This is also true when the meso-
several square kilometer surface dimensions, all other cosm modeler departs from the purely aquatic systems
factors aside, would be dominated by true plankters, and enters the realm of wetlands, marshes, and swamps,
normally living most of their lives suspended in mid where the key species are either large individuals or the
and surface waters, with little benthic (or bottom) influ- very nature of the community (e.g. a marshland) requires
ence, whereas the shallow stream or narrow lagoon of a a large area compared to water and sediment volume.
few meters in depth is very much benthic dominated. Each of the aquaria, microcosms, and mesocosms
Light enters only through the air–water interface of a described in Chapters 20–23 illustrates the process of
water ecosystem, and the shape of the containing body designing envelope (tank) shapes to fit the functional
of water relative to depth, as well as water turbidity, requirements of the enclosed ecosystems. Whether they
determines the basic photosynthetic vs heterotrophic are fully successful or not is limited only by the ingenu-
(nonphotosynthetic feeding) character of the ecosystem. ity and financial resources of the human builders
The direction of current flow and wave action through (Figure 2.1).
an aquatic system relative to the position and orienta- Ideally, the microcosm or mesocosm envelope would
tion of the communities present is critical to simulate in be like that of the boundary of the mathematical modeler,
any ecosystem model, or else the character of the com- a theoretical boundary controlling access but not having
munities and the abundance of its various species will any inherent characteristics. Of course, that is not possi-
change in the microcosm or mesocosm. ble, for two primary reasons. First, walls, whatever their
The all-glass aquarium, ranging from about 40 liters nature (unless rather esoteric measures are used to pre-
(10 gallons) to 1000 liters (250 gallons) is a standard vent organisms and organic molecules from using their
and highly reliable piece of equipment in the aquarium surfaces) are effectively hard bottoms. In an aquatic
industry (Color Plates 1 and 2). Likewise, because of its model of an ecosystem dominated by hard bottom com-
low cost and availability, every effort is generally made munities that may not make a difference (remembering
to use all-glass aquaria for microcosm work. Indeed, by however, that especially in marine and estuarine systems
drilling holes to attach pipes and linking all glass tanks that some species have larvae that must escape into the
in complex arrays, many aspects of wild ecosystems plankton for the early part of their lives). The important
can be modeled with reasonable accuracy. of the walls is less, as is often the case in an all-glass sys-
We talk about the issue of scaling later, but anyone tem, if the walls are frequently scraped. However, for
wishing to simulate the planktonic aspects of an ecosys- a small model of a planktonic system, the presence of
tem, not overwhelmed by the benthic communities, uncleaned walls may prevent the system from being
is likely to be seeking tanks with radii greater than plankton dominated. Second, walls of living models
14 2. The Envelope
FIGURE 2.1 Diagrammatic illustrations of two very different types of ecosystem models (a coral reef and a mangrove/swamp
sandy shore) showing spatial configurations, water movement, controls, and energy supply as well as the basic materials used in
construction. Both of these models are streated in considerably more detail in Chapters 20 and 22.
consist of real materials. To some degree, they interact characterized environmentally by their long-term stabil-
with the water of the ecosystem they contain. For most ity and a lack of leachable compounds.
purposes, glass and many plastics are ideal in this
respect. There are few aquatic systems in which the slow
leaching of silica into the water column would be a prob-
lem, and barring the significant presence of ultraviolet Glass tanks constructed commercially offer many
radiation, most plastics that one might use for walls advantages to the hobbyist and even to the scientist
(polyester, polyvinyl chloride (PVC), polyethylene) are and aquarium distributor. Technically, a glass is any
The Envelope 15
molten rock that has cooled so rapidly that crystals We have used heat-strengthened, laminated glass suc-
have not had a chance to form. In the context of this cessfully. With three 0.5-inch panels and two 0.030-inch
book, glass is silica (SiO2) or uncrystallized, amor- plastic laminate layers, little visual distortion occurs
phous quartz. In practice, commercial glass is an alloy and cost is minimal.
typically also containing oxides of sodium (Na2O) and
calcium (CaO). This soda and lime glass is the oldest,
cheapest, and easiest to fabricate. Many other glasses
now exist. For example, borosilicate (borax, sodium The primary competitor with glass for small aquar-
borate, plus silica) is the base of chemical and kitchen- ium construction or for ports in larger tanks is acrylic
ware glasses such as Pyrex and Kimax. Lead is used in sheet (Plexiglas, Lucite, etc.). Acrylics are made of syn-
“crystal” glasses. Some commercial “glasses” for spe- thetic hydrocarbons and can be colorless and transpar-
cialized uses do not even contain silica (see e.g. Bansal ent (see e.g. Levy and DuBois, 1984). Like glass, their
and Doremus, 1986). strengths in actual practice are significantly lower than
Soda–lime glass (simply glass in the rest of this dis- the theoretical values. The strength of acrylic is gener-
cussion) is quite transparent and very hard. Very few ally taken to be somewhat less than that of glass. Where
minerals, such as diamond and carborundum, are weight is a factor, acrylic is about 40% the density of
harder or more resistant to weathering and most chem- glass, a feature readily apparent to anyone who has car-
icals. Theoretically glass is stronger than steel even in ried glass and plastic aquaria. Using the same care as
tensile strength. Also, most glass components (silica, for silicone cement attachment of glass, acrylic-soluble
calcium, and sodium) in microquantities not only are cements can be used to fuse acrylic sheets together.
nontoxic, but they are also needed micronutrients for While some brands of acrylics are harder than others,
almost any ecosystem. Most of these points are well all acrylics are more or less subject to intensive scratch-
known and along with the viewing characteristics are ing by organisms with shells or teeth. Also algal, bacter-
the primary reasons for the traditional aquarium use of ial, and protozoan growths (aufwuchs) are inevitable
glass. It is the theoretical qualification in the strength (and desirable) on available surfaces of all ecosystems.
characteristics of glass that is puzzling and sometimes If visibility is to be maintained, the glass or acrylic sur-
leads to the choice of other materials. Glass is brittle. faces must be regularly cleaned either by organisms or
It shows little plastic deformation or give before frac- by hand. In time, this process tends to reduce the trans-
ture. A very carefully drawn rod of glass can have parency of the hardest acrylic. Care also has to be taken
extraordinarily high strength and, theoretically, could in construction of complex structures to allow for the
replace steel in rigid steel cable. However, it flaws eas- considerable flexibility of acrylic sheets. In public view-
ily and cracks can start at flaws, greatly reducing ing areas, where absolute safety is demanded, and
strength. Also, even though glass has great weathering where unplanned impact from a hard object, such as a
resistance, it does in fact react slowly with water (some tool or a bottle, is possible, acrylics have much to offer.
SiO2 groups being replaced by SiOH). This effect is par- Nevertheless, in the past we have chosen safety glass
ticularly seen at flaw points on the glass surface from (multilayered glass with thin acrylic sheets molded
which crack development is accelerated. between) in these situations. This laminated glass prod-
Glass is relatively cheap. Silicon is one of the more uct provides the advantages of both materials in aquaria
abundant elements of the Earth’s crust. As long as and microcosm construction.
weight is not a significant factor (and this is likely true
in aquarium situations because of the proportionally
large weight of water), 10 to 1 safety factors placed on
normal working strengths will easily solve the indeter- In the mid-size enclosure range of 300–10 000 gallons,
minant strength characteristics. There is a considerable composite plastic tanks are preferable to all-glass or
literature that relates glass thickness to dimension char- acrylic units. The base material for these tanks is poly-
acteristics currently in use in the commercial aquarium ester resin, usually with glass cloth or mat reinforcing.
field (see, e.g. Adey and Loveland, 1991). This applies to Polyester resins have good strength, toughness, and
all glass tanks or glass in steel or concrete structures. chemical resistance characteristics. Most importantly,
Generally, in all glass tanks it is the sealant that begins polyesters adhere well to other materials, particularly
to fail with minor leakage long before there are glass glass and wood. The composite material of polyester
problems. In very sensitive situations, safety glass or resin and glass cloth or matting has a flexural strength of
tempered glass can be used as an extra safety factor, nearly 10 times the practical strength of glass and can
although safety glass eventually delaminates and tem- exceed that of magnesium alloys. Equally important, the
pered or “heat-strengthened” glass can fail explosively. polyesters are catalyzed resins, and setting time as a
16 2. The Envelope
function of temperature and catalyst quantity (which is controlling elements of biological function. DDT is a
on the order of drops per gallon) is relatively uncritical. classic case, and Silent Spring (Carson, 1962) presents
As in all plastics, avoiding contamination, especially a grim reality that could have been (and may yet
by oils and greases, in mixing and application is critical. be – PCBs followed and now a new generation of syn-
Although almost any technique will “work,” strength thetic herbicides, pesticides, and hormones are escap-
and longevity will be severely compromised by any, but ing into our streams and rivers). DDT was, hopefully,
a technique of scrupulous cleanliness and reasonable caught in time (it is still found in whales and birds
adherence to time, temperature, and catalyst quantity in the remote reaches of oceans). Also, many pesticides
tables. Fiberglass unfortunately is not transparent, and banned or highly controlled in the United States are
therefore glass or acrylic panels must be used where used in massive quantities elsewhere (including DDT).
side viewing is required. Chlorine used for water “purification” in swimming
pools, sewer outflows, and drinking water supplies
deserves close attention. We may yet destroy ourselves
and our higher animal and plant associates through
Where weight and space are not factors, and tank size chemistry intended for “better living” if we do not rap-
exceeds 10 000 gallons, reinforced cement block or con- idly learn more care in this regard. These matters we
crete is the material of choice. Particularly in larger discuss further in Chapter 4.
dimensions, these structures should be designed by The aquarist operates mini ecosystems that, because
experienced engineers. However, it is essential to convey of their small size, are particularly susceptible to contam-
the special problems of water, salt water, and ecosystems ination by external and internal pollutants. In Chapter 4,
to the responsible engineers. An engineer will easily we discuss the potential problems that can derive from
appreciate the corrosion problems, but the sensitivity of the water source. Here, we briefly discuss potential mate-
ecosystems to contamination by metals must also be con- rial problems that apply equally to the envelope, plumb-
veyed. Also, concrete is porous and blocks can gradually ing, heating and cooling, tide creation, and light supply
disintegrate when constantly submerged. The inside sur- elements as well as to the substrate. These involve mostly
faces of these construction materials must be coated with structural elements and thus primarily metal contamina-
an impervious layer. Because this is the same problem, in tion, though many other possibilities exist.
reverse, as the leaking of building foundations in wet Glass, acrylics, epoxies, polyesters, polypropylenes,
areas, engineers and contractors will understand the polyethylenes, nylons, Teflon, and silicones, among
sealing problems. However, the final internal coatings others, are structural materials commonly used in aquar-
should be epoxy or butyl rubber to prevent any water ium construction. When properly cured these materials
contamination. The function of one of the largest meso- are generally inert, nonbiodegradable, and nontoxic. In
cosms attempted to date was severely compromised by some cases fungicides might be added to the materials in
unsealed concrete (Marino and Odum, 1999). use, and these should be guarded against. Many metals
find their way into construction processes and must be
avoided. Except for perhaps lead, mercury, cadmium,
Toxic Elements and Compounds
chromium, nickel, and silver, metals can have micronutri-
Many chemical elements and compounds are toxic ent uses in organic processes (e.g. iron, zinc, and copper)
to life. Some of these are only mildly poisonous and are and are not a problem in small quantities. Nevertheless,
often required by organisms as elements in small quan- in abundance even these can cause severe problems.
tities and only become toxic in excess. Others are Copper is one of the most insidious of metal problems
always toxic and only concentration determines effect. for the aquarist. In ionic form it is placed in municipal
Many organisms have evolved the ability to produce water systems to kill algae; it is also abundant around
poisonous organic compounds, primarily as a means human and aquarium situations as copper wiring and
of defense or to facilitate food capture. piping. Stainless steel, in addition to iron (which is prob-
Humans have been highly successful at learning the ably the most acceptable of metals, often a micronutri-
chemical possibilities of the Earth, both inorganic and ent), has alloy metals such as chromium and nickel.
organic. Some of the toxic productions of humans are While possibly acceptable in fresh-water use, stainless
solely for industrial purposes, but in many cases have steels should be avoided around salt-water ecosystems.
been allowed to leak into the wild environment. Other Titanium may be acceptable, especially in cooling sys-
elements and compounds have been developed specifi- tems, though the final environmental word has not been
cally to kill undesirable organisms. Unfortunately, many received on this metal.
chemicals that are directed toward specific pest species Zinc as “galvanizing” is often used to coat iron and
work their way through ecosystems and become major steel to reduce corrosion. It is particularly toxic when
dissolved, and in abundance, and should be strictly gradual uptake and storage of carbon dioxide (CO2) as
avoided. Galvanized and stainless steel will be recom- well as the release of oxygen (O2) by plants, over geo-
mended by engineers to solve structural problems where logic time, has created an atmosphere and biosphere
corrosion is a potential difficulty; however, they should that greatly limits temperature extremes on planet
not be allowed into aquatic life processes in abundance. Earth. The vegetated surface itself limits temperature
Many plants take up metals and incorporate them variation because of its large water content and indi-
into their structure. Some geological prospecting can rectly through the control of water movement. In part,
be carried out by looking at the plants that either con- this phenomenon is the basis of the Gaia concept: the
centrate the element of interest or show a characteristic presence of life on Earth has progressively made a rel-
response. If algal turf scrubber (ATS™) control systems atively inhospitable environment ever more conducive
are used, the algal turfs, also take up many metals to even more sensitive and complex life.
(including heavy metals) preferentially, and with the
ultraviolet component of especially metal halide
lamps, many toxic organics are also broken down. We
discuss these issues in Chapter 25. Under water, the temperature extremes are much
smaller than they are on land. However, some very
important temperature-controlled factors are operating
Plumbing and Electrical
in addition to direct temperature effects. For example,
PVC piping has become a standard part of western oxygen solubility, and thus the amount of oxygen avail-
human society, and once manufactured appears to able to the gills of an aquatic animal, is quite tempera-
offer no toxicity concerns either to aquatic systems or ture dependent (low at tropical temperatures and nearly
humans. PVC pipe does have surfaces that are ideal for twice as high near 0°C). Tropical and temperate zones
the attachment of many organisms. If this is a problem have existed for billions of years on the Earth. Arctic and
either ecologically or from a maintenance concern, subarctic zones, on the other hand, have come and gone.
then design and construction must allow ports or sim- Only a few million years have been available for the evo-
ilar devices for regular cleaning. lution of new organisms, and cold-water mechanisms
Likewise, electrical systems should be designed as and ecology, in the most recent set of glacial cycles
they would be for wet areas in general, using equip- (Pleistocene, Quaternary). This basic limiting factor, along
ment for exterior and all-weather use as well as ground with the strong seasonal cyclicity, is the main reason
fault interrupters (GFIs) or breakers. GFIs are relatively why colder regions have fewer species and thus less
expensive and prone to random failure and short life. complicated ecologies than the tropics.
However, they are necessary to preserve human life. The most important factor limiting the majority of
Thus, the consequences of their unreliability must be organisms to relatively narrow temperature or biogeo-
avoided by design; for example, critical pumping, graphic zones is a basic chemical limitation. Rates of
lighting, or heating functions must consist of dual units chemical reactions, including those characteristics of
on separate breakers. organic processes, are a function of temperature, and
the thousands of different reactions that occur in any
organism are mutually tuned to a limited temperature
TEMPERATURE range. Chemists and physiologists say that Q10 ranges
from 2 to 3, meaning that any given chemical reaction
While the temperature of stars ranges from about doubles or triples its rate for every 10°C rise of temper-
3000°C to 20 000°C, the mean temperature of the uni- ature. Since many mutually dependent chemical reac-
verse is about –235°C. The surface of most of the plan- tions in an organism are not likely to have the same Q10
ets of the solar system generally ranges from below values, relatively small temperature changes can quickly
–100°C to 100°C, beyond the range of most life as we unbalance an organism’s critical chemistry. Thus, organ-
know it. The Earth is in a narrow range of distance isms are at a constant risk of poor health and death when
from the sun that allows liquid water to be present, and the temperature exceeds the ranges, too high or too low,
the size of the Earth ensures that it can be present in the to which they have become genetically and environmen-
atmosphere. tally adapted.
Abundant water is a major element in limiting the There are two generally applicable subrules that
temperature range on Earth from about –50°C (–68°F) apply to the physiological temperature extreme capa-
to about 50°C (122°F). However, to a large extent this bilities of organisms. First, most organisms can accli-
extremely small temperature range also results from matize considerably given the time to do so. This rule
the activities of organisms over billions of years. The applies to both individuals (within a time frame of
18 2. The Envelope
FIGURE 2.2 Activity and mortality of marine/aquatic organisms is much more sharply
tied to higher rather than lower temperatures. (A) Intertidal barnacle activity (upper inter-
tidal, solid line; lower intertidal, dotted line). (B) Mortality rates of a number of marine crus-
taceans as they approach their upper temperature limits. After Levinton (1982). Reprinted
by permission of Prentice Hall, Englewood Cliffs, New Jersey.
days to months) and populations (many years). Thus, a in Chapter 21, Strongylocentrotus drobachiensis, the green
subarctic clam that might quickly expire given a tem- sea urchin, an algal grazer, is a keystone species in the
perature of 15°C in March would find that same tem- North Atlantic Subarctic. At higher temperature levels,
perature quite optimal in August. A second rule of but still well below its lethal temperature, S. drobachien-
thumb is that individual organisms, as well as whole sis is subject to a protozoan disease. Because of this, at
populations, are typically nearer their lethal point at temperatures only a few degrees above optimum, pop-
the high-temperature end of the scale of survivorship ulations are subject to alternate build-ups and crushes,
than at the colder end (Figure 2.2). Temperatures sev- as peak summer temperatures vary from year to year.
eral degrees above the normal high temperature range An even bigger issue concerns the very future of coral
of a population would likely be more dangerous than reefs. Temperatures just a few degrees higher than
temperatures several degrees below the normal low normal in tropical waters cause corals to lose their
temperature. zooxanthellae, with many dying. With global warming
This relationship can be both complex and far- coral reefs will likely radically change their community
reaching. For example, as we will discuss in more depth structure and combined with additional atmospheric
would show something similar for the use of a
gardener, though not usually with the natural water
supply component. Although perhaps more muted (as
is temperature change), the same kinds and ranges of
life zones or biomes occur under water. These biomes
are partly determined by temperature, and substrate
becomes more crucial and rainfall only indirectly of
In general, fresh-water streams follow a temperature
pattern similar to that of the terrestrial life zones. How-
ever, small spring-fed, especially forested area streams
are more controlled by ground-water temperature and
therefore have a small temperature range (Figure 2.5).
Passing downstream, as branches meet and the flow
grows, streams warm or cool according to air tempera-
ture and range becomes quite large. Finally in larger
streams and rivers, temperature fluctuations tend to
reduce again as the greater volume is more subject to
long-term factors. Rivers can become complex biomic
entities as they flow for hundreds or thousands of miles
changing radically in temperature characteristics, and
therefore in the organisms that make up their biological
FIGURE 2.3 Gonad development in the starfish Pisaster ochraceus communities.
from the intertidal of northern California. Note that while some sea-
sonal reproductive cycles are tied to day length, this animal reaches its
peak reproduction shortly after average temperatures reach their min-
imum for the year [1955 (•); 1956 ( )]. After Levinton (1982). Reprinted
Temperature Characteristics of Lakes
by permission of Prentice Hall, Englewood Cliffs, New Jersey. If they are large enough, lakes can have a consider-
able ameliorating effect on the local terrestrial climate.
In temperate and colder regions, the lake climate itself
CO2 (and lower ocean pH) may stop growing alto- is always considerably more moderate than the sur-
gether (see Chapters 10 and 20). rounding terrestrial climate. Because the maximum
Beyond concern for the extreme ranges and the density of water (including the ice phase) lies at about
short-term survivorship of organisms and their popu- 4°C, cold-climate lakes in the winter have relatively
lations, there is also a need to consider normal life cycles, warm deep water (the hypolimnion) while the surface
whether temperature determines breeding (as it often is frozen and the upper few meters lie near 0°C (Figure
does) (Figure 2.3), and whether feeding patterns (and 2.6). During the summer, lake surface waters warm
the availability of feed) and migration are also deter- considerably and, barring strong winds or other fac-
mined by temperature. tors, become stable and stratified. The surface layers
(or epilimnion) become nearly as warm as the average
monthly terrestrial air temperatures, while the bottom
Temperature Characteristics of
water temperature typically ranges from 6°C to 15°C,
Biomes and Rivers
in temperate climates. The temperature change from
Most people are aware that the major biomes (ter- shallow to mid depths, called the thermocline, is often
restrial life zones) of characteristic terrestrial plants sharp. Because the hypolimnion is often relatively iso-
and animals change radically with temperature. From lated, in lakes excessively rich in organic material, bot-
the polar north southward, the polar south northward, tom waters can become anaerobic in summer if they lie
and downward from the tops of high cold mountains, beyond the maximum penetration of light. In the fall,
the tundra, taiga (conifer forests), and hardwood forests as surface temperatures chill and the water becomes
form circumpolar or circummountain bands. Around heavier, these lakes “overturn,” mixing the water and
the warm equatorial and subequatorial bands of the taking on the same temperature from top to bottom.
Earth, water supply rather than temperature is the pri- Tropical lakes, on the other hand, while showing the
mary factor determining biome type. These bands, same basic tendency to stratify, may have a surface to
generalized for all continents, are shown in Figure 2.4. bottom temperature difference of only a few degrees
A standard plant hardiness map for North America centigrade. Similarly, though much colder, Arctic lakes
20 2. The Envelope
FIGURE 2.4 Idealized terrestrial biomes or large areas of similar climate, mostly determined by
temperature and to a lesser extent rainfall. I. Tropical zones: (1) equatorial rain forest; (2) tropical rain
forest with trade wind, orographic rain; (3) tropical-deciduous forest (and moist savannas); (4) trop-
ical thornbush (and dry savannas). II. Extratropical zones of the Northern Hemisphere: (5) hot desert;
(6) cold inland desert; (7) semidesert or steppe; (8) sclerophyllous woodland with winter rain;
(9) steppe with cold winters; (10) warm-temperate forest; (11) deciduous forest; (12) oceanic forest;
(13) boreal coniferous forest; (14) subarctic birch forest; (15) tundra; (16) cold desert. III. Extratropical
zones of the Southern Hemisphere: (17) coastal desert; (18) fog desert; (19) sclerophyllous woodland
with winter rain; (20) semidesert; (21) subtropical grassland; (22) warm-temperate rain forest;
(23) cold-temperate forest; (24) semidesert with cushion plants, or steppes; (25) subantarctic tussock
grassland; (26) inland ice of the Antarctic. After Walter (1979).
can have the same temperature from top to bottom in temperature range throughout the world’s oceans, out-
summer. side of very restricted salt ponds or tidal pools, is about
32°C (58°F), as opposed to about 100°C (180°F) in the
land environments. The yearly ranges in any one locality,
even coastal localities, are much more restricted, rang-
Even more than in lakes, the marine environment ing from as much as 20°C (36°F) in some temperate or
varies relatively little in temperature, and marine subarctic coastal areas to as little as 3–5°C (5.5–9°F) in
organisms have evolved to be able to withstand only some tropical, boreal, and arctic coastal zones. In gen-
small changes in ambient temperature. The maximum eral, the daily and weekly changes at a given depth in
FIGURE 2.5 Maximum daily temperature range as a function of stream order (0 spring,
then numbered as streams join). The smallest, spring-fed streams and larger rivers are least
affected by local climate. Mid-level streams can change radically on a day-to-day basis and fol-
low atmospheric climate closely. From Vannote and Sweeney (1980).
coastal and ocean waters are measured in no more than Coastal marine ecosystems have characteristic
tenths of a degree centigrade (Thurman and Webber, yearly temperature ranges, usually following a more
1984). or less sinusoidal pattern with a peak and a minimum
Most organisms in the biosphere are “cold” or following solar peak and minimum by 1–2 months.
“cold-blooded,” poikilothermic in scientific terminol- Marine temperature patterns are related to ocean cur-
ogy. Unlike birds and mammals (homeotherms), which, rents, the orientation of coastlines, and the relative
with adequate energy or food supply, can handle a wide “continentality” of the coast, as well as to latitude.
range of temperatures, invertebrates, most fish, amphib- Figure 2.7 shows a contour plot of miles of coastland
ians, reptiles, and plants can do little or nothing to con- for the world’s oceans. Clearly, there are extensive
trol their temperature. They function in accordance with lengths of coastline for some summer/winter tempera-
the temperature provided to them by the ecosystem ture signatures (what we will loosely call shore climate)
or ecosystems to which they are adapted. Some of and very little or none at other signatures.
these species function over relatively wide temperature The last 2–5 million years has been characterized by
ranges (eurytherms); others are much more limited alternating glacial and interglacial stages. Fortunately,
(stenotherms). Any given species is subject to a wide the ocean surface temperatures, summer and winter for
range of environmental variables, and the regional tem- the last glacial stage at 18 thousand years, have been
peratures over which a species ranges are not all likely determined by studying the fossil planktonic commu-
to be optimum for growth and reproduction. Those opti- nity that has rained into the extensively core-drilled
mum temperatures are narrow and generally changing ocean sediments (Climap Project Members, 1976). Using
with time, but lie within the regional range. a similar plot for 18 thousand years overlain on the plot
Embedded in the terrestrial biomes shown in of Figure 2.7, it has been possible to estimate what shore
Figure 2.4, which depend on temperature and rainfall climate signatures were constant over the last several
(more generally climate), are biogeographic regions. million years (Adey and Steneck, 2001). Shown as a con-
For example, the narrow equatorial zones are charac- tour plot in Figure 2.8, these are the shore climates to
terized by tropical rainforest which has similar physi- which most current existing rocky shore species have
cal, chemical, and ecological characteristics around the evolved. These are the biogeographic regions of the
world. However, South American, South African and rocky shore biome and they are shown geographically
South Asian, and the Australasian rainforests are occu- in Figure 2.9. They correspond closely with the classic
pied by different species; they have developed in tune biogeographic regions determined from the distribution
to the same kind of environment, but the genera and of marine fish and invertebrates (Briggs, 1974). In
species that have resulted from evolution over the last Chapter 21, we discuss in more depth what this means
100 My, largely in isolation, are quite different. to the modeler of ecosystems.
Marine ecosystems have the basic equivalent of the
biomes; e.g. oceanic plankton/nekton systems, deep-
Model Ecosystems and Temperature
water benthic or bottom systems, and a wide variety of
coastal muddy, sandy, rocky, and coral reef shores, all Matching the temperature pattern of any given
under a wide variety of temperature conditions. Here, ecosystem model with that of its wild analog is not a
we will concentrate on the shore systems, the rock difficult technical problem given the enormous diver-
shores, and coral reefs most likely to be modeled. sity and sophistication of the equipment available. To
22 2. The Envelope
FIGURE 2.6 Yearly temperature (°C) ranges surface to deep water in arctic to tropical lakes.
(A) Arctic; (B) tropical; and (C) temperate, continental. After Hutchinson (1957). Reprinted by
permission of John Wiley & Sons, Inc.
achieve a high precision of measurement, recording in the long term, to be the controlling cost element. Since
and controlling can be a significant cost factor. However, the situations are likely to vary widely, for each of the
it is the resulting requirement for heating and especially myriad systems to be considered, we discuss heating and
cooling, depending on the circumstances, that is likely, cooling for each of the examples given in Chapters 20–23.
Water Motion 23
FIGURE 2.7 Distribution of temperature characteristics of rocky ocean shore in the world’s oceans. Each contour repre-
sents one nautical mile square (1 minute of latitude; a nautical mile 6080 feet or 1870 meters). Note that overlapping coast
patterns (e.g. Indo-Pacific and tropical East Pacific; New Zealand and Australia) are separated by the amounts shown to reduce
confusing overlap. This diagram shows that large areas of coastline occur under certain temperature regimes. For example,
hundreds of nautical miles of coast (in the Mediterranean) have a temperature regime of 24–26°C in summer and 10–16°C in
winter; on the other hand there is virtually no rocky shore that is 20–24°C in summer and 6–10°C in winter. From Adey and
This will give the modeler a perspective on the heating WATER MOTION
and cooling problems likely to be encountered in a spe-
cific case (Table 2.1). Natural waters, to varying degrees, are very much
Temperature sensing and control units can provide chemical soups. The possibilities for chemical interac-
significant contaminating problems; for example, cop- tions on a large scale are greater in water than in any other
per heating or cooling coils are rarely acceptable. environment on the Earth. They are probably greater than
Beyond contamination issues, for the simplest situa- anywhere else in the universe, except where water might
tions, we suggest the control heating/cooling equip- be present. On the other hand, simple diffusion of an
ment available at larger, more sophisticated aquarium element or an ion through water can be very slow. As we
outlets or the options suggested by Spotte (1995). For discuss in Chapter 4, even though water allows most ele-
more sophisticated systems with greater precision of ments and many compounds and gases into its loose
control, especially when daily and seasonal ranges are chemical structure, often as weakly charged ions, the rate
to be matched, the equipment offered by most of the of mixing and interacting can be limited in the short term
larger scientific and laboratory supply or medical com- by the rate of diffusion. Indeed, the very structural factors
panies provides a full range of options. Glass, plastic, that allow water to be the ultimate solvent, and thus the
or ceramic surfaces in contact with water are almost chemical soup, also provide significant limitations to dif-
always preferred to metal surfaces or contacts. fusion and therefore to the rates of reactions.
24 2. The Envelope
FIGURE 2.8 Distribution of average temperature characteristics of rocky ocean shores in the world’s oceans for the
past 3 million years (Pleistocene). This diagram is derived by obtaining the glacial coastal temperature range (after Climap
Project Members, 1976) and multiplying (for each degree square) times existing coastal temperature range (Figure 2.7).
Basically it shows expected species concentrations for rocky coasts. From Adey and Steneck (2001).
Organisms are rarely static? (though resting It is now recognized that wave action and the orbital
overwintering, overdrying stages, and seeds can be water motion it creates in the upper layers of oceans
amazingly long lasting). The basic unstable nature of and lakes can increase phytoplankton photosynthesis
individual life requires a constant flow of energy and (Marra, 2002).
materials to keep the biological and ecological processes Figure 2.10 shows the contrast between the muddy
operating. Whether it is the stirring of water in the bottom infaunal biomass, with depth, in fresh and
home or laboratory, the wind blowing across a lake, marine waters. Nixon (1988) relates the approximate
waves crashing on a rocky shore, or tides coursing in one-half order of magnitude difference between marine
and out of a bay, all significantly contribute to ecologi- and fresh waters to the driving effects of tide and wind
cal and ecosystem processes. These physical energy (waves and current). Note that the one lake that
inputs force the mixing required to varying degrees by approaches marine situations in benthic biomass is the
living organisms to carry out an active life. Scientists large Lake Michigan.
have been examining the direct effects of waves and All forms of mixing accelerate chemical and there-
currents on physical variables such as oxygen and tem- fore biological processes up to a certain saturation
perature and directly on individual species for a long point beyond which other factors (light intensity, tem-
time. These forms of physical energy have a major perature, chemical concentration, etc.) begin to be lim-
impact on primary ecosystem processes such as photo- iting. Thus, waves, currents, and tides should not be
synthesis and respiration (Leigh et al., 1987; Nixon, omitted from the ecosystem model any more than from
1988; Adey and Hackney, 1989; Carpenter et al., 1991). the wild community (Color Plates 9, 41, and 46). They
Water Motion 25
FIGURE 2.9 Major biogeographic provinces of rocky shore in the world’s oceans. These are the coastal areas that one would expect to have
strongly distinctive flora and fauna; the unhatched areas between the provinces are transitional. From Adey and Steneck (2001).
TABLE 2.1 Heating and Cooling of Selected Model Ecosystems Described in Chapters 20–22
(Normal temperature Type Heat Type Heat
range) exchanger exchanger
3000-gallon reef, Smithsonian 2000 W, titanium coated, None Two titanium immersion None
(25–28°C) immersion heater (Process water chillers, 1 hp each
Technology, Inc.) (Aqua-Logic)
130-gallon reef, home system Two 100-W glass aquarium None Air-conditioned room held at
(25–28°C) heaters for winter minimum 23°C; no supplemental cooling
750 000-gallon reef Great Barrier Open air at Townsville, QLD, Water chiller Plastic tubing
Reef Marine Park Australia; supplemental heating coils in tidal
(25–29°C) from scrubber lights and immersion reservoir
heater if necessary
Chesapeake estuary Temperature-controlled room; no Air-conditioned room and
(20–28°C, summer) supplemental heating input sea-water cooled
(4–6°C, winter) with an immersion chiller
Florida Everglades estuary Propane-heated greenhouse None One titanium water chiller, Plastic tubing
(25–28°C, summer) Three 4000-W immersion 2 hp (Universal Marine coils in water
(18–21°C, winter) heaters (Process Technology, Industries) distribution
Florida Everglades fresh water Propane-heated greenhouse None One titanium water chiller, Plastic tubing
(25–28°C, summer) Immersion heater as necessary 2 hp (Universal Marine coils in
(20–22°C, winter) Industries) upper pool
2500-gallon Maine rocky shore None needed Three titanium immersion water None
(12–15°C, summer) chillers, 1 hp each (Aqua-Logic)
26 2. The Envelope
FIGURE 2.10 Comparison of the biomass of soft bottom infauna in marine, estuarine, and
fresh-water environments. After Nixon (1988), with mean curves fitted by eye. Weights are
shell-free, ash-free dry weights. The wider curve to the right represents salt and brackish water.
The narrow curve to the left/center represents fresh water.
need not be, and often cannot be, of the great force and in colder climates, by autumn and spring overturns
energy that they sometimes are in the wild. However, (Figure 2.6). Overturns result from surface cooling in
wild levels during storms are often far above satura- the autumn (or heating in early spring) when the sur-
tion levels in terms of their effects on ecological face waters become heavier than deeper waters. Under
processes. On the other hand, storm or even weekly or some conditions, particularly in warmer and less
monthly high waves or currents may determine com- windy seasons, or in the tropics where lakes can be
munity structure in many cases. If these high-energy warm at the surface year round, the surface waters
communities are to be simulated, at least in a localized become warm, light, and strongly stratified. When this
way within a model system, then steps need to be taken happens, mixing with deep-water stops. If the bottom
to provide strong point sources of physical energy. sediments are even moderately rich in accumulated
organic material, bacteria, worms, and clams in the
mud can use up all of the available oxygen and leave
Currents in Fresh Waters
the bottom sediments and even some of the bottom
Currents, sometimes extreme, occur in streams and water virtually dead. This is more likely to happen in
rivers. Those currents control mixing and circulation, lakes with greater nutrient input, and therefore higher
as well as the nature of bottom sediments (see below). productivity levels (Figure 2.12). Lake Tanganyika in
That currents also occur in lakes and are of great East Africa is a well-known example of such a lake,
importance is not as widely recognized (Figure 2.11). with about 90% of its total volume being permanently
As we noted above, lakes are also mixed by wind and, devoid of oxygen.
Water Motion 27
FIGURE 2.11 Surface current patterns in Lake Constance, Switzerland. Average rates in shallow water are 10–20 cm/s and reach 27 cm/s at
some localities. After Hutchinson (1957). Reprinted by permission of John Wiley & Sons, Inc.
FIGURE 2.12 The relationship of stratification (as shown by temperature curves) and oxygen in different types of lakes (Feforvatn: biologi-
cally sterile; Breiter Lucin: intermediate; Green Lake: highly productive). [O2] oxygen observed; [O2]s saturation level at temperature;
temperature; bottom. From Hutchinson (1957). Reprinted by permission of John Wiley & Sons, Inc.
It is also not unusual for even quite large lakes and and the dead zone has continued to grow (Price, 2005).
estuaries to become unnaturally anaerobic due to the Unfortunately in these cases, since phosphorus does
nutrifying effects of human activity. Chesapeake Bay in not diffuse easily through oxygenated sediment, slight
eastern North America, one of the largest estuaries in deoxygenation releases stored phosphorus in large
the world, is just such an example. A deoxygenated quantities. This triggers more surface productivity and
layer began to appear in deeper waters during the sum- a “snowballing” of deoxygenation. Many lakes in pop-
mer in the 1950s. In spite of great effort and expense to ulated or heavily farmed areas have reached a similar
reduce nutrient loading over the last 30 years, popula- state, and now the northern Gulf of Mexico, off the
tion growth in the watershed has offset improvements Mississippi River, has developed a large, hypoxic zone.
28 2. The Envelope
Currents in the Marine Realm primarily by density as established by salinity and tem-
perature (Figure 2.14). As in lakes, the limited circulation
In open, shallow-water marine environments con-
in deep water results in oxygen depletion (Figure 2.15).
stant and relatively rapid turnover of living biomass is
However, in this case because of the enormous depths
the rule, longevity the exception. Organic-rich sedi-
involved, the organic material raining from the surface is
ments, equivalent to marshes on land, can form in deeper
largely broken down within the upper 1000 meters. The
water, in the extensive shelf environments and in pro-
oxygen minimum occurs in the 500–1500-meter range,
tected lagoons and bays. These organics can become geo-
and oxygen concentrations generally increase in even
logically stored for hundreds of thousands or millions of
deeper water. The deep and bottom waters are generally
years. However, the short-term in-situ storage of biomass
very cold and relatively oxygen-rich, being derived from
as in terrestrial forests and swamps does not readily
very slow-moving bottom currents from the surface
occur in the near-coastal marine or aquatic realms. A
waters of the Arctic and Antarctic.
rapid exchange of gases (oxygen, carbon dioxide),
metabolites (food, nutrients, nitrogenous wastes), and
salts and minerals between aquatic organisms and their
watery environment is the normal state in high-energy While the larger-scale circulation of the ocean is in
environments. On the other hand, these low-biomass, large measure driven by long-term wind stress, wave
high-water quality zones remain in that state in large action more directly and strongly mixes the surface
measure because of export and storage of organics else- layers of water. Figure 2.16 shows how a wave, whether a
where, whether in deeper water or in lagoons and bays. wind wave or swell, disturbs, and mixes surface waters
The world’s oceans develop major surface currents by its motion. Waves driven for several hours or more
(Figure 2.13). These currents are created primarily by by any wind over 12–15 knots and for a distance of over
prevailing winds, modified by Coriolis (Earth rotational) several miles can have large effects on the shore and the
and density forces as well as by land geography. While biological and ecological processes of that shore. Most
moderate in rate, ocean currents can, however, reach sev- oceanographic text books provide tables or graphs for
eral knots (e.g. the southern Gulf stream). Ocean currents predicting wave heights, wavelengths, and their fre-
provide mixing and heat transfer for the entire ocean, quency. Marine literature, including sailing directions,
and consequently the atmosphere. They are major factors and maritime forecasts, provide similar information.
in determining weather patterns. Below several hundred Waves can accomplish more than circular internal
meters, circulation generally is slower and is driven motion and turbulance when they are driven against
FIGURE 2.13 Surface circulation of the world’s oceans. After Kennett (1982).
Water Motion 31
FIGURE 2.17 Oxygen reduction at night in water driven over a Caribbean coral reef by the trade wind sea and swell. 1, Front of fore-
reef; 2, back of forereef; 3, front of backreef; 4, back of backreef. Note the oxygen increase at night between forereef and backreef (i.e. 2–3),
in the surf zone, due to input from the atmosphere. After Adey and Steneck (1985).
FIGURE 2.18 Wave surge and current in the Smithsonian coral reef model. See Figure 20.1. The mean inflow (across the reef)
is about 0.1 ft/s, but the oscillation (or surge) is very marked.
a surge. Filter devices usually have associated drive (though see our discussion on the effects of bubblers and
pumps. However, they are rarely used to establish cur- centrifugal pumps, below). In shallow coastal and shore
rent or waves, although that possibility sometimes communities, marine or fresh water, on which this book
exists. Even a pump of very high rating could provide focuses, water motion occurs as a result of simulated
little flow if the filter unit itself is partially clogged. tides, currents, wave action, and its resulting surge.
Newer pumping devices often include “power heads” Many devices have been constructed to create
and are capable of producing locally high current zones waves in tanks for experimental purposes, including
32 2. The Envelope
FIGURE 2.19 Reduction of oxygen production with reduced wave action in coral reef
microcosm algal scrubber (Adey and Hackney, 1989).
FIGURE 2.20 Pneumatic wave drive system used in Australian Great Barrier Reef aquarium at Townsville.
Water Motion 33
push boards and large pistons. Most recently a pneu- strong wave action. It is often necessary in models of
matic device has been extensively used for creating these systems, especially in the smallest microcosms and
waves in swimming pools, and a version of this device aquaria, to create occasional unusual turbulence either
has been used on several large mesocosms (Figure 2.20). by hand or with apparatus designed for this purpose.
For most mesocosms and aquaria a variation of the sim-
ple dump bucket (Figure 2.21) is the most reasonable
approach in terms of cost and maintenance. If the dump
rate is matched to the natural frequency of the tank
(determined by “rocking” or seiching the tank water Among the wide variety of pumps available for mov-
mass by hand), a high surge rate can be created. Often, ing water in microcosms, mesocosms, and aquaria, the
however, it is desirable to slightly mismatch wave dump most commonly used is the centrifugal/impellor pump.
with natural frequency to avoid waves that become These can be inexpensive, reliable, and quiet, and a wide
excessive. If diaphragm pumps are used (Figure 2.22), a choice exists to fit almost any system design. Submersible
surge or seiching motion can also be created by periodic impellor pumps are readily available and can be quieter
suction. and esthetically more desirable than those designed
Moderate waves, created by the techniques described for operation in air as they can be hidden within a tank.
in this chapter and in Chapters 20–23, are normally suf- However, with plumbing failure they also have the
ficient to maintain community structure on the scale of potential for pumping a tank virtually dry unless the
days and perhaps weeks. However, many ecological intake is placed very high. Submersible pumps also tend
communities, especially those of rocky shore and reef to raise system temperatures, and some varieties have
environments, are partly structured by occasional the potential for leaking oil.
FIGURE 2.21 Photographs of dump-bucket wave maker. Note that these devices are highly sensitive to weight shift
and easily become unbalanced with algal growth. Proper setting of the hinge axis and the use of friction-minimum bear-
ings that will not corrode are essential. We have found that Teflon against Teflon is the only foolproof method, although
Teflon against other plastics is usually acceptable. We have also used Nylatron, as the axis against a Teflon bearing.
34 2. The Envelope
FIGURE 2.22 The 30-rpm, 5-gpm diaphragm pumps as installed in a 130-gallon scrubber-operated reef aquarium (see Figure 20.18). The
dark area to the right is a refugium. The scrubber unit is off the photo to the right (see Color Plates 8A and 8B). Photo by Nick Caloyianis.
The unfortunate difficulty with most impellor extensively used the bilge pump system shown in Figure
pumps is that their internal turbulence, pressure, and 2.22 on many small aquarium systems (see Chapters
shear forces kill many plankters and the swimming or 20–23). Sophisticated engineering and manufacture for a
floating reproductive states of plants and animals. We mass market could make these pumps “standards.”
have been able to demonstrate a greater than 90% mor- Archimedes’ screw pumps are ancient devices used
tality of large zooplankters, such as Artemia salina, on centuries ago, particularly in irrigation. Today, they
passing through such a pump. Impellor pumps select still merit usage in sewage plants where a simple, vir-
plankton populations in a system, killing some and tually uncloggable pump to move large quantities of
effectively enhancing others. This is the basis for the water at minimal height is desired.
development of tinted waters (yellow or green) in We have had experience with several, large
some systems and not in others (see also discussion in Archimedes’ screw pumps in mesocosm systems. They
Chapter 6). are unexcelled at lifting large quantities of water without
We have experimented with alternatives to the ubiqui- significantly disturbing plankton, or even larger inverte-
tous impellor pumps. Among the possibilities are rela- brates and fish (typically they lift to a distribution reser-
tively large diameter diaphragm pumps that contain voir). However, Archimedes’ screw pumps have a
“flapper valves” and alternate relatively slowly from a tendency to burn out drive motors, during restart (under
slight suction to a slight pressure (Color Plates 2, 4–6). heavy water loading) during power outages. Also, the
Some compressed-air-driven types for transferring cor- primary lower bearing is subject to corrosion and wear.
rosive slurries in the chemical and other industries work Both of these issues are minor engineering problems.
quite well and are easily available. However, they are Recently, a promising “bubble-lift” pump that uses
expensive and often quite noisy. We have designed and large bubble “bursts” injected into a chamber from a
Tides: Simulating the Effects of Sun and Moon 35
low-pressure, high-volume compressor has been devel- Many factors determine actual pumping rate com-
oped. This is basically a smaller version of the wave gen- pared to the rate given on the pump or pumps. Besides
erator shown in Figure 2.20. Because a single bubble on the pump rating, water delivery rate is a function of
the order of several hundred milliliters to a liter or two both suction and delivery heights, length of flow, and
(depending on pump dimension) will lift a relatively the size of the pipe, as well as any restrictions to flow.
large volume of water, the bubble surface that traps Bacterial filtering devices can greatly reduce actual out-
plankton is greatly limited. Thus, the “skimming effect” put, as well as destroying plankton. It is inappropriate
of standard aerators or bubblers, which removes plank- to use such filters in model aquatic ecosystems unless
ters, particulates, and large organic molecules, is partly they mimic a desirable feature of a wild system (e.g. a
avoided. large filter feeder). In our discussions below we refer to
Centrifugal pumps that lack impellors and have sim- actual flow.
ple discs, or discs with grooves or ridges, called disc- In general, if algal scrubbers are used to control
flow pumps, are used in the food-processing industry to water quality, a minimum rule-of-thumb flow rate over
pump a wide variety of foods. These pumps are an the scrubbers is 40 liters (10 gallons) per minute per
acceptable alternative to the impellor pump replace- one square meter (10.6 square feet) of scrubber surface.
ments described above when the values of a centrifugal If this rate is not acceptable for achieving the currents
pump are needed. Since disc-flow pumps are not yet desired, then a separate recycling pump can be used,
being built for the mass market, they tend to be rela- either on the primary tank or on the scrubbers. A sim-
tively expensive. On the other hand, we have found ple device that combines scrubbing with current, wave
them to be highly reliable (see Chapter 22) and accept- action, and wave surge is shown in Color Plate 9 and
able in maintaining diverse plankton communities. Figure 2.1. This “dump scrubber” is particularly effec-
Pumping rates vary from system to system. At the tive when minimum space is available in a small system
Smithsonian, the coral reef system overturned approx- and the desirability of mounting all apparatus directly
imately every 60 minutes, and the Maine rocky-shore, on top of the tank is a foremost consideration.
mud-flat tank overturned approximately every 45 min- It is best to split up the pumping among as many
utes. The small, home, 130-gallon reef described in small pump units as economically and physically feasi-
Chapter 20 overturned every 20 minutes. The 750 000- ble, thereby lessening the threat to the whole system
gallon reef system at Townsville, Australia (Chapter when a pump breaks down, as it inevitably does. There
20), is completely pumped around every 2.9 hours should always be backup pumps readily available.
(Jones, 1988). There is no way to arrive at an ideal rate Beyond the inevitable contamination, we remind the
without taking oxygen measurements in the fully func- modeler, whatever the level, that the single most fre-
tioning system (see Chapter 8) and comparing actual quent source of massive failure is catastrophic leakage
currents and surge, depending on design, with the usually from plumbing. Also, pumps and electricity
wild analog. The mean flow rate across the St. Croix will fail. If there is a dynamic water mass (i.e. water in
analog coral reef is 10 cm/s, three times as high as that transit) in a system, adequate sump volume (e.g. the
in the Smithsonian model at 3 cm/s. On the other hand, tank itself) must be allowed.
turnover time (ocean water replacement) on the wild
reef averages about 6 hours compared to 1 hour in the
model mentioned above. Thus, these related parame- TIDES: SIMULATING THE EFFECTS OF
ters are both within the right order of magnitude, but SUN AND MOON
displaced in opposite directions because of critical size
restrictions in the model. A secondary and related The ebb and flow of tides is one of the most fascinat-
parameter, water quality in the model as measured by ing aspects of the sea. Even though lakes show sea-
dissolved oxygen concentration, is remarkably close to sonal or meteorological changes in level, tidal effects
that in the wild (see Figure 8.9). This kind of give and are virtually absent, and on some ocean coasts (e.g. the
take matching is crucial to the modeling process. In southwestern coast of Norway), tides are small enough
general, warmer and smaller microcosms and aquaria to be more or less negligible. However, as we pointed
should turn over more frequently than larger and out above, bottom biomass in lakes is generally less
colder systems. Oxygen solubility in cold water is than in the sea, probably in large part due to tidal
almost twice that in tropical waters (see Chapter 8). effects (Figure 2.10). Many biological communities (e.g.
Therefore, drawdown for a given biological load is less salt marshes and rocky intertidals) depend entirely on
critical in cold water. Also, smaller systems will usually tides, and it has been demonstrated that the mixing
be more overloaded than larger ones. Thus, greater cir- effects of tides provide an energy subsidy to ecosystem
culation in proportion to volume is desired. function (Figure 2.23). In addition, many organisms
36 2. The Envelope
FIGURE 2.23 Energy flow diagram developed for the Narragansett Bay ecosystem. Note that
tide has been given a major controlling role both on solar input and on export from the bay. The
boxed form of tidal attachment also indicates tidal effects driving all levels of the ecosystem.
After Kremer and Nixon (1978).
key important elements of their life cycles, particularly before being washed out to sea, it provides a more pre-
reproduction, to the tides and to the moon (Palmer, cise way to ensure fertilization of large numbers of
1995). Sophisticated lighting control systems for home eggs. Also, the tide pool situation is one that is difficult
aquaria have begun to include a moon component. for many fish to occupy. Wrasses, for example, would
As an example of the complex ways in which tides otherwise eat the eggs as they are released. Thus, the
and moon, together and separately, can affect an organ- tide pool provides relative freedom from fish predation
ism (and therefore a community), we cite the case of and it seems likely that in part this also has resulted in
the Caribbean/West Indian magpie shell, Cittarium the evolution of this curious pattern. A similar repro-
pica. This large, rocky intertidal and upper subtidal ductive keying to spring – higher high tides on sandy
snail, characteristic of exposed wave-beaten shores, California beaches – is practiced by a fish, Leuresthes
achieves some gastronomic use in the Caribbean. Three tenuis, the grunion. Thurman and Webber (1984)
to five days after the new moon (i.e. during the darkest describe this process and its relationships to tide in
nights of the month), the males and females crawl into some detail.
exposed tide pools at high tide. When tide level lowers The intertidal zone itself is truly the interface between
sufficiently to isolate the pool, the snails start releasing the terrestrial and the marine, and this area is the most
eggs and sperm into the water. (It is not known easily accessible of marine environments. Many scientific
whether elevated temperatures, hydrostatic pressure, studies have been carried out in the intertidal zone and
lack of wave action, or some other factor alerts the ani- some excellent books describe it (Raffaelli and Hawkins,
mal that the pool is isolated.) Fertilization takes place 1996; Haywood, 2004). One of the finest of the classic
in the pool and the developing larvae are washed into works is Between Pacific Tides (Ricketts et al., 1985), first
the ocean as the rising tide floods the pools. This com- written in 1939 and now in its fifth edition. In particular,
plex and multi-keyed reproductive pattern offers the rocky intertidal and salt marshes, restricted to the
many advantages. To an animal living on a wave- intertidal zone, are important subjects for model ecosys-
beaten shore where eggs and sperm released into the tems and we describe several of these models in later
water would have a difficult time coming together chapters.
38 2. The Envelope
FIGURE 2.25 A variety of tidal curves from ports scattered around the Earth, September
1958. After Gross (1982).
can be, for those organisms able to withstand its rigors tides); (2) a periwinkle snail or littorinid snail zone
successfully, competition and predation are generally (roughly the upper half of the tide zone); (3) a white
reduced and for the plants both maximum light and a and very rough barnacle zone (the lower half of the reg-
very reliable water supply can be achieved. ular tide); and finally (4) a mussel zone between neap
The intertidal zone itself is often strongly subzoned, and spring low tides. Specific areas have even more char-
and such zonation can be related to patterns of tidal acteristic communities, such as the rockweeds (brown
form and height. Typically, worldwide, the basic pat- algae) and Irish moss (red algae) of the North Atlantic
tern of zonation from top to bottom in the rocky inter- (see Chapter 21). Some of the most interesting marine
tidal is: (1) a black band of blue green algae and lichens and estuarine plants and animals richly occupy the inter-
(in the spray zone or just at or above the highest regular tidal zone and form unique and highly productive
Tides: Simulating the Effects of Sun and Moon 39
communities (Figures 2.26 and 2.27). In more protected Whether tides should be considered a factor in a
areas salt marshes and mangrove swamps cover many microcosm depends on the marine community being
square miles and provide extensive habitats for inter- simulated. None of our coral reef tanks, all based on
tidal organisms, insects, and birds. These too are Caribbean reefs, has had a tidal element. While in some
strongly zoned to the tide (see Color Plate 40), even places of very high wave energy the intertidal algal ridge
when beyond the limit of salt water (Odum et al., 1984). is one of the most fascinating communities on Caribbean
Extensive mud flats, often found in protected areas reefs, for most reefs in this region tides are relatively
having extreme tide ranges, can become rich reservoirs unimportant. On the other hand, on the Australian Great
of organic particulates. These organic-rich, muddy bot- Barrier Reef, tides of 3–10 feet (1–3 meters) are an
toms are largely derived by wash-in from more extremely important ecological element. The Great
exposed areas and from streams and rivers. Tidal flats Barrier Reef Marine Park reef aquarium in Townsville,
are occupied by a host of small invertebrates, including Australia, provides a moderate tide range. In the simula-
many clams prized as human food. tions of the rocky Maine coast and Chesapeake Bay and
the Florida Everglades described in this book, tides were
too important to ignore and are critical elements.
Tides and the Model Ecosystem
Developing a tidal system in a closed microcosm is
While a few research systems have been built partic- in part a matter of time-regulating higher and lower
ularly to investigate the effects of oil on rocky shores water levels. This is most easily accomplished by tem-
and marshes, and some of the more progressive public porarily storing water at times of low tide in a separate
aquaria have constructed ecological models to show reservoir (Figure 2.28, and Figures 22.8 and 22.9). The
the effects of tides in appropriate tanks, tidal models tidal reservoir can also serve as a fine-sediment settling
are rarely constructed. This situation is peculiar since trap and refugium for the numerous worms and small
accomplishing a rather accurate intertidal simulation is crustaceans that characterize deeper-water mud bot-
not difficult. toms. As we discuss throughout this book, refugia and
FIGURE 2.26 The vertical zonation of organisms occurring on intertidal rocky shores on the Pacific coast. Reprinted from Ricketts et al.
(1985), revised by David W. Phillips, with the permission of Stanford University Press.
40 2. The Envelope
FIGURE 2.27 The vertical zonation of intertidal organisms on hard bottoms of the Atlantic coast.
Modified after Gosner (1978). Reprinted by permission of Houghton Mifflin Co.
FIGURE 2.28 Photograph of tidal controller attached to a tidal reservoir on the Maine coast microcosm.
The center motor rotates approximately twice a day to create the semidiurnal component. The outer motor
rotates once every 2 weeks to create neaps and springs.
Tides: Simulating the Effects of Sun and Moon 41
settling traps are critical elements of model ecosystems submergence) times in the microcosm are the same as in
that allow the simulation of much larger wild environ- the wild. Marsh vertical ranges are always much smaller
ments. If it is desirable to save space, two separate than the total tide, generally occupying only the upper
reservoir systems or two separate parts of the same half of the tide range.
tank can be operated on alternate tide cycles. In our
Florida Everglades mesocosm, the estuary served as
the tidal reservoir for the Gulf of Mexico portion of
the system. Pumps first pumping in one direction (to the References
reservoir) and then in the other direction (back to the Adey, W. and Hackney, J. (1989) Harvest production of coral reef
main tank) can also be used; however, unless a compli- algal turfs. In: The Biology, Ecology and Mariculture of Mithrax spin-
osissimus Based on Cultured Algal Turfs. W. Adey (Ed.). Mariculture
cated multiple pump arrangement is employed, the
Institute, Washington, DC.
result is a sawtooth tidal pattern rather than the sine- Adey, W. and Loveland, K. (1991, 1998) Dynamic Aquaria: Building
type curve of the wild. The sawtooth curve reduces by Living Ecosystems, 1st and 2nd edn. Academic Press, San Diego.
about 25% the total times of high and low tide. Adey, W. and Steneck, R. (1985) Highly productive eastern
We have designed a water-level tidal management Caribbean reefs: synergistic effects of biological, chemical, physi-
cal and geological factors. In: The Ecology of Coral Reefs. M. Reaka
system based on interval timer control of stepping
(Ed.). NOAA Symposium Series on Underwater Research, Vol. 3.
motors (Figure 2.28 and Color Plate 41; see also Figures Washington, DC.
22.7–22.9). This method creates pure semidiurnal tides Adey, W. and Steneck, R. (2001) Thermogeography over time creates
and provides for biweekly springs and neaps as well as biogeographic regions: a temperature/space/time-integrated
for the 50 minutes’ daily timing advance to “follow the model and an abundance-weighted test of benthic marine algae.
moon.” The approach is generally trouble-free and J. Phycol. 37: 677–698.
Bansal, N. and Doremus, R. (1986) Handbook of Glass Properties.
inexpensive. The system can easily be adapted to a Academic Press, Orlando, Florida.
diurnal tidal cycle simply by changing the timing on Briggs, J. C. (1974) Marine Zoogeography. McGraw-Hill, New York.
the primary stepping motor drive. Stepping motor Carpenter, R., Hackney, J., and Adey, W. (1991) Measurements of pri-
control can be modified to simulate virtually any tidal mary productivity and nitrogenase activity of coral reef algae in a
cycle, even a mixed diurnal/semidiurnal tide. chamber incorporating oscillatory flow. Limnol. Oceanogr. 36: 40–49.
Carson, R. (1962) Silent Spring. Fawcett Crest, New York.
Mud flats and rocky shores are relatively easy to Climap Project Members (1976) The surface of the ice-age earth.
establish and manage in an intertidal microcosm. Some Science 191: 1131.
care should be taken to stock organisms at their proper Gosner, K. (1978) A Field Guide to the Atlantic Seashore. Petersen Field
zonal level, and this can be quite difficult when a large Guide Series, Houghton Mifflin, Boston.
vertical tidal zone in the wild analog is reduced to a rel- Gross, M. G. (1982) Oceanography: A View of the Earth. Prentice Hall,
Englewood Cliffs, NJ.
atively narrow zone in the model. However, commu- Haywood, P. (2004) A Natural History of the Seashore. Collins, London.
nity adjustments in the microcosm generally develop Hutchinson, G. E. (1957) A Treatise on Limnology, Vol. 1. Wiley, New
slowly over many months without detrimental effects. York.
Rocky intertidals in particular are adjusted in the wild Jones, M. (1988) The Great Barrier Reef Aquarium: A Matter of Scale.
Northern Reg. Eug. Conf. (Australia), Townsville, June 10–13.
to wave action, with given zonal bands being higher
Kennett, J. (1982) Marine Geology. Prentice Hall, Englewood Cliffs, NJ.
with increased wave action (Figure 2.27). Also, rocky Kremer, J. and Nixon, S. (1978) A Coastal Marine Ecosystem Simulation
intertidals are notoriously patchy, with the effects of and Analysis. Springer-Verlag, Berlin.
settlement, wave action, local terrain, and local preda- Leigh, E., Paine, R., Quinn, J., and Suchanek, T. (1987) Wave
tion varying widely. These effects have been favorite energy and intertidal productivity. Proc. Natl. Acad. Sci. USA 84:
subjects for studying the dynamics of community
Levinton, J. (1982) Marine Ecology. Prentice Hall, Englewood Cliffs, NJ.
structure (see Haywood, 2004). In an aquarium or Levy, S. and DuBois, J. H. (1984) Plastics Product Design Engineering
small mesocosm, the available shore can become a sin- Handbook. Chapman and Hall, New York.
gle patch changing from time to time. The process can Marino, B. D. V. and Odum, H. T. (1999) Biosphere 2, Research Past and
be altered and directed by the “disturbance” of the Present. Elsevier Science. An Elsevier Science Publication, Ireland.
Reprinted from Ecological Engineering Spec. 13(1–4).
aquarist. Algal, mussel, and barnacle zonation on the
Marra, J. (2002) Approaches to the measurement of plankton produc-
rocky intertidal of an aquarium system, with the graz- tion. In: Phytoplankton Productivity. P. J. leB. Williams, D. Thomas
ers and predators that occupy the same environment, and C. Reynolds (Eds). Blackwell Science, Oxford.
can be an exciting model to manage. Nixon, S. (1988) Physical energy inputs and the comparative ecology
Marsh communities are considerably more sensitive of lake and marine ecosystems. Limnol. Oceanogr. 33: 1005–1025.
Odum, W., Smith, T., Hoover, J., and Mclvor, C. (1984) The Ecology
to tidal levels than rocky intertidals. In microcosms of
of Tidal Freshwater Marshes of the United States East Coast: A
small or microtidal ranges (less than 2 feet in the wild), Community Profile. U.S. Fish and Wildlife Service OBS-83/17.
it is important to place the sod surface of marsh grasses Palmer, J. (1995) The Biological Rhythms and Clocks of Intertidal Animals.
at the equivalent tidal level so that total exposure (and Oxford University Press, London.
42 2. The Envelope
Price, J. (2005) Chesapeake Bay an Undeclared Ecological Disaster. Thurman, H. and Webber, H. (1984) Marine Biology. Addison-Wesley
Chesapeake Bay Ecological Foundation. On-line piece, Sunday, Educational Publisher, Menlo Park, CA.
October 23, 2005. Vannote, R. and Sweeney, B. (1980) Geographic analysis of thermal
Raffaelli, D. and Hawkins, S. (1996) Intertidal Ecology. Chapman and equilibria: a conceptual model for evaluating the effect of natural
Hall, London. and modified thermal regimes on aquatic insect communities.
Ricketts, E., Calvin, J., Hedgpeth, J., and Phillips, D. (1985) Between Am. Nat. 115: 667–695.
Pacific Tides, 5th edn. Stanford University Press, Stanford, CA. Walter, H. (1979) Vegetation of the Earth, and Ecological Systems of the
Spotte, S. (1995) Captive Seawater Fishes. Science and Technology. Wiley, Geo-Biosphere. Springer-Verlag, New York.
C H A P T E R
The Active Role of Rock, Mud, and Sand
In the first two editions of this book, we emphasized last decade to bring the relatively new science of plate
the construction of living models or microcosms and tectonics into a modern framework that includes the
mesocosms of aquatic ecosystems. Our logic at that life sciences (e.g. Redfern, 2001; Marshak, 2004). That
time in presenting a background chapter on geology, review should be followed by a more detailed examina-
including the origin of the rocks that provided the base tion of local geology and sedimentation.
of some aquatic ecosystems and the sediments that pro- Lithospheric activity, centered on plate tectonics,
vided the base of other ecosystems, was that the nature determines the shapes of seas and oceans and greatly
of the substrate was critical to the character and func- constrains open ocean currents. The position of conti-
tion of the ecosystem being modeled. Also, the salinity nents, also constantly moving, relative to the Earth’s
of the oceans and coasts and the chemical composition axis, along with the major ocean currents, over geolog-
of fresh waters is determined by the nature of the rocks ical time is a very important factor in global climate.
over and through which the water flows. This might Even more directly, along coastlines and mid-ocean
have seemed quite remote for the oceans, but now we ridges, and of course in fast-moving streams and along
know more about the hydrothermal vents along ocean the shores of larger lakes, rock provides a surface to
ridges and how sea water is constantly circulating and which organisms attach and from which they interact
chemically interacting with hot and even liquid ocean in myriad ways with the aquatic environment.
crust (van Dover, 2000). Also, with human mining, and The processes of weathering, transportation, and
coal and oil extraction from the Earth’s crust, we have sedimentation, whether on continental shelves or in
become aware of the extensive changes to streams and the deep ocean, result in the constant geological-scale
rivers, the Earth’s atmosphere and even the chemical sequestering of carbon and other nutrient and mineral
character of the oceans (e.g. Kleypas et al., 1999). (i.e. elemental) requirements used in the building of
In this edition, we have changed our focus some- living cells and tissues. Thus, ultimately, the underly-
what and argued that all ecosystems on Earth are con- ing lithosphere or rock, in its interaction with the
trolled by human activity and are in effect macrocosms. atmosphere and the hydrosphere, or liquid water enve-
It is simply a matter of scale between the microcosms lope, determines the concentrations and thus the avail-
and mesocosms that we build for research, education or ability of many of the basic chemical building blocks of
hobby, and those macrocosms, altered by human activ- life in the ocean. Except in closed basins and areas of
ity, that we seek to restore to a pre-industrial state (or at high evaporation relative to precipitation, fresh waters
least rehabilitate). In ecosystem restoration, it is even are transient sites for elements, mostly in low concen-
more important that the restorer understand the geo- trations, on their way to the sea.
logical background and framework of the ecosystem It is perhaps not unreasonable for the modeler or
being treated. Although here we present a basic back- aquarist working on an oceanic plankton community
ground in geology and sedimentology, we recommend to regard the ocean characteristics, for all practical pur-
that the modeler and restorer, before initiating work, poses, as independent from the lithosphere. For the
review one of the broader texts that have evolved in the ocean restorationist, however, that would not be the
44 3. Substrate
case, for most ocean and coastal pollution today Our planet still has considerable heat (from gravita-
derives from land/river/bay run-off. And for benthic tional collapse and radioactivity) in its hot, liquid or
(bottom), shoreline, and of course stream, river, and semi-liquid interior. The hard, semi-plastic crust of the
lake shore situations, the presence and nature of the Earth caps a slowly churning mantle cauldron. This has
rock bottom, and the sediments derived from those given rise to a rather remarkable evolution of the surfi-
rocks, can be crucial to the function of both a wild cial crust that has been a major catalyst to the evolution
ecosystem and its model. It might make the modelers’ of life and in many ways determines and constrains its
endeavors easier to regard that surface of rock as a the- ecology today. The “boiling up” of this mantle cauldron
oretical boundary, an attachment but nothing more, has gradually concentrated relatively light minerals par-
like the glass of the model’s wall. Perhaps in some ticularly rich in silica, aluminum, and potassium in scat-
cases, a smooth basalt bottom for example, this might tered “floating mounds” called continents, which are
actually be the case. In most cases, however, the geo- raised above the generally heavier calcium-, magne-
logical world is less remote from the needs of the sium-, and iron-rich crust of the Earth (Figure 3.1). The
modeler or ecological restorer than a preliminary look oceans, occupying primarily the deeper parts of this two-
might suggest. level surface (Figures 3.2 and 3.3), have a mean depth of
3730 meters, while the continents are slightly raised
(above sea level) to an average height of 870 meters.
THE SOLID EARTH AND LIFE Through the process of plate tectonics (continental drift),
the boiling up of the Earth’s cauldron is constantly split-
The Earth, as viewed from space, with approximately ting the crust, changing the shape of both continents and
70% of its surface covered with water, would be most oceans (Figure 3.4). When pieces of the crust driven by
appropriately called “planet water.” The size of the the cauldron collide, earthquakes, mountain chains, and
Earth, its distance from the sun, and its moderate level sometimes very active volcanoes are created and ocean
of internal energy production have allowed it to retain a levels are changed (Marshak, 2004).
massive volume of water (in the liquid state). This water, Thus, there has been throughout much of the Earth’s
as we described in Chapter 1, was probably brought to history, and is certainly on-going today, a very active
Earth early in its development by comets. However, the relationship between the Earth’s lithosphere, with its
retention of the water, more than any other single factor, minerals and elements, and the hydrosphere, the origi-
has led to the development and evolution of life. nator of life. This relationship is strengthened by the
However, if the hard surface of the Earth, the litho- continuous formation of limestone and other sedi-
sphere, were smooth (i.e. nearly spherical), then the ments in which living or recently dead organisms play
solid Earth would be covered uniformly with approxi- a crucial role. Sedimentary rocks or structures include
mately 2600 meters (8000 feet) of ocean. Although life those that are formed largely by the skeletons or even
probably would have developed and evolved under the organic matter of dead organisms (coal, oil shales).
such a regime, without a more active inclusion of the The Earth’s crust is a melange of rocks created by tec-
lithosphere in the atmosphere–hydrosphere interaction, tonic and volcanic activities, and the results of the
it would certainly be far less diverse. Probably it would reworking of those rocks by atmospheric and hydros-
still be very primitive, as it was several billion years ago. pheric processes.
FIGURE 3.1 Schematic section of the crust of the Earth at about 3.8 billion years BP. Prior
to this point most of the crust was oceanic (basaltic), and creation of crust at ocean-spreading
centers (a) was followed by subduction back into the mantle with little change. At the time
shown, the fractionated lighter material of future continents (b) has been minimal and usually
subducted with the basaltic crust (1). However, larger pieces (2) are beginning to survive, even-
tually leading to full continent formation. From Lowe (1994).
The Solid Earth and Life 45
FIGURE 3.2 Hypsographic curve of the distribution of the amount of Earth surface at
different elevations. After Kennett (1982).
FIGURE 3.3 Worldwide plate system showing the placement of “raised” continents and oceanic crust with its deep ocean.
Continental margins are shallow coastal areas, presently submerged but belonging to continents, and are shown cross-hatched.
The ocean ridges form over hot up-flowing areas in the underlying mantle and are sites of new ocean crust formation. Ocean
crust slides away from the ridges and sinks and melts in the subduction zones. Volcanic hot spots are mostly on ridges or sub-
duction zones, though a few (like the island of Hawaii) are isolated beneath either ocean crust or continents. After Gross (1982).
46 3. Substrate
FIGURE 3.4 Development of oceans through seafloor spreading: (A,B) formation of rifts; (C) rift valley
with lakes stage (see Figure 3.5); (D) “Red Sea” stage; (E) young ocean stage, subduction started on right;
passive margin on left. After van Andel (1985).
Crucial additions to an already active rock, water, in solar radiation and the orbit and rotation of the Earth,
and atmosphere interface, changing mostly on the scale and partly due to the change of the positions of conti-
of many millions of years, are major alterations of over- nents and sea bottom relative to ocean currents, cooling
all Earth climate on the scale of tens to hundreds of of the poles results in large-scale glaciation. These “con-
thousands of years. Partly due to slight cyclical changes tinental” glaciers produce both radical alterations in
The Solid Earth and Life 47
FIGURE 3.5 Formation of large continental lakes by rifting of the Earth’s crust. After Burgis
and Morris (1987).
rock weathering (by ice) and sea-level changes. Even in North America are an example of this process.
in mid-latitudes, sea-level changes resulting from the Elsewhere, a variety of local factors such as volcanism,
locking of water in ice caps near polar regions and the beach drift along the shore, rivers that change their
bending of the Earth’s crust as weight distribution of ice course, and of course human activities result in lake
and water changes result in marked alterations of both and estuary formation. Stream formation results from
coastal areas and, as the gradient changes, the lakes and the run-off of rain working against tectonism, that is,
streams that drain into them. In addition, while some major Earth movements, and the relative resistance of
lakes and rivers can result from tectonic effects, for the underlying rocks to stream erosion. Clearly human
example, the African Rift Valleys (Figure 3.5) and the activity can radically alter many of the above described
Andean lakes, the majority of lakes and drainage in relationships and ecological restoration is equally pos-
high latitudes results from either the scouring or the sible as long as these relationships are understood and
mounding-up of sediment by glaciers. The Great Lakes managed.
48 3. Substrate
CHEMICAL RELATIONSHIPS BETWEEN logarithmic curve. In small planets near the sun, such as
ROCKS, SEA WATER, AND ORGANISMS the Earth, the lightest elements are lost to space. The net
result for the crust of the Earth (Figure 3.6) is a skewed
The universe is heavily dominated by the very light logarithmic, normal curve of abundance with the lightest
elements of hydrogen and helium in the atomic fires of elements depleted, the light to mid-weight elements from
the stars (see Figure 1.1 in Chapter 1). As the tempera- oxygen to iron most abundant, and heavier elements
tures of these fires degrade, as a star ages or as frag- scarce to rare. The very unreactive noble gases, helium,
ments are spun off in collisions or super novae, heavier neon, argon, etc., are anomolously low in abundance.
elements are formed. In general, with increasing atomic Pure water, possibly fractionated from the crust
weight, elements decrease in abundance according to a early in the Earth’s cooling cycle, was more likely
FIGURE 3.6 Diagram showing the abundance of chemical elements in the Earth’s crust in relation to the use of those elements by living
organisms. The principal elements of life (CHON) are light, relatively abundant, and also form water and the Earth’s atmosphere. It is signif-
icant that nitrogen is the least abundant of the principal life elements in the crust, requires energy to remove from the atmosphere, and is the
most critically limiting nutrient in the aquatic environment. The remaining organic macronutrients are drawn from the elements that form the
salts of the sea, which in turn are the next heavier and most abundant elements of the Earth’s crust. The micronutrients (with the outliers
molybdenum and iodine) are the lesser abundant and/or heavier elements of the main group. Note that aluminum, titanium, chromium, and
nickel lie within the main group and are essentially unused by organisms. Modified after Bricker and Jones from Salbu and Steinnes (1995)
and Parker (1967).
Chemical Relationships between Rocks, Sea Water, and Organisms 49
FIGURE 3.7 Concentration of some elements of sea water in relation to residency time of those elements in sea water. Data derived
from Millero and Sohn (1992) as mean of river input and sediment rate calculations.
“rained-in” from space later. Virtually all chemical ele- react more with the water cycle than the igneous rocks.
ments occur in the sea, as we shall see in Chapter 4. Ultimately, the concentration of elements in sea water
However, the heavier elements are poorly represented. is a function of their residence time (Figure 3.7) as
The dominant elements dissolved in ocean water are determined by rate of incoming (from rivers) and out-
mostly those that are also moderately abundant in going (to sediments).
the Earth’s crust. However, the proportions are not Thus, of the top 12 elements, by weight, in the salts
the same primarily because in the Earth’s crust most of sea water, chlorine at 19 000 mg/liter in sea water
elements appear as components of minerals. As the forms only about 0.03% of the Earth’s crust, while sil-
minerals of a rock exposed to atmosphere, rain, and ica, the dominant element of the Earth’s crust (28.5%) is
inorganic and organic acids dissolve in water, some an important, but minor component of sea water
elements are very mobile and move easily into streams (4 mg/liter). The top six elements of sea salt (chlorine,
flowing to the sea. Others tend to be re-bound in new sodium, magnesium, sulfur, calcium, and potassium)
minerals and stay in the crust or in sediments. To make are all “conservative.” They are required by organisms
matters more complex, sedimentation tends to further and concentrated to some degree, especially calcium.
fractionate some elements (e.g. calcium, carbon, and However, their relative requirement is minimal and the
magnesium) into new sedimentary rocks, and these concentration of the large quantity in the sea is not
rocks, common in terrestrial environments, tend to affected by the activities of organisms. Many of the
50 3. Substrate
primary chemical components of organisms (carbon, mesocosm. However, because of the scaling factor the
nitrogen, and oxygen) relate more to the Earth’s atmos- substrate can be crucial when interfacing with a small,
phere (and are gases dissolved in sea water) than to sea enclosed body of water. Of course, rocks (or gravel)
salts. Oxygen and hydrogen can enter the biosphere that are iron-rich, lead-rich, arsenic-rich, etc., particu-
through the splitting of water in photosynthesis. larly in a small system, cannot be used without an
However, phosphorus, iron, and silica, ultimately understanding of the export mechanisms of those ele-
derived from dissolution of the Earth’s crust, are ments from the system (see, e.g. Chapter 11). It is par-
organically required elements in sea water that can be ticularly important to ask what rock substrate is in
very limiting to the production of plants and therefore contact with the ecosystem to be modeled in the wild:
animals. In very pure (oligotrophic) waters, other ele- for example, carbonate rock for a reef, marine, or any
ments can also limit plant production, though such hard-water system, or a silica-rich hard rock for a black
limitation usually relates only to calcium, magnesium, or other soft-water ecosystem. Buffering and the car-
or potassium. bon dioxide/pH cycle in relationship to carbonate sub-
In general, the chemistry of life utilizes light elements strate are specifically discussed in depth in Chapter 8.
(less than atomic number 35) that are also abundant and Rock substrate is often crucial in structuring a com-
reactive. However, elements that tend to form insoluble munity in that it supplies a secure base for those organ-
compounds or become locked up by mineralization isms able to tightly attach. In addition, the spaces of
processes have generally been “avoided” by organisms. cracks or voids, sometimes abundantly available, pro-
In the universe, aluminum is more abundant than vide greatly increased surfaces for attachment and
sodium and calcium, and in the Earth’s crust it is lesser spaces for hiding. The aquarist should try to match the
only than oxygen silica in abundance. However, it configuration, or spatial heterogeneity, of the wild ana-
approaches being rare in sea water, having a residence log as closely as possible, and the restorationist may
time of about 100 years, and is unused by organisms. need to consider the changes that could have occurred
Iron is also one of the more abundant elements in the due to human activity (e.g. a sediment coating on rock
universe and in the Earth’s crust. Because it readily oxi- surface). However, the sediments, in themselves, are a
dizes to insoluble forms, its abundance in the sea is very more critical concern, and that is what we concentrate
low. However, it is crucial to all organisms. It can be sur- on here.
mised that before algae provided oxygen gas (dioxygen) Generally, whether dealing with a fresh- or a salt-
in abundance to the Earth’s atmosphere (and ocean) iron water environment, there is a strong relationship
was abundant and it became key to many life processes. between current and wave energy and the coarseness or
It is possible that “life” nearly extinguished itself, a few fineness of the bottom sediments (Figure 3.8). In micro-
billion years ago, by producing oxygen, which then cosms, mesocosms, and aquaria, sediments that have
combined with iron (as iron oxide) to deplete this ele- the same physical characteristics as those in the systems
ment from the seas. Some scientists have suggested that being modeled should be used. Strong wave action or
replacing iron in the open ocean, through a massive, currents, whether on exposed lake or ocean coasts or in
human industrial chemistry-type operation could solve a mountain stream, give rise to exposed bedrock or large
the problem of excess atmospheric carbon dioxide by cobbles or boulders providing a bare (or usually algal-
increasing open ocean photosynthesis now limited by colonized) rock. In an aquarium or mesocosm environ-
lack of sufficient iron. More recent field research has ment, if these surfaces are to be preserved as in the wild,
indicated that the effects are minimal and the costs high, equivalent or at least sufficient wave or current action
and as we discuss in Chapter 25, there are other routes to must be present. Otherwise the surface will become
increasing photosynthesis at large scale that are more coated with fine sediment and will fail to recreate the
efficient and provide additional benefits (see ATS). wild ecosystem. There is a major difference between a
However, this is the kind of global scale restorationist bare rock bottom to which organisms must attach (or
thinking that is required to solve our overwhelming bore as in softer rocks), and over which water must have
dominance of the biosphere. considerable motion, and a sediment bottom. As we dis-
cuss further in Chapter 23, in fresh-water environments,
human changes have often meant changing the water
THE SOLID EARTH, ROCK, AND energy/sediment relationships, and these are the first
MODEL ECOSYSTEMS corrections that need to be made.
In Chapters 20–23, we discuss a variety of ecosystems
It may seem remote to equate the activity of the lith- in mesocosms and aquaria with and without bare rock
osphere with the Earth’s water on a geological scale to and coral rock substrate. It is best to discuss these on
that relationship over a few years in an aquarium or an individual basis, because the very layout of this
Sediments and Model Ecosystems 51
FIGURE 3.8 Relationship between the movement of sediment and the grain size of the
sediment as a function of water velocity. After Davis (1983).
substrate often provides the primary habitat for the sandy beach between a dune and a wave-broken sandy
ecosystems. This chapter mostly deals with finer sub- bottom within a few meters. It does not work in the
strate, and although there is considerable overlap with wild, as many coastal landowners have found to their
Chapters 6 and 18, the generalities will be discussed here. chagrin, and it does not work in an aquarium or meso-
cosm (Figure 3.11; Chapter 22). With difficulty, sandy
beaches can be simulated in mesocosms. In aquaria
SEDIMENTS AND MODEL ECOSYSTEMS and microcosms, it is extremely difficult, unless it is the
only community included.
As quieter water is approached, whether in widened As we discuss in Chapter 12, the break between
areas or billabongs (ox bow lakes) in a stream, in a lake high-energy shores with rock or mobile sand substrate
small enough to prevent large waves, or in a bay or and a quieter mud or sandy-mud bottom is ecologi-
coastal lagoon along a sandy coast, the sediment cally great. We treat them as separate biomes, the high-
becomes progressively finer from gravel, to sand and silt, est community level differentiation. Generally, algae
to a soupy, silty-clay mud. Coarse sands or gravels are occupy the highly disturbed but stable rocky shores
perhaps the most difficult benthic environments for and higher plants (marsh plants and submerged aquat-
organisms to adapt to, and there are relatively few ics) dominate the finer, less energetic shores. Even in a
species within sand and gravel habitats. To remain sand, lake this differentiation is apparent. Large lakes lack
the bottom must stay in motion (and clay and silt remain reed beds on most shores (except in protected coves),
suspended), and therefore special adaptations are and very small lakes are usually continuously rimmed
required by any organisms that will inhabit such bot- with emergent aquatic flowering plants. In the ocean,
toms. A few larger animals, such as the Donax clam and this relationship is also apparent. The outer shores,
the amphipod Neohaustorius have developed rapid bur- depending on sediment supply, range from rock
rowing techniques (Figure 3.9). The mole crab familiar to with more or less abundant macroalgae to bare sand.
beach naturalists along the extensive mid-Atlantic US Mostly, the only plants from the high-water line sea-
outer banks is another example. Otherwise, organisms ward on rocky bottoms are algae (including lichens).
must be small (less than 0.5 millimeter) and worm-like, On the other hand, in deeper waters, in protected bays,
so that the sand grains appear large to them, and have or behind reefs and barrier islands, mud bottoms pre-
the capability to rapidly burrow: these are the relatively vail and the marsh communities and their flowering
poorly known meiofauna (Higgins and Thiel, 1988) plants dominate the landscape.
(Figure 3.10). Even bacterial numbers tend to be limited Finer sediments, sandy-silt to silty-clay mud, typi-
in sand and gravel since their organic substrates are often cally have a very rich fauna, usually richer than a rock
“washed out” (Table 3.1). or boulder surface, though probably not richer than a
Sandy shores have a rather long profile in the energy coral reef. On a typical rocky shore, there are dozens of
regime required to keep them sandy. In model con- common species of algae, barnacles, snails, and small
struction there is little use in trying to sandwich a crustaceans in what appears to be an extremely rich
Sediments and Model Ecosystems
FIGURE 3.13 Results of the analysis of the soft bottom macroinvertebrate (greater than 1 µm) communities from Delaware Bay in two successive years (1972; 1973).
Although most of the same species occur in the 2 years, none of the “community” groupings is obviously the same. This analysis includes 169 species: 40.8% annelid
worms; 28.9% arthropods; 17.8% molluscs; 7.1% bryozoans; and 5.4% miscellaneous phyla. By feeding types the species could be grouped as 45% deposit feeders; 24.8%
suspension feeders; 18.3% carnivores; 10.7% omnivores; and 2.2% miscellaneous. After Maurer et al. (1978).
56 3. Substrate
FIGURE 3.14 Life cycle and predators of mayflies. The flying stage is reproductive only
and lasts for quite a short time. The larval stages of many species are burrowers in soft sedi-
ments of lakes, ponds, and streams. After Burgis and Morris (1987).
FIGURE 3.15 Distribution with depth of oxygen and hydrogen sulfide in a muddy bottom.
This profile typically occurs over a few to at most a few tens of centimeters from the mud/water
surface. After Levinton (1982). Reprinted by permission of Prentice Hall, Englewood Cliffs,
TABLE 3.2 Plants Dominating Sediment Bottoms in Temperate Lakes and Their Patterns of Change with Time (Succession)a
The English (Cumbrian) lakes Trout Lake (Wisconsin)
Successions in deep water Successions in shallow water Exposed to
slight waves; Severe wave
Very fine, rich, Stony and sandy Fine inorganic Sheltered silted and action; rather
inorganic silted Increase in substrates poor in soils with Largely organic soils rich in sandy soils coarse gravelly
Soil substrates with fineness and basic silts, and continued Increase in soils with silt and with some and sandy
type little organic matter richness of silt eventually organic silting organic content sparse silting organic sediment organic sediment substrates
Najas (Nitella) Isoetes Littorella Lobelia Ceratophyllum
Submerged linear- Potamogeton (Nitella) Potamogeton Myriophyllum Funcus
Overall line succession and decrease in
leaved association pusillus bulbosus
Potamogeton spp.) fluitans Myriophyllum– (Chara)–
Potamogeton Potamogeton Potamogeton Funcus (Chara)–
obtusifolius praelongus perfoliatus bulbosus Najas–
depth of water
Sparganium Potamogeton Nymphaea Potamogeton Nymphaea– Elodea–
minimum alpinus or Nuphar natans Potamogeton– Najas–
Sagittaria Potamogeton Isoetes–
Nymphaea Potamogeton Typha Schoenoplectus– Carex Sagittaria– Eleocharis–
and natans Phragmites or Sparganium– Equisetum–
Nuphar Equistum Typha Schoenoplectus
In all the above successions, only the dominant(s) of each community is indicated. Algal dominants are enclosed in brackets. After Sculthorpe (1985).
58 3. Substrate
FIGURE 3.16 Characteristic marine flowering plants from muddy sand and muddy bottoms: (A) the tropical Thalassia
testudinum (turtle grass), a dominant of many reef lagoons; (B) the cold-water Northern Hemisphere Zostera marina (eel-
grass). Note that neither species is a true grass. After Dawes (1981). Reprinted by permission of John Wiley & Sons, Inc.
variety and capability of the bacteria are limited. Few pathway for recycling nitrogen and phosphorus.
or no animals are present to eat the bacteria and, in Another pathway is through the root hairs, rhizomes,
turn, fish and larger invertebrates do not have a rich, and up into the leaves of higher plants, to be eaten by
smaller invertebrate bottom on which to browse. Thus, fish or snails or become more detritus. Some nitrogen
aquarium procedures in the past have tended to short- in the anaerobic sediments is denitrified to a gaseous
circuit the natural cycling processes. This results in loss form and lost to the atmosphere.
of valuable energy to the many larger members of the As long as the sediment surface is aerobic, phospho-
community. Microcosms, mesocosms, and aquaria that rus tends to remain locked in the sediments, since iron
by design do not have a fine sediment community oxides under these conditions link up with and trap
should have a separate sediment trap that periodically phosphorus. When, because of excess organic material,
can be partially drained of sediment. Particularly if a the normally subsurface zero-oxygen levels extend
system needs to be driven faster than normal for scal- into the water column, producing dead zones, stored
ing reasons, or if import and export are desired because phosphorus tends to be released. Sulfur also is utilized
of the size and coverage of the model ecosystem, by bacteria and becomes the very odiferous hydrogen
organic sediments can be used as an export tool. sulfide that one associates with anaerobic conditions.
In the wild, nutrients are exchanged between sedi- In nutrient-poor lakes, phosphorus tends to become
ments and the water column in a variety of pathways. the limiting nutrient because it is locked in sediments
Detritus to bacteria to worms to fish is an important by high oxygen levels. In richer lakes and estuaries
Geological Storage 59
FIGURE 3.17 Generalized feeding patterns in a typical shallow-water, soft-bottom community.
with large amounts of sediment in contact with the 26, we discuss large-scale, photosynthetic procedures
water, phosphorus tends to be released in abundance for solving these problems, combining nutrient removal
and is responsible for algal blooms if nitrogen is avail- with oxygen injection.
able. In the open ocean where fine organic sediments
are deep and to a large extent out of reach of the shal-
low water column, nitrogen and phosphorus tend to be
closer in importance with the final limitation usually GEOLOGICAL STORAGE
belonging to nitrogen.
For the restorer of degraded lakes and estuaries, this Bioturbation (or bottom disturbance) by animals and
is frequently the first and foremost issue to be the rooting and shooting activities of flowering plants in
addressed. Once human eutrophication has allowed shallow water are processes that continuously return the
spring planktonic algal blooms to increase bottom energy and chemical elements of organic sediment to the
organic biomass and bring the anaerobic zone up to the water column. However, in many cases sedimentation is
sediment surface and into the water column during the rapid enough to bury organic materials out of reach of
summer, previously stored phosphorus is released living processes for geological time. This could be thou-
causing a further cascade of degradation. Simply cut- sands of years for lakes or fresh-water environments or
ting off the nutrient supply will no longer work in millions of years for marine situations. On the Earth, a
these cases, and radical methods such as chemical pre- significant part of the plant primary production that has
cipitation or sediment dredging are extremely expen- occurred in the past 500 million years has been stored as
sive and sometimes prevent full restoration. In Chapter coal, oil, gas, and oil shales.
60 3. Substrate
Limestone production likewise is indirectly related destroyed by increased run-off, with heavy sediment
to the photosynthetic process. As we shall discuss fur- loadings, related to logging and shore development. If
ther in Chapter 8, virtually all carbon on the Earth’s this is past activity, and significant sedimentation is no
surface and in its crust has been cycled through organ- longer present, then transplantation of a new commu-
isms, yet it has been estimated that greater than 1600 nity of reef organisms from a viable host reef is proba-
times as much organic carbon is buried in the Earth’s bly appropriate (Precht, 2006). If moderate run-off is
crust as exists in the biosphere proper. Most of this still occurring, then it is possible that the ATS system
buried carbon was derived from the process of photo- described in Chapter 25 can assist in ameliorating the
synthesis and was removed, as carbon dioxide, from effects. Heavy sedimentation will have to be blocked by
the atmosphere. Photosynthesis, in the first few billion physical settling ponds or lagoons or any restoration
years of Earth’s history, also resulted in the evolution efforts on coral reefs are likely to be unsuccessful.
of oxygen into the atmosphere.
During the past century, most human management
of the Earth’s organic resources (historically including References
sewage treatment and aquarium management) is Burgis, M. and Morris, P. (1987) The Natural History of Lakes.
philosophically based on rapid recycling of readily Cambridge University Press, Cambridge.
available raw materials (nutrients). In more recent pre- Davis, H. (1983) Depositional Systems: A Genetic Approach to Sedimentary
Geology. Prentice Hall, Englewood Cliffs, New Jersey.
human history of the Earth’s biosphere, organic stor-
Dawes, C. (1981) Marine Botany. Wiley Inter-Science, New York.
age and great limitation of available nutrients has been Gross, M. G. (1982) Oceanography: A View of the Earth. Prentice Hall,
the rule. This is undoubtedly a major factor providing Englewood Cliffs, New Jersey.
long-term stability to our biosphere. Likewise in mod- Higgins, H. and Thiel, H. (1988) Introduction to the Study of the
ern organic waste management, it is important to keep Meiofauna. Smithsonian Institution Press, Washington, DC.
nutrients locked in biomass, either active or stored. Kennett, J. (1982) Marine Geology. Prentice Hall, Englewood Cliffs,
In addition to algal turf scrubbing (or other plant Kleypas, J., Buddemeier, R., Archer, D., Gattuso, J.-P., Langdon, C.
removal) to simulate model communities characterized and Opdyke, B. (1999) Geochemical consequences of increased
by organic sediment burial, a storing or exporting sedi- carbon dioxide on coral reefs. Science 284: 118–120.
ment trap is necessary. There are many ways to do this, Levinton, J. (1982) Marine Ecology. Prentice Hall, Englewood Cliffs,
and several units are described in Chapters 20–26. New Jersey.
Lippson, A. J. and Lippson, R. L. (1997) Life in the Chesapeake Bay, 2nd
Sometimes, when export, in the time frame of the model edn. Johns Hopkins University Press, Baltimore.
planned, is not desired, and bottom disturbance is not Lowe, D. R. (1994) Early environments, constraints and opportuni-
excessive, the basin of the tank itself becomes the sedi- ties for early evolution. In: Early Life on Earth. S. Bengtson (Ed.)
mentation trap and organic storage facility. Separate set- Columbia University Press, New York.
Marshak, S. (2004) Essentials of Geology. Norton and Company,
tling traps, within the model plumbing, with tap-off
valves, can also be used as refugia (Chapter 12). Maurer, D., Watling, L., Kinner, P., Leethem, W., and Wethe, C. (1978)
Benthic invertebrate assemblages of Delaware Bay. Marine Biol.
Aquatic Ecosystem Restoration and Parker, R. (1967) Data of Geochemistry, 6th edn. USGS Prof. Paper
Precht, R. (2006) Restoration of Coral Reef Ecosystems. Coral Reef
In several subsections in this chapter, we have noted Restoration Handbook Taylor and Francis, CRC, Boca Raton.
the relationship of anthropogenic sedimentation, both Redfern, R. (2001) Origins: The Evolution of Continents, Oceans and Life.
increased and decreased on the health of wild ecosys- University of Oklahoma Press, Norman.
tems needing restoration. In general, ecosystems domi- Rheinheimer, G. (1985). Aquatic Microbiology, 3rd edn. Wiley,
nated by submerged aquatic vegetation (SAV) tend to
Salbu, B. and Steinnes, E. (1994) Trace Elements in Natural Waters. CRC
be damaged by excessive siltation from land develop- Press Boca Raton, FL.
ment and farming and ecosystems dominated by emer- Sculthorpe, C. (1985) The Biology of Vascular Plants. 1985 reprint of
gent aquatic vegetation (EAV) tend to be damaged by 1967 edn. Koeltz Scientific Books, Konigstein.
the removal of periodic sedimentation (see also Chapter Thurman, H. and Webber, H. (1984) Marine Biology. Merrill Publishing,
14). However, other aquatic ecosystems can also be
van Andel, T. (1985) New Views of an Old Planet. Cambridge
highly sensitive to sedimentation processes. Among the University Press, Cambridge.
most important of these are coral reefs. Frequently these van Dover, C.-L. (2000) The Ecology of Deep-Sea Hydrothermal Vents.
tropical systems have been damaged or virtually Princeton University Press, Princeton, NJ.
C H A P T E R
Management of Salinity, Hardness, and Evaporation
Virtually, all chemical elements dissolve in water. overall course of organic evolution, cell walls developed
Many are rare in natural waters and of little conse- very early, perhaps 3.5 billion years ago, perhaps in a
quence; most of the more common elements occur in pre-life chemical process; they would have provided an
ionic form and often in element combinations. Some efficiency advantage to many organic processes that
elements are fairly common in many natural waters previously had to compete in the larger oceanic soup.
and sea water has a suite of elements that are largely Likewise, the first closure of vascular or blood systems,
fixed in their percentage composition. Many chemical some 1 billion years ago, took the previously open sea
elements occur in aquatic organisms; some are essen- water that used to carry food and oxygen to each cell
tial to organism function and are highly concentrated and isolated it, as a transporting medium, in blood ves-
over their concentration in the ambient water. Those sels and body cavities. This isolating device provided
that are concentrated more than about 104 times can be more control and allowed the development of larger
limiting for the growth of organisms; however, when organisms. However, to obtain oxygen from water,
these elements greatly exceed normal concentrations in gills, devices basically arranged to bring water in as
ambient water, they can also lead to the disruption of close a contact as possible to the flowing blood, had to
community structure and function. These latter ele- be developed.
ments are called nutrients (mostly nitrogen, N; phos- Even more recently, in a geologic sense, perhaps 400
phorus, P; iron, Fe; and silicon, Si); they require special million years ago, fish entering fresh waters for the first
attention and we treat them in greater detail in Chapter time evolved kidney glomeruli. Once the salt balance
9. The conservative elements provide those salts that between inside and outside changed, these were neces-
change little in abundance except for freshwater dilu- sary to constantly pump out the fresh water that now
tion. Here we also cover the micronutrients and the continuously flowed into the blood through the gills
relationship of all chemical elements of the hydros- (Evans, 1993). These bony (teleost) fish then returned
phere and the Earth’s crust. In our view, “natural to the sea, millions of years later, having evolved to a
waters” significantly unaffected by human activity lower level of salts in the blood. Then, for the marine
have virtually ceased to exist, and in this chapter we teleost, the problem changed to a need to continually
introduce the more important nonnutrient additions of drink water and excrete salt. Gills and bladders also
industrial and agricultural societies. became involved in this need for osmotic balance
The chemistry of the aqueous medium or hydros- (Jobling, 1995). While kidneys have gradually evolved
phere as a whole is highly variable over the face of the to become much more complex and varied structures,
Earth. Even the ocean, the most constant of waters, the problem of sensitivity to the aqueous medium
varies considerably in some aspects of its chemical remains. Many algae and small invertebrate animals,
composition as coasts and rivers are approached. At being essentially isotonic (same internal salinity) with
the same time, aquatic organisms are much less chemi- sea water, remain extremely sensitive to changes in
cally removed from the water medium than their ter- the chemical composition of water. Others, such as
restrial counterparts are from the atmosphere. In the anadromous fish, can move salts or water in or out as
Ocean Salinity 63
bodies of water in colder climates would freeze to the (Na at 30.61%) and chlorine (Cl at 55.04%) make up
bottom, and only the surface would melt in summer. over 85% of this salt, and only four additional elements,
Even more important to life as we know it is the dis- 2
sulfur as sulfate (SO4 at 2.71%), magnesium (Mg2 at
solving power of water. Allowing virtually every natu- 2
3.69%), calcium (Ca at 1.16%), and potassium (K at
rally occurring element and most compounds into its 1.10%), bring the composition to over 99%. As we dis-
semi-open liquid structure, in the natural environment cussed in Chapter 3, the residence time of an element in
water becomes the universal soup in which a very large sea water (between river delivery and sedimentation
number of chemical interactions become possible. The removal) determines the ultimate concentration in sea
clusters or “spheres of hydration” shown in Figure 4.1 water. When sea water is diluted by rivers and streams,
also form around many ions and minerals and organic along an ocean coast, the proportional chemical compo-
aggregates providing for most of the extraordinary sition remains essentially unchanged, though the total
characteristics. quantity of salts drops with dilution. Evaporation, pre-
cipitation, and river supply certainly affect sea-water
salt composition, and for that reason the surface waters
OCEAN SALINITY of the major oceans and seas can vary slightly in salinity.
Also, variation can occur on a geologic time scale. For
The salinity of the open oceans has a rather uniform example, it is known that epicontinental or enclosed
chemical composition in both time and space (Tables 4.2 seas have often dried up, leaving large salt beds. In the
and 4.3) that ranges from about 34 to 37 parts per thou- case of the Mediterranean in the late Miocene epoch, 5–6
sand (ppt) or 3.4% to 3.7% by weight. In the chemist’s million years ago, repeated isolation and complete evap-
language, this is 34 000–37 000 mg/liter (ppm). Sodium oration probably also affected salt composition of the
TABLE 4.1 Unusual Physical Properties of Water and Their Importance in Biological/Ecological Systemsa
Property Comparison with other substances Importance in physical/biological environment
Heat capacity Highest of all solids and liquids except liquid Prevents extreme ranges in temperature
NH3 Heat transfer by water movements is very large
Tends to maintain uniform body temperature
Latent heat of fusion Highest except NH3 Thermostatic effect at freezing point owing to
absorption or release of latent heat
Latent heat of evaporation Highest of all substances Large latent heat of evaporation extremely important in
heat and water transfer of atmosphere
Thermal expansion Temperature of maximum density decreases with Fresh water and dilute sea water have their maximum
increasing salinity. For pure water it is at 4°C density at temperatures above the freezing point. This
property plays an important part in controlling
temperature distribution and vertical circulation in lakes
Surface tension Highest of all liquids Important in physiology of the cell
Controls certain surface phenomena and drop formation
Dissolving power In general dissolves more substances and in Obvious implications in both physical and
greater quantities than any other liquid biological phenomena
Dielectric constant Pure water has the highest of all liquids Of utmost importance in behavior of inorganic dissolved
substances because of resulting high dissociation
Electrolytic dissociation Very small A neutral substance, yet contains both H and OH ions
Transparency Relatively great Absorption of radiant energy is large in infrared and
ultraviolet. In visible portion of energy spectrum there is
relatively little selective absorption, hence is “colorless.”
Characteristic absorption important in physical and
Conduction of heat Highest of all liquids Although important on small scale, as in living cells, the
molecular processes are far outweighed by eddy
From Sverdrup et al. (1942). Reprinted by permission of Prentice Hall, Englewood Cliffs, New Jersey.
64 4. Water Composition
TABLE 4.2 Elements Present in Sea Watera (at greater than 6.10 6
Element mg/kgb Cl 19.00 0/00 mg-atoms/liter Cl 19.00 0/00 Atomic weight (1940) 1/atomic weight
Chlorine 18980 548.30 35.457 0.02820
Sodium 10561 470.15 22.997 0.04348
Magnesium 1272 53.57 24.32 0.04112
Sulfur 884 28.24 32.06 0.03119
Calcium 400 10.24 40.08 0.02495
Potassium 380 9.96 39.096 0.02558
Bromine 65 0.83 79.916 0.01251
Carbon 28 2.34 12.01 0.08326
Strontium 13 0.15 87.63 0.01141
Boron 4.6 0.43 10.82 0.09242
Silicon 0.02–4.0 0.0007–0.14 28.06 0.03564
Fluorine 1.4 0.07 19.00 0.05263
Nitrogen (ionic) 0.01–0.7 0.001–0.05 14.008 0.07139
Aluminum 0.5 0.02 26.97 0.03708
Rubidium 0.2 0.002 85.48 0.01170
Lithium 0.1 0.014 6.940 0.14409
Phosphorus 0.001–0.10 0.00003–0.003 30.98 0.03228
Barium 0.05 0.0004 137.36 0.00728
Iodine 0.05 0.0004 126.92 0.00788
Arsenic 0.01–0.02 0.00015–0.000 74.91 0.01335
Iron 0.002–0.02 0.00003–0.000 55.85 0.01791
Manganese 0.001–0.01 0.00002–0.000 54.93 0.01820
Copper 0.001–0.01 0.00002–0.000 63.57 0.01573
Zinc 0.005 0.00008 65.38 0.01530
Lead 0.004 0.00002 207.21 0.00483
Selenium 0.004 0.00005 78.96 0.01266
Cesium 0.002 0.00002 132.91 0.00752
Uranium 0.0015 0.00001 238.07 0.00420
Molybdenum 0.0005 0.000005 95.95 0.01042
Thorium 0.0005 0.000002 232.12 0.00431
Cesium 0.0004 0.000003 140.13 0.00714
Silver 0.0003 0.000003 107.880 0.00927
Vanadium 0.0003 0.000006 50.95 0.01963
Lanthanum 0.0003 0.000002 138.92 0.00720
Yttrium 0.0003 0.000003 88.92 0.00125
Nickel 0.0001 0.000002 58.69 0.01704
Scandium 0.00004 0.0000009 45.10 0.02217
Mercury 0.00003 0.00000001 200.61 0.00498
Gold 0.000006 0.00000002 197.2 0.00507
Radium 0.2 3 10 0.8 12 10 13 226.02 0.00442
Virtually all the gases of the atmosphere are also present, and together these provide a wide variety of organic and inorganic chemical
compounds. Adapted from Sverdrup et al. (1942). Reprinted by permission of Prentice Hall, Englewood Cliffs, New Jersey.
The salinity for which these element concentrations are tabulated is 34.3 ppt. Each value should be multiplied by 1.043 to obtain an
equivalent to a salinity of 35.8 ppt, a level more appropriate for coral reef systems.
world’s oceans by several parts per thousand. (This in algae. The concentration of other mostly very minor ele-
turn may have affected world climate by increasing sea ments can also be affected by chemical reactions, espe-
ice formation because of general lowered salinities.) cially in sediments. Sea water near sea floor spreading
Marine chemists have traditionally separated the zones where there is active interchange between hot,
chemical elements dissolved in sea water into conserva- forming ocean crust and sea water can be locally altered
tive and nutrient categories. The conservative elements (van Dover, 2000).
are relatively abundant in sea water, particularly in pro- Table 4.4 shows the relationship between the princi-
portion to their requirements by organisms. The nutrient- pal elements in oceanic phytoplankton (excluding car-
type elements are relatively low in concentration in sea bon, hydrogen, and oxygen) and the mean sea-water
water and are needed in proportionally large quantities concentrations of those elements. Clearly, limiting sta-
by organisms, particularly phytoplankters and other tus is conferred both by the functional requirements of
Ocean Salinity 65
TABLE 4.3 Ionic Composition of Sea Watera (at greater than 10 12
Element Chemical species Molar µg/liter (ppb)
H H2O 55 1.1 108
He He (gas) 1.7 10 6.8 10 3
Li Li 2.6 10 180
B B(OH)3, B(OH)4 4.1 10 4440
C HCO3 , CO2 , CO2
3 2.3 10 3
N N2, NO3 , NO2 , NH4 1.07 10 1.5 105
O H2O, O2 55 8.8 108
F F , MgF 6.8 10 1.3 103
Ne Ne (gas) 7 10 1.2 10 1
Na Na 4.68 10 10.77 106
Mg Mg2 5.32 10 2
Al Al(OH) 4 7.4 10 2
Si Si(OH)4 7.1 10 2 106
P HPO2 , PO3 , H2PO4
4 4 2 10 6
S SO2 , NaSO 4
4 2.82 10 2
Cl Cl 5.46 10 18.8 106
Ar Ar (gas) 1.1 10 4.3
K K 1.02 10 3.8 105
Ca Ca2 1.02 10 2
Ti Ti(OH)4 2 10 1
V H2VO 4, HVO 2 4 5 10 8
Cr Cr(OH)3, CRO2 4 5.7 10 9
Mn Mn2 , MnCl 3.6 10 0.2
Fe Fe(OH) 2, Fe(OH) 4 3.5 10 2
Ni Ni2 2.8 10 8
Cu CuCO3, CuOH 8 10 0.5
Zn ZnOH , Zn2 , ZnCO3 7.6 10 8
As HAsO2 , H2AsO 4
4 5 10 8
Se SeO2 3 2.5 10 9
Br Br 8.4 10 6.7 104
Kr Kr (gas) 2.4 10 0.2
Rb Rb 1.4 10 120
Sr Sr2 9.1 10 5
Mo MoO2 4 1 10 7
Cd CdC12 1 10 0.1
Sb Sb(OH) 6 2 10 0.24
I IO 3, I 5 10 60
Xe Xe (gas) 3.8 10 5 10
Cs Cs 3 10 0.4
Ba Ba2 1.5 10 7
U UO2(CO3)4 2 1.4 10 8
From Spotte (1979). Reprinted by permission of John Wiley & Sons, Inc.
the phytoplankton and by the abundance of the Nitrogen, phosphorus, and iron are the classic limit-
element in sea water. Sodium and chlorine have ing nutrients. Nitrogen and phosphorus (also the prin-
higher concentrations in plankton than any other ele- cipal eutrophication nutrients) we treat in depth in
ment except carbon, nitrogen, and oxygen. However, Chapter 9. Iron requires special mention, not because it
because of the high concentration of these elements is likely to be either limiting or superabundant in
in sea water, neither can ever be limiting. Silica, on the microcosms and mesocosms, but because it has been
other hand, is moderately abundant in sea water. Yet, suggested that it is limiting for photosynthesis, far
its great requirement by diatoms for their cell walls, from shore in the large southern ocean; some scientists
when they explode in spring blooms, results in frequent have suggested that it might be possible to counter
limitations. global warming by introducing iron into the southern
66 4. Water Composition
TABLE 4.4 Relative Abundances of Elements in Marine Phytoplankters and in Sea Watera
Concentration in Concentration in
phytoplankton sea water Concentration
(wt./100 g) (wt./m3) factor SW/Plankton
N u t r i e n t
Nitrogen (N) 5g 300 mg 0.06*
Phosphorus (P) 0.6 g 30 mg 2.105 0.05*
Silica (Si) (diatoms) 10 g 500 mg 2.105 0.05*
Iron (Fe) (other than diatoms) 1g 500 mg 2.105 0.05*
Vanadium (V) 3 mg 0.3 1.105 0.1
Silica (other than diatoms) 0.5 g 500 mg 1.104 1.0
Carbon (C) 30 g 28 g 1.07.104 1.0
Iron (diatoms) 40 mg 50 mg 0.8.104 1.3
Copper (Cu) 5 mg 10 mg 2
Cobalt (Co) 0.05 mg 0.1 mg 5.103 2
Manganese (Mn) 2 mg 5 mg 4.103 2.5
Zinc (Zn) 20 mg 5 mg 40.108 4
C o n s e r v a t i v e
Aluminum (Al) 1 mg 120 mg 83 120
Magnesium (Mg) 0.4 g 1.3 kg 3.07 300
Potassium (K) 1g 390 g 25.8 390
Calcium (Ca) 0.5 g 416 12.02 830
Sulfur (S) 1g 900 g 11.1 900
Fluorine (F) 1g 1.4 g 7.15 1400
Boron (Bo) 2 mg 5g 4 2500
Sodium (Na) 3g 10.75 2.8 3600
Chlorine (Cl) 4g 19.3 kg 2.07 4800
Bromium (Br) 2.5 66 g 0.37 26 000 (Rejected)
* Frequent limitations
Modified after Millero and Sohn (1992).
ocean. This we discuss in more depth later in this chap- outer ring of the atom, thereby dictating basic chemical
ter. Even the elements most frequently limiting pri- reactivity. The elements in each column have a chemi-
mary production by algae, nitrogen, and phosphorus are cal similarity, but the atoms are progressively heavier
not limiting in very low-nutrient coral reef environments. and larger lower in the table. Thus, cadmium (Cd) and
In most reefs, strong current flow from the open ocean mercury (Hg) chemically react like zinc (a minor nutri-
constantly brings a new supply of low-concentration ent) but being larger atoms are likely to replace zinc in
nutrients. Many algae are quite capable of obtaining an organic molecule but then twist the molecule out of
those nutrients even at very low concentrations; this is shape. Thus, the general toxicity of these elements.
so as long as there is abundant physical energy (current Likewise, arsenic (As) below phosphorus and nitrogen
and wave action) that prevents microzones of low con- is a general biotic poison.
centration against cell walls, where there is an active Most important for the modeler, who is typically
uptake gradient. In addition to carbon, nitrogen, and working with a relatively limited volume of water, any
phosphorus (and of course hydrogen and oxygen as element present in organisms could theoretically be
water and ions), another six elements (sodium, potas- limiting and thereby function as a nutrient-type ele-
sium, calcium, magnesium, sulfur, and chlorine) are ment. For example, in the operating of coral reef envi-
essential to all life. Ten other elements, including iron, ronments in aquaria or mesocosms, due to potentially
manganese, silica, copper, zinc, and boron, are required high calcification rates in those systems, calcium can
by most organisms and another ten by a few organisms. enter “geological” storage. Even though it is returned
Figure 4.2 shows diagrammatically the relationship from geological storage by boring organisms net calci-
between the chemical elements, in the standard frame- fication rates can be very high, resulting in depletion in
work of the periodic table, and their function in living the water column. In some reef systems, we have also
organisms (see also Frausto da Silva and Williams, 1991). seen reductions in strontium and potassium, though
Here, it is possible to see the role that some toxic ele- those reductions in concentration were probably not
ments play in the basic chemistry of life. Each column of concern. However, any element on the upper two-
in the table signifies the number of electrons in the thirds of the list in Table 4.4 could be a problem at
Hardness of Fresh Waters 67
FIGURE 4.2 The chemical elements of living organisms and their primary function in relation to the periodic table of the elements. Modified
from Frausto da Silva and Williams (1991).
model scale and should at least be occasionally moni- above 0.2 ppt, barring human effects or the localized
tored. The primary nutrients, including nitrogen, phos- leaching of salt beds. The River Jordan reaching 7.7 ppt
phorus, silica, carbon, and calcium, we treat in depth in is an example of salt bed leaching and evaporation
later chapters. In practice, in any model system in effects.
which import and export of organics is similar to that in The ionic composition of fresh waters, even those of
the wild analog and, in the case of salt- or hard-water far less extreme characteristics, can have significant
systems, it is necessary to maintain a minimal water effects on biota. Hutchinson and Edmonson (1993) offer
exchange to prevent salt drift. Chemical elements can numerous examples of control or rejection of some
be lost to the atmosphere, as anyone who has operated species because of water composition. In the modeling
salt-water systems in a greenhouse can attest. of freshwater systems, basic considerations of design, in
Fresh waters, on the other hand, vary widely in most cases, will include salinity or hardness.
salinity (generally called hardness) from those of virtu-
ally pure water to very high levels for lakes with no
outflow, that is, endorheic lakes (Table 4.5). The Dead HARDNESS OF FRESH WATERS
Sea (226 ppt) and the North American Great Salt Lake
(203 ppt) have salinities far above that of the ocean and Water hardness is handled a little differently from
chemical compositions that vary considerably from salinity in that in some countries the degree is the unit
those in the ocean. On the average, rainwater has a of measure. One German degree of hardness equals
salinity of about 0.008 ppt and is slightly enriched in 10 mg/liter (ppm) of calcium and magnesium oxide or
calcium and sulfate, though near sea coasts a consider- 17.8 ppm of CaCO3 in the USA. This is not at all equiv-
able increase in chlorine can be found (Hutchinson, alent to salinity in that a relatively low salinity water
1957). River waters average 0.1–0.16 ppt, though those rich in calcium and magnesium could have a relatively
draining predominantly igneous rock areas are high degree of hardness. On the other hand, a fresh water
typically below 0.05 ppt. Rivers usually do not extend rich in sodium chloride alone could have a very low
68 4. Water Composition
TABLE 4.5 Chemical Composition of Selected Lakes Dominated by Different Anions (%)a
Na K Mg Ca CO3 SO4 Cl SiO2 (AlFe)2O3 Salinity (mg/kg)
Upper, Wyoming 4.49 6.86 23.69 52.68 5.76 2.68 3.84 – 185
Lower, Utah 20.54 4.76 10.12 21.53 8.16 32.36 – 2.53 637
Great Salt Lake, Utah 33.17 1.66 2.76 0.17 0.09 6.68 55.48 – – 203 490
Jordan at Jericho 18.11 1.14 4.88 10.67 13.11 7.22 41.47 1.95 1.45 7700
Dead Sea 11.14 2.42 13.62 4.37 Trace 0.28 66.37b Trace – 226 000
Montreal Lake, Saskatchewan 4.9 2.3 10.8 16.8 56.5 1.8 2.5 3.9 0.5 150.5
Redberry Lake, Saskatchewan 12.0 0.85 12.3 0.56 2.58 70.5 1.1 0.03 0.07 12 898
Little Manitou Lake 16.8 1.0 10.9 0.48 0.47 48.4 21.8 0.019 0.21 106 851
Silvies River, Oregon 10.42 2.45 3.13 12.88 34.76 7.35 2.88 25.13 0.08 163
Malheur Lake, Oregon 24.17 5.58 4.13 5.58 44.63 7.64 4.55 2.89 Trace 484
Pelican Lake, Oregon 29.25 3.58 2.62 2.27 30.87 22.09 7.97 1.21 0.02 1983
Bluejoint Lake, Oregon 37.70 2.62 0.63 0.53 38.68 5.67 13.85 0.55 0.02 3640
Moses Lake, Washington 19.86 7.25 8.41 51.56 2.87 3.88 5.06 1.11 2966
After Hutchinson (1957). Reprinted by permission of John Wiley & Sons, Inc.
And 1.78% Br.
TABLE 4.6 Hardness Scales for Fresh Watersa of the standard hardness test kit. If one is creating a
synthetic system, the best manuals describing standard
dGH dKH pH
aquaria fish usually provide optimum numbers for each
GH total hardness (dGH German total hardness)
KH carbonate hardness (dKH German carbonate hardness) species. Many fish species can adapt to a wide range of
PH permanent hardness hardness, particularly if it is changed gradually. Gener-
Carbonate hardness based on bicarbonate is not permanent because ally, with freshwater systems, as long as evaporation is
the CO2 can be driven off by boiling. The remaining calcium and not excessive and the hardness of the replacement
magnesium by definition determines permanent hardness.
water is not too high, occasional small volume changes
Total hardness can be illustrated as follows:
Degrees of hardness (1 gallon a week for a 70-gallon system) are sufficient to
0–4° dGH very soft 12–18° dGH fairly hard prevent salt buildup and the effective development of
4–8° dGH soft 18–30° dGH hard an endorheic or salt lake in the aquarium or mesocosm
8–12° dGH medium hard over 30° dGH very hard environment. As discussed below, algal scrubbers tend
One degree of hardness 10 mg/liter of CaO or MgO
to adjust disproportionate elements as long as the
system is not allowed to become too unbalanced. The
Partly after Riehl and Baensch (1987). difficulties arise in fresh- or salt-water microcosms or
aquaria when the fresh water being used to replace
evaporated water is excessive in certain ions, typically
hardness. Nevertheless, the mean river of Hutchinson those of the elements calcium, iron, sulfur, or magne-
(1957) with a salinity of 0.13 ppt would have a hardness sium. Even in models of soft to medium-hard water
of about 1.9° (i.e. very soft). The standard terminology ecosystems, it is important to occasionally carry out an
relating degrees of hardness to descriptive elements is analysis of the spectrum of inorganic elements. A stan-
given in Table 4.6. dard commercial test for tap or drinking waters will
Unfortunately, hardness through calcium is tied to usually suffice.
the very nonconservative carbonate system, as meas- We have worked with a hard water on the Atlantic
ured by pH. The pH is very much affected by organism Coastal Plain that is rich in both iron and sulfur. Even
respiration and photosynthesis and is treated at length though a standard water softener is used on the well
in Chapters 8 and 10. In practice, these two can be han- water, the taps and sinks have excessive iron staining
dled separately as long as one remembers that there can and water out of the tap has a sulfurous odor, particu-
be a connection. Hard waters usually have a high pH. larly in dry years. The water softness, as an ion exchange
The status of a wild freshwater community that one system, also introduces a small amount of sodium chlo-
wishes to simulate can be determined within the range ride. We have successfully solved this problem by using
Hardness of Fresh Waters 69
TABLE 4.7 Concentrations of Selected, Analyzed Chemical Elements, Ions, and Compounds
from a Variety of City Water Suppliesa
Parts per million, mg/liter
Element, ion, San Washington,
or compound Boston Chicago Dallas Baltimore Los Angeles Francisco DC
*Aluminum ? 0.45–0.5 ? 0.08–0.16 ND–0.2 0.02–0.08 0.042–0.2
Arsenic 0.005 0.005 0.005 0.005 ND–0.02 ND 0.000–0.001
Barium 0.1 0.05 0.05 0.021–0.03 ND ND–0.01 0.028–0.07
Cadmium 0.002 0.001 0.001 0.001 ND ND 0.0–0.00
*Chlorine-free ? 2.12–2.29 ? 0.4–0.7 1.6–2.1
*Chloride 12–44 10.9–11.1 15–27 18–22 18–127 2–19 15.6–29.0
Chromium 0.005 0.003 0.01 0.001 ND ND–0.001 0.0–0.006
*Copper 0.01–0.08 0.003 0.01–0.02 0.004–0.006 ND ND–0.015 0.001–0.110
*Fluoride 0.06–0.98 0.92–0.93 0.77–0.78 0.9–0.97 0.1–0.7 0.3–1.2 0.93–1.14
*Iron 0.02–0.16 0.010 0.01–0.01 0.02 ND–0.07 ND–0.06 0.001–0.07
Lead 0.002 0.003–0.010 0.005 0.001 ND ND–0.001 0.0–0.001
Manganese 0.01–0.05 0.001–0.002 0.005 0.01 ND ND–0.01 0.001–0.004
Magnesium .5–2.4 12.3–12.5 3–5 4.4–6.2 5.7–27 ? 6–11
Mercury 0.001 0.0005 0.001 0.0005 ND ND 0.0000–0.0003
Nickel ? 0.003 0.01–0.01 ? ? ? 0–0.003
*Nitrate (as N)b ? 0.25–0.26 0.22–0.45 1.7 ND 0.04–0.1 1.29–2.67
*Phosphate (as P)b ? 0.010–0.018 0.03–0.09 0.01 0.02–0.07 0.002–0.017 00–0.14
Potassium 0.9–2.3 1.5 3.7–4.8 2.2–2.6 3.6–4.8 0.2–0.8 2.11–3.27
Selenium 0.005 0.001 0.001–0.001 0.005 ND ND 0.0–0.002
Silver 0.005 0.001 0.01 0.005 ND ND 0.0
*Sodium 7.2–26.3 5.8–6.0 11.0–28.5 7.1–8.3 37–86 1.0–15.5 4.8–15.6
Strontium ? 0.119–0.142 0.10–0.25 ? ? ? 0.093–0.24
*Sulfate 8.3–14 26.4–27.5 31–50 13.6–15 28–232 1.6–3.6 22.1–48.9
Zinc 0.02 0.004–0.005 0.01–0.02 0.028–0.038 ND ND–0.010 0.0–0.005
Total trihalomethanes ? ? 0.0227 41 13–72 0.063–0.075 26–137
Endrin (pesticide) ? ? ND 0.04 ND ND ND
2.4-D (pesticide) ? ? ND 0.05 ND ND ND
Note: Tap waters can have additional or increased contamination levels. ND, not determined. These data are from the 1980s. Few, if any,
large metropolitan water systems would lack free chlorine or trihalomethanes today.
Sources: Indicated metropolitan water authorities.
*Added in treatment, in part or whole.
a separate water softening algal scrubber system. Excess that of an endorheic, or closed basin lake, if topping up
calcium, iron, and sulfur are either taken up by the algae for evaporation continues for some time and water
or precipitated out on the surfaces of the cells and exchange with waters of the character of the analog of the
removed at harvest time. A reverse osmosis (RO) unit model is not carried out. However, the primary prob-
can be used following a water softener if the volume lem with city tap water is the additives used to control
requirements are not too great. human pathogens, to adjust the taste, to control algae in
The character of well waters varies widely, and it artificially eutrophic reservoirs, or to reduce corrosion
would be impossible to cover the problems of micro- in pipes (Table 4.8). The addition of chlorine is well
cosm and mesocosm water supplies for all cases. In known and is the primary characteristic that renders
general, if a standard water softener does not solve the tap waters objectionable to humans. It is added to kill
problems, we have found that a separate algal turf pathogens, but the chlorine also would kill most of the
scrubber (ATS) managed water reservoir (see Chapter animals that one would wish to maintain in an ecosys-
11) adjusted for nutrient levels and pH can remove tem. Fortunately, being in the gaseous state it is more
almost any contaminant including heavy metals. or less easily removed by bubbling or allowing the
In general, city or town waters provide more serious water to stand for several days.
problems. While rarely are city tap waters saline or Since chlorine in combination with organic com-
hard compared to average natural waters (Table 4.7), pounds occurring naturally forms compounds (tri-
the salinity of an aquarium or microcosm can become halomethanes; see Table 4.7) that have been shown to be
70 4. Water Composition
TABLE 4.8 Chemicals Typically Used in the Treatment of City Water Suppliesa
Aluminum as aluminum sulfate (Al2(SO4)3, 18 H2O) Clarification
Ammonium hydroxide (NH4OH) Taste and odor control
Carbon, activated (C) Taste and odor control
Chlorine or chloramines (Cl2) (NH2Cl, NHCl2, NCl3) Sterilization
Copper sulfate (CuSO4) Algal reduction
Fluorosilicic acid (H2SiF6) Dental decay reduction
Ferric chloride (FeCl3) Clarification
Hexametaphosphate (PO3)6 Reduce corrosion in metal pipes
Lime (CaO, Ca(OH)2) pH adjustment
Sodium chlorite (NaClO2) Taste, odor, and algae control
Sources: Metropolitan water authorities as given in Table 4.7.
carcinogens, some cities have started to add chlor- these and other anthropogenic organic compounds
amines instead of chlorine to control human pathogens. (which are now banned in the USA) are extremely low
Unfortunately, chloramines are more toxic than chlorine in sea water, they tend to be concentrated “up food
to fish and invertebrates and are more slowly lost to the chains,” especially in fatty tissues, until very toxic levels
atmosphere than chlorine. are developed in top predators (e.g. Laws, 1993). While
Copper sulfate is added to many drinking water the half-life of many of these compounds in the sedi-
systems that include reservoirs to prevent the excessive ments of lakes and estuaries may be only 10–15 years,
algal growth that sometimes results from artificially in the biosphere they can be 150 years or more. For
high nutrient levels. Unfortunately, the copper is also example, while 7–16 ppm of PCBs in milk is highly
toxic to the algae that is necessary to maintain virtually toxic to infant monkeys, Beluga whales were found in
all natural, aquatic ecosystems. Finally, a major prob- the St. Lawrence estuary (which is a highly mixed body
lem of many city tap waters is that they are eutrophic, of water with extensive deep water oceanic injection)
that is, excessive, particularly in dissolved nitrogen with 575 ppm PCB in their livers and 1750 ppm in their
and phosphorus. While additional chemical treatments milk (Laws, 1993).
are available to remove all of these contaminants, we Heavy metals from industrial activities and sewage
prefer physical (RO) and plant production (algal scrub- (e.g. mercury, Farago, 2000), and organometals like trib-
bing) methods for cleaning tap waters to levels accept- utyl tin (a now banned antifouling agent) tend to be
able for ecosystem management. Scrubbers utilized in thought of as local pollutants, mostly in harbors where
this way are typically dominated by blue-green algae. boats are concentrated and mixing minimal (and
We have limited our discussion of water composition where very serious and lethal effects on mollusks have
to the inorganic elements, mostly those existing in solu- been documented). However, years after use was dis-
tion as charged ions, either alone or in combination with continued in the USA and Canada, the livers of Beluga
oxygen and sometimes hydrogen. However, natural whales in the St. Lawrence estuary (again, a very large
waters also include abundant particulates both inorganic and well-mixed body of water) were still contaminated
and organic, and aquatic ecosystems cannot function with tributyltin (Preston, 2002).
normally without the particulate “soup” that is often The problem of toxic compounds has gone well
present in the wild. Many of the smaller organic particu- beyond immediate solution in the ocean. Only time
lates can be regarded as dissolved organics, the bound- (probably measured in decades and centuries) and
ary between particulate and dissolved being quite future prevention of release of toxic compounds to natu-
arbitrary. In this book we treat the particulate compo- ral waters can eventually solve this problem. Even when
nents primarily in Chapters 3, 6, 17, and 18. concentrations of many of the newer industrial, agricul-
Finally, anthropogenic pollutants, inorganic and tural, and pharmaceutical compounds are not directly
organic, cannot be ignored in any natural waters that lethal, they can function as endocrine disrupters pre-
might be used for source or exchange. POPs (persistent venting or reducing reproduction and having drastic
organic pollutants), like DDT and its breakdown prod- effects on invertebrate and fish populations (Pellerito
ucts, and PCBs have reached every corner of the globe et al., 2002). As we discuss in depth in Chapter 25, most
(Turosov et al., 2002). Penguins, seals, and whales in if not all of these compounds can be removed from lake
Antarctica and polar bears in the Arctic have DDT and and river waters along with nutrients, though consider-
PCBs in their tissues. Although often concentration of able public and political will is required to do so.
Algal Scrubbing and Water Composition 71
WATER AND MODEL ECOSYSTEMS disease and toxic introduction, and a pre-treatment
water system with ATS clean-up is desirable.
In earlier editions, we discussed our preference for Once a microcosm, based on the principles discussed
using natural waters from unpolluted habitats to initiate in this book, is established, water changes should be min-
model ecosystems. On occasion, in the 1980s and 1990s, imal and aimed primarily at preventing evaporative
we went as much as 50 miles offshore in the mid-Atlantic “salt drift” in sea waters and the change in the propor-
region to obtain water suitable for starting large model tional salt content caused by evaporative accumulation
coral reef systems. However, for most aquarists, includ- in fresh waters. In short, very minor water changes
ing university researchers modeling ecosystems, high- should be made to avoid drift in conservative elements
quality natural waters may simply not be available. that would create a “Great Salt Lake” or endorheic basin.
To emphasize the magnitude of the problem, we cite As we discuss in Chapters 7–11, nonconservative or
Turosov et al. (2002) (National Library of Medicine). nutrient-type elements should be maintained dynami-
“Due to its stability and its capacity to accumulate in adi- cally by balanced system loading.
pose tissue, it (DDT) is found in human tissues, and there
is now not a single living organisms on the planet that
does not contain DDT.” PCBs, mercury, and probably ALGAL SCRUBBING AND WATER
numerous other compounds of modern civilization have COMPOSITION
already achieved or are approaching the same state.
However, the microflora and microfauna appropri- In both our mesocosm and aquarium endeavors, we
ate to a model system is likely to be obtained only from have emphasized the use of plants, mostly algae, to
natural waters. The rational approach today is to use manage water quality. This is part of a broader tendency
RO water adjusted to salinity with the highest-grade in environmental water management today called phy-
sea salts, or prepared with reagent, or better, analytical toremediation, and we treat the subject in some detail
grade chemicals appropriate to the type of hardness in Chapter 25. As we discuss in many places in this
desired (for fresh waters) to fill the system. Once an book, the key to ecosystem management is stability
aquarium, microcosm or mesocosm is operating as a achieved by locking nutrients up in biomass rather
physical plant, algal scrubbers (see Chapter 11), and than by using bacterial filtration to rapidly reduce all
5–10% additions of natural water can be added to intro- nonliving organics and organism excretions to freely
duce microflora and microfauna and clean up micro available elements and ions. The algal scrubber is the
contaminants. The gradual introduction of macro organ- principal technology in this management system and is
isms to build up community structure can then be car- discussed in depth in Chapter 11.
ried out with the occasional natural water aliquot. As we Algal scrubbing is used primarily to maintain a bal-
describe in depth in Chapter 11, if the ATS methodology ance, to simulate the effects of the larger body of low-
is employed (with routine harvest), heavy metals will be animal biomass water that balances out the requirements
captured by the algae and most organic pollutants will of high-biomass systems. This might be smoothing out
be broken down and the carbon removed from the water the differences between day and night in small model
column of the system along with the algal harvest. ecosystems or between seasons in large mesocosms. If
When substrate and organisms from the natural envi- there is no import to a system, because it is large
ronment are introduced, as we describe above, micro- enough and rich enough in photosynthetic plants to
organisms will be brought in with them. They cannot be provide sufficient energy to the community of organ-
avoided, unless one wishes to select all organisms, isms maintained, then export is not required. The algae
including protozoans and microbes, individually (a vir- are removed by scrubbing as a daily, weekly, or seasonal
tually impossible task) and then pass them through sub- requirement and are dried and eventually returned to
lethal or other baths selective for the desired organisms. the system. Thus, there is little chance for the removal of
The sterilization approaches of modern medicine are not critical elements from the water medium. However,
applicable to the synthesis of most ecosystem models. when the aquarist is running a dynamically balanced
Quarantine of fish, especially those purchased, and par- system with significant input (usually dried or live
ticularly those from fresh water, is essential to avoid food) and export, either because the model has exces-
occasional serious disease problems. On the other hand, sive biomass and is being driven hard or because the
if the organisms are in a healthy environment and the input and export simulate similar features in a wild
ecosystem is managed properly, disease will be mini- ecosystem, then imbalances are theoretically possible.
mal. We discuss these matters further in Chapters 19 and The algal turfs of scrubbers are communities, typi-
26. However, as we have recently learned from hard cally with many species from most algal divisions, and
experience, today, any coastal waters are suspect for thus tend to be self-balancing. Algae and other aquatic
72 4. Water Composition
plants synthesize a wide variety of organic compounds
including many vitamins (Ragan, 1981). It is unlikely in
diverse communities of fifty to several hundred species
of plants that contain many herbivores, even in relatively
small models, that lack of algal-synthesized organic
compounds would hinder ecosystem development. On
the other hand, many algae have requirements for inor-
ganic micronutrients, such as iron, calcium, manganese,
molybdenum, boron, cobalt, copper, and iodine that
could theoretically provide such limitations by locking
up elements of concern. Moe (1989) discusses removal
of trace elements particularly by ozonation and protein
skimmers, but also through uptake by algae. Iodine,
particularly needed by crustaceans for molting, was
cited as a characteristic problem. We refer to a general
pattern of crustacean success in our systems (Chapters
20–23), where extensive algal scrubbing has been used
for many years. For one particularly successful coral
reef model, we describe more than 9 years of continu-
ous molting in a single individual of rare reef lobster. In
addition, after 10 years of continuous operation that
never included a mass water change (beyond a standard
2% per month to prevent salt drift), the Smithsonian
Coral Reef contained concentrations of iron, manganese,
silica, copper, and strontium that remained very close to
or slightly above concentrations in Delaware coastal
waters (the source of top-up water at that time). FIGURE 4.3 Conversion graph for obtaining salinity from specific
On the other hand, as we describe in detail in gravity and temperature.
Chapters 10 and 20, in coral reef models with abundant
calcifiers, high temperatures and light levels with
extensive photosynthesis, the “sinking rate” of calcium
living and dried foods; (3) in the long term utilize small
and carbon in carbonate skeleta and shells is very high
water changes (constant “new water” exchange is
(see also Chapter 3, re: geological storage). This can
a feature of wild ecosystems); and (4) where calcifica-
lead to calcium and alkalinity depletion followed by
tion is an important and extensive feature of a model
slower growth rates of calcifying organisms. It is essen-
ecosystem, be certain that calcium carbonate, espe-
tial in this situation to maintain calcium and alkalinity
cially as aragonite, is readily available and alkalinity is
concentrations at or above levels typical for the open
within normal range (see also Chapters 8 and 10). For
ocean (420 mg/liter and 2.43 meq/liter). The addition
the latter, standard, inexpensive test kits are available.
of calcium and bicarbonate in this case simulates deliv-
However, especially for calcium, the accuracy and pre-
ery to wild reefs by equatorial and tidal currents as well
cision are marginal.
as trade wind seas, and cannot be regarded as “undesir-
able”; if one’s purpose is modeling, these additions are
equivalent to that in the wild and are required for
ecosystem function. MARINE MICROCOSMS AND AQUARIA
In a research laboratory, the limiting or potential
limiting of chemical elements in ecosystem models can An attempt to faithfully re-create a marine system
be extensively monitored and appropriately adjusted. must include monitoring of salinity levels and a knowl-
For the researcher with more limited resources or a edge of daily, weekly, and monthly salinity variations in
hobbyist, a commercial water analysis service may do, the wild. Normal ranges of salinity for most nonestuar-
although sufficient accuracy and precision needs to be ine coastal situations are 28–34 ppt for colder waters
demanded. Following a few simple rules (that are, in (with a variation of no more than several ppt a day) and
effect, what happens in the wild) will avoid most prob- 34–37 ppt for tropical oceanic situations (varying no
lems: (1) do not run import and export highly out of more than 0.5 ppt daily). (The idiosyncrasies of brackish
balance (see Chapter 11); (2) use a wide variety of water aquaria are discussed in Chapter 22.)
provides about the same precision. Both devices require
very careful observation and conversion for effective
use on reef systems. For other coastal communities and
estuaries, either device is quite adequate.
The infrared-level sensors, now easily available, are
generally quite accurate. The sensors themselves need to
be wiped off every few weeks to avoid failure. Failure of
a water-delivery system can be just as disastrous as the
jamming of a heater. A check of the tank twice daily can
prevent the problem from becoming critical. However,
continuous pumping of fresh water for hours can
destroy a sensitive marine microcosm. We use manually
filled freshwater reservoirs for replacement water. The
reservoirs contain the maximum amount of water that
can safely be pumped in between checks.
QUALITY OF TOP-UP WATER
For coral reef systems, high-grade distilled water is
recommended for evaporative replacement water,
because many contaminants continually placed in a
closed tank are generally not removed by evaporation.
Poor input water quality is a key element tending to
degrade model ecosystems. As we discuss in depth in
Chapters 11 and 25, many pollutants are broken down
and removed from ecosystem models through the use of
algal turf scrubbers. The reverse osmosis and laboratory-
grade deionizer system that we used for the Chesapeake
mesocosm are illustrated in Figure 4.4. In this case an
FIGURE 4.4 Tap water cleaning system consisting of a laboratory-
algal scrubber unit is also used because it produces lower
grade RO unit, a reservoir, and an algal scrubber. nitrogen input levels than the reverse osmosis unit. Such
a system will also remove heavy metals and synthetic
organic contaminants where that is necessary. City tap
waters and many private well waters are unsuitable
Evaporation is an on-going process with all open for direct long-term evaporative water replacement to
tanks, and generally at least daily replacement of evap- ecosystem models.
orated water is necessary. Manual topping up to a The long-term result of intensive evaporation of
mark is acceptable for cold-water or brackish systems water is an alteration of the salt composition of a sys-
that normally experience wide salinity swings. But for tem. A 0.5–1.0% per day exchange with a high-quality
controlling salinity in tropical reef tanks, precision lev- “make-up” water of appropriate salinity or hardness
eling devices now available from most aquarium stores (as we discussed above) will generally avoid this prob-
and laboratory supply houses should be used. The lem. Hardness in fresh water is usually much less of a
hydrometer measures salinity by specific gravity (or problem than salinity maintenance in salt waters.
density) and is the least expensive and most trouble- Nevertheless, in special cases it can be critical, and the
free device of this type. A conversion is required (Figure 0.5–1.0% exchange may also be appropriate.
4.3) because temperature is also an important parameter
relating salinity to specific gravity. Also, hydrometers
must be calibrated for reading variation as a function of References
temperature away from the standard for which they are
calibrated at the factory. However, even the larger Evans, D. (1993) Osmotic and ionic regulation. In: The Physiology of
Fishes. D. Evans (Ed.). CRC Press, Boca Raton, Florida.
hydrometers are difficult to read with a consistent effec- Farago, M. E. (2000) Mercury in Marine Environments. In: Chemical
tive precision of better than ±0.2 ppt. A refractometer Processes in Marine Environments. A. Gianguzza, E. Pelizzetti,
costs a little more and is easier to use. However, it and S. Sammartano (Eds). Springer, New York.
74 4. Water Composition
Frausto da Silva, J. and Williams, R. (1991) The Biological Chemistry of Preston, M. (2002) Endocrine-disrupting chemicals in the marine envi-
the Elements. Oxford University Press, Oxford. ronment. In: A. Gianguzza, E. Pelizzeti, and S. Sammartano (Eds).
Horne, R. (1969) Marine Chemistry. Wiley, New York. Chemistry of Marine Water and Sediments. Springer, New York.
Hutchinson, G. E. (1957) A Treatise on Limnology, Vol. 1. Wiley, Ragan, M. (1981) Chemical constituents of seaweeds. In: The Biology
New York. of Seaweeds. C. Lubban and M. Wynne (Eds). University of
Hutchinson, G. E. and Edmondson, Y. (1993) A Treatise on Limnology, California Press, Berkeley, California.
Vol. IV. Zoobenthos. Wiley, New York. Riehl, R. and Baensch, H. A. (1987) Aquarium Atla. Mergus-Verlag, Melle.
Jobling, M. (1995) Environmental Biology of Fishes. Chapman and Hall, Spotte, S. (1979) Seawater Aquariums. Wiley-Interscience, New York.
London. Sverdrup, H., Johnson, M., and Fleming, R. (1942) The Oceans, Their
Laws, E. A. (1993) Aquatic Pollution, An Introductory Text, 2nd edn. Physics, Chemistry and General Biology. Prentice-Hall, Englewood
John Wiley and Sons, New York. Cliffs, New Jersey.
Millero, F. and Sohn, M. (1992) Chemical Oceanography. CRC Press, Thurman, H. and Webber, H. (1984) Marine Biology. Merrill,
Boca Raton, Florida. Columbus, Ohio.
Moe, M. (1989) The Marine Aquarium Reference. Green Turtle Pub- Turosov, V., Rakitsky, V., and Tomatis, L. (2002) Dichlorodiphenyl-
lications, Plantation, Florida. trichloroethane (DDT): ubiquity, persistence and risks. National
Pellerito, L., Barbieri, R., DiStefano, R., Scopelliti, M., Pellereito, C., Library of Medicine, Pub. Med. Environ. Health Perspect. 110: 125–128.
Fiore, T., and Triolo, F. (2002) Toxic Effects of Organometallic Van Dover, C.-L. (2000) The Ecology of Deep Sea Hydrothermal Vents.
Compounds Towards Marine Biota. Ibid. Princeton University Press, Princeton, NJ.
C H A P T E R
The Input of Solar Energy
In many ways, this is the key chapter in this book. they are rather rare, requiring an anaerobic environ-
Photosynthesis not only provides virtually all the energy ment in conjunction with abundant solar energy, a
that drives ecosystems, it provides our food and the envi- somewhat unusual situation on today’s Earth
ronment in which humans have evolved. This has not (Rheinheimer, 1985).
always been so. Finally, about a billion years later, the blue-green
The early atmosphere and ocean, rich in carbon algae (treated today as cyanobacteria since they lack a
dioxide, ammonia, and perhaps hydrogen sulfide and well-defined nucleus) developed the ability to use the
without oxygen or ozone, was bombarded with short- most abundant compound available in the Earth’s
wave radiation. Possibly the radiation impacting the oceans (water) in this same basic process of energy
elemental soup created a wide variety of physically supply (Figure 5.1). Photosynthesis eventually became
synthesized simple “organic compounds,” or possibly a highly sophisticated chemical process of two basic
they “rained in” with comets that also provided the steps, the first requiring light and using chlorophyll
water. The earliest proto “organisms” evolved from and associated pigments, as antennae or catalyzers, to
chance combinations of these compounds, perhaps capture light energy and to split water to provide elec-
with the involvement of the intense energy of lightning trons and hydrogen ions (and incidentally release oxy-
strikes. Some researchers think that the structural pat- gen). The second step can take place in the dark. It uses
terns of clay minerals, which can replicate, may have the energy carried by excited electrons from the first
provided the proto-genetic organization, while the sur- step and the hydrogen ions to build simple sugars or
face tension of water combined with simple “organic” alcohols (C6H12O6 or 6CH2O) from carbon dioxide,
created cellular-like bubbles. These developing “organ- thereby providing the basic chemical energy supply for
isms” likely made direct use of simpler, energy-rich the plants, and for the animals that eat them.
compounds, much as many present-day heterotrophic It is still true that in oceans, at sea floor spreading
bacteria are able to do, and were able to grow. This pat- zones and on anaerobic mud flats, as well as in hot
tern of energy supply continued for perhaps a billion springs on land, some biological sources are chemo-
years or more and probably could have been effective autotrophic and probably not even indirectly derived
only in the absence of oxygen. from solar energy. A prime example, discovered in the
early 1980s, is provided by the thermal vent communi-
ties and their ecosystems, along mid-ocean ridges. These
PHOTOSYNTHESIS AND ITS ORIGIN ecosystems are based on energy supplied from the Earth.
However, interesting as these systems are, and as inter-
About 3 billion years ago, some bacteria developed esting as they would be to bring into a microcosm, it is
the ability to absorb sunlight and to split a variety of sunlight that drives the vast majority of ecosystems
abundantly available noncarbon compounds with likely to be of interest to the ecologist and the aquarist.
hydrogen and an available electron, such as H2S and Also, in environments such as deep soft bottoms where
H2. The same or similar bacteria still exist today though no light is present, the ecosystem’s driving energy is
76 5. The Input of Solar Energy
FIGURE 5.1 Evolution with time of the major groups of organisms, the process of photo-
synthesis, and the composition of the atmosphere. After Mathews and van Holde (1996).
Reprinted by permission of Addison Wesley Longman.
obtained through the rain of organic matter from shal- more complex life forms on Earth. Since the dawn of the
low water or possibly through turbidity or other cur- industrial revolution, human society has been massively
rents. Tropical jungle streams survive largely through extracting energy from fossil fuels and forests (both
the breakdown of leaves that fall into them or are made stored carbon) and simultaneously releasing nutrients to
available to the community during floods of the adja- surface waters with little regard for the consequences. To
cent forest floor. In simulating such systems one would prevent a collapse of human civilization when the fossil
perhaps wish to “feed” them with appropriate organic oil runs low (see e.g. Diamond, 2005; Lovins et al., 2004)
particulates or leaf litter rather than primarily with and the Earth overheats, we need to greatly expand our
light through a second model ecosystem. However, the solar energy capture systems (including photosynthesis
most interesting systems for aquaria, and microcosm bioenergy). At the same time we need to de-nutrify and
models, as well as wild aquatic systems currently need- de-toxify our surface waters. In the second edition of this
ing restoration, are high light systems. Even the source book, we reasoned that while we could build ecosystem
water for blackwater streams might be best “scrubbed” models that operated in pre-industrial environments, we
first, as we described at the end of the last chapter, and could not economically repair the existing damage to our
then acidified to rain level pH with CO2 bubbling. atmosphere and natural waters. The principal focus of
We examine the light-driven reactions of photosyn- the earlier edition was to provide enough public and sci-
thesis in greater depth, because they provide the keys to entific understanding of the workings of aquatic ecosys-
the operation of model ecosystems, as well as to the tems to redouble conservation efforts at preventing
restoration of most damaged ecosystems. The evolution, further damage. Conservation is essential, but a more
increasing sophistication and globalization of photosyn- pro-active approach is now necessary. In this edition, we
thesis, and its corollaries, an oxygenated, low carbon replace that more pessimistic, but hopeful view, with
atmosphere and mostly low nutrient-shallow waters, one of greater optimism. We describe how our natural
provided the basis for the further evolution of higher, ecosystems can be recovered with economic advantage.
Photosynthesis and Its Origin 77
FIGURE 5.2 Electron microscope and diagrammatic view of chloroplast structure. After Keeton and Gould (1986). Reprinted by
permission W. W. Norton & Co., Inc.
This optimism is based in an understanding of chloro- constructors of most coral reefs. These coelenterates
phyll and photosynthesis, and in an application of that build reef “infrastructure” that is then colonized by the
understanding to environmental restoration. highest diversity of animals and algae in the oceans.
Chlorophyll is the basis of photosynthesis. The This feat of calcification and growth is accomplished
magnesium-centered chlorophyll molecules, porphyrin- by a photosynthesis-enhanced metabolism that accrues
ring structures (like the iron-centered hemoglobin) were from the capture of algal cells (zoothanthellae), and
no doubt the end result of hundreds of millions of years the combining of the physiologies of both animal and
of improving the biochemical processes of photosyn- alga. There are many animals in coral reefs that are
thesis. The cellular synthesis of the chlorophylls and herbivores of free-living algae, and many that hide in
hemoglobin is part of the same biochemical complex of the free-living algae that grow on the reef surface, but
processes that synthesizes the cytochromes (electron- only the symbiosis of an animal and an alga could
transferring molecules of photosynthesis), the phyco- create the largest and most diverse ecosystem in the
bilins (light capturing accessory pigments of red and shallow ocean.
brown algae) and cobalt-centered vitamin B12, among In algae and higher plants, the chlorophyll mole-
many others. Some photosynthetic bacteria have chloro- cules are held on the lipid membrane surface of the
phyll pigments that are zinc-centered porphyrins. These granae by a convoluted protein and have long hydro-
are all molecules configured to easily pick up and lose carbon tails embedded in the membrane. As shown in
excited electrons and to bind oxygen. In the algae and Figure 5.3, chlorophyll “a” (the primary photosyn-
higher plants, chlorophyll and photosynthesis occur in thetic molecule) is tuned to light capture in two differ-
chloroplasts, membrane enclosed cellular organelles ent ways. Photosystem II, absorbing light at 680 nm
that contain membrane-bound platelets (granae) (Figure (red), produces excited electrons that escape from the
5.2). Chloroplasts have their own DNA, quite different chlorophyll molecules, and then, in a poorly understood
from the cell’s nuclear DNA, and many researchers process (Pace, 2005; Melis, 2005), replaces those elec-
think that these represent cyanobacteria, first captured trons from water molecules resulting in the “splitting”
over a billion years ago by algal ancestors (Lee, 1999). of water and the production of oxygen. In the light, the
Thus, algal (and now higher plant) photosynthesis was lipid membrane surface of the granae, which is studded
the result of a symbiosis similar to the coral symbiosis with molecules like cytochrome and ferredoxin, that
with zooxanthellae that we describe later. The light pick up and lose excited electrons easily, is a “sea” of
capture process occur on the surface of the granae. The moving, excited electrons. Some of the cytochrome mol-
so-called dark reactions of the synthesis of sugar ecules, as an electron attaches and detaches, use elec-
(Chapter 7) occur in the intergranae spaces, the stroma. tron energy to pump hydrogen ions into the internal
As we will discuss in greater depth in Chapters 19 spaces of the granae. Employing the hydrogen ion gradi-
and 20, stony corals are the primary framework ent, enzymes, also embedded in the membrane, function
78 5. The Input of Solar Energy
FIGURE 5.3 Process of photosynthesis and the sequence and location of light-sensitive phases on the membranes of plant chloroplasts. After
Keeton and Gould (1986). Reprinted by permission of W. W. Norton & Co., Inc.
as hydrogen-ion-driven pumps to attach phosphorus much as 80%; Melis, 2005) by the chemical storage
ions to ADP to in turn create the energy transporting process. Nevertheless, the overall process of photosyn-
ATP in the intergranae spaces. The membrane also has thesis and primary production remains considerably
chlorophyll “a” molecules that are tuned slightly dif- more efficient than current industrial methods of solar
ferently, to 700 nm (Photosystem I), and serve to simply energy capture.
re-excite electrons traveling along the membrane with- Many scientists are attempting to find the keys for
out splitting more water. Finally, ferredoxin molecules, carrying out photosynthesis industrially, physically
on picking up excited electrons, are able to attach those independent of algal or plant cells. This is certainly logi-
electrons to NADP to produce the energy carrier cal. The chemical process of photosynthesis is highly
NADPH. efficient and produces electrons, oxygen, and hydrogen.
In the light, activated NADPH and ATP molecules In the laboratory, some algae have been induced to pro-
are constantly released from the surface of the granae duce hydrogen gas, which could be used in fuel cells
membranes into the stroma (intergranae spaces) where (Melis, 2005). Hopefully, if this can be accomplished
they are available to drive sugar synthesis (Chapter 6) without negative side effects (as in atomic energy), then
and then return to the granae surface for reactivation. perhaps with a more or less inexhaustible energy source
This process of photosynthesis, evolved over a billion we could concentrate on environmental recovery. How-
years or more, is highly efficient at solar energy capture ever, as we have shown, photosynthesis is a highly com-
and also supplies energy storage in chemical bonds. plex process, and chlorophyll does not function when
Solar cells and wind generation also capture energy in it is stripped from its supporting protein molecules
the form of moving electrons, albeit far less efficiently and lipid membrane. Perhaps the new science of nano-
than photosynthesis. However, storage of energy technology (the physical manipulation of molecules and
acquired with these devices is far more problematical, atoms) can help us out with this problem. While human
requiring expensive, inefficient batteries, or more eso- understanding of physical and biological processes, and
teric methods. It is interesting to note that the highly our achievements at engineering that knowledge for
efficient chlorophyll, energy capturing process of algae practical human use, is phenomenal by any measure,
and higher plants is greatly reduced in its efficiency (as not all natural processes can be reduced to practical
Solar Radiation and Water 79
human use, especially in the time frame we may require.
As we discussed in the Introduction, our approaching
socio-political collision with the exhaustion of oil energy,
coupled with an ever-growing pollution of the Earth’s
atmosphere and water, and increasing disruption of nat-
ural ecosystems gives us little lead time. We cannot wait
on the engineering of photosynthesis to solve these prob-
lems. In this book, we describe how we can achieve that
“symbiosis” with photosynthesis, not only for the man-
agement of aquaria and ecosystem models, but also for
the restoration of wild environments and the recovery of
our socioeconomic system. However, above all, it
requires an understanding of photosynthesis, both in
algae and in the higher plants.
SOLAR RADIATION AND WATER
Any atom or physical mass, including the sun, radi-
ates electromagnetic energy in accordance with its tem-
perature. Beginning at about 800 K (degrees centigrade
plus 273), visible light in the red end of the spectrum
begins to be radiated. As the temperature increases, emit-
ted wavelengths (and the amount of energy radiated)
increase. An incandescent bulb has a color temperature
of 2800 K and is quite red; a cool-white fluorescent bulb
radiates at about 4000 K and is strongest in the red- FIGURE 5.4 Attenuation of PAR in different types of water. After
orange. Daylight fluorescent bulbs and the sun radiate at Kirk (1994). Reprinted with permission of Cambridge University
about 6000 K. Unfortunately, the magnitude of visible Press.
radiation is measured in many ways. Wherever possible,
we use an energy measure: microeinsteins per square
meter per second (millimoles). For rough comparison,
2000 µE/m2/s is approximately 100 000 lux or 10 000
In the middle of a bright sunny day, early summer at
high latitudes and year-round in the tropics, approxi-
mately 2000 µE/m2/s of visible or photosynthetically
active radiation (PAR) is received at the Earth’s surface.
Depending on the clarity of the water in question, this
radiation can extend to great depth or be limited to a few
meters (Figure 5.4). The total solar radiation received per
day over the Earth is shown by month for various lati-
tudes in Figure 5.5. The yearly total is shown in Figure 5.6.
Generally, higher latitudes have greater seasonal vari-
ability in incoming light. While progressively north
and south of latitude 40 total yearly radiation is consid-
erably reduced, in a broad range of mid-latitudes total
incoming radiation is mostly a function of cloudiness or
Light incoming to the Earth’s outer atmosphere has
roughly the spectrum shown by the top curve in Figure
FIGURE 5.5 Change in incoming solar radiation at the top of the
5.7. By the time it passes through the atmosphere and atmosphere calculated seasonally and for different latitudes. After
reaches the sea surface through clear sky or clouds, it Kirk (1994). Reprinted with permission of Cambridge University
looks more like the second or third curves. Shaded areas Press.
80 5. The Input of Solar Energy
FIGURE 5.6 Mean annual insolation (solar radiation) on the surface of the Earth (calories/cm2/year 103). Note that the greatest yearly
totals occur in the horse latitudes rather than in the tropics proper. However, the seasonality is considerably greater in the horse latitudes, with
higher levels in summer and considerably lower levels in mid-winter (see also Figure 5.5). After Gates (1980).
FIGURE 5.7 Spectral quality of incoming solar radiation, light reaching the Earth’s sur-
face (through clear and clouded sky), and light transmitted through terrestrial vegetation.
After Gates (1980).
Solar Radiation and Water 81
without significant local reflection and those under The resulting attenuation at different wavelengths
green foliage are the fourth and fifth curves. Further, varies greatly depending on depth and water character.
attenuation in lakes or the sea provides a color balance Curves for light distribution with depth for open ocean,
that is even more removed from the original spectrum. clear coastal water, and a lake are shown in Figure 5.8.
FIGURE 5.8 Spectral quality of solar radiation transmitted through natural waters
(marine and fresh) of varying character. After Kirk (1994). Reprinted with permission of
Cambridge University Press.
82 5. The Input of Solar Energy
In general, pure water absorbs longer wavelengths
above 550–600 nm and thus, given enough depth, will
appear green or ultimately blue. Suspended particu-
lates and dissolved substances absorb the shorter
wavelengths, and typically as one passes from open
ocean to coast, to estuary, and then to river and lake,
more of the wavelengths below 500 nm and eventually
even 600 nm are absorbed. Thus, depending on the
extent of matter in the water, one passes from blue, to
green, to yellow, to red or brown in making such a tran-
sect. This is also an indication of the kind of light that is
available at depth. Further upstream, into mountain
lakes and streams (at least when they lack glaciers), the
number of particulates usually decreases along with FIGURE 5.9 Spectral absorption of the freshwater macrophyte
nutrients and planktonic algae. Under these condi- (flowering plant) Vallisneria spiralis. After Kirk (1994). Reprinted with
tions, water clarity and the blue-green character of the permission of Cambridge University Press.
community, particularly an algal community, the pho-
tosynthetically active pigments cover the visible spec-
LIGHT ABSORPTION BY trum. As stated by Mathews and van Holde (1996)
WATER PLANTS “scarcely a photon can come through that cannot be
absorbed by one chromophore (pigment) or another.”
Plants, including algae, utilize a wide variety of acces- Heldt (2005) demonstrates how the red and blue pig-
sory energy-absorbing pigments in addition to the all- ments of red algae and cyanobacteria, phycoerythrin,
important chlorophyll. Each of these pigments requires and phycocyanin (structural relatives of chlorophyll)
specific wavelengths to be photosynthetically efficient. are in effect “extra antennae” that are arranged on the
Plants are generally classified into evolutionary group- surface of the granae membranes on top of or near
ings, most easily designated by color and therefore by chlorophyll “a” Photosystem II reaction centers. Photons
their photosynthetically active pigments. The green are captured by the accessory pigments and subse-
plants include the flowering plants such as marsh quently the energy transferred (as a fluorescence process
grasses and all submerged aquatic vegetation as well as or excitons) to the chlorophyll “a” reaction centers,
green algae including Ulva (sea lettuce) and Enteromorpha. allowing these algae (and cyanobacteria) to use light
The brown algae, with virtually no fresh water or terres- thru the middle of the visible light range where the
trial representatives, include large marine plants such as chlorophylls are inactive.
Laminaria (kelp) and Sargassum. The red algae, mostly
marine with a few species in fast-running streams,
include Chondrus (sea moss) and Rhodymenia (dulce). LIGHT INTENSITY AND PLANTS
The blue-green algae (Cyanobacteria) are filamentous
or unicellular plants that form slimy crusts, ribbons, or In addition to color balance or spectrum of solar
cushions of varying hues (green, red, black, etc.) that radiation, a major concern in photosynthesis is the total
are common in most lighted wild environments as well intensity of the radiation. Many plants including
as in many fresh- and saltwater aquariums. Finally, marine and aquatic plants are highly adaptive to avail-
a number of widespread algal groups particularly able light. Plants of a given species grown at high light
important as plankton include golden-brown algae intensity will perform more poorly under low light
(diatoms) and yellow-brown algae (dinoflagellates). than plants raised at low intensity. It is characteristic of
The chlorophylls and the accessory pigments used by many algae that with a major change in solar radiation
higher plants, and marine and aquatic algae absorb light the plants will die or die back and develop new growth
for photosynthesis at particular wavelengths or groups adapted to the new light levels.
of wavelengths. These absorption peaks tend to be in Terrestrial plants from normal sunny habitats typi-
the blue-green and the far-red wavelengths. However, cally show a pattern of photosynthesis with available
the actual absorbance by plants and the action spectra light similar to that of the bean (Figure 5.11). At cool
(or photosynthetic activity) of those plants, including temperatures leaves of this plant show a more or less
the major phyla of marine algae (Figures 5.9 and 5.10), direct and strong increase of photosynthesis up to
are more smoothed or spread out. In general for a plant about one-third of full tropical sunlight. Above that
Light Intensity and Plants 83
FIGURE 5.10 Action (- - - -) and absorption (—) spectra of photosynthesis in vari-
ous marine algae. While the two curves usually coincide and light absorbed is utilized
in photosynthesis, that is not necessarily the case, particularly at the ends of the spec-
trum. (A) Ulva (green); (B) Coilodesme (brown); (C) Delesseria (red); (D) Chlorella (green);
(E) Skeletonema (diatom). After Kirk (1994). Reprinted with permission of Cambridge
level up to the strongest natural light possible, photo- surface light, and at higher intensities it is actually
synthesis continues to increase but at a slower rate. On inhibited. The same results are obtained in more recent,
the other hand, at high midday leaf temperatures pho- sophisticated computer modeling (Behrenfeld et al.,
tosynthesis considerably increases up to the most intense 2002). On the other hand, benthic plants, both flowering
solar light possible on Earth. Most physiological studies plants and algae, do not show an obvious inhibition
of plants are carried out on small specimens or pieces of (Figure 5.14).
those plants. As shown in Figure 5.12, there is a major One might conclude from these data that while
difference between the photosynthetic performance of many land plants, given no limitation by other factors
whole plants compared to their parts. The relationship (e.g. carbon dioxide or temperature), can use all of the
between light and photosynthesis for entire trees is possible solar radiation available for photosynthesis,
almost direct to the full intensity of sunlight. marine and freshwater plants saturate or even lose pro-
An often quoted pattern of underwater photosyn- duction at levels of one-quarter to one-half of available
thesis is that of phytoplankton, as shown in Figure 5.13. surface radiation. However, if one looks at production
Here, photosynthesis peaks at about one-quarter of by entire benthic plant communities in the wild, almost
84 5. The Input of Solar Energy
FIGURE 5.13 Photosynthetic rates of Sargasso Sea (•) and Lake
FIGURE 5.11 Light response at different temperatures of the Windemere (• ) phytoplankton as a function of light levels (labora-
bean Phaseolus vulgaris, a tropical plant characteristic of sunny sites. tory experiments). After Kirk (1994). Reprinted with permission of
At lower temperatures photosynthesis is limited by molecular and Cambridge University Press.
chemical processes controlled by temperature, rather than by light
itself. After Gates (1980).
FIGURE 5.12 Photosynthesis rate for two terrestrial, woody plant species – individual
leaves as compared to the entire trees. After Oliver and Larson (1990). Reprinted with
permission of John Wiley & Sons, Inc.
invariably primary production (or water purification, if While 50% of production is achieved when 500 µE/m2/s
one is thinking in those terms) is limited seasonally and is reached (a few hours after dawn), full production is
daily by the available solar radiation (Figures 5.15–5.18). only achieved at noon, at light intensities close to full
Figure 5.15 illustrates the relationships particularly well. tropical sunlight. Below maximum intensity (and down
Light Intensity and Plants 85
FIGURE 5.14 Photosynthetic rates of (A) various submerged macrophytes (flowering
plants) and (B) algae as a function of light levels. After Kirk (1994). Reprinted with permission
of Cambridge University Press.
86 5. The Input of Solar Energy
FIGURE 5.15 Photosynthesis (day) and respiration (night) as measured on a
Caribbean coral reef (Panama): (A) oxygen exchange vs time; (B) oxygen exchange vs
light in situ on reef; (C) oxygen exchange vs light for an in situ microcosm of the reef.
After Griffith et al. (1987). Reprinted with permission of The American Society of
Limnology & Oceanography.
to about 500 µE/m2/s) every 10% reduction in intensity
causes a 5% reduction in production. Likewise in a cold-
water kelp community (Figure 5.16), light and tempera-
ture are not in phase. Yet yearly photosynthesis closely
follows available light independent of temperature.
Factors other than light may also limit plant produc-
tion. Plankton production in higher latitudes in lakes
and oceans, for example, typically rises sharply in the
spring, as the light returns and no nutrient limitation
exists. There may be dips in production in midsummer,
but this is usually due to nutrient limitation or grazing
by zooplankton. Phytoplankton production and more
FIGURE 5.16 Photosynthetic rates of kelp as related to light lev- rarely benthic plant production can be limited by ultra-
els (at depth of growth) throughout a 1-year cycle. After Kirk (1994). violet (UV) radiation near the surface. This limitation is
Reprinted with permission of Cambridge University Press. minimal, however, and likely more than made up for
Light Intensity and Plants 87
FIGURE 5.17 Diurnal oxygen exchange of a tropical coral reef community by season. After Adey and Steneck (1985).
FIGURE 5.18 Gross primary productivity of four sections across a well-developed
shallow-water tropical coral reef community (St. Croix, U.S. Virgin Islands) as a function
of light, season, available surface, and biomass. After Adey and Steneck (1985).
88 5. The Input of Solar Energy
FIGURE 5.19 Generalized spectral characteristics of natural water bodies and the artificial
light typically required to provide underwater light in aquarium and mesocosm models of
those water bodies.
by increased plant production in deeper water, particu- Calvin cycle and reduce CO2 to make the sugar phos-
larly in benthic communities. phoglyceraldehyde and eventually glucose (a process
called carbon fixation). The simplest way to determine
the magnitude of photosynthesis is to measure oxygen
PHOTORESPIRATION release. All of the measures of photosynthesis dia-
grammed above were based on determining oxygen
As we pointed out above, photosynthesis involves release. However, primary production refers to the
two primary steps: (1) the capture of solar energy in completion of the process and the net fixation of carbon
electron excitation, with the electrons derived from the (from carbon dioxide) in simple carbohydrates.
splitting of water molecules (with the release of Ribulose 1,5-bisphosphate (RuBP or Rubisco) carboxy-
gaseous oxygen, O2) and (2) the transfer of electrons to lase is a critical enzyme in the fixing or incorporation of
NADP and ADP, the energy transfer molecules, on the carbon dioxide in the dark phase of photosynthesis (the
granae of chloroplasts. The resulting NADPH and ATP Calvin cycle). It has been known for some time that in
are then available in the chloroplast stroma to drive the many higher plants, under some conditions (especially
Light and Model Ecosystems 89
high temperatures and low carbon dioxide availability) 1978). Algal turf communities in exposed reef flats reach
RuBP carboxylase acts as an oxidizer, “respiring” the peak production at midday light intensities of about
intermediate products of photosynthesis without provid- 1500 µE/m2/s (Adey and Hackney, 1989). Small and
ing net energy or biomass to the plant. Adey (2001) demonstrate system calcification rates equal
Some groups of higher plants, particularly the to the faster growing coral reefs in the wild, as well as
grasses or C4 plants, have developed mechanisms to the fastest, published Acropora growth rates, using six,
avoid the effects of photorespiration. Others, with the C3 160-W VHO fluorescent lamps on a 130-gallon coral
or standard Calvin cycle, simply perform poorly when reef system (see Chapter 20). At the distance involved
matched with C4 plants in intense light at high tempera- in the formal coral growth studies, light received would
tures. Although all or most algae appear to have C3-like have been about 1500 µE/m2/s.
pathways, photorespiration seems to generally be sup- When planning light simulation in microcosms,
pressed in algae (Lobban and Harrison, 1994). In algal mesocosms, and aquaria, our rule of thumb is to match
turfs under coral reef environmental conditions, which both light spectrum and light intensity as closely as
we discuss at some length in later chapters, studies have possible to those of the wild ecosystem being modeled.
shown no evidence of photorespiration (Hackney and In general, if desired for reasons of economics, light
Sze, 1988). It has been assumed that bicarbonate (HCO3) intensity may be reduced by 20–30% of that in the wild
under normal conditions in aqueous environments, without major effects, but greater reductions would
especially in the sea, is available to algae as a carbon seriously compromise the system biologically and eco-
source and this prevents the significant occurrence of logically. Likewise, if there were considerable benefits
photorespiration. It is unlikely that carbon, as a nutrient, to be derived, one might omit some of the green-yellow
can ever be limiting in marine environments (see coral part of the light spectrum, but it is likely that some part
calcification, Chapter 10). However, this may not be so of the ecosystem would be compromised.
in highly productive freshwater environments (see A great number of artificial light sources are now
Chapter 25). available for use in model ecosystems. Delbeck and
Sprung (2005) provide an excellent summary of the more
recent lighting developments as they apply to the build-
LIGHT AND MODEL ECOSYSTEMS ing of coral reef aquaria. These produce a diverse range
of intensity and spectra (Color Plates 7 and 8). Tungsten-
Until the 1980s, because of the rule of thumb that filament lamps produce light useful to plants. However,
aquatic plants used only a fraction of available sun- a tungsten lamp produces little green and blue light,
light, model ecosystems tended to be operated with whereas it is in the blue-green end of the spectrum that
relatively low light levels. In the aquarium world, light aquatic plants carry out a major part of their photosyn-
was largely considered to be solely for the viewer and thesis. They are also relatively inefficient in terms of PAR
perhaps for the activities of fish. Particularly in marine produced compared to heat. On the other hand, the gas
tanks, if algae were present, they were primarily the lamps – fluorescent and metal halide – produce a wide
encrusting blue-greens that could manage the low light variety of light spectra, much of it within the photosyn-
levels (and low water quality). Because these algae thetically useful range (Color Plates 7 and 8). In addition,
were often black (and slimy), even such a minimum they are quite efficient in terms of power usage. Many
presence was not desired. spectral types of fluorescent lamps are available and,
Moe (1989) documents this history and provides an with appropriate mixing of color types, the spectrum of
excellent review of the changes in attitude among incoming sunlight to a marine or aquatic community
aquarium hobbyists, particularly those specializing in can be reproduced. The intensity of the standard fluo-
reef tanks. In the reef aquarium world, the approach rescents is, however, relatively low and, although they
has shifted radically, and now we find many of the are strong enough to supply the light requirements of
more advanced hobbyists seeking out the various the deepest-water or heavy-shade communities, they are
actinic, 10 000 K or even 20 000 K, lamps. These lamps not generally suitable for most sun-dependent ecosys-
have a spectrum that is shifted far to the blue. If the pri- tems, especially those from shallow tropical areas.
mary interest is to culture deeper water corals or a deep High-output (HO) and very-high-output (VHO) flu-
reef ecosystem, this approach is perhaps warranted. orescent lamps can be found in most of the spectral
On the other hand, most Acropora, Millepora, and Porites types of standard fluorescents. The same size as stan-
species, among many others, grow most rapidly where dard lamps, they put out approximately twice and four
they receive greater than 1000 µE/m2/s, at the equivalent times as much radiation, respectively. (Output is roughly
of 5000–7000 K (i.e. little shift from the natural spectrum proportional to wattage.) For most small systems (less
of sunlight), through the middle of the day (Adey, than 200 gallons), especially fresh- and cold-water coastal
90 5. The Input of Solar Energy
microcosms, these lamps are suitable. For coral reef or effective depth of the microcosm. The light at the bot-
similar brightly lit communities it is possible to use tom of the reef tanks at 6 feet is equal to that measured
VHO lamps, particularly if the tank is relatively shal- at 40–60 feet in the natural reef environment. The result
low. However, the light levels of the shallowest coral is that the microcosm contained in this tank is essen-
reefs cannot be effectively produced by this means, and tially a scale model, relative to light, and includes
the number of lamps that have to be used require major 40–60 feet of reef profile (relative to light) in only 6 feet
wiring efforts. of water. Many opportunities and problems are pre-
For large (deeper) microcosms and mesocosms, and sented by this compression of depth zones.
even larger coral reef aquaria, only the high-intensity dis- The cold-water and temperate microcosms, as we
charge lamps, which can be obtained from 250 to 1000 W, have arranged them, are also lighted at least partially by
provide sufficient light to simulate shallow-water inten- metal halide lamps. The bottom in the Maine tank slopes
sities. For larger systems, of all commonly available light steeply, and the turbidity is moderate. The community
sources, metal halide lamps have been found to provide represents a cross section that reaches from the intertidal
the best combination of spectrum and intensity for zone nearly to the limit of the photic zone. While sum-
simulating natural sunlight (Color Plates 7 and 8). These mer radiation in the Maine intertidal zone can be close to
lamps are now available in 2000–6000 K and much that received by an exposed reef, or algal ridge, in the
higher models, solving the most acute spectrum prob- tropics, even during times of strongest sunlight, the
lems. However, achieving an even distribution of 6000 K energy that reaches the subtidal organisms in the coastal
light at 1000 µE/m2/s for a shallow reef flat requires a Gulf of Maine is much less than that in the clear water of
dense aggregation of the highest wattage lamps. the tropics. Turbidity is caused by runoff from the land,
In ecosystem models, the intensity and period for tidal stirring of sediments, and the bloom of planktonic
which artificial lighting is used can be varied to suit organisms responding to high nutrients and the sea-
conditions in the native environment of the commu- sonal increase in light. A light measurement equivalent
nity being supported. For instance, the microcosms to a depth of about 50–60 feet is registered at the bottom
holding the coral reef communities (see Chapter 20) are of the Maine tank, while the intertidal zone receives
modeled after areas in the tropical Caribbean between light levels close to those found in the wild. As we dis-
10° and 25° north latitude. Day length at those locali- cuss in Chapter 21, the lights are raised and the daylight
ties (photoperiod) ranges from about 11 to 13 h over the period shortened to simulate winter light levels.
year, and incoming light intensity at noon, just beneath In the Smithsonian Chesapeake estuarine meso-
the water surface, measures about 1800 µE/m2/s in cosm, the shallow and emergent marshes required
summer and 1400 µE/m2/s in winter. The “cold tank” maximum intensity, and we used four 1000-W metal
(Chapter 21) represents the Maine coast, 2000 miles to halides, at a height of about 3 feet above the soil sur-
the north, where photoperiod and light intensity change face, for about 20 square feet of marsh area. It is inter-
significantly with the season. In summer the sunlight is esting to note that while radiation of 1200–1800 µE/m2/s
almost as strong as that of the tropics and the day is is characteristic of the upper third of the marsh plants,
even longer. However, in the winter, light intensity many will grow well into the high-intensity cone of
drops dramatically to about 800 µE/m2/s just below light, exceeding 4000 µE/m2/s, with apparent healthy
the water surface at noon and there are only 6–7 daylight color ceasing only when temperatures finally become
hours. Lighting for these microcosms was planned with too high. On the deeper end of the Chesapeake tank,
these conditions in mind, and the diagrams of the eight 160-W VHO lamps are used to simulate reduced
arrangements that reproduce them are shown in light in the highly turbid bay analog. Thus, for the
Chapters 20 and 21. Clear 500–1000 W lamps are used marsh, a maximum equivalent intensity of 200 W/ft2 is
to light the tropical tanks, the brighter lamps over the used whereas in deeper water levels drop to 32 W/ft2
deeper areas. Although output directly beneath indi- (electrical rating).
vidual bulbs exceeds the intensity of natural sunlight The period of illumination of each mesocosm, micro-
in the tropics, the light level decreases rapidly with dis- cosm, and aquarium that we have constructed (i.e. the
tance from the center of concentration. The physical “day length”) is controlled automatically by timers that
size of the light units prevents there being more than open and close the light circuits according to a preset
one bulb for every 3 square feet of tank surface; thus program. However, full intensity is not delivered to the
the mean light intensity per unit surface is lower than microcosms for the entire period of illumination, but
that found in the tropics. Peak intensity is, however, changes gradually to imitate the periods of dawn and
stretched out over a longer period each day. On the other dusk. This is accomplished by lighting or extinguish-
hand, lower intensity in midday results in a rapid dwin- ing parts of lights in sequence over a period lasting up
dling of light as it penetrates the water and increases the to 2 h between each light and dark cycle. This allows
the tank inhabitants a transition period between day can be greatly reduced before morning. Many shallow
and night activities. Most marine organisms are sensi- marine and aquatic environments have relatively dense
tive to light changes. Some animals are nocturnal, func- populations. However, in the wild, during the night,
tioning only during dark periods, while others are the constant flow of water from less populated areas of
active in the daytime. In some cases, these transitions the open ocean, lake, or river supplements the supply
are striking. Parrotfish, for instance, rest in a secreted of oxygen and removes wastes.
bag of mucous in the dark hours and feed continuously This situation where one ecosystem supplies the
during the day. A reasonable twilight or changeover needs of another is common in the wild and can be
time is desirable. adopted to preserve the nighttime balance in an aquar-
The total light energy available to a microcosm is a ium. Rather than using a large reservoir to replenish the
function of period as well as intensity, the length of water at night, a method of ensuring continuous water
time as well as the brightness. To a limited extent, a conditioning by plants can be utilized. Our microcosm
deficiency of light intensity can be compensated for by systems are connected to separate units that are reserved
lengthening the period, but probably with some loss of for the cultivation of a specialized community of algae.
accuracy in simulation results. Many plant and animal These units are lighted at night when the microcosms
responses are related to day length, especially in popu- are in darkness, and they supply a constant flow of
lations from higher latitudes where seasonal variation oxygenated, decontaminated water. This process (algal
is significant. Often growth and reproductive cycles turf scrubbing) and the mechanisms built to support it
can be closely connected with light period. are described fully in Chapter 11.
As Delbeck and Sprung (2005) discuss, there are a Light measurement is an important part of micro-
multiplicity of new lighting shapes, sizes, and color cosm management. It is also one of the most difficult of
temperatures, as well as increasingly sophisticated con- physical factors to quantify. A number of instruments
trolling systems available to the aquarist and modeler. are available for sensing intensity. Examination of
However, the basics have not changed over the last spectral characteristics, while not difficult, requires
decade. There is great hope for the potential of LED light- even more sophisticated instrumentation. In general, if
ing, but the intensities required for coral reefs or most proper light measuring equipment is not available, the
shallow-water ecosystems are not yet available. It is guidelines provided above will suffice if the bulbs are
hard to imagine how one could use a metal halide replaced on a regular basis (every 6 months).
lamp of 10 000 K, except possibly for a very large deep-
water ecosystem. Those authors do point out that with
the now available lighting, it would be possible to pro-
vide harmful UV light to corals and they suggest SUMMARY
means for measuring and avoiding the problem. The
approach we have shown in Figure 5.19 can be adapted The light phase of photosynthesis is highly efficient,
to some of the newer lighting types. perhaps more so than any other process in nature (and
certainly far more than industrial creations, Barter et al.,
2002). However, the second or dark phase is limited
LIGHT AND PHYSIOLOGICAL in several ways by the basic inefficiencies of the key
CONSIDERATIONS enzyme Rubisco. The light phase in many planktonic
algae is inhibited by high light levels and is therefore
The reprocessing of animal and bacterial metabolic reduced in production capability. This may in part be a
wastes and oxygen production occur as natural parts result of the UV that accompanies the useable part of
of algal metabolism in well-lighted situations. However, the light spectrum, but is more likely the result of
a sufficient biomass of plant material must be main- excess O2 production, and oxidation of the photosyn-
tained to provide the production of plant food needed thetic centers. In most benthic algae and the higher
to accommodate the full requirements of plant-eating plants, it is the dark reactions that are more limiting.
animal populations. It is possible to balance this inter- In the higher plants, “photorespiration” (basically a
action within a single large tank, but usually this requires chemical “confusion” between CO2 and O2) can be a
that the number of animals be limited to their average problem especially when temperatures are high. Some
abundance in the natural environment, especially if desert and tropical plants (C4 and C5 plants) have
herbivorous species that might deplete the algae are developed mechanisms to concentrate CO2 at reaction
included. When the lights go out at night the plants centers and thereby avoid photorespiration. However,
stop producing oxygen and, if the animal population is this reduces the efficiencies of those plants under more
large, the oxygen supply dissolved in the tank water equable conditions. Benthic algae are at least mostly C3
92 5. The Input of Solar Energy
plants and rarely have to deal with excessive tempera- Barter, L., Bianchietti, M., Jeans, C., Schilstra, M., Hankamer, B.,
tures and photorespiration. Diner, B., Barber, J., Durant, J., and Klug. D. (2002) Biochemistry
The process of ATS (algae turf scrubbing) that we Behrenfeld, M., Esaias, W., and Turpie, K. (2002) Assessment of pri-
describe in this book, is a way to optimize photosynthe- mary production at the global scale. In: Phytoplankton Productivity.
sis for ecosystem modeling and environmental restora- P.J. Williams, B. le, D. Thomas, and C. Reynolds (Eds). Blackwell
tion. This solar–algal process removes many of the Sci, Oxford.
deficiencies of “wild” photosynthesis, and could well be Delbeck, C. and Sprung, J. (2005) The Reef Aquarium, Science Art and
Technology, Vol. 3. Ricordea Publishing. Coconut Grove.
a critical tool to stabilize the earth’s environments until Diamond, J. (2005) Collapse, How Societies Choose to Fail or Succeed.
the scientific community can create a viable artificial Penguin.
photosynthesis without negative side effects. ATS Gates, D. M. (1980) Biophysical Ecology. Springer-Verlag, Berlin.
avoids both photorespiration and photo-oxidation/ Griffith, P., Cubit, I., Adey, W., and Norris, J. (1987) Computer auto-
inhibition. By forcing water/cell contact through surg- mated flow respirometry: metabolism measurements on a
Caribbean reef flat and in a microcosm. Limnol. Oceanogr. 32:
ing, it also avoids the additional serious problem of 442–451.
nutrient deficiency that occurs in most benthic and GTE/Sylvania (1987) Color Is How You Light It. Catalog. Sylvania
planktonic algae (as well as higher plants). “The same Lighting Center, Danvers, Massachusetts.
surging motion provides for light flashing on cells, Hackney, J. and Sze, P. (1988) Photorespiration and productivity
avoiding inhibition due to “over-lighting” and shading. rates of a coral reef algal turf assemblage. Marine Biol. 98: 483–492.
Heldt, H.-W. (2005) Plant Biochemistry. Elsevier, Amsterdam.
The latter problem is so severe in the more typical algal Keeton, W. T. and Gould, J. L. (1986) Biological Science, 4th edn.
reactors, that some groups of scientists are working to Norton, New York.
genetically engineer planktonic cells to both operate at Kirk, J. T. O. (1994) Light and Photosynthesis in Aquatic Ecosystems,
lower light levels and to reduce light absorption (Melis, 2nd edn. Cambridge University Press, Cambridge.
2005). ATS is a planar, rather than a volume system, ren- Lee, R. (1999) Phycology, 2nd edn. Cambridge University Press,
dering harvest an efficient process of scraping or suction Lobban, C. and Harrison, P. (1994) Seaweed Ecology and Physiology.
rather than filtering. In the terrestrial plants, primary Cambridge University Press, Cambridge.
production has a basic limitation resulting from the cou- Lovins, A., Datta, E. K., Bustnes, O.-E., Kooney J., and Glasgow, N.
pling of CO2 uptake and water loss. When carbon diox- (2004) Winning the Oil Endgame. Rocky Mountain Inst. Snow-
ide uptake and energy production is being considered, mass. CO.
Mathews, C. and van Holde, K. (1996) Biochemistry. Benjamin/
water for enhanced terrestrial production (irrigation) is Cumming, Menlo Park, California.
rapidly becoming a serious issue; this is not a factor in Melis, A. (2005) Bioengineering of green algae to enhance photosyn-
large-scale ATS systems. thesis and hydrogen production. In: Artificial Photosynthesis.
A. Collings and C. Critchley (Eds). Wiley-VCH, Weinheim.
Moe, M. (1989) The Marine Aquarium Reference. Green Turtle
References Publications, Plantation, Florida.
Oliver, C. and Larson, B. (1990) Forest Stand Dynamics. McGraw-Hill,
Adey, W. (1978) Coral reef morphogenesis: a multidimensional
model. Science 202: 831–837.
Pace, R. (2005) An integrated artificial photosynthesis model. In:
Adey, W. and Hackney, J. (1989) Harvest production of coral reef
Artificial Photosynthesis. A. Collings and C. Critchley (Eds). Wiley-
algal turfs. In: The Biology, Ecology and Mariculture of Mithrax spin-
osissmus Utilizing Cultured Algal Turfs. W. Adey (Ed.). Mariculture
Rheinheimer, G. (1985) Aquatic Microbiology. Wiley, New York.
Institute, Washington, DC.
Small, A. and Adey, W. (2001) Reef corals, zooxanthellae and free-
Adey, W. and Steneck, R. (1985) Highly productive eastern
living algae: a microcosm study that demonstrates synergy between
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calcification and primary production Ecol. Eng. 16: 443–457.
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(Ed.). NOAA Symposium Series on Underwater Research, Vol. 3,
C H A P T E R
The Input of Organic Energy
Particulates and Feeding
The treatment of suspended particulates has been flagellated microalgae, by removing the larger plank-
largely ignored in most aquatic models used for ters from the water column. Depending on the exact
research and in virtually all aquaria. Unfortunately, in nature of the filter involved, and the turnover time of
most cases standard filtration methods remove, or at the system (all the water in the system passing through
least attempt to remove, the particles, radically altering a pump or filter several times an hour will have a far
their size and quality distribution and rarely is this greater effect than a turnover of once in several days,
quantified. Traditionally, the filters employed by aquar- particularly on reproductive stages), filters are likely to
ists have been standard bacterial (biological) types, have far more significant effects than pumps alone. As
though more recently trickle filters, protein skimmers, we describe in Chapter 20, we have had repeated coral
and in some cases resin columns have been used. These larval settlement out of the water column in systems
devices are designed to trap particulates as well as sup- without centrifugal pumps and with very low turnover,
port biofilms. Less obtrusive “nonfiltration” methods and we have not seen significant coral settlement in
such as rotating drums employing bacterial or algal systems with impellor pumps.
films have also been employed in aquaculture, though
rarely in aquarium or ecosystem models. In this book,
we emphasize the use of algal turf scrubbers (ATS) PARTICULATES, ENERGY SUPPLY, AND
to control water quality (oxygen, pH, nutrients, etc.). AQUATIC ECOSYSTEMS
Some capture of particulates occurs in these devices
(see e.g. Adey et al., 1993); however, relative to particu- All organisms and therefore their ecosystems require
lates, ATS act more like biofilms than filters. energy to function. For most higher plants and algae,
Particles, whether of inorganic or organic material, that energy source is solar, through the process of pho-
are an integral part of all aquatic ecosystems. In some tosynthesis. Energy from chemosynthesis, and particu-
cases, the use of bacterial or simple physical filtration larly from volcanic vents along mid-ocean ridges, is
(or better biofilm capture) might be a valuable compo- quite interesting, but globally is very small as compared
nent of modeling, for example, to simulate the sinking to photosynthesis. For many animals and bacteria, the
of plankton and other particulates out of an open, sur- energy source, through food webs, is based directly in
face-water system. However, when such methods are higher plants and algae. However, for some very large
used, the modeler or aquarist needs to insure that the water ecosystems (e.g. the deep ocean and deeper parts
filters are functioning in the manner intended and are of lakes), most of the direct organic energy supply is
not radically altering the model to a state very different derived from particulates originally created by photo-
from that desired. Although we have not studied the synthesis and primary production in shallow water.
effects of a variety of filtration systems on a commu- It is well known that small, planktonic algae, proto-
nity of plankters (including reproductive stages), we zoa, and bacteria (which can be considered particulates)
have examined the effects of standard impellor pumps. are fed on by a wide variety of larger filter feeders, and
In general, an impellor pump will select the very small provide the base of open-water food webs. It is not as
94 6. The Input of Organic Energy
FIGURE 6.1 Diagrammatic representation of the “mass balance” of particulates in a bottom-
dominated aquatic ecosystem. Modified after Johnson et al. (1990).
widely recognized, at least in aquatic systems modeling, from the capture of oceanic plankton (Chapter 20). In
that the ocean, lake, or river “soup” is in large measure some very large ecosystems (e.g. the mid-ocean and
made up of suspended particles, in part inorganic, but deep ocean), the only energy supply is through
in large measure organic but nonliving. This is the the organic particulates or “marine snow” from surface
detritus of the more obvious organisms and their food waters. This particulate transport route is so important
webs; it consists of the body parts of animals and higher to biosphere function that it can determine ocean
plants, algal fragments, and fecal material, usually chemical composition (Stumm, 1987; Boyd et al., 2000;
coated with fungal hyphae and/or bacteria, and is called see also Chapter 3). Finally, marine snow is probably
particulate organic material (POM). As it degrades, the “sink route” for about one-half of the anthropoge-
POM ranges down to the state of dissolved organic nic carbon as carbon dioxide that is currently released
material (DOM). These particulates are not, by any yearly into the atmosphere.
means, the end point. They continue to be an energy The “sinking” of organic material in the open ocean,
source in mid-water detrital food webs. Even in the after both trophic (food web) and microbial loop
dissolved or extremely small particulate state, these reworking, can be quite substantial. Because of this, in
organic materials can be absorbed by bacteria, some the 1990s a plan was developed and eventually tested
animals, and algae, they can aggregate to form larger to increase planktonic photosynthesis in the Southern
particulates again, or they can be adsorbed onto larger Ocean (Boyd et al., 2000), hopefully to greatly increase
particles and organic films that have developed on sur- carbon dioxide removal from the atmosphere. In this
faces (Figure 6.1). global-encircling ocean, where land contact is mini-
In addition, ecosystems are rarely closed in the mum, the potential for iron limitation of photosyn-
sense that the energy supply is only directly from solar thesis (Table 4.4) becomes a reality. The concept was to
sources. Almost invariably there is an input from an greatly increase photosynthesis by spraying very fine
adjacent ecosystem of living or dead organisms and iron particulates on the ocean surface from freighters.
organic particulate materials that are derived from Theoretically, this iron would dissolve and be uptaken
dead organisms, including fecal materials. Coral reefs by phytoplankters previously limited in production
are among the strongest and most efficient photosyn- potential. Eventually, the increased organic material
thetic communities on Earth, and yet a significant developed would form “marine snow” that would fall
( 10%) part of a typical reef’s energy supply is derived to the deep ocean, taking carbon out of the atmosphere
Organic Particulates 95
semi-permanently and reducing the effects of global moving waters. Particularly in large and very deep
warming. After several trials, this “ocean-seeding” waters, such as the open ocean, clays can provide the
process did not turn out to be as effective as first primary source of bottom sediment. Ocean sediments
thought, and because of additional environmental con- are dominated throughout much of the shallow open
cerns, the idea is on hold. ocean by calcium carbonate provided by the rain of
Carbon is often used as a proxy for bioenergy tests or shells from coccolithophore planktonic algae;
exchange and storage. However, the largest volume at more moderate depths, sediments become domi-
of stored carbon near the surface of the Earth lies in nated by shells of foraminifera and pteropods, and
inorganic limestones and dolomite, bearing no energy deeper by the siliceous particles derived from diatoms
storage. By far the largest proportion of organic (energy- and radiolarians. Both calcium carbonate and siliceous
bearing) carbon on Earth is in coal, oil, gas and kero- particulates slowly dissolve as they sink. In the deepest
gen, stored over the last 300–400 million years. Only ocean waters only the red clays remain.
1/3000 of the organic carbon on Earth occurs in the Many groups of animals, particularly some
biosphere, and only 1/20 000 occurs in the atmosphere. foraminifera (and other protozoans), and many poly-
The current scientific evidence strongly indicates that if chaete worms in the sea and chironomids (mayfly larva)
a fraction of this stored carbon were to be released into and caddisfly larva in fresh water build their external
the atmosphere, especially considering that human skeleta by “glueing” together primarily inorganic par-
society is continuously reducing the potential for pho- ticulates. Although organism-derived, these are mostly
tosynthetic production and accumulation in the bios- inorganic and do not bring an energy component; we
phere, the Earth would be driven into a super-heated, treat these particulates in Chapters 3 and 18.
dead Venus-like state. Why wouldn’t it just return us to To chemists and atomic scientists, all matter includ-
the “ocean soup” of billions of years ago? Probably ing atomic and subatomic materials is particulate, and
because the Earth’s mantle is out-gassing and continu- dissolved inorganic elements and ions we treated in
ously producing “new carbon.” While that rate is very Chapter 4, under water chemistry. This was done, even
small, over the more recent 300–400 million years it has though we recognize that there is no sharp line, relative
produced much of the organic carbon currently on to organism function, between dissolved and particu-
Earth. In addition, it is generally thought that the sun late. Here, as is standard in the field, we use 0.45 µm in
produces more radiation now than it did during early diameter as the practically useful boundary between
Earth time (see e.g. Figure 5.1). In short, we cannot go particulate and dissolved. For a greater depth of treat-
back; we must keep the stored carbon out of the atmos- ment we recommend the book by Roger Wotten (1990a),
phere, but managing oceanic particulates alone is The Biology of Particles in Aquatic Systems.
unlikely to accomplish this need.
Assuming that some of the energy supply remains
unconverted to organism function and low-level heat, ORGANIC PARTICULATES
material input to an ecosystem must be balanced by
internal storage of organic materials. This will happen In terrestrial stream–river systems, large logs can be
by the buildup of nutrients and other elements, by a displaced by bank erosion or beaver activity and even-
temporary buildup of living biomass (e.g. a newly set tually carried into the open ocean. In time, these become
mussel bed), or by equivalent export. We discuss the water logged and sink to the ocean floor, where they
storage and export equivalents in model ecosystems in continue to be broken down into smaller and smaller
Chapters 3, 9, and 11. The form and magnitude of pieces. Maser and Sedell (1994) describe this process of
organic particulate input is the primary subject of this mass transfer and degradation of organic materials that
chapter. encompasses virtually all aquatic environments.
The source of a much greater mass of organic partic-
ulate and dissolved material is that of wood and leaf
INORGANIC PARTICULATES fragments that enter streams or lakes as larger particu-
lates, either from soil erosion or simply by being blown
In many aquatic environments inorganic particu- in. These fragments are continually reduced through
lates are derived from the terrestrial erosion of rocks clipping, shredding, masticating, and partial digestion
and the soils produced by the precipitation and atmos- by a host of invertebrates, particularly insect larvae
pheric weathering of rocks. Sand to silt-size particles in fresh waters, as they “spiral” through the food webs
do not remain suspended for long (Figure 3.8). of freshwater complexes, and finally into estuaries and
However, fine clay particles do remain in suspension the sea. Particularly along rocky or coral coasts, algal
for long periods and can be carried great distances by production adds to the detrital/food-web loops and
96 6. The Input of Organic Energy
FIGURE 6.2 The movement of particulates (POM) and dissolved organic (DOM) and inorganic (DIM)
matter through aquatic systems from the terrestrial realm to the open ocean. Modified after many sources (see
especially Kranck, 1984).
the suspended and dissolved supply of particulates. In larger streams and rivers, as tree shading is
Mud flats and muddy bay bottoms, rich in organic reduced and sufficient light reaches the water column,
detritus mostly derived from elsewhere, are rich dumps stream banks, and bottoms, phytoplankton populations
of energy as particulates. A host of invertebrates work with zooplankter grazers develop in the water column.
these muddy flats and bottoms for their food supply In addition, bacterio-algal surface biofilms (epilithon,
(see Chapter 18). periphyton, or aufwuchs) begin to form on substrates
Particulates and Aquatic Models 97
freshwater, and soil organic degradation. As polymer
compounds, they are highly varying combinations of
organic molecules (carbohydrates, amino acids, and
fatty acids) and are also highly resistant to further
microbial degradation. Terrestrial and freshwater humic
substances generally contain recognizable lignin, while
marine humic substances do not. Also, marine and ter-
restrial humic substances differ in isotopic composition,
so that it has generally been assumed that terrestrial
organics are largely trapped by the estuarine “filter” or
at least do not make it across the shelf in any significant
proportion (Millero and Sohn, 1992).
Although the process is poorly understood, it is
widely accepted that humic substances are gradually
integrated into sediments and become the kerogen or
“oil” of oil shales, probably the largest single reservoir
of carbon on Earth. Kerogen, in turn, subject to appro-
FIGURE 6.3 Relationship of the “microbial loop” to the standard
open-water food chain. The reality is far more complex than this dia- priate geological heating and pressure, is thought to
gram. However, it is useful in emphasizing that even at the level of develop into crude petroleum. Kerogen formed in the
dissolved organics the biochemical energy originally formed in pho- marine environment is often called algal kerogen. This
tosynthesis continues to be aggregated and inserted back into the organic “waste” is largely derived from humic sub-
food chain. Dissolved organics in an aquatic ecosystem, wild or
stances originating in phytoplankton production in the
modeled, can be an important aspect of function. Modified after
Wotten (1990). ocean, especially along continental shelves and in shal-
low epicontinental seas.
(Figure 6.2). Both of these communities can interact with
the terrestrially derived organic particulates, degrading PARTICULATES AND AQUATIC MODELS
them physically and chemically, and can even uptake
DOM. Wood and leaf particles are not a high-quality food Microcosms, mesocosms, and aquarium models have
source. However, as they are worked over, a new and largely ignored the existence of particulates and their
higher quality organic particulate with feces and body relationship to equivalent processes in the wild analogs.
parts mixes with the wood and leaf-derived detritus. Often particulates and unfortunately any plankton,
As the rivers reach estuaries, the flocculating effect of including reproductive states, are removed by a wide
salt ions causes much of the DOM and smaller POM to variety of filtration processes. Sometimes, particularly in
aggregate into irregular masses and sink to the bottom. display systems, dissolved organics and humic sub-
At the same time, laterally, sometimes very extensive stances are oxidized or greatly reduced by ozonation or
marshes and mangroves develop that are both trapping resin column and charcoal treatment. Since very few
river-derived particulates and massively producing ecosystems operate exclusively by direct primary pro-
woody and leafy detritus of their own. In the extensive duction, with degradation up a food web and all par-
tidal channels of marshes and among the prop roots of ticulates exported to another ecosystem (and none
the mangroves, the same basic organic conversion and imported), an important element of internal recycling is
cycling occurs as in the rivers that feed the system. omitted. If bacterial filtration is the reason for the cap-
Passing out to sea, much of this material is reduced ture of particulates, the filtration system acts like a single
in abundance by sedimentation, incorporation in large and often very important filter feeder and removes
organisms through the microbial food web (Figure 6.3) or greatly reduces normal filter-feeding populations and
of bacteria, ciliates, and plankton, or simple dilution. their energy contribution to the model. As Tables 6.1–6.4
Further offshore, phyto- and zooplankton come to demonstrate, many filter feeders are able to extract con-
dominate the organic particulate spectrum. siderable food value from detritus as well as from dis-
solved organics. While the food value in leaf and wood
fragments and humic (refractory) substances is very
HUMIC SUBSTANCE low, the food value in mucus, organic films, and some
detritus can be as high as that of phytoplankton.
Humic substances, in the past called “gelbstoff” As we discussed in Chapter 2, pumps can have a
or yellow compounds, are the end points of marine, considerable effect on plankters and reproductive
98 6. The Input of Organic Energy
TABLE 6.1 Assimilation Efficiency (AE) of Freshwater TABLE 6.3 AE of Freshwater and Marine Shredders
Filter and Deposit Feeders on Organic Particulatesa Feeding on Organic Materialsa
Taxon AE (%) Food Taxon AE (%) Food
Oligochaete worms 3–6 Particulates in sediments Pteronarcys 9–16 Detritus
Hexagenia 68 Detritus Asellus 23 Decayed leaves
Simulium (8) 17–25 Organic particulates Asellus 26–44 Decomposing leaves
including plankters Gammarus 10 Decaying leaves
Crustacea Gammarus 73–96 Fungal protein
Cladocera (2) 10–30 Detritus Hyalella 22 Elm leaf protein
Daphnia 2–18 Detritus Hyalella 7–15 Lake sediments
Daphnia 50 Bacteria Hyalella 14–23 Sediment protein
Ostracoda cypridopsis 85 Detritus Palaeomonetes 91 Detritus
Ostracoda dolerocypris 73 Decomposed blue-greens
Ostracoda dolerocypris 27 Decomposed green algae a
After Wotten (1990b). Reprinted with permission from CRC
After Wotton (1990).
Note: In this and following tables – repeated citations of a taxon TABLE 6.4 AE of Freshwater and Marine
refer to different experimental trials with usually somewhat Browser/Scrapers Feeding on Organic Particulatesa
different results. Reprinted with permission from CRC Press.
Taxon AE (%) Food
TABLE 6.2 AE of Marine Filter and Deposit Feeders on Insecta
Organic Particulates (Including Dissolved Organics)a Spaniocerca 69 Surface organic layer
Pycnocentrodes 18 Surface organic layer
Taxon AE (%) Food Helodid beetles 30–31 Surface organic layer
Coelenterata, Gorgonian Potamopyrgus 4 Detritus
Coral 22 Coral mucus Potamopyrgus 74 Surface organic layer
Mollusca 14 Refractory particulates Hydrobia 5–19 Dead green algae
Crassostrea 1 Refractory particulates a
After Wotten (1990b). Reprinted with permission from CRC
Acartia 47 Mucus and
Acartia 50 Coral mucus systems of small volume compared to the wild analog.
Mysidium 44 Mucus and In Chapter 11, we discuss ATS, a process emphasizing
microorganisms primary production that is designed to control nutrients,
Corophium 82–92 Surface of particles
oxygen, and carbon dioxide/pH without significantly
Echinodermata 30 Organic sediments affecting the particulate spectrum. When low-oxygen
Parastichopus 17 Organic sediments
and low-pH environments are desired, rotating drum
Chordata 42 Kelp detritus units can similarly provide a large bacterial film sur-
Pyura face for removing ammonia and DOM. DOM, including
humic substances, can probably be controlled for view-
After Wotten (1990b). Reprinted with permission from CRC ing situations, where extreme clarity is necessary, by
Press. using ultraviolet light at high oxygen levels. The nega-
tive effects of ultraviolet light on plankton can be
stages, drastically altering ecosystem function. While reduced by limiting application to either a small part of
the direct effects of pumping on nonliving or bacterial- the model or only a small part of the pumped overturn
coated POM and DOM are probably small, the effect of of system volume.
preventing flocculation (coagulation) and thus the
building of organic particulates to a size that is utiliz-
able by many filter feeders is a serious issue for many
model ecosystems. Bacteria in the environment have generally been
Bacterial or algal films (Figure 6.4), in which trap- regarded as primarily planktonic in nature, free in the
ping of particulates is minimal, provide a solution to water column or attached to organic particulates until
the need to control water quality and nutrient export in those particles are broken down. A newer view regards
Particulates and Aquatic Models 99
FIGURE 6.4 The relationship of a river biofilm to dissolved (DOM), colloidal (COM) and particulate (POM) organic matter in the water
column. These dynamic interactions apply to all biofilms, to varying degrees, in all ecosystem models. From Lock et al. (1984). Reprinted
with permission of Munksgaard International Publishers, Ltd.
bacteria as primarily components of a mini but extremely cleaned. In reef and rocky shore models, this may not
widespread set of “benthic” ecosystems called biofilms matter, and these surfaces can be regarded as additional
(Harrison et al., 2005). In this latter view, biofilms are “bottom” or pore space. However, in many models,
diverse communities of bacteria (and protists) in which these surfaces may well provide a significant biologic/
species are “organized” into consortia to perform differ- ecologic presence, with their biofilms, that cannot be
ent functions in community maintenance, including the ignored. This is also true of the inside surfaces of piping.
releasing of the polysaccharide and protein slime that In general, piping is minimized in the design of any
provides the matrix and protection to the communities. ecosystem model for hydraulic and energy reasons.
Individual bacterial cells within a biofilm exchange However, biofilms will form wherever such surfaces
metabolites and even DNA (Figure 6.4). “Reproductive,” exist and these biofilms will capture particulates, organic
free-swimming cells, of bacteria as well as protists, are and inorganic, and become a part of microcosm/aquar-
released into the water column to colonize other surfaces ium metabolism. Petersen et al. (2003) describing scaling
extending the biofilm. work on mesocosms demonstrate how system volume
In the construction of enclosed marine/aquatic must be above a certain level so that wall benthic com-
ecosystems, piping and walls add surfaces that do not munity does not overwhelm a plankton community.
appear in the wild example or type system. While these However in many systems, the inner surface of piping
surfaces are initially neutral, they soon acquire biofilms. with its biofilm could easily exceed tank wall surface. If
The glass walls of tanks are usually present to provide this is to be avoided, piping should be of large diameter
visibility and are likely constantly cleaned to prevent and short. In Chapter 25, we discuss a specialized situa-
biofilm formation. However, especially in larger systems, tion of high ammonia loading where biofilms in piping
there may well be significant nonglass walls that are not became a very serious issue of water quality control.
100 6. The Input of Organic Energy
Whether this process is significant or not in any given sit- Particulate processes in model aquatic systems are
uation is up to the modeler to determine. poorly understood. We make a plea for more research
In lower-energy environments, even on shallow, in this area to test against design concepts. While many
well-lighted surfaces that contain photosynthesizing of the model systems described in this book have an
algae, biofilm communities can become very complex organic input based on known inputs in wild analogs,
autotrophic or subautotrophic ecosystems (Burkholder, none have made a serious effort to develop a reason-
1996). We discuss this issue in many chapters, espe- able size or quality spectrum for that input.
cially the higher energy variant algal turfs, and the eco-
logically engineered subset ATS.
AQUATIC ECOSYSTEM RESTORATION
PARTICULATE IMPORT IN In Chapter 3, we discussed the role of inorganic sed-
AQUATIC MODELS imentation in the problems of restoration of damaged
aquatic ecosystems. While inorganic and organic sedi-
In most ecosystems, particulate import or export to mentation can occur together, generally the problem of
or from external sources (other ecosystems) is normal. excess organic sedimentation is more likely correlated
It can be at very high levels, as in tidal mud flats, or with excess nutrient loading. These issues we discuss
it may be moderate, as in coral reefs. In a model this in depth in Chapter 25.
provides the opportunity to control organic input by
“feeding.” As we discuss in Chapter 20, inputs into References
coral reef models were based on fine mesh plankton
Adey, W., Luckett, C., and Jensen, K. (1993) Phosphorus removal from
tows upstream (in the trade wind current) of the reef
natural waters using controlled algal production. Restor. Ecol.
systems in St. Croix, US Virgin Islands. Unfortunately, 1: 1–11.
these tows did not include very fine organic particu- Boyd, P. W. et al. (2000) A mesoscale phytoplankton bloom in the
lates, or DOM, and import to these models at roughly polar southern ocean stimulated by iron fertilization. Nature
15% of total organic energy supply may have been low. 20: 695–702.
Burkholder, J. (1996) Interactions of benthic algae with their
On the other hand, export from the model systems was
substrata. In: Algal Ecology, Freshwater Benthic Ecosystems.
in the form of algal filaments from scrubbers (POM in J.R. Stevenson, M. Bothwell, and R. Lowe (Eds). Academic Press,
the wild), so DOM was also not exported. San Diego, California.
Some coral reef microcosms and mesocosms have a Harrison, J. J., Turner, R. J., Margues, L.L.R., and Ceri, H. (2005)
faint yellow color at lighting levels less than 5000 K. Biofilms: a new understanding of these microbial communities is
driving a revolution that may transform the science of microbiol-
However, careful microscopic examination has indicated
ogy. Am. Sci. 93: 508.
that this coloration is provided by very small suspended Johnson, B. D., Kranck, K., and Muschenheim, D. K. (1990)
algae rather than significant humic substances. The sys- Physicochemical factors in particle aggregation. In: The Biology of
tems that have this coloration are impellor pump-driven Particles in Aquatic Systems. R. S. Wotton (Ed). CRC Press, Boca
units. Even in a situation where waters and organisms Raton, Florida.
Kranck, K. (1984) The role of flocculation in the filtering of particu-
are mixed between two separate tanks, one with impel-
late matter in estuaries. In: The Estuary as a Filter. V. Kennedy (Ed).
lor pumps another with bellows pumps, only the impel- Academic Press, San Diego, California.
lor pump unit has the yellow coloration. It is very likely Lock, M. A., Wallace, R. R., Costerton, J. W., Ventullo, R. M., and
that the impellor pumps select out the small algae by Charlton, S. E. (1984) River Apilithon (Biofilm): Toward a Structural
killing off their larger predators and competitors. Functional Model. Munksgaard International Publishers Ltd.,
There is considerable question whether refractory
Maser, C. and Sedell, J. (1994) From the Forest to the Sea, the Ecology of
humic substances have any negative effect on system Wood in Streams, Rivers, Estuaries and Oceans. St. Lucie Press,
function, though esthetic issues might be of concern. Delray Beach, Florida.
At the Great Barrier Reef Marine Park Authority reef Millero, F. and Sohn, M. (1992) Chemical Oceanography. CRC Press,
aquarium in Townsville, Australia (see Chapter 20), Boca Raton, Florida.
Peterson, J., Kemp, W. M., Bartleson, R., Boynton, W., Chen, C. C.,
ozone is used periodically to reduce yellow coloration,
Cornwell, J., Gardner, R., Hinckle, D., Houde, E., Malone, T.,
solely for esthetic reasons. This is probably having detri- Mowitt, W., Murray, L., Sanford, L., Stevenson, J. C., Sundberg, K.,
mental effects on the microbial and planktonic popula- and Suttles, S. (2003) Multiscale experiments in coastal ecology:
tions, though no study has been carried out to determine improving realism and advancing theory. Bioscience 53: 1181–1197.
whether ozone is a factor in system function. Large Stumm, W. (1987) Aquatic Surface Chemistry. Wiley, New York.
Wotten, R. S. (1990a) The Biology of Particles in Aquatic Systems. CRC
impellor pumps are utilized on this system and since the
Press, Boca Raton, Florida.
planktonic microflora and fauna have not been studied, Wotten, R. S. (1990b) Particulate and dissolved materials as food.
it is quite possible that the coloration observed has the In: The Biology of Particles in Aquatic Systems. R. S. Wotten (Ed).
same origin as the systems described above. CRC Press, Boca Raton, Florida.
P A R T
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C H A P T E R
and Biological Loading
To maintain a human being or almost any terrestrial can provide us with a good supply of water, we need
mammal or bird, the “hotel” requirements seem rela- to worry only about the temperature, salinity, light,
tively simple, at least on the surface. Unfortunately, it is space, and food needs of those few species. But what
this apparent simplicity that has placed the human about good water quality? That is hard to get from
race in its present increasingly difficult environmental most municipally supported taps and many river, lake,
situation. As long as there were relatively few of us, and ocean shores these days. When the authors were
and our tools and access to the Earth’s great store- young, tap water was still mostly drinkable, and, on a
houses of short- and long-term “fossil” energy were hike, one could drink from most streams. Now that is
limited, we took for granted many essentials that the rarely the case, and reverse osmosis (RO) created bot-
natural ecosystems of the Earth’s surface provided. No tled water is carried by most of us wherever we go. But
longer can we assume that good-quality water and RO is very expensive at large scale, and many profes-
atmosphere will automatically be available or that the sional production aqua-culturists are increasingly find-
products of our daily activities can simply be discarded ing themselves in great controversy because of the
for “processing” by nature. With our increasing num- pollution of natural waters that their intense and mas-
bers and intense energy use, we are massively chang- sive cultures are producing.
ing our planet. With a thorough understanding of In ecosystems, modeled or wild, we do not neces-
organism metabolism at the ecosystem scale, particu- sarily want organisms to grow fast, as if we were going
larly plant metabolism, and the conditions under to eat them, like a herd of cows in a feedlot or chickens
which solar capture by photosynthesis can be opti- in a coop, but we do want them to behave normally.
mized in engineered systems, many of these problems This is the context in which we have passed more than
can be solved (Chapter 25). However, with time, if 99% of our evolution, one in which thousands of
human numbers remain uncontrolled, relative to our species around us behaved “normally” in a mutual
large-scale ecosystem management capabilities, our environment or biosphere. Water quality is even more
future looks dim indeed. important to an aquatic organism than it is to us. When
For the hobbyist and scientist the problem of main- our primary water requirement is for drinking, at least
taining aquaria, microcosms, and mesocosms is similar in much of the world we can collect rainwater, use
on a small scale to the global environmental problem solar stills, or use a variety of filtering and de-ionizing
for the environmental restorationist. Several extremely devices. However, the entire bodies of underwater ani-
important wild ecosystem-based fisheries have col- mals are immersed, including their gills and, effec-
lapsed. We have had a spectacular example in the loss tively, their internal vascular or blood transfer systems.
of what was at one time the largest fishery in the world, So far in this book, we have discussed physical and
in the northwest Atlantic. The Atlantic cod fishery is environmental factors, factors that to a large extent
still heavily restricted by the Canadian government 15 modern humans immediately understand as part of life
years after closure. We can operate aquacultures for a in an industrial society. Now we approach life in a bio-
few species, and assuming local aquatic ecosystems chemical context. We also come to a most appropriate
104 7. Metabolism
question that should precede our attempts to re-create our planet’s surface. The oxygen-rich atmosphere that
or restore living ecosystems based on hundreds of living allows the rapid time scale of animal life, and has in
species. In the introduction to this volume, we asked part given us equitable temperatures for several billion
the question: “How did life originate on planet Earth?” years, the very soil that supports so much terrestrial
As we discussed, the scientific community is gradually biomass, and the organic-rich sediments that become
piecing together a “most likely” scenario. However, we an integral part of Earth’s geology (perhaps, as some
did not entertain the question of: “What is life?” A typi- would have it, even allowing continental drift and the
cal dictionary definition would be “a quality that dis- essential features of the Earth’s geology) are all part of
tinguishes a plant or animal from the inanimate such the accomplishments of life. These are the unique fea-
as rocks, earth, or water,” sometimes followed by “espe- tures of the “living Earth” and probably other living
cially characterized by reproduction and growth by planets scattered through the cosmos. They are con-
accreting materials from the surroundings.” To say that trary to what the physical evolution of the solar system
something alive is not dead is rather circular reasoning; offers when life does not evolve.
in any case, many mineral crystals not only reproduce The ability to reduce entropy and produce highly
and grow; they often “look alive,” at least in the plant unlikely levels of organization through energy capture
sense. Life, of course, is rich in complex molecules of might be the modern physicist’s answer to the nature of
carbon, hydrogen, and oxygen, but that is also true of the basic entity that we call life. One biologist’s answer
the plastics that we now routinely manufacture. Viruses seems different (see Mayr, 1988): life is uniquely charac-
are not alive; they are packets of information that can terized by information, the information encoded in the
utilize living cells to make more information. So, what genes. If that is so, then a virus is alive, and so is a clay
is the state of “alive”? mineral. Also, a cell from which a nucleus has been
Beginning nearly 40 years ago, the U.S. National extracted is already dead, even though it might func-
Aeronautics and Space Administration began to have tion as any cell in that state for some time. Perhaps, for
this problem when they proposed to find out, as their now, we should retain the ability to store and process
space probes and landers touched down elsewhere in energy definition, recognizing that information from
the solar system, whether life was present. Dr. James the distant past is required to do this.
Lovelock, the author of Gaia (1979) and The Ages of Gaia Several billion years ago life evolved the process of
(1988), proposed an answer, outlined below, that is still respiration. The information that allows, through
both workable and instructive relative to how we energy conversion, the structural and functional ele-
approach life both on Earth and in our mesocosms. ments required to do this has been passed through
In a physical context, the science of thermodynamics countless generations of organisms. Every cell in our
tells us that energy is always moving to a lower level body has the age-old code for respiration. Hundreds of
of intensity or organization. The disorganization of this millions of years ago our distant relatives added
energy in the form of the bonding and motion of mole- another level of respiratory complication. Oxygen and
cules and atoms (entropy) is always increasing. Thus, carbon dioxide are exchanged in the lungs from the
in Earth’s time frame, the universe has been running ambient atmosphere or water to the bloodstream. The
down like a battery, as matter flies out from the big blood in turn meets each cell to provide the raw
bang. Some billions of years from now this almost materials for respiration. Every cell in our bodies also
inconceivable collection of matter and energy is head- “knows” this. Whether a cell acts to “pull its weight” at
ing for death close to absolute zero. Perhaps once it has this level depends on whether it is part of this higher-
converted all its energy to the gravitational form, it will level respiratory pathway.
collapse to another big bang and a rebirth. Our concern Life has what we can call a self-organization capabil-
here, however, is the running-down process. On the ity that occurs at many levels. While we humans may
time frame of hours to years rather than a few billion well be very bright as animals go, we still do not fully
years, life temporarily reverses this apparent process of understand the intricacies of most ecosystems. Yet most
senescence. It is capable of collecting small amounts of of these complex systems preceded us by many millions
mostly solar energy and chemically organizing, stor- of years, without the benefit of our brains and powers of
ing, and directing that energy to rather intensive usage. organization. Throughout this book we suggest that
On the scale of the individual, life can literally store since we know only vaguely how to internally organize
and concentrate solar energy, eventually to defy grav- and operate ecosystems in a long-term stable fashion, or
ity; on the scale of the community, life can store and even in the short term, we should let those ecosystems
concentrate energy to be released as heat a few or mil- be “free” to do what they are more than capable of
lions of years later; on the scale of the biosphere, life doing. They “know” because they consist of organisms
has been and still is capable of massive alterations of with information that dates back millions of years,
encoded in their genes. Thus, broadly, but in the context transfers the energy of sunlight to hydrogen and elec-
of this book, the modeler or the restorationist should trons obtained by the splitting of water and the release
supply the right environment as closely as possible, sup- of oxygen (see Chapter 5). Thus, in an ecological sense,
ply the right genetic material, then sit back and watch or given light, plants are purifiers: they are constantly
begin the experiment as one’s endeavor directs. It is removing nutrients, including carbon as carbon dioxide,
often necessary, because of the small scale and location from their surroundings and adding oxygen. Plants are
of a given mesocosm or wild ecosystem needing restora- purifiers in many other ways, such that their use in an
tion, for the human operator to participate to supply environmental sense is now known by the general term
energy, to fill the role of missing larger organisms, or phytoremediation.
to offset patchiness. However, given the right outside Animals, on the other hand, eat plants or other ani-
parameters (light, temperature, salinity, nutrients, as mals. When they are no longer growing they return all
well as appropriate import and export), the “captured” intake materials in reduced form to their environment.
ecosystem will generally take care of itself. Even while growing, food-transfer efficiency is low
With this statement of philosophy, let us move on to and therefore a large part of the ingested materials is
the nitty-gritty of the chapter. A basic understanding of released to the surroundings for breakdown by bacte-
metabolism in living organisms and how it relates to ria. As long as the delivery rate of animal plus bacterial
the chemistry of the environment is required to develop wastes to the local environment is no faster than the
a husbandry capability for captured or managed uptake of the plants that require those “wastes,” then a
ecosystems, what Adey (2006) called the “operational balance is present.
imperative.” The references will provide the interested An idealized model of animal vs plant requirements
reader with a more in-depth treatment of the subject. is shown in Figure 7.1A. If excess plant production
occurs, and direct-feeding animals as well as detritus
feeders are not available to consume all of plant pro-
METABOLISM duction, assuming plenty of water, light, and carbon
dioxide from the atmosphere, and some nutrient input,
Life in the whale, the tree, the alga, or the protist sur- then plant material accumulates. Given the right condi-
vives by the same very basic process: the chemical tions, as in a swamp, this excess organic material could
“burning” or oxidizing of organic matter (food) at the go into geological storage as coal for tens of thousands
cellular level. Although it is possible to obtain some to millions of years. As we described in Chapter 6, algal
energy without oxygen (e.g. by fermentation), cellular remains, as complex and refractory unreduced organic
respiration using oxygen is the most efficient pathway. molecules called humic substances, give rise to the very
The food, a carbon, hydrogen, and oxygen complex, large quantity of petroleum and kerogen (oil shales)
sometimes with nitrogen, phosphorus, sulfur, and stored in the Earth’s crust. Under natural conditions,
minute quantities of other elements, is produced inter- excess animals occur only under unusual conditions
nally (by plants) or is taken from another organism. that do not last long, usually because the food supply
The energy stored biochemically in the food is directed runs out or predators arrive to enjoy the excess. In a cul-
to the production of chemical compounds that are ture or human-operated environment, as in a human city,
transferred to specific sites in the cell for release as heat where plants do not or cannot balance animals, and
or motion or to the building of structural materials for food is artificially introduced, something entirely differ-
reproduction or growth. ent happens. Here waste products accumulate (carbon
Generally, plants are producers of food and capturers dioxide, as well as nitrogenous, phosphorus, and sulfur-
of solar energy. Whether bacteria, algae, or nonvascular rich compounds). Bacteria use the excess waste products.
or vascular plants, through photosynthesis and acquisi- However, bacteria, which in most cases metabolically
tion of solar energy, photosynthetic organisms build act like miniature animals, when in excess can also rad-
sugars, starches, and oils. By this means, plants, algae, ically alter environmental chemistry. In addition, when
and photosynthetic bacteria store the captured energy atmospheric access is slow, in water and muds, for
for building the even more complex structural and example, oxygen can be used up, creating an anaerobic
chemical compounds needed, such as cellulose, lipids, situation that few higher plants and animals can toler-
proteins (including the enzymes that drive reactions at ate. This metabolism, occurring out of environmental
biological rates), and the informational nucleic acids. context, or organic pollution, is the primary subject of
The needs of photosynthetic organisms are great: water, this chapter.
carbon dioxide, nitrogen, phosphorus, and many The basic picture of metabolism in a generalized
micronutrients. On the average, growing photosynthetic plant cell is shown in Figure 7.2. If the segment involv-
organisms are also oxygen producers. Photosynthesis ing photosynthesis in the lower right is removed, and it
106 7. Metabolism
FIGURE 7.1 (A) Simplified schematic diagram of the movement of essential compounds
by organisms in an idealized closed ecosystem. (B) “Unbalanced” community of plants in
which excess plant production is being stored (e.g. in sediments). (C) “Unbalanced” commu-
nity of animals in which food is provided.
is assumed that glucose and basic nitrogen (and other molecules of a cell are stable with time and can even be
nutrients) are derived from digested food not from the stored in excess of immediate need, proteins tend to be
water column, then the diagram also applies to a typi- unstable, constantly breaking down and being replaced
cal animal cell. Much of the structure of an animal cell by new synthesis.
is built up from sugars digested from plant or other
animal foods. Some amino acids, for protein construc-
tion, are derived directly from food; others are synthe- RESPIRATION
sized from ammonia derived from the simultaneous
bacterial breakdown of food (in a stomach or intestine). Animals come in a wide variety of sizes and com-
In general, the construction or anabolic reactions or plexities. They range from unicellular protozoa (now
steps do not occur at the same site in a cell as the break- typically placed in a separate kingdom, the Protista), a
down or catabolic reactions. Also, while most complex fraction of a millimeter long, to elephants and whales
FIGURE 7.2 Generalized process of metabolism in a living cell. Plant cells normally add the photosynthetic
component on the lower right and dispense with the nitrogenous excretory function on the lower left. Modified
after Mathews and van Holde (1996). Reprinted with permission of Addison Wesley Longman.
in which tons of complex tissues and multimillions of (Mathews and van Holde, 1996) for a discussion of all
cells work together. The basic pattern, based on the cell components. Here we concentrate on the cyto-
cell, is the same in all cases. In the more complex ani- plasm and the mitochondria, because it is in these
mals, individual cells become highly organized parts locales that the basic respiration and glycolysis processes
of tissues and organs specialized in one or a few of the take place.
many functions of cells. A generalized animal cell is When an animal eats a plant or another animal, a
shown in Figure 7.3. The reader is referred to texts on complex digestive process begins. In the stomach and
biology (e.g. Keeton and Gould, 1986) or biochemistry small intestine or their equivalents, digestive acids and
108 7. Metabolism
FIGURE 7.3 Idealized animal cell with its multiplicity of internal organelles. After Keeton and Gould (1986).
Reprinted by permission of W. W. Norton & Co., Inc.
numerous enzymes break down food particles to their ammonia. The blood stream delivers these basic mole-
molecular constituents and then the large organic mole- cules directly to each cell in the animal body where res-
cules to smaller, simpler molecules. These small mole- piration and the collective anabolic and catabolic
cules can be absorbed through the walls of the intestine processes (as in Figure 7.2) can occur. Within each cell,
and then enter directly into either the blood stream or the basic energy removal is that of the oxidization or
the lymph system. The blood vessels along the small “burning” of sugars. Simplistically, this is C6H12O6 6O2
intestine return directly to the liver where glucose is 6CO2 6H2O 670 kcal/mol of energy: the cell cannot
stored and re-released to manage constant levels in the simply burn the sugars. Instead, it uses a small-scale
bloodstream, and amino acids are broken down to chemical transfer process. Respiration of glucose
FIGURE 7.4 Simplified diagram showing the process of the complete breakdown of glu-
cose, in respiration, to achieve 36 ATP for energy transfer elsewhere in a cell. After Keeton and
Gould (1986). Reprinted by permission of W. W. Norton & Co., Inc.
produces adenosine triphosphate (ATP) and CO2. ATP and some tissues within organisms to live in an anaero-
carries away small packets of energy in chemical bonds bic or partially anaerobic environment.
(about 1/100 that of an entire glucose molecule) and When an animal feeds on a plant or another animal,
delivers that energy throughout the cell for many pur- it obtains many organic chemicals more complex than
poses. Figure 7.4 shows a very condensed version of the sugars for digestion. Proteins and fats are essential to
entire process of breakdown of a simple sugar and con- the animal in many ways, providing vitamins, miner-
version of its energy to ATP. Carbon dioxide and water als, and other important compounds. However, much
are the by-products. One critical feature to note in this of the protein and fats is also simply digested and
diagram is that some ATP can be produced without oxy- respired to produce energy, much as sugars (Figure
gen. The amount is small, but this primitive process 7.5). Herein lies a crucial element of the effects of ani-
(glycolysis or fermentation), probably the dominant one mals on their environment: the production of nitroge-
in the early eon of life on Earth, allows some organisms nous wastes and, to a lesser extent, phosphorus.
110 7. Metabolism
In more complex organisms, water control and excre-
tion have tended to be joined together. In a sense, the
unit of the mammalian kidney, the nephron (Figure 7.8),
is an advanced flame cell. Because water loss can be cru-
cial in land animals, the nephron and the kidney came to
reabsorb much water, leaving more concentrated nitro-
gen compounds as urea. In fish, on the other hand, the
primary excretory product remains ammonia and, par-
ticularly in fresh water, large quantities of water and
ammonia are excreted through the kidneys (Bond, 1979).
The kidneys are by no means the only site of excretory
activity. The liver, in addition to being a digestive organ,
excretes waste compounds. Also, the digestive system
itself excretes, along with the nondigested wastes of the
feces, nonabsorbed nitrogen- and phosphorus-rich com-
pounds that have been broken down both by the animal
itself and by bacteria in the gut. In animals with gills,
including fish, much ammonia is excreted through the
gills, along with carbon dioxide.
FIGURE 7.5 Generalized process of breakdown of proteins and
fats to achieve introduction of these compounds into the respiration BACTERIAL METABOLISM
process. After Keeton and Gould (1986). Reprinted by permission of
W. W. Norton & Co., Inc. Bacteria are neither plants nor animals and today are
placed in a separate kingdom called the Monera. Some
In many of the tiny protozoans, digestion and excre- bacteria (including the very important cyanobacteria or
tion can be seen in their basic form. For example, in blue-green algae) are capable of photosynthesis, thereby
Figure 7.6, a small plant or animal is shown being cap- acting like plants. Most bacteria act like animals and
tured, engulfed and enclosed in a vacuole (phagocyto- break down dead organisms or are predators acting as
sis). The golgi apparatus, through the lysosomes, parasites in living organisms. Bacteria are very simple
provides digestive enzymes to the food-filled vacuole. cells, filaments, and colonies. They lack a nucleus and
After the food is broken down, undigested particles other cellular organelles enabling them to carry out the
(e.g. a diatom silica wall), along with ammonia and complex cellular digestive/excretion process we dis-
phosphoric acid, are transported to the cell membrane cussed above. Bacteria excrete their digestive enzymes
and simply excreted to the exterior of the cell by exocy- into their surroundings and absorb through their cell
tosis. Sugars, amino acids, and nutrients needed are membranes the simple sugars and reduced nitrogenous
taken into the cytoplasm through the vacuolar mem- and phosphorous compounds that they require. Nitroge-
brane. Also shown in Figure 7.6 is the more general nous and other wastes develop at least partly external to
process of recycling of organelles by capture in lyso- the cell. In a sense, when bacteria are abundant, because
somes and eventual excretion (B) and even the destruc- dead organic material is abundant, the external environ-
tion of a whole cell (D). Pathway (A) refers to the ment locally becomes like that of the stomach or small
excretion of digestive enzymes to the surroundings, intestine. We discuss this in depth later, but excess dead
such as would occur in some protists. organic material free in a relatively closed space pro-
Early in evolutionary history another process vides an environment like a stomach: acid, rich in carbon
entered into the excretory picture. In any water less dioxide, methane, and ammonia, devoid or nearly devoid
than full ocean salinity, outside fresher water continu- of oxygen, and having many enzymes capable of organic
ously moves into the cell by diffusion. The resulting breakdown. This is a specialized environment, which in
cell dilution is called osmosis, and it often results in a the open world could be the subsurface of an organic-rich
pressurized internal environment. To avoid dilution of mud flat; however, it is not one that many higher organ-
the cell to the point of death, some vacuoles (contrac- isms can tolerate. It is also an unsatisfactory environment
tile) function to collect this water, eventually expelling for the open water of most aquaria, microcosms, and
it to the exterior. A more advanced form of this process, many wild ecosystems.
including a specialized cell, the flame cell, is seen in the And now we briefly return to Figure 7.1 and the
simple planarian (Figure 7.7). basic ecological point of this chapter. Animals and
Bacterial Metabolism 111
FIGURE 7.6 Digestion of food by idealized protozoan cell. After Mathew and van Holde (1996). Reprinted by
permission of W. W. Norton & Co., Inc.
most bacteria require complex organic foods, plants, produced. In the more-or-less restricted localities
and other animals, dead or alive. The principal require- where wastes do accumulate, in some cases entering
ment is simple sugars for energy. While a small amount into geological storage, they create a special environ-
of vitamins, amino acids from protein, and many other ment in which a few specialized organisms are capable
micronutrients are required, only a small part of the of functioning. The biosphere/lithosphere combina-
nitrogen, phosphorus, and sulfur in complex com- tion has the means of storing the components of excess
pounds is needed. The rest becomes organic waste, organic production – organic-rich sediments and even-
some of which is toxic, when concentrated in quantity, tually coal and oil, for example. The same basic storage
to many organisms. On the other hand, these wastes equivalent can be accomplished in a mesocosm, and,
are required by living, photosynthesizing, and grow- with a little more difficulty, in the aquarium. When one
ing plants and algae to build their tissues. In a balanced is dealing with restoration of an aquatic ecosystem that
system and in most natural ecosystems, organic wastes is receiving excess anthropogenic waste products, the
do not accumulate; they are used as fast as they are storage option may not be possible without changing
112 7. Metabolism
the entire character of the ecosystem. However, as we
discuss in Chapter 25, prevention of organic import
may be possible.
Nearly all the organic energy stored in the Earth’s
crust and held as biomass in the biosphere, as well as
that used by humans since they have evolved, has been
solar energy, captured in the process of photosynthesis.
Most of this solar energy has been captured within the
chloroplasts of plant cells (Figure 7.9). Nuclear energy
remains a miniscule portion of energy used by humans
and is likely to also remain problematic. In Chapter 5,
we discussed how that energy capture occurs and how,
through oxygen release, the process has changed the
surface of the Earth, making life possible for more than
just microbes. The light reactions of photosynthesis are
highly efficient and produce energized electrons and
hydrogen ions that end up energizing two transport
compounds ATP and NADPH . However, this is just
the beginning – the chemical energy built into these
compounds has to be efficiently stored and used to
build more complex organic compounds and cell struc-
ture, plant and eventually animal bodies or it will
quickly be lost as heat to the environment.
Early in the development of the biosphere, roughly
from 2.5 to 3.5 billion years ago, a number of chemical
FIGURE 7.7 Planaria flame cell. A cell specialized for water reg- pathways evolved that would allow the anaerobic bac-
ulation – a primitive kidney. Keeton and Gould (1986). Reprinted by
permission of W. W. Norton & Co., Inc.
teria of the time to use the energy of ATP, NADPH ,
and perhaps other energy carriers, to capture, or fix,
CO2 (or possibly –HCO3 in some cases) and build
organic compounds (Raymond, 2005). Some of these
ancient pathways still exist in more or less rare, anaero-
bic bacteria. However, at about 2.5 billion years ago,
cyanobacteria evolved the Calvin cycle (see Heldt, 2005
and Figure 7.10). Probably by symbiotic “capture” of
cyanobacteria cells by protists, this has been passed on
to all algae and eventually to higher plants. The basic
Calvin cycle produces fructose and other sugars in the
stroma of chloroplasts (see Figure 5.2), and these
sugars, mostly translocated throughout the cells or to
other cells in tissues, become the building blocks for
more complex compounds. The uptake of CO2 in the
Calvin cycle, as shown in Figure 7.10, is catalyzed by the
highly abundant but very inefficient enzyme Rubisco.
Much as in animal cells, the energy-rich sugars pro-
duced by plant cells are respired as needed to produce
ATP. The ATP-stored energy derived from photosyn-
thesis is then transferred throughout the cell and used
FIGURE 7.8 Diagram of the principal cellular element of the to build walls (cellulose), nucleic acids, proteins, phos-
human kidney. After Keeton and Gould (1986). Reprinted by permis- pholipids (on cell membranes), and more chlorophyll,
sion of W. W. Norton & Co., Inc. to name a few. All of these are needed as cells grow and
FIGURE 7.9 Idealized plant cell. To compare essential similarities and differences to an animal cell see Figure 7.3. After Keeton and Gould
(1986). Reprinted by permission of W. W. Norton & Co., Inc.
divide. These building processes result in a need for these compounds are left for bacteria degradation, the
nitrogen, phosphorus, sulfur, and other micronutri- result will be lower water quality, perhaps even an
ents, which are primarily taken up as dissolved salts anaerobic environment.
(phosphate, nitrate, sulfate, etc.). Ammonia, at least in Plant cells also respire, much as animal cells, and at
small concentrations, is a preferred source of nitrogen. night generally require oxygen and release carbon
Often, especially in algae and aquatic plants, higher dioxide. In some cases, both in the wild and in closed
forms of the most essential requirements, such as urea, ecosystems, the combination of animal and bacterial
can also be taken up. In the aquatic environment respiration in the dark can be crucial to ecosystem
removal of these compounds by plants can be crucial, function. The practical aspects of this situation are dis-
as, in abundance, they are toxic to most animals. If cussed in Chapter 8.
114 7. Metabolism
for all the various elements of organic function. Carbon
dioxide is produced by this process, and a typical
measure of respiration is O2 use or CO2 production. Most
important in this context is that the use or production
of O2 and the use or production of CO2 are among the
most critical and obvious ways in which marine or
aquatic organisms change the chemistry of their sur-
roundings and the most immediate factors to be dealt
with in an enclosed system.
In a closed ecosystem, the respiration process is
basically no different than that in the wild community,
but several factors have to be kept in mind. For example,
a high-biomass (and high-metabolic-rate) rocky-bottom
community typically relies on constant movement of
water from the overlying or off-lying water mass, often
a planktonic community, which normally has much
lower loading effects. The community in a tank might
FIGURE 7.10 Movement of photosynthetic productions in a very well be functioning exactly as in the wild and yet
typical plant cell, including most marine and aquatic plants (C3). not have sufficient oxygen to survive at night because
After Mathews and van Holde (1996). Reprinted by permission of of lack of contact with the equivalent larger adjacent
Addison Wesley Longman. Note that in most algae (other than green
body of water. Indeed, this basic situation happens nat-
algae) the storage products are often not starch, but a wide variety of
oils, alcohols, and starch-like compounds. urally in the wild in a mud-flat environment where the
oxygen needs of the community as a whole cannot be
met because of inadequate oxygen-exchange mecha-
nisms for the large metabolic requirement. A mud-flat
BIOLOGICAL LOADING community is adapted to this situation. A rich rocky-
bottom community would probably not survive, either
As must be very clear from the above discussion, in the tank or in the wild, if this need is not met.
living organisms can radically change the chemistry of There are many other metabolic effects of marine
their surroundings. From the study of geology and and aquatic organisms that lead to changes, buildups,
atmospheric chemistry, we know that global-scale or exhaustion, of elements or compounds in the water
changes have been introduced over billions of years by in which they live. Chief among these are the variety of
living organisms. In shorter time frames, the same compounds that result from nitrogen metabolism. The
effects are very obvious during a red tide, or near an primary problem in this case is the excretion of ammo-
odiferous mud flat, and become particularly noticeable nia and related products, toxic compounds in large
when one “walls off” a piece of that environment. quantity, that results from the constant breakdown of
When scale modeling a living ecosystem, the buffer proteins in animal cells and by some bacteria. In a
effect of the larger surroundings is gone and one loses broadly considered wild marine ecosystem, ammonia
the normal dynamic balances that result from commu- is very much needed by the photosynthetic organisms,
nity-level patchiness in the larger ecosystem. Biological whether phytoplankton, algae, or higher plants that
loading is the term that we use to describe the effects of inhabit the community. Thus, it should never be a crit-
the organisms present on the physical and chemical ically toxic element either in the wild or in a micro-
environment. In a simulation system, biological load- cosm. However, in both cases potential imbalances
ing can be classified in two general categories: chemi- exist. On an organic-rich muddy bottom, animal bio-
cal exchange and its requirements, discussed in this mass often greatly exceeds plant biomass, which in
chapter and the remainder of Part II, and behavioral deeper waters could be totally absent. While bacteria
requirements and interactions, discussed in Part III. may then take over the role of plants in taking up and
While there is some connection between the two, they utilizing ammonia, the levels of ammonia present are
are largely independent of each other. likely to be much higher than those in a community
Metabolism refers to the complex of chemical reac- frequented by plants.
tions that occur inside a living organism. Respiration Thus, in aquarium science, when a bacterial filter is
refers specifically to the basic energy-exchange mecha- used to break down ammonia, not only is more oxygen
nisms that involve the use of oxygen to “burn” (chemi- used, but the ammonia concentrations are likely to be
cally) the appropriate organic matter to provide energy considerably higher than they would be in a plant-rich
community like a shallow-water coral reef or a rocky of its organic production in the reef itself, and there is
shore. Also, dilution plays a major role in potentially major loss of plant fragments to lagoons by most reefs.
transferring toxic ammonia from an animal-rich site of This potential organic loss to a reef is partially made up
production to a broad area of dilute but more than suffi- for by the capturing of zooplankton swept in by cur-
cient plant production. There are many other ways in rents from the open ocean.
which use of a bacterial filter can negatively affect many Such mass balances need to be carefully considered
marine organisms and communities, and that relates to in microcosm work. For example, in a coral reef micro-
a tendency in aquarium science to turn to other method- cosm, if 1 g of dried shrimp is fed to the system each
ologies, especially foam fractionation. The same prob- day to simulate the planktonic input from the open
lem applies to wild communities, especially streams, ocean in the wild, then more than 1 g (dry) of algae or
lakes, and bays with large adjacent human communi- other organics must also be removed from the tank.
ties. Sewage plants are nothing but large bacterial filters, This may not necessarily be carried out daily or even
and large bodies of water can be destroyed by the ill- weekly – the import/export schedule is a function of
considered use of these systems (e.g. Chesapeake Bay). how much imbalance a system will normally take.
In some cases, use of a foam fractionator can remove There are several ways in which this can be done, as we
excreted particulates and even large molecules, but they discuss in depth later:
cannot remove ammonia and CO2 already formed and,
in addition, remove the plankton and reproductive 1. weeding of macroalgae;
stages that are key elements of most aquatic ecosystems. 2. sediment settling traps that include organic particu-
Trickle filters, basically water trickling over abundant lates and foam fractionators that remove those par-
surfaces with bacterial biofilms, are a great improve- ticulates as well as large molecules of dissolved
ment over the more traditional bacterial filters in that organics (see Chapter 3);
atmosphere exchange is greatly improved; however, the 3. removal of larger organisms that have grown in the
same basic problems remain. These matters are dis- systems (fish, invertebrates); or
cussed in detail in Chapter 9. 4. the use of an algal turf scrubber (Chapter 10).
The basic concept under discussion here can be It is also possible to scrape the diatoms or other algae
extended to carbonate metabolism, silica metabolism, that grow on the walls of the microcosm or aquarium,
and all of the potential water chemistry-altering activi- and to mechanically filter out those scrapings for a short
ties of organisms. When one is considering microcosm period. However, a major part of the algae removed
or mesocosm simulation of a community, the question tends to be diatoms, and the net result after periods of
should be asked: “How does the wild community in several months can be silica depletion. While this might
question avoid the problems created by metabolic not be undesirable in some cases, generally it results in
imbalances?” If they are solved within the community considerably reduced numbers of both planktonic and
on a daily as well as hourly basis, then faithful repro- benthic diatoms.
duction of environment and community in microcosm In the next three chapters we discuss the primary
will produce the same result. However, if the problem chemical problems of biological loading, respiration,
of metabolic imbalance in a wild situation is solved by and nitrogen metabolism, and the generalized means of
interaction with another community, or effectively by simulating the required adjacent ecosystem effects. In
dilution, then either the alternate community or the Chapters 20–23, in discussing the major types of micro-
dilution must be supplied or its effects simulated. cosms and mesocosms on which we have worked,
Another aspect of biological loading is long- or other generally less crucial aspects of biological loading
short-term storage of organism tissues or organic mate- are considered further. Finally, in Chapters 24 and 25,
rials derived from those tissues. Some entire ecosys- we discuss the landscape and global implications of
tems, such as bogs, are accumulating storage biomass. human loading on wild ecosystems and the biosphere,
In these situations, some high-level organic com- and discuss large-scale methods for dealing with those
pounds that could be available to organisms are not problems.
being used for a variety of reasons. Fossil fuels derive
from long-dead ecosystems that functioned in this
manner. Other biological communities, such as reef References
lagoons, mud flats, and temperate forests are charac-
Adey, W. (2006) Lessons learned in the construction and operation of
terized by the accumulation of organic detritus in part
coral reef microcosms and mesocosms. Chapter 17 in: Coral Reef
of the system (e.g. the soil or lagoonal sediment), Restoration. Handbook. W. Precht (Ed.). Taylor and Francis Group
where it is gradually used by organisms specialized to CRC Press, BocaRaton.
the environment. A coral reef system stores very little Bond, C. E. (1979) The Biology of Fishes. Saunders, Philadelphia.
116 7. Metabolism
Heldt, H.-W. (2005) Plant Biochemistry, 3rd edn. Elsevier, Amsterdam. Mathews, C. and van Holde, K. (1996) Biochemistry. Benjamin/
Keeton, W. T. and Gould, J. L. (1986) Biological Science, 4th edn. Cummings, Menlo Park, California.
Norton, New York. Mayr, E. (1988) Toward a New Philosophy of Biology. Harvard
Lovelock, J. (1979) Gaia: A New Look at Life on Earth. Oxford University Press, Cambridge, Massachusets.
University Press, Oxford. Raymond, J. (2005) The evolution of biological carbon and nitrogen
Lovelock, J. (1988) The Ages of Gaia: A Biography of Our Living Earth. cycling – a genomic perspective. Rev. Miner. Geochem. 59: 211–231.
Norton, New York.
C H A P T E R
Organisms and Gas Exchange
Oxygen, Carbon Dioxide, pH, and Alkalinity
The metabolism of living organisms affects water water body lacks organisms and organic materials, an
chemistry in two basic ways: (1) gas exchange (mostly equilibrium or saturation is established that is a func-
oxygen and carbon dioxide) and (2) exchange of dis- tion of temperature, salinity, and pressure. Nitrogen is
solved nutrients (nitrogen, phosphorus, and a variety of the most abundant gas in the Earth’s atmosphere.
micronutrients). However, animals also release undi- However, while it is abundantly present as a dissolved
gested food in the form of feces and plants lose or detach gas in water, it is largely inert (as a gas) and is little
parts, which relative to the environment are dead organic affected by biological activity. We discuss nitrogen fix-
materials undergoing further breakdown primarily by ation and denitrification (exchange from the gaseous
microbes. They also excrete organic compounds such as state to the organic or dissolved state and the reverse)
ammonia and urea that undergo further microbe degra- in Chapter 9. Here, our concerns are primarily for the
dation. All of these processes ultimately use oxygen, next most abundant atmospheric gases, oxygen and
release carbon dioxide, and produce nutrients. carbon dioxide. The concentration of these gases is rad-
In this chapter and Chapter 9, we discuss gas and ically and constantly altered by organic activity in
nutrient exchange, respectively. In Chapter 10, we exam- aquatic and marine environments. The carbon dioxide
ine the issue of biomineralization, the formation of bone of the Earth’s Northern Hemisphere atmosphere varies
and shell, and particularly the crucial subject of calcium seasonally due to the activity of plants (about 5 of almost
carbonate formation by organisms. Calcification is 380 ppm today, it was 320 in 1965). Indeed, so great is
important to the entire biosphere, as well as to many the potential for exchange of these gases by biological
ecosystems and thousands of abundant species, and is activity that the Earth’s atmosphere has been drasti-
inextricably linked to carbon dioxide and its reaction cally changed (over billions of years) primarily by plants.
with water. For perspective, we briefly discuss selected In addition, a considerable percentage of the rock on
wild aquatic and marine environments followed by the Earth’s surface is limestone or marble (primarily
examples from a variety of captured ecosystems. In CaCO3), ultimately derived from carbon dioxide through
Chapter 11, we examine methods of controlling gas, the shell-creating or environment-changing activities of
nutrient exchange, and calcification in microcosms, plants and animals. Other rocks, such as shales (derived
mesocosms, and aquaria. In these model ecosystems, from muds), can also be very rich in organic carbon
control or compensation is needed because of the small derived from the bodies of ancient organisms.
size of the system in a day–night cycle, the presence of Tables 8.1 and 8.2 give the saturation values, that is,
an unnaturally large biomass, or the lack of compensat- concentration at equilibrium, for oxygen and carbon
ing larger adjacent body of water. Finally, in Chapter 25, dioxide, respectively, at different temperatures and
we show how these same methodologies, at landscape salinities. These values apply to surface waters, and,
and even global scale, can lead to the repair of ecosys- for “nonliving” waters, they are good reference points.
tems damaged by human organic overloading. However, they hardly ever occur in nature because
Gases from the atmosphere diffuse into and out of of the constant exchange activities of organisms. In
any water body that the atmosphere contacts. If the aquatic and marine ecosystems oxygen is generally the
118 8. Organisms and Gas Exchange
TABLE 8.1 Saturation Levels of Oxygen Gas Dissolved such as many submerged aquatic plants and mangroves,
in Water as a Function of Salinity and Temperaturea are adapted to living on oxygen-deficient soils or sub-
strates and have spaces within their tissues for the storage
Temp. and transport of oxygen. Nevertheless, an oxygenated
(°C) 0 5 10 15 20 25 30 35 40 water column or atmosphere is required. Some animals
and plants can temporarily use nonoxygen-requiring
5 14.8 14.4 13.9 13.5 13.0 12.5 12.1 11.6 11.2 metabolic pathways to derive energy from food. These
10 13.0 12.6 12.2 11.8 11.4 11.0 10.6 10.2 9.8
15 10.3 10.0 9.7 9.4 9.2 8.9 8.6 8.3 8.1
pathways can be utilized in low-oxygen environments
20 9.4 9.1 8.8 8.6 8.4 8.1 7.9 7.6 7.4 or to carry out “extra” metabolism (e.g. the emergency
25 8.5 8.3 8.0 7.8 7.6 7.4 7.2 6.9 6.7 heavy use of muscles) over and above oxygen transport
30 7.8 7.6 7.4 7.2 7.0 6.8 6.6 6.4 6.2 capabilities. Such pathways are, however, much less
efficient than those using oxygen.
Recalculated from data of Home (1969). Reprinted by permission of
John Wiley & Sons, Inc. Values given as mg/liter.
Unicells, or simple filaments, such as bacteria, proto-
zoa, and fungi, take up oxygen directly from the envi-
ronment through their cell membranes. Multicellular
aquatic animals have evolved a variety of organs called
TABLE 8.2 Solubility of Carbon Dioxide in Water as a gills to remove oxygen from the water column. They
Function of Salinity and Temperaturea
have also evolved a number of blood pigments to carry
Salinity (ppt) oxygen in the bloodstream (Table 8.3) so that cells situ-
Temp. ated deep inside their bodies receive oxygen. In gen-
(°C) 0 5 10 15 20 25 30 35 40 eral, it is the microbes, bacteria, yeasts, and some fungi,
0 3.39 3.31 3.22 3.15 3.07 2.99 2.90 2.83 2.75
protozoans, and certain parasites that are adapted to
6 2.72 2.65 2.59 2.52 2.46 2.39 2.34 2.28 2.21 the anaerobic environment.
12 2.21 2.16 2.11 2.07 2.02 1.97 1.93 1.88 1.83 A number of alternate energy, “chemosynthetic,”
18 1.83 1.80 1.75 1.72 1.67 1.64 1.60 1.57 1.53 and nonoxygen-using carbohydrate breakdown path-
24 1.54 1.51 1.52 1.45 1.42 1.39 1.36 1.33 1.30 ways exist. Some produce compounds like hydrogen
30 1.32 1.29 1.27 1.25 1.22 1.20 1.17 1.15 1.13
sulfide, which are quite poisonous to most animals.
Recalculated from data of Richards (1965). Values given as g/liter. Many organisms are adapted to aqueous environments in
Note that oxygen (in Table 8.1) is given in mg/liter. Effectively, the which anaerobic sediments are overlain by oxygen-rich
solubility of CO2 is hundreds of times greater than that of O2. water or the atmosphere. However, where oxygen
depletion is permanent and extends up into the water
column, along with the concomitant H2S, the envir-
onment becomes largely “dead” except for anaerobic
most important and straightforward of the two gases.
microbes. This can happen on a very large scale, such
Carbon dioxide reacts with water to form carbonic acid
as in the Black Sea where deep waters are isolated by
and its ionic forms. It is also involved with both inor-
the shallow sill at the Bosporus and the rain of organic
ganic and organic calcification. We discuss carbon diox-
material to deep water exceeds the diffusion and cur-
ide second. Note that in a water body not significantly
rent transport requirements for oxygen. Unfortunately,
affected by the activity of organisms, much more carbon
today such oxygen depletion is also happening in
dioxide will be dissolved (including its ionic forms) than
many lakes, bays, and even coastal waters, ultimately
due to human eutrophication.
In the surface waters of the open ocean, oxygen is
generally supersaturated (Figure 8.1). While extensive
OXYGEN EXCHANGE surface exchange (wave action) under conditions of low
biomass would not allow a large negative difference
The vast majority of organisms, animals and plants, from saturation values, either seasonally or diurnally,
living on the surface of the Earth and within its waters excess plant biomass and photosynthesis in the well-
require an oxygenated environment. While plants pro- lighted zones tend to keep ocean surface waters above
duce oxygen, often in great overabundance (to their saturation levels. The ocean is a major original and con-
immediate needs), photosynthesis requires light, which tinuing source of oxygen to the atmosphere. It can be
is rarely continuous. Most algae and higher plants can- argued that before humans evolved and utilized oxygen
not store oxygen and must remove some from their in the burning of forests and fossil fuels, maximum
environment at night (even if they produced a great atmospheric oxygen levels had been attained. The use of
overabundance during the day). More complex plants, fire in hunting by Stone Age humans probably already
Oxygen Exchange 119
TABLE 8.3 Respiratory (Oxygen-Carrying) Pigments in
the Animal Kingdoma
Hemocyanin: Copper-containing protein, carried in solution.
Molecular weight 300 000–9 000 000
Mollusks: Chitons, cephalopods, prosobranch, and pulmonate
gastropods: not in lamellibranchs.
Arthropods: Malacostraca (sole pigment in these): Arachnomorpha:
Hemerythrin: Iron-containing protein, always in cells,
Molecular weight 108 000
Sipunculids: All species examined
Priapulids: Halicryptus, Priapulus
Brachiopods: Lingula FIGURE 8.1 Oxygen saturation levels of the surface waters of the
Chlorocruorin: Iron-porphyrin protein, carried in solution. South Atlantic Ocean. After Richards (1965).
Molecular weight 2 750 000
Restricted to four families of Polychaetes:
Sabellidae, Serpulidae, Chlorhaemidae, Ampharetidae
Prosthetic group alone has been found in starfishes, Luidia
Hemoglobin: Most extensively distributed pigment; iron-
porphyrin protein, carried in solution or in cells.
Molecular weight 17 000–3 000 000
Vertebrates: Almost all, except leptocephalus larvae and some
Antarctic fishes (Chaenichtys, etc.).
Echinoderms: Sea cucumbers
Mollusks: Planorbis, Pismo clam (Tivella)
Arthropods: Insects Chironomus, Gastrophilus. Crustacea
Annelids: Lumbricus, Tubifex, Spirorbis (some species have
hemoglobin, some chlorocruorin, others no blood pigment).
Serpula, both hemoglobin and chlorocruorin.
Flatworms: Parasitic trematodes
Protozoa: Paramecium, Tetrahymena
Plants: Yeast, Neurospora, root nodules of leguminous plants
After Schmidt-Nielsen (1975).
significantly lowered oxygen concentration and raised
that of carbon dioxide. The domination of Australian FIGURE 8.2 Dissolved oxygen levels in the sea (in ml/liter). After
forests by eucalyptus and the abundance of parklike Dietrich (1963).
grasslands and sedge lands in place of the previously
dominant Nothofagus and Araucaria forests were proba-
bly caused by the aborigines’ burning activities (Flood, trigger glacial periods (reverse global warming) and set
1983). Atmospheric oxygen levels prior to human influ- another kind of limit on photosynthesis.
ence were in part limited by the natural combustion In somewhat deeper water (100–700 meters) in the
levels of forests. In short, “the world is (or at least was) open ocean, oxygen levels reach their minimum (Figure
green.” Plants probably have the capability to raise 8.2). This is below the lighted or photic zone of plant
atmospheric oxygen concentrations higher than they activity. It is also a level at which the rain of algal and ani-
are, perhaps to 22%. The potential for subspontaneous mal waste material from the surface provides relatively
combustion of forests on land, the release and oxidation high animal and bacterial activity. Finally, in the lower
of methane from anaerobic deposits, and perhaps the half of the deep ocean, oxygen concentrations return
reduction of carbon dioxide to the point where photo- to near-surface values. These deep waters are cold
synthesis becomes very slow set the limit to atmospheric and largely derived by deep currents from Arctic and
oxygen levels (see Lovelock, 1979). Although there is Antarctic zones. At their high-latitude sites of origina-
much debate on the subject, low CO2 levels could also tion, oxygen saturation levels were initially high. Also, at
120 8. Organisms and Gas Exchange
cold temperatures plant photosynthesis is relatively biomass (Stumm and Morgan, 1981). Also, in oxygen-
more efficient than either plant or animal respiration. poor environments, glycolysis and fermentation result
Open coastal waters are similar to the open ocean, in the partial breakdown of plant-produced organics
though fluctuations are greater. without the use of oxygen. This is how oxygen derived
Lakes and rivers tend to operate under similar oxygen from the photosynthetic splitting of molecular water has
distributions but, on the average, show a shift to lower gradually built up to high levels in the atmosphere.
oxygen levels. This situation derives from the addition of Even if the Earth has now reached a balance (independ-
terrestrial organic matter from the surrounding water- ent of humans) in oxygen production, and levels are no
shed. There are almost as many oxygen distribution and longer building up in the atmosphere, the excess oxygen
exchange patterns as there are lakes. For more detail see required by methane, coal, and oil as they are exhumed
Chapter 2 and the extensive discussion by Hutchinson on the surface of the Earth is not generally recycled by
(1957) and Dodds (2002). In summary, oxygen concentra- organisms in aquatic environments. Thus, most natural
tions in the surface waters of most lakes are near satura- water ecosystems not made eutrophic by humans, par-
tion levels. Relatively clear, unproductive lakes in which ticularly shallow-water environments, will tend to be
a more ordered organic and oxygen exchange occurs can supersaturated or at least rich in oxygen.
average supersaturated levels of oxygen at the surface
and moderate oxygen levels at depth. At the other
extreme, in eutrophic or nutrient-rich lakes, variations in OXYGEN, MODEL ECOSYSTEMS, AND
oxygen concentration can be very large. Under the right ECOSYSTEM RESTORATION
conditions in the spring or summer, such lakes bloom
with intensive plant growth. In these cases, oxygen In microcosms and mesocosms where one is attempt-
supersaturations of 50% or more are eventually followed ing to simulate all aspects of a particular environment
by a “crash” in oxygen levels by late summer. Such and ecosystem, presumably one provides enough light
eutrophic lakes build up biomass to the point where and the appropriate plant community to simulate wild
oxygen diffusion at night is not sufficient to prevent levels of photosynthesis. If diurnal and season oxygen
anaerobic conditions resulting from the very large oxy- measurements show oxygen levels below those in the
gen requirements. Extensive fish kills often result. Unlike natural community then there is a serious problem that
the oceans, lakes, and rivers acquire significant organic should be corrected. This is often the simplest proxy
loads from the terrestrial environment. Where depths measurement for the overall model veracity. Assuming
extend well below the photic zone, mean oxygen deficits that community structure is more or less correct and
can exist, and a lake will use more oxygen than it pro- photosynthetic plant biomass and animal biomass are
duces or can diffuse through its surface. properly balanced, a problem of low oxygen levels is
Estuaries lie between lakes and rivers and the ocean likely to be caused either by inadequate light or by a fail-
with regard to mean oxygen concentration and can be ure to simulate water flow from areas of higher oxygen
more like one or the other depending on the nature of concentration, particularly at night. The first problem
the organic and nutrient input of the fresh waters and was discussed in depth in Chapter 5. We discuss the
the amount of exchange with the ocean. In lakes, rivers, solution to the second problem in Chapter 11.
and estuaries, organic and nutrient inputs by humans In microcosms and mesocosms, even if the builder
are crucial to oxygen levels and organic stability. Indeed, and operator are attempting to maximize equivalences
oxygen depletion often becomes the most essential ele- between the wild environment and the aquarium, scal-
ment of human degradation of aquatic environments – ing and inadequate ratios of water surface to water vol-
more on this below. Mesocosms and aquaria are similar. ume can provide great difficulties relative to oxygen
Photosynthesis and respiration are often summed up concentration. In the aquarium, where display is a pri-
as CO2 + H2O + energy (light/chemical) CH2O + O2. mary function and volume is small, animal biomass is
Ecologically, this implies a balance in which all energy- likely to be higher than normal, particularly for the
rich organic compounds created by the photosynthesis marine environment. Also, artificial feeding in excess of
of plants are either metabolized by the plants them- wild equivalents is almost invariably provided to an
selves or metabolized by animals through a food chain. aquarium. Thus, except for the relatively unusual envi-
However, this is not the case. Much plant and some ani- ronments normally low in oxygen that one might try to
mal organic material goes into geological storage, even- model, it is difficult to simulate a proper oxygen envi-
tually becoming peat, organic-rich shale, coal, gas, and ronment by simple aeration. While trickle filters and
oil. It is estimated that over 14 000 times as much organic foam fractionaters may improve oxygen exchange, with-
material and other carbon of organic origin lies in geo- out using bottled oxygen, they cannot achieve the super-
logical storage as presently exists in the biosphere as saturation of wild systems.
Carbon Dioxide Exchange 121
Many lakes and ponds have become hypoxic or down photosynthesis to some degree. However, in most
anaerobic and unaesthetic and useless for recreation due aquatic and virtually all marine environments there is
to nutrient overloading by sewage plant outfalls, farm usually a very large supply of this essential compound
runoff and runoff from urban/suburban development (as bicarbonate ion, HCO3 ) available for all biological
(Livingston, 2006). This widespread problem has activity. On the other hand, excess carbon dioxide tends
expanded and moved downstream, so that in recent to increase the acidity of an environment and renders the
decades one of the largest estuaries in the world calcification requirements of an organism more difficult.
(Chesapeake Bay – Blankenship, 2005) and even coastal As shown in Figures 8.3 and 8.4, the proportion of the
areas (Gulf of Mexico – USGS, 2005) have developed primary components of the carbonate system (carbon
large “dead” (anaerobic) areas during the summer. In a dioxide, bicarbonate, and carbonate and hydrogen ion,
case of minimum overload (e.g. a pond with human-fed pH) present in any given water mass is a function of the
ducks), a water fountain aerator might temporarily interaction of several chemical equilibria dependent on
solve the problem. Restoration of these large-scale envi- temperature, salinity, and pressure. The status of the
ronments can be accomplished, and we discuss the oxy- entire system under any given set of conditions can be
genation and denitrification methodology in Chapter 25. determined by measuring any of two of the following
components: pH, total alkalinity, total CO2 (CO3 +
HCO3 + CO2), and the partial pressure of CO2 (e.g.
CARBON DIOXIDE EXCHANGE Millero and Sohn, 1992). In practice, this is usually done
by measuring pH and total alkalinity. Total alkalinity for
The other major gas involved in exchange between sea water consists of bicarbonate (HCO 3, approximately
organisms and their environment is carbon dioxide. The 89%), carbonate (CO3 , approximately 6.7%), borate
activity of CO2 is, in a sense, the inverse of oxygen, the (B(OH)4, 2.9%), and several minor components (includ-
two being primarily cross-exchanged between plants ing OH ) adding up to less than 0.5%. In most meso-
and animals (Figure 8.3). However, it is also very differ- cosm work, where great precision is not needed,
ent from oxygen in that it reacts chemically with water. inexpensive analytical kits are available to measure total
Also, CO2 is intimately bound to calcification or shell and alkalinity or carbonate alkalinity. However, pH should
wall formation in many organisms (bacteria, protists, be measured with high-quality probes and meters using
plants, and animals) and to the chemical precipitation of high-quality buffers for standardization.
limestones. Photosynthesis and calcification by organ- Calculating the expected changes in the carbonate
isms are intimately linked through carbon/carbonate system of any body of water can be done using the
chemistry (McConnaughey, 1994; Small and Adey, 2001). equations discussed in depth by Millero and Sohn (1992).
In synergistic fashion the two processes enhance each In field work on coral reefs, for example, alkalinity deple-
other and have thus given rise to many animals/algal tion from ocean water pouring over a reef has been
symbioses in the ocean. Unlike oxygen, relative to respi- used repeatedly to determine rates of community calci-
ration, the lack of carbon dioxide in special terrestrial and fication. In practice, in mesocosm and aquarium work,
aquatic environments (including greenhouses) may slow Figure 8.4 can be used to estimate magnitude and
direction of change due to biotic effects, and actual
measurements of pH and alkalinity can be taken to
verify the expected changes. With some minor modifi-
cation, the nomographs for evaluating bicarbonate and
carbonate alkalinity and carbon dioxide given in the
seventeenth edition of Standard Methods for the Examina-
tion of Water and Wastewater (Cleseri et al., 1989) can be
used to quickly and precisely evaluate the status of the
carbonate system in both wild and captured systems.
Note that while removing carbon dioxide through pho-
tosynthesis, in a closed system, raises pH with little
effect on alkalinity, calcification lowers both pH and
alkalinity. Thus, photosynthesis supports calcification
by removing the excess CO2 produced and preventing
acidification. Calcification, in turn, supports massive
FIGURE 8.3 Chemical and biological movement of carbon diox- photosynthesis (and oxygen production) by preventing
ide in aquatic and marine ecosystems. After Horne (1969). Reprinted depletion of the carbon supply. We discuss these matters
by permission of John Wiley & Sons, Inc. in greater depth in Chapter 10. A specific example
122 8. Organisms and Gas Exchange
FIGURE 8.4 The distribution of dissolved compounds in the carbonate/water reaction
chain as a function of pH. Note that sea water is buffered and occurs only over a limited pH
range, while pure water can range widely. After Home (1969). Reprinted by permission of
John Wiley & Sons, Inc.
applied to a coral reef microcosm is given in Chapter 20 the surface where, partly through the atmosphere,
and described in depth by Small and Adey (2001), with organisms can again turn over that stored carbon. All of
the primary elements of the carbonate system shown in the carbon on the surface and in the continental crust,
Figure 8.5. except for a small amount of new carbon arriving from
In the CO2–CaCO3 system, the oceanic parallel to deep in the Earth, mostly through volcanoes, has been
high photosynthesis, high levels of oxygen in the sur- cycled through organisms several times. At least prior to
face photic zone, is seen in calcium carbonate satura- the use of fossil fuel by humans, it is likely that the
tion (Figure 8.6). In tropical oceans, ultimately due to storage of “organically derived” carbon in the Earth’s
photosynthesis, there is a great excess of calcium car- rocks was continuing to grow slowly as the continents
bonate in crystalline form as shells. However, in deeper enlarged (Chapter 3).
water, carbonate concentration rapidly falls and calcite
becomes undersaturated (i.e. shells begin to dissolve as
they sink). Where the oxygen minimum and the carbon
dioxide maximum meet, sea water has only 70% of sat- CARBON DIOXIDE AND GLOBAL
uration levels. Finally, below about 4500 meters the AQUATIC RESTORATION
rate of supply of calcium carbonate from the surface is
exceeded by dissolution and carbonate shells are virtu- Most people are aware of the concept of acid rain
ally absent from sediments. and understand that many lakes in largely igneous and
Most of the carbon on the surface and in the crust of metamorphic regions such as New England and
the Earth does not occur in organisms or in the atmos- Scandinavia, where there is little carbonate buffering,
phere. At any one time, carbon occurs mostly in lime- have had their fish populations radically altered by
stones, in coal and oil, and in other organic rock such rain from upwind industrial areas. Carbon diox-
derivatives (Figure 8.7), mostly deposited in shallow ide in the atmosphere does make rain acidic, as we
waters. However, the exchange rate, primarily through describe below; however, in the case of lakes it is excess
carbon dioxide, is very large. For example, carbon SOX from coal-fired power plants, effectively sulfuric
turnover between the atmosphere and organisms occurs acid in the rain that is the primary problem. However,
on the order of every 20 years. Also, as large as the reser- the ever-increasing CO2 in the atmosphere, resulting
voir of carbon is in the rocks, on a time scale of about 400 from the burning of all fossil fuels, is also having a seri-
million years, geological processes bring the carbon to ous effect on the pH of natural waters.
Carbon Dioxide and Global Aquatic Restoration 123
FIGURE 8.6 Factors affecting the distribution of calcium carbon-
ate as calcite, with depth, in the equatorial Pacific Ocean. After Kennett
Sea water is strongly buffered for pH and generally
ranges from 8.00 to 8.40. Because of the ions present,
great changes in carbon dioxide are necessary to effect
a small change in pH. Nevertheless, most marine
organisms are particularly susceptible to small pH
changes, and in this respect, environmental status is
crucial. Despite the buffering, the pH of sea water can
be reduced as a function of the interaction of sea water
with the CO2 in the atmosphere as well as photosyn-
thesis and calcification in shallow water. Roughly one
half of the anthropogenic CO2 released into the atmos-
phere does not show up in the many standard meas-
urements taken of the atmosphere. It has generally
been thought that this was a good thing, as it has so far
saved human civilization from the worse complications
of elevating atmosphere CO2. However, researchers
FIGURE 8.5 The daily state of the carbonate system and pH in a have now begun to document drops of pH in oceanic
coral reef microcosm. (A) mean pH levels during a 24-hour cycle for
one year; (B) mean Talk (total alkalinity) during a 24-hour cycle for waters. This process is expected to reduce calcification
one year; and (C) mean state of daytime carbonate system calculated by 14–30% by mid-century (Kleypas et al., 1999; Osmond,
by nomogram from Talk and pH. From Small and Adey (2001). 2004). While there is little question that this will have
124 8. Organisms and Gas Exchange
of sand- or silt-size aragonite, the least stable form of cal-
cium carbonate, is invaluable. The shells of some cal-
careous algae (e.g. Halimeda) or crushed coral skeleta can
provide the aragonite (when clean of organic material).
Oolitic or nearly pure Bahamian aragonitic sand is mar-
keted in bulk in the United States. Spotte (1992) has
argued that in an aquarium system, such carbonate (as
calcite) has its potential dissolution surfaces “blocked”
by magnesium overlays. Organic material can have
the same effect. Thus, even though boring and scraping
constantly make new surfaces available in a high diver-
sity, properly functioning mesocosm, it is good practice
to use a fine aragonite sand or silt and to arrange for
frequent delivery of fresh sand.
In part, by reducing carbon dioxide production and
removing carbon dioxide through “excess” photosyn-
thesis one can achieve a status of the pH/carbonate
complex that is equivalent to most shallow sea waters.
FIGURE 8.7 The carbon cycle on Earth showing the approximate However, if significant calcification is occurring in a
quantities of carbon and relative exchange between compartments. closed system and maintaining the rate of such calcifi-
Mass exchange rates are given as microgeomoles/year (1014 moles/ cation is a primary feature of the model, it will likely be
year). Carbon mass is given as geomoles (1020 moles). After Stumm and
important to replace alkalinity depletion with an out-
Morgan (1981). Reprinted by permission of John Wiley & Sons, Inc.
side source, much as occurs in the wild. This process is
discussed in greater depth in Chapters 10 and 20.
However, it is important to emphasize that many prop-
disastrous effects on already damaged coral reefs world- erly operated shallow water microcosms, especially
wide, the more dangerous effects on biosphere health coral reef systems, will have calcification rates that are
may be in changing the role of calcifying coccolithores, so high that both alkalinity and calcium ion need to be
the dominant phytoplankters in tropical and temperate monitored and re-supplied, just as in the wild.
shallow ocean waters.
As we noted above, the exchange rate of carbon
dioxide between the biosphere and the atmosphere is
very high, overturning on the order of 20 years. This is Rainwater from an unpolluted atmosphere typically
a good thing, in that it means that the undesirable has a pH of less than 5.6 (i.e. moderately acidic due to
changes that we have brought about in our atmosphere the interaction of atmospheric carbon dioxide with the
can be reversed relatively quickly, by reducing fossil water while it cycles through the atmosphere. On lime-
carbon export and increasing photosynthesis. We dis- stone and related substrates, this natural acidity can be
cuss just such a scenario in Chapter 25. Here, we simply strongly buffered. In some cases, however, particularly
note that for a fraction of the cost of going to war we can on largely unbuffered granitic rock basements, and with
solve one of our most serious environmental problems. the addition of organic acids from some vegetation, the
natural acidity of the rainwater can be significantly
increased in the surface and groundwater. Freshwater
lakes, ponds, and rivers typically vary from slightly
MANAGING CARBON DIOXIDE AND pH IN
acidic (pH 6) to moderately basic (pH 9). Extremes occur
MICROCOSMS AND MESOCOSMS
from acid volcanic lakes (near pH 1) to soda lakes (at pH
12), though these would be of concern only to a few
aquarists. Because of great concern over the polluting
Within a model system it is possible to increase the effects of acid rain and the resulting environmental acid-
buffering effect of sea water using calcium carbonate ification, considerable study has been directed to the
chips or substrate. Since most shallow marine waters are negative effects of acidification on flora and fauna
highly supersaturated with calcium carbonate, this is an (Figure 8.8). The interested reader is referred to Cresser
essential fail-safe feature for any marine microcosm or and Edwards (1987).
aquarium. In small and difficult situations with heavy In the modeling of freshwater systems, the aquarist
animal loads or high calcification requirements, the use seeks to simulate waters of a given pH. For basic
Gas Exchange and Selected Model Ecosystems 125
geologically and biologically, and has been studied in
some detail. The water moving onto the reef due to wave
and current action typically has an oxygen concentration
close to 6.5 mg/liter, a level that varies by only a few
tenths day and night (Figure 8.9). This is essentially the
saturation point. As this sea water flows in over the reef,
driven by the constant trade winds, it picks up extra oxy-
gen, becoming highly supersaturated during the day
because of excess photosynthesis, that is, photosynthesis
that exceeds respiration. On the other hand, at night the
same water loses oxygen, due to the respiration (without
photosynthesis) of both plants and animals in the reef.
The effect of extensive wave breaking on the exchange of
oxygen can also be marked on rough days and causes
oxygen loss during the day and oxygen gain at night, the
net effect being to smooth out metabolic effects on the
gas concentrations. This is not an unusual pattern for a
well-developed, open-water coral reef, whether Indo-
Pacific or Caribbean (see Chapter 20).
To simulate this typical reef environment in a micro-
cosm system, the aquarist would need to obtain a
night-to-day oxygen concentration range from 5.5 to
FIGURE 8.8 Lower pH tolerance limit of common molluscs and 8.5 mg/liter, 6.3 mg/liter being the approximate satura-
crustaceans found in Norwegian fresh waters. After Cresser and tion level. The traditional marine aquarium, with its
Edwards (1987). Reprinted with permission of Cambridge heavy animal oxygen requirement, increased by bacter-
University Press. ial action in biological filters, cannot achieve supersatu-
ration. Trickle filtering and foam fractionation release
waters, above pH 8.0, the same rules previously dis- oxygen from the water and actually prevent supersatu-
cussed for salt waters apply. On the other hand, if neu- ration, though oxygen rather than or mixed with air
tral or acidic waters are desired, the situation becomes might produce the appropriate effect. Even if well
more complex. Certainly if a high-nutrient, low-pH lighted, such a system is likely to remain undersaturated
environment is desired and oxygen levels are not a for oxygen and may well go below 5 mg/liter at night.
concern, then bacterial filtration is an ideal approach to The lower limit of oxygen for water overlying a reef com-
system management, preferably using a rotating drum munity is probably typically about 4 mg/liter under
or trickle system instead of a “filter” unit to avoid exceptionally calm conditions. Extensive periods lower
removing plankters. On the other hand, if a low-nutrient, than this level in the main mass of overlying water
low-pH (e.g. a black-water stream) environment is would likely be detrimental to reef plants and animals,
needed, the situation becomes considerably more diffi- especially because oxygen concentration would be con-
cult. In mesocosm and microcosm simulations of siderably lower in the interstices of the reef. Intensive air
black-water streams where fish and invertebrate bio- bubbling carried out in well-kept and reasonably loaded
mass are kept appropriately low and where energy traditional tanks could produce minimum oxygen levels
input is derived largely from slowly breaking down at or above 4–5 mg/liter. However, without intense light-
leaf litter, minimum mechanical filtration or, prefer- ing and abundant photosynthetic plants (or an oxygen
ably, settling traps may be all that is required. For sim- bottle) it would not be possible to raise oxygen concen-
ulating highly acidic natural waters, acidification can trations above 6.5 mg/liter and likely not even to that
be derived from CO2 bubbling. level. The “dry”-type trickle filter is excellent for raising
oxygen levels from the lower potential values. However,
it too loses oxygen during the day. A dry trickle filter
GAS EXCHANGE AND SELECTED could be attached to the system at night and separated
MODEL ECOSYSTEMS during the day to overcome this problem.
The oxygen concentration in a Smithsonian coral reef
The southern bank barrier coral reef on the Caribbean microcosm compared to that in the wild reef is shown in
island of St. Croix can be regarded in many ways as a Figure 8.9. As described in Chapter 11, by using an algal
generalized tropical reef. It is mature, well developed turf scrubber rather than a bacterial filter, even during
126 8. Organisms and Gas Exchange
FIGURE 8.9 Comparison of oxygen levels in the open sea and on a St. Croix coral reef with
levels in a coral reef microcosm (see also Chapter 20). After Adey (1983). –, Oxygen saturation.
the dark hours oxygen levels are stabilized just below thereby lowering pH even while oxygen remains at sat-
saturation levels. During the day oxygen levels in this isfactory levels; therefore both O2 and pH levels through-
well-lighted reef tank (see Chapter 20) rise well above out the day should be checked at least occasionally.
saturation and in most respects match wild reef values Equally important, as discussed in Chapter 9, nitroge-
closely. nous exchange between plants and animals is not sig-
Using an oxygen meter, one can measure the rate of nificantly affected by atmospheric exchange. Even if
oxygen uptake in a mesocosm or aquarium system oxygen is artificially kept above 5 mg/liter by physical
during the dark at near saturation levels to determine atmospheric exchange methods, it does not mean that
if the community respiration load is equivalent to that water quality is not otherwise rapidly degenerating. It is
in the environment one wishes to simulate. This meas- wise to have either adequate water buffer to carry a sys-
urement must be taken at or near saturation so as not to tem through the night or a plant-compensating system.
have to account for exchange with the atmosphere. The critically important variable of photosynthesis,
In one of the early 1800-gallon reef tanks, for example, or primary production, is treated in several chapters.
the dark respiration rate was about 2 g O 2/m2 of reef However, it is so inextricably linked to oxygen, carbon
surface/hour or about 24 g O 2/m2/day. This is only dioxide, pH, and system loading that its role is repeated
about one-half of the wild St. Croix reef rates, which again here in the context of a coral reef model. Net pri-
presumably means that we could have doubled our mary production (in terms of oxygen) for the St. Croix
animal respiratory load, assuming that wave or other reef is shown in Figure 8.10. If oxygen loss due to respi-
exchange keeps oxygen concentrations at a minimum ration, which we presume to be roughly constant at all
of about 4 mg/liter. Later tanks have had rates of times, is removed from the data (by dropping the zero
3–5 g O 2/m2/h, rather closer to rich reef levels. line approximately 2.5 g O 2 /day), a curve of approxi-
Oxygen is relatively soluble in water and exchanges mate total photosynthesis is derived. Several important
rapidly with the atmosphere in bubbling or wave action. pieces of information can be derived from this diagram.
However, carbon dioxide exchanges more slowly and First, total photosynthesis is very high, at approximately
even though sufficient oxygen may be supplied to a 40 g O 2/m2/day. If this is converted to actual plant pro-
microcosm, CO2 concentration may well increase rapidly, duction (leaving out what the algae themselves use),
Gas Exchange and Selected Model Ecosystems 127
FIGURE 8.10 Mean yearly diurnal oxygen exchange for several reef transects on the island of St. Croix. After Adey and
one finds a rate of about 25 g ( dry weight)/m2/day. In activity for short periods in the summer and essentially
the laboratory, measured rates of actual algal production shut down for the colder, darker part of the yearly
consistently achieve 10–20 g ( dry weight)/m2/day on cycle. However, examination of primary production in
flat screens. Since a typical reef has several times the Gulf of Maine rocky-bottom kelp and rockweed com-
mean surface of a flat screen, the reef value measured munities shows that this is hardly the case (Figure
by oxygen seems not unreasonable. Also production 8.11). Photosynthetic efficiency, or available light con-
(photosynthesis) continues to increase during the morn- verted to biological use, on a wave-beaten rocky shore
ing, peaking around 12:00 h when sunlight is at its great- is about the same, in proportion to available light, as on
est intensity. In summer, it appears that there is a slight a coral reef. Interestingly enough, on the rocky shore
drop by noon, but this is probably at least partly due to itself, grazing rates are relatively low and thus there is
saturation of metabolites. Unlike what most scientists an actual excess of production. In the wild, roughly
have thought with regard to other marine algae, the reef three-quarters of the plant production is eventually lost
plants (primarily algal turfs) can use most of the avail- from the rocky bottom to beach drift and finally deliv-
able sunlight and as a community do not seem to be ered by tides and currents to the inshore mud flats. In
inhibited by the intense light (see Figure 5.15). The high short this community is a strong net exporter of biologi-
respiration and biomass levels of a shallow-water reef, cal production, and this must be taken into account
and a well-designed and operated reef microcosm, are when designing such a system.
internally driven by a high level of plant production that In the rocky Maine shore microcosm, oxygen levels
needs full sunlight to fully perform. averaged higher than on a coral reef, as a reflection of
We have based our discussion of oxygen and carbon this system as a net producer and exporter of plant bio-
dioxide exchange to this point on field studies and mass. At 8.5–9.5 mg/liter of dissolved O2, average oxy-
models of coral reef systems. However, the points gen concentration remains above saturation for most of
made are equally true in other model ecosystems. One the year. This occurs in spite of the fact that considerable
tends to think of cold-water northern ecosystems as wave action was present, continuously, in the model
highly seasonal ones that may reach high levels of (see Chapter 21).
128 8. Organisms and Gas Exchange
FIGURE 8.11 Yearly productivity of benthic algae (in wet weight) in rocky intertidal and sub-
tidal zones in the northern Gulf of Maine. After Adey (1982).
References Cresser, M. and Edwards, A. (1987) Acidification of Freshwaters.
Cambridge University Press, Cambridge.
Adey, W. (1982) A resource assessment of Gouldsbaro Bay, Maine. Dietrich, G. (1963) General Oceanography. Wiley-Interscience, New York.
Report to NOAA, Marine Sanctuary Program. NA81AA-D-Cz076. Dodds, W. (2002) Freshwater Ecology. Academic Press, San Diego,
Adey, W. (1983) The microcosm: a new tool for reef research. Coral California.
Reefs 1: 194–201. Flood, J. (1983) Archaeology of the Dreamtime. Collins, Sydney.
Adey, W. and Steneck, R. (1985) Highly productive eastern Horne, R. A. (1969) Marine Chemistry. Wiley, New York.
Caribbean reefs: synergistic effects of biological, chemical, physi- Hutchinson, G. E. (1957) A Treatise on Limnology, Vol. 1. Wiley,
cal and geological factors. In: The Ecology of Coral Reefs. M. Reaka New York.
(Ed.). NOAA Symposium Series on Underwater Research, Vol. 3, Kennett, J. (1982) Marine Geology. Prentice Hall, Englewood Cliffs,
Washington, DC. New Jersey.
Blankenship, K. (2005) Bay experiences largest recorded anoxic zone Kleypas, J., Buddemeier, R., Archer, D., Gattuso, J.-P., Langdon, C.,
this summer. www.bayjournal.com. and Opdyke, B. (1999) Geochemical consequences of increased
Cleseri, L., Greenberg, A., and Prussell, R. R. (Eds) (1989) Standard atmospheric carbon dioxide on coral reefs. Science 284: 118–120.
Methods for the Examination of Water and Wastewater, 17th edn. Livingston, R. (2006) Restoration of Aquatic Ecosystems. Taylor & Francis,
American Public Health Association, Washington, DC. Boca Raton, Florida.
Lovelock, I. (1979) Gaia: A New Look at Life on Earth. Oxford Schmidt-Nielsen, K. (1975) Animal Physiology. Cambridge University
University Press, Oxford. Press, Cambridge.
McConnaughey, T. (1994) Calcification, photosynthesis and global Small, A. and Adey, W. (2001) Reef corals, zooxanthellae and free-
carbon cycles. Bull. l’Inst. Ocean. Monaco 13(Specl.): 137–161. living algae: a microcosm study that demonstrates synergy between
Millero, F. and Sohn, M. (1992) Chemical Oceanography. CRC Press, calcification and primary production. Ecol. Eng. 16: 443–457.
Boca Raton, Florida. Spotte, S. (1992) Captive Seawater Fishes. Wiley-Interscience, New York.
Osmond, B. (2004) Changing the way we think about global change Stumm, W. and Morgan, J. (1981) Aquatic Chemistry. Wiley, New York.
research: scaling up in experimental ecosystem science. Global USGS. (2005) Resource Data Base for Gulf of Mexico Research.
Change Biol. 10: 393–407. www.gulfbase.org.
Richards, F. (1965) Dissolved gases. In: Chemical Oceanography.
J. Riley and G. Skirrow (Eds). Academic Press, London.
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C H A P T E R
The Primary Nutrients – Nitrogen,
Phosphorus, and Silica
Limitation and Eutrophication
Open ocean sea water contains about 35 parts per to primary production in ocean waters far from land.
thousand (ppt; 35 000 ppm) by weight salts and other This situation is highly unlikely in model ecosystems
elements, in addition to the hydrogen and oxygen that and human-controlled aquatic ecosystems because of
make up the remaining 965 ppt (mostly as water). Over the abundance of iron in human environments. Carbon
99.6% of the “salt” weight is made up, in order of abun- (as CO2 and alkalinity) could also be limiting in some
dance, of chlorine, sodium, magnesium, sulfur, calcium, community models (e.g. coral reefs). This potential
and potassium. These elements are conservative. They problem is treated in Chapters 8, 10, and 20.
vary little in their proportions over the entire world’s
oceans and even into most estuaries. Several gases,
nitrogen, oxygen, and carbon dioxide, are also more or NUTRIENTS IN NATURAL WATERS
less abundant; these we discussed in Chapter 8. Most of
the remaining chemical elements occur in sea water, in A typical tropical open ocean distribution pattern
extremely small quantities. However, there are a num- of dissolved (reactive) nitrogen and phosphorus
ber of elements, required by some or all plants, that with depth is shown in Figure 9.1. Surface values of
occur normally at concentrations of a small fraction of a these essential compounds are typically less than 1 µM
ppm to perhaps as much as 0.2 ppm. The most impor- (0.014 ppm) nitrogen as nitrite plus nitrate and less
tant of these elements to organisms are nitrogen, phos- than 0.1 µM (0.003 ppm) phosphate. Below the photic
phorus, and silica. See Table 4.4 for a summary of these zone, and a little below the oxygen minimum and car-
relationships. bon dioxide maximum, where phytoplankton and zoo-
In fresh waters, the conservative elements are gener- plankton are being eaten or are breaking down without
ally present in very small quantities with salt lakes in light for recycling, nutrient levels climb to about 20–30
basins without an outflow being striking exceptions. In times surface values. In the deepest waters, which are
salt lakes, the dominant salts vary widely, depending on cold with very slow currents derived from Arctic and
the rocks present in the drainage basin (see Chapter 4). Antarctic surface waters, nutrient levels are moderate
However, the same basic nutrients as in the sea tend to be at all times. Largely inaccessible to plants except at
limiting to plant production in the Earth’s fresh waters. unusual points of current upwelling, reactive nitrogen
In this chapter we discuss the primary nutrients, and phosphorus remain in storage for hundreds to
nitrogen, phosphorus, and silica. After the basic physi- thousands of years in the deep ocean.
cal parameters, temperature, light, etc., the abundance In relatively shallow coastal waters the picture is rather
of these elements is critical in determining the character different, especially outside the tropics where surface
and function of an aquatic ecosystem. Other nonconser- warming in the summer tends to prevent mixing. The
vative elements might be limiting in special cases. Iron yearly cycles of nitrogen and phosphorus levels for
has recently been under heavy investigation as a limiter the English Channel are shown in Figure 9.2. Here, the
132 9. The Primary Nutrients – Nitrogen, Phosphorus, and Silica
oxygen reverses this reaction and allows reactive phos-
phorus to escape into the lower water column. How-
ever, being generally below the photic zone except in
the smallest lakes, it remains largely unavailable for
Silicon is one step up from carbon in the periodic
table of the elements. Thus, chemically it is quite similar
to carbon, but is a little over twice as heavy. Forming an
enormous number of compounds as minerals in the
Earth’s crust, it is to the lithosphere what carbon is to the
biosphere. Diatoms are the only primary producers that
make an ecologically important use of the element.
FIGURE 9.1 Distribution with depth of phosphate and nitrate in Diatoms use silicate, instead of cellulose or related com-
the tropical and subtropical portions of the oceans. Microgram atoms pounds, to form cell walls. They are essentially alone in
per liter µM; concentrations of N as nitrate with depth are this use, although a few other heterotrophs (secondary
0.3–0.6 ppm; P as phosphate are 0.06–0.09 ppm. After Sverdrup et al. producers) such as radiolarians and some sponges make
(1942). Reprinted by permission of Prentice Hall, Englewood Cliffs, silica skeletons. Radiolarians can be extremely abundant
both in the plankton and on the bottom in specialized
localities. While silicon (as silicate) is moderately abun-
dant in water environments (about one-tenth of carbon
mixing of tides and winter storms accompanied by low and six times that of reactive nitrogen), it can sometimes
light allows moderate levels of nutrients to build up in be limiting to plant production when that production is
winter. Note, however, that in the winter at 5–8 µM dominated by diatoms (see Table 4.4).
nitrogen as nitrite plus nitrate, levels are still well below Today human influence on the biosphere is massive
deep ocean levels. Most aquatic animals excrete ammo- and rapidly growing; thus, it is critical for the modeler,
nia. This very toxic compound is metabolized by bacte- the aquatic restorer, and the hobbyist to keep the above
ria to the mildly toxic nitrite and finally to the relatively described relationships in mind. Under pre-human
benign nitrate. Both ammonia and nitrite occur at a conditions, in all aquatic and marine environments,
fraction of the concentration of nitrate in the water except relatively rare naturally eutrophic situations,
columns of most aquatic ecosystems. Algae and bacte- the low concentrations of nitrogen, phosphorus, silica,
ria both compete for these compounds as sources of and sometimes iron provided considerable restrictions
nitrogen and energy, and if it is possible to measure on the level of plant activity and therefore on the level
ammonia and nitrite by any but the most sophisticated of total biological activity. An upwelling zone with
of chemical analytical processes, that is, if either is over a prevailing offshore wind, a whale washed up on
about 0.5 µM (0.0007 ppm), they are probably much too the shore of a restricted inlet, a marshy basin on a
high, as we discuss in some depth below. recently burned slope, organic detritus concentrated
The nutrient picture in fresh waters not subject to on a beach or a mud flat by a storm – these were natu-
intensive human activity is similar to that of the ocean, rally eutrophic or nutrient-rich situations. However,
but different in some critical ways. First, nitrogen has they were restricted in space and time. In the plank-
many potential sources of atmospheric bacterial fixa- tonic environment, the flow of nutrients to the algal
tion on the land. The equivalent process is not available cells could also be greatly limited by the diffusive
for phosphorus, and thus phosphorus tends to be lim- boundary layer (DBL); understanding the conditions
iting for plant production, rather than nitrogen. It is under which the effect of the DBL is reduced is a sci-
phosphorus that operates on a yearly cycle to limit pri- ence by itself (Riebesell and Wolf-Gladrow, 2002).
mary production. Figure 9.3 shows typical summer Much of the practical and operational water quality
patterns on several lakes with low levels of phospho- control measures discussed in this book will deal with
rus at the surface markedly increasing below the ther- ways of reducing the effects of the DBL.
mocline. On the other hand, near the bottom, additional Some heterotrophic bacteria, primarily under anaero-
mechanisms quite different from those applicable to bic conditions, but as we now know also under some
nitrogen are active (Figure 9.4). Under aerobic conditions, aerobic conditions (Sprent, 1987), utilize nitrate or nitrite
phosphate combines with ferrous iron in the sediments. and produce the gases nitrous oxide and nitrogen. This
The precipitate that forms remains locked in those sed- process of denitrification removes nitrogen from an
iments until they approach anaerobic conditions. Thus, aqueous medium or sediments to the atmosphere. In the
under stratified and stagnant summer conditions, low water column of most lakes and the oceans, this process
Nutrients in Natural Waters 133
FIGURE 9.2 Yearly cycles of nutrients in the English Channel. Milligrams per cubic
water µg/liter; for nitrate, 100 µg/liter 7µM; for phosphate, 30 µg/liter 1 µM. After
Gross (1982). Reprinted by permission of Prentice Hall, Englewood Cliffs, New Jersey.
is negligible. However, in the anaerobic sediments of when that is achieved largely by macrophytes or
eutrophic bodies of water (enriched by human activi- attached algae.
ties) denitrification rates can be considerable, in some In summary, below about 15–20 µM (N as NO2
cases at the levels of primary production (Seitzinger, NO3) (0.2–0.3 ppm) denitrification is negligible. Below
1988). On the other hand, in noneutrophic shallow about 1–2 µM (N as NO2 NO3) (0.014–0.03 ppm) nitro-
waters, low in nitrogen, denitrification, mostly from gen fixation from gaseous N2 begins to be a significant
underlying sediments, occurs at rates an order of mag- factor (Lucid, 1989; Chapter 20). The net effect is that in
nitude or more below primary production, particularly most modeling and restoring efforts, where achieving
134 9. The Primary Nutrients – Nitrogen, Phosphorus, and Silica
FIGURE 9.3 Phosphate concentration in several temperature lakes during the summer. , temperature °C; phos-
phorus: PT, total; PS, soluble; PST, in particulates. After Hutchinson (1957). Reprinted by permission of John Wiley &
the original, nondegraded, ecological environment is bacteria (including H2S) provides environmental condi-
desired, denitrification (nitrogen loss to the atmosphere) tions that are suitable for very few organisms.
is not a significant factor and a small amount of nitrogen As we discuss under Bacteriological Filtration in
fixation (from the atmosphere) is likely. Chapter 11, it has become customary for modern human
societies to avoid the most serious problems of excess
concentration of organics (generally sewage) by provid-
EUTROPHICATION AND ing large bacteria-operated industrial plants to break
HYPEREUTROPHICATION OF NATURAL down these organics. A sewage plant releases carbon
WATERS dioxide to the atmosphere, reducing biochemical oxygen
demand (BOD) in the water effluent (but adding to
Excess concentration of organics and nutrients by global warming). The bacterial biomass that develops
human activities leads to a variety of problems in wild (sludge) is hauled away to environments of less concen-
ecosystems that are not adapted to such excesses. Most tration. Ocean dumping is rarely allowed today; how-
critical for marine and freshwater environments is ever, spreading or spraying sludge on farm fields simply
ammonia. When this very toxic nitrogenous excretion of moves the problem to another location. Most of the nutri-
many waterliving organisms (see Chapter 7) is available ents in solution, as nitrites, nitrates, and phosphates, are
in abundance, and sufficient plant or microbe activity is then dumped into estuaries, lakes, and streams. While
not present to remove it, it can become deadly. A number this process has avoided the most immediate difficulties
of bacteria and fungi also perform nitrification, or break- of mass sewage, namely disease transmittal and local
down of ammonia to nitrite and nitrite to nitrate, though low oxygen, when carried out with large human popula-
they generally require oxygen and release carbon diox- tions it only extends the basic problem a few years. After
ide. Excess organic material without consequent plant a half-century of adding and upgrading sewage plants,
return to the stored “fixed” carbon state also leads to a as a “half solution,” the nutrients have simply built up
drawdown of oxygen and eventually anaerobic condi- downstream in lakes, bays, and now the ocean.
tions. The combination of anaerobic conditions in the Many algae and some aquatic plants are adapted to
water column and the often-toxic products of anaerobic make use of the temporary mass availability of nutrients
Eutrophication and Hypereutrophication of Natural Waters 135
FIGURE 9.4 Seasonal cycling of oxygen, iron as Fe2 , and phosphate just over the deepest
mud, at 14 meters in an English lake. After Hutchinson (1957). Reprinted by permission of John
Wiley & Sons, Inc.
in wild ecosystems (the dead whale, for example, or the moderate levels increases the growth rates of many
school of fish on the beach). The life strategy of these plants (other factors being equal) and most animals
“opportunists” is extremely rapid growth, given ade- including corals are not directly affected by this increase.
quate light, temperature, and a large peak of nutrients. Thus, in human cultured environments, it may be desir-
Given summer long or permanently high nutrients, able to elevate nutrients (as in farming). However, at the
these plants multiply rapidly, choking bodies of water risk of overstatement, we note again that such increases
and eventually reducing oxygen, killing themselves as almost always change ecosystem community structure,
well as many invertebrates and fish at the same time. sometimes radically. Direct control methods (e.g. weed-
Given elevated nutrients and typically higher tempera- ing, light control) can affect these changes; however, this
tures some blue-greens (cyanobacteria) in fresh water can be very difficult and costly to achieve. It has not been
and dinoflagellates in coastal waters can bloom, pro- unusual to apply herbicides (to kill off the offending
duce abundant toxins, and provide mass kills of fish and submerged aquatic vegetation (SAV) or algae), but this
sometimes birds and humans (e.g. Livingston, 2006). is a very short-term solution. Also, dredging of eutrophic
To many humans, it is the fast-growing algae or the sediments merely puts the problem off a few years and
equivalent macrophyte such as Hydrilla or water hyacinth can rarely return an ecosystem to its original state.
that is the problem, not ourselves who have created the In wild ecosystems, this is not simply a matter of
unnatural high nutrient situation. Increasing nutrients to esthetics. The loss of major fisheries and their associated
136 9. The Primary Nutrients – Nitrogen, Phosphorus, and Silica
jobs, and the impending loss of recreational value, in problem in traditional aquarium management, and in
Lake Okeechobee, Pensacola Bay, Chesapeake Bay, and most model ecosystems for that matter, has been pre-
now the northern Gulf of Mexico (to name just a few) venting the “pollution” of the system by these excre-
is only a prelude of things to come. Serious fish and tory compounds. It is primarily to solve this very basic
invertebrate diseases, and red tides that cause human problem that the biological filter was developed.
illness and even death, are not far behind. Chemical and Unfortunately, in many cases reliance on the bacterial or
bacterial methods of dealing with human-concentrated “biological” filter is counterproductive in that the solu-
nutrients have been developed (BNR: biological nutri- tion to the ammonia problem is accompanied by a num-
ent removal), and are beginning to be used in the US ber of negative side effects that render natural ecosystem
(Zickefoose, 2004). However, they are difficult, erratic, management difficult or impossible to achieve.
and costly (Chesapeake Bay Commission, 2004). After Marine and freshwater planktonic algae actively
roughly 25 years of major effort by governments and photosynthesizing and growing have a continuous and
NGOs, and billions of invested dollars, Chesapeake Bay, often production-limiting requirement for nitrogen and
for example, is more eutrophic than when the effort other nutrients. Approximately 1 nitrogen atom is needed
began. Nutrient inputs in the rivers of the Bay have not for every 7 carbon atoms built into plant tissue and 1
been reduced, and the dead zone in the Bay in the sum- phosphorus atom for every 100 carbon atoms. Benthic
mer of 2005 (Blankenship, 2005) was larger than ever. algae, on the other hand, are capable of producing at a
Some of this degradation can be put down to increasing considerable deficit when nutrients are low (Figure 9.5).
population in the watershed, and indeed this cannot go Likewise many fleshy algae are noted for their “luxury”
on indefinitely. Mostly, however, it is a failure to recog- or excess consumption of nutrients when they are avail-
nize basic biology and ecology, and to develop counter- able. Most algae accept ammonia as a nitrogen source
ing methodologies. In Chapter 25, we bring together the and are capable of rapidly taking it up. The nitrification
rationale and methodology for a full solution to this products of ammonia, nitrite, and nitrate, as well as
ever-increasing problem. more complex nitrogenous excretory products such as
NUTRIENTS AND MODEL ECOSYSTEMS
Basically, the organic pollution problems are the
same for the aquarist as they are for human society at
large. Only the scale is different. It is instructive to
compare wild ecosystem nutrients discussed above
with those for traditional aquaria. We quote from
Spotte (1979): “It is inevitable that seawater aquariums
will become eutrophic . . . inorganic nitrogen levels in
aquarium water can be staggering.” Great improve-
ments in culture techniques have been made since the
first edition of this book was written. However, these
improvements apply to a limited set of organisms, in a
garden-like environment; in an ecological context, con-
siderable improvement is still needed.
As we discussed in Chapter 7, animal tissue that
has become food for other animals or for bacteria or
fungi undergoes a continuous process of breakdown
and assimilation. Carbohydrates and most fats in this
breakdown process are metabolized using oxygen and
result in the release of carbon dioxide. On the other hand,
proteins, nucleic acids, and phospholipids (along with
other compounds) provide an excess of nitrogen and FIGURE 9.5 Carbon, nitrogen, and phosphorus ratios in marine
phosphorus in addition to the basic carbon, hydrogen, plants. Note that temperate algae were apparently not nutrient defi-
and oxygen of organic tissues. The net result is a require- cient, tropical algal turfs were not nitrogen deficient (due to nitrogen
fixation) but were slightly phosphorus deficient, and larger tropical
ment for the excretion of nitrogen-rich and phosphorus- algae were deficient in both nutrients. Productivities as measured by
rich compounds into the ambient water. Chief among biomass increase were approximately equivalent in all groups (Adey,
these excretory compounds is ammonia. The central 1987).
Nutrients and Model Ecosystems 137
urea, can also be used by many algae. In reef tank radiation or equivalent light levels can induce disas-
ecosystems, with dense algal and higher plant commu- trous planktonic algal blooms at the nutrient concentra-
nities, nitrogen salts, measured with autoanalyzers, tions of traditional aquarium tanks. It has been
typically occur at a concentration of less than 1–1.5 µM demonstrated that moderate nutrient levels ( 5 µM
(14–21 ppb). This is equivalent to the situation nor- N–NO3, 70 ppb) are not directly damaging to some reef
mally encountered in a wild reef and yet is at great corals (Atkinson et al., 1995). However, experiments
variance with traditional aquarium systems in which have shown calcification disruption in corals by even
nitrogen levels of over 100 ppm are acceptable. The lower nutrient levels (Marubini and Davies, 1996). At
limiting of sensitive organisms in aquarium systems the very least, excess nutrients can allow benthic algae
by ammonia, nitrate, and nitrite, as well as the unsta- to outcompete corals. Even if grazing levels are greatly
ble environment these nutrients create in excess, is a increased, this can provide a level of disturbance that is
major element in the erratic nature of the traditional destructive to stony corals.
aquarium. Maine rocky shore and temperate estuarine systems
Tropical reef communities in particular are character- such as the Chesapeake Bay, as well as other communi-
ized by low nutrient levels. Nitrate levels in incoming ties that have been involved in microcosm or mesocosm
ocean water in St. Croix reefs are about 0.4 µM (6 ppb). simulation, have relatively high concentrations of dis-
More open ocean or equatorial current situations (such solved or reactive nitrogen (Figures 9.6 and 9.7). Those
as Grand Turk, for example) are even lower, on the order naturally rich ecosystems, however, at 5–10 µM
of 0.1 µM. Blue-green algae in reef waters are known to (N–NO3 ) for unpolluted waters, and 10–80 µM (NO3 )
fix gaseous nitrogen much as the bacteria of the root for polluted waters, are still far below the older type
nodules of legumes do in the terrestrial environment. aquaria at 5000 µM (N–NO3 ) or higher. Note that in
However, these blue-greens are either not present or Figure 9.7, 25 µM (0.38 m/liter) N–(NO2 NO3 ) and
unable to fix nitrogen in any but the most nutrient- 13 µM (0.38 mg/liter) (total phosphorus as PO3 ) are
minimum environment. High nutrient levels cause a noted as critical levels, above which algal or aquatic
shift in algal community structure, a shift that can be plant blooms occur with disastrous consequences. Both
very detrimental to an attempt to simulate an ecosys- systems are also characterized by having both a sediment
tem. It has long been known that perhaps next to silta- sink and an open ocean sink for such nutrients. If rocky
tion, elevated nutrients (or eutrophication) is one of the shore and estuarine communities are managed properly,
primary factors causing degeneration of wild reefs. with considerable nutrient importation, then a “nutrient
A serious problem for coral reefs as well as most open sink” is required to prevent eutrophication and radical
shallow-water ecosystems is the relationship of such alteration of the biological communities. Most such
high nutrient levels to the growth capabilities of some coastal marine communities are characterized by run-
species of both planktonic and benthic algae. Solar off from the adjacent land. Without the ocean sink to
FIGURE 9.6 Nitrate concentration as a function of salinity in the Sheepscot estuary
(Maine), September 1986. After Fefer and Schettig (1980).
138 9. The Primary Nutrients – Nitrogen, Phosphorus, and Silica
FIGURE 9.7 Nitrate plus nitrite and total phosphorus as PO4 concentrations on the upper Potomac estuary, summer,
1972–1975. After Lippson et al. (1979).
eventually dilute and remove those nutrients, eutrophi- Some aquarists have advocated using the process of
cation would result. The data given in Figure 9.7 shows denitrification in special anaerobic traps to remove
the Potomac River leading into the upper-mid Chesa- excess nitrogen from mesocosm and aquarium environ-
peake Bay, as it was in the 1970s – already eutrophic. As ments. Indeed, this process probably occurs to a limited
we discussed above, this eutrophic character, in 2005, has extent in virtually all closed systems and in many wild
extended to the entire upper half of this 200-mile-long systems. In eutrophic aquaria with rich sediment bot-
Bay. In the simulations of Chesapeake Bay and the rocky toms, it will certainly be an important process. However,
Maine shore described in Chapters 21 and 22, dissolved in sediments and their overlying waters that are not
nitrogen concentrations are normally maintained in the enriched far beyond natural levels, denitrification rates
1–10 µM range, far below presently existing levels in the are likely to be below 30–50 µM N/m2/h (Seitzinger,
wild ecosystem, but probably slightly above pre-human 1988). This is one to two orders of magnitude below the
levels. removal rates of nitrogen in primary production or
photosynthetic removal of nitrogen. In addition, denitri- SUMMARY
fication does not remove the balanced array of nutrients
that are taken up in primary production. A number of The handling of nitrogenous and phosphorus
schemes have been developed to enhance denitrification wastes in aquarium simulations of ecosystems can be
(NO3 to N2) in coral reef systems, and these have been summed up by several critical requirements:
reviewed by Delbeek and Sprung (2005). Some of these
1. An animal load that is at least close to that in the
methods add sulfur so as to use sulfur bacteria to drive
wild (an excessive load technically can be managed;
the process, and they can then work efficiently.
however, it makes the system more equivalent to an
However, all of the other criticisms remain, and one is
aquaculture or farming unit and presents numerous
operating a potentially deadly system in tandem with
ecological balancing problems).
the highly oxygenated system desired. The chance for
2. A built-in system for rapidly exporting ammonia
disaster is always present, and one has to ask: why not
and other waste compounds. In most aquarium sys-
stick with the primary production processes that work
tems this is the bacterial or “biological” filter. In
so well in the wild?
most natural shallow-water ecosystems, and in the
In recent years perhaps the most favored methodol-
examples in this book, this requirement is accom-
ogy for maintenance of high water quality in aquarium
plished directly by plants or by export/mixing with
systems is foam fractionation, more commonly known
an adjacent community (a larger open body of
in the aquarium trade as protein skimming. This
process provides a fine stream of bubbles in a vertical
3. A means of ultimately exporting added nutrients. In
column with a means for collecting the foam generated
the wild this is partly accomplished by oceanic dilu-
(Delbeek and Sprung, 2005) and has numerous varia-
tion and sinking to deep water, although burial in
tions and methods for increasing efficiency. The pri-
marshes, sediments, and soils acts as a primary,
mary purpose is to remove dissolved organics and
thus, unlike denitrification “filters” and similar to algal
“filtration” systems, it will remove a cross section of The first requirement, that of an appropriate animal
nutrients. Foam fractionation does not directly remove load for the area and volume involved, is discussed in
dissolved nutrients and therefore cannot achieve the depth in a number of the following chapters. The second
oligotrophic levels of open ocean waters, although requirement can be met by providing the appropriate
schemes have been developed to enhance water col- photosynthesizers for the system being worked, and the
umn bacterial action (e.g. by adding alcohol – vodka) right environmental factors, light, and water motion to
to enhance bacterial production and therefore increase enable those plants to function. These elements are dis-
skimmer removal of nitrogen and phosphorus. How- cussed primarily in Chapters 12 and 14. Finally, the
ever, most important as a consideration for a technology effects of an open-water sink relative to nutrients can
for operating closed ecosystems, foam fractionation also be provided by plants and algae (MAPS: managed
cannot differentiate between dissolved and particulate aquatic plant systems), given a proper control mecha-
organics and the planktonic and reproductive flora and nism. Several mechanisms, particularly algal turf scrub-
fauna. While foam fractionation cannot be used to bing (ATS), have been devised and are discussed at
accurately model most ecosystems, it could have been length in Chapter 11.
used where a more limited result of the culture of indi- The management and restoration of wild ecosystems
vidual organisms does not directly or indirectly utilize subject to human eutrophic degradation differs only as a
a natural planktonic or particulate community (see matter of scale. Sewage plants at cities and towns and
Chapters 2, 6, and 17). If a “garden” is desired, this buffer strips and best management practices (BMPs) on
could be an excellent way to go, one for the aquarist farms are essential at the primary, particulate level and
and one for the aquarium (i.e. vodka). for disease control. New BNR methods have been devel-
Ion exchange media, including charcoal and newer oped for nitrogen and phosphorus, but they are batch,
resins and plastic materials with great porosity and ion one nutrient at a time, processes and are very sensitive
absorption characteristics, can also be used to reduce to minor environmental changes. Computer control and
nutrients as well as dissolved organics. These media all expert staff are necessary to achieve success. However,
suffer from difficulties of control and balance in the only solar-capture, photosynthetic (MAPS) methods can
chemical soup that is a “living” water, especially sea efficiently solve the eutrophication problem at land-
water. Also, as in all filtration methods, plankton and scape scale. These low cost methods have been demon-
larval stages are trapped and mostly destroyed (see strated at large scale (20 mgd modules) and are
also Chapters 6, 11, and 17). discussed in Chapter 25.
140 9. The Primary Nutrients – Nitrogen, Phosphorus, and Silica
References Lucid, D. (1989) Effects of Dissolved Inorganic Nitrogen Concentrations on
Primary Productivity, Nitrogen Fixation, and Community Composition
Adey, W. (1987) Food production in low-nutrient seas. Bioscience 37: of Coral Reef Algal Turf: A Microcosm Study. M.S. Thesis, University
340–348. of Maryland.
Atkinson, M., Carlson, B., and Crow, G. (1995) Coral growth in high Marubini, F. and Davies, P. (1996) Nitrate increases zooxanthellae pop-
nutrient, low pH seawater: a case study of corals cultured at the ulation density and reduces skeletogenesis in corals. Mar. Biol. 127:
Waikiki Aquarium, Honolulu, Hawaii. Coral Reefs 14: 215–223. 319–328.
Blankenship, K. (2005) Bay experiences largest recorded anoxic zone Riebesell, U. and Wolf-Gladrow, D. A. (2002) Supply and uptake of
this summer. www.bayjournal.com. inorganic nutrients. In: Phytoplankton Productivity. P.J. le B.
Chesapeake Bay Commission (2004) Cost effective strategies for the Williams, D. Thomas, and C. Reynolds (Eds). Blackwell Science,
Bay. www.chesbay.state.va.us. Oxford.
Delbeek, C. and Sprung, J. (2005) The Reef Aquarium: Science, Art, and Seitzinger, S. (1988) Denitrification in freshwater and coastal marine
Technology, Vol. 3. Ricordea Publishing, Coconut Grove, Florida. ecosystems: ecological and geochemical significance. Limnol.
Fefer, S. I. and Schettig, P. (1980) An Ecological Characterization of Coastal Oceanogr. 33: 702–704.
Maine, Vol. 2. US Fish and Wildlife Service, Boston, Massachusetts. Spotte, S. (1979) Sea Water Aquariums: The Captive Environment. Wiley,
Gross, M. C. (1982) Oceanography, 3rd edn. Prentice Hall, Englewood New York.
Cliffs, New Jersey. Sprent, J. (1987) The Ecology of the Nitrogen Cycle. Cambridge
Hutchinson, C. E. (1957) A Treatise on Limnology, Vol. 1. Wiley, University Press, Cambridge.
New York. Sverdrup, H., Johnson, M., and Fleming, H. (1942) The Oceans: Their
Lippson, A. J., Haire, M. S., Holland, A. F., Jacobs, F., Jensen, J., Moran- Physics, Chemistry and General Biology. Prentice Hall, Englewood
Johnson, R. L., Polgar, T. T., and Richkus, W. A. (1979) Cliffs, New Jersey.
Environmental Atlas of the Potomac Estuary. Environmental Center, Zickefoose, B. (2004) Improving the Design of the BNR Process in
Martin Marietta Corp., Baltimore, Maryland. Wastewater Treatment Plants from an Operations Perspective. M.S.
Livingston, R. (2006) Restoration of Aquatic Systems. CRC Press, Taylor Thesis, Engineering Department, Florida State University.
and Francis, Boca Raton, Florida.
C H A P T E R
Biomineralization and Calcification
A Key to Biosphere and Ecosystem Function
Under very special circumstances of burial and Muscles certainly greatly pre-date the Cambrian as
preservation the soft tissues of animals and their part of multicellular organisms. However, muscles are
imprints in sediments can be preserved in the fossil more efficient, the required distance of movement
record. Woody plants of the last 400 million years have being less, if they are attached to and pulling against
been preserved, especially under swamp conditions. something hard. Thus, whether for capture or escape,
However, the tremendous library of organic evolution mineralized skeleta for muscle attachment provided
of fauna over the last 543 million years, the paleonto- major advances in evolutionary “races.” Finally, sens-
logical record, is primarily written in mineralized ing and balance systems gain greater precision, in many
skeleta. This is a complex record of comings and goings, cases, if they are not jell-like in texture, and instead are
of changes in the kinds of organisms that are dominant, heavier than water and “rock-firm.” Many organisms
that depends, at least in part, on small changes in the developed mineralized otoliths or their equivalent.
chemistry of the sea (Knoll, 2003). Thus, mineralized hard parts have become an indelible
For nearly a century, geologists drew the practical line and critical element of many organic lines, both aquatic
between living and nonliving at the pre-Cambrian/ and terrestrial.
Cambrian boundary, about 500 million years ago. The The realm of geology is dominated by silicate chem-
principal paleontological question of the first half of this istry. However, except in science fiction, this is the
century was: why did a large, complex fauna suddenly province of geology, the lithosphere, rather than the
show up at the Cambrian? Intensive paleontological biosphere, where carbon is the key element. The ele-
work through the middle and later part of the 20th cen- ment silicon is used by many living organisms to form
tury has demonstrated life over 2 billion years further hard parts, and diatoms are a very abundant example
back, with numerous complex, taxonomic lines at least in aquatic environments; however, such use is as amor-
several hundred million years before the Cambrian. The phous silica (SiO2) not as a crystalline silicate. Silica is
event that changed apparent life on Earth so radically an important biomineral; however, it follows the car-
was the widespread development of an ability on the bonates in abundance. Of the hundreds of minerals
part of many evolutionary lines to make mineralized known, nearly half are not silicates, and about 50 have
hard parts. That these fossils were easily seen in sedi- been developed by many phyla of living organisms as
mentary rocks, and their predecessors were not, formed hard parts (skeleta, teeth, and sensory devices). Table
the principal character of early paleontology. 10.1 shows the more important minerals of aquatic sys-
The development of mineralized hard parts was an tems and the phyla in which they occur.
inevitable step in evolution. Protection by external For very good reasons, as we shall see, carbonate
skeleta in aqueous environments was an obvious way minerals overwhelmingly dominate the biominerals.
to lessen predation pressure, though, almost as quickly, Nevertheless, a dozen phosphatic minerals are also
predators upped the ante of the arms race (Chapter 16) extremely important in the biosphere, for example as
by developing mineralized teeth and radula. In reef vertebrate bone (calcium hydroxyapatite), and iron
systems, calcification by many organisms also became oxides and calcium oxalates come into play in a few
a competitive device to obtain space and light. groups (especially as teeth and skeleta, respectively).
142 10. Biomineralization and Calcification
TABLE 10.1 Principal Mineral Formation by Aquatic Organisms
Rhodophyta (including Corallines)
Chlorophyta (including Halimeda)
Chordates (mostly bony fish)
Calcite (Ca(Mg)CO3) * * * * * * * * *
Aragonite (CaCO3) * * * *
Opal (SiO2) * * *
Note: *Biomineralization of widespread occurrence and of special significance to mesocosm and aquarium operation. Modified after Simkiss
and Wilbur (1989).
Since such a large number of minerals of quite dif- conditions under which biomineralization occurs.
ferent chemical composition are used in such a large Before entering into our principal concern in this chap-
percentage of phyla of living organisms, it seems likely ter, biomineralization that is potentially controlled or
that there are some basic physiological and biochemical limited by the basic parameters of living models and
The Carbonate System and the Formation of Calcite and Aragonite 143
degrading ecosystems, we examine biomineralization the framework of a more complex hard-part structure
in general. (such as a tooth or bone).
In some species, mineralization occurs simply because Thus, the basic principles for the construction of
of the chemical changes caused in the surrounding organism hard parts, with minerals both known in the
waters by the metabolism of the organism. This occurs lithosphere and specific to organisms, whether skeletal,
most often in bacterial and blue-green algae (cyanobacte- sheathing, or sensory, are known. The minerals employed
ria) films and can involve the precipitation of sulfides in are numerous, with undoubtedly more to be discovered.
the first case and carbonates in the second. See also the In general, the process of membrane formation followed
discussion on the green algae Halimeda below. Mostly, by ion pumping requires energy and can therefore work
however, biomineralization is under some direct control against considerable environmental gradients. In the end,
(and at some energy expenditure) of the organisms however, a basic ecological trade-off must apply. The sur-
involved, as is the case for most skeletal hard parts, such vival benefits provided by the skeleta or sensory appara-
as vertebrate bone, mollusc shells, and a wide variety of tus must exceed the survival losses inherent in the energy
tooth-like structures. given up. Also, in many cases, behavioral aspects requi-
site to the use of hard parts can have considerable bearing
on survivorship. A very striking example in the aquatic
THE PROCESS OF BIOMINERALIZATION environment is the required molting phase of crus-
taceans: during the soft intervals, while the skeleta are
Control of the production of hard parts by an organ- being “calcified,” individuals of many species are in large
ism involves two key elements: measure defenseless and subject to considerable losses
due to predation.
1. The enclosure of a very small volume of water by tis-
sues, cells, a membrane-bound vacuole, or a macro-
molecular sheath produced by the organism. This
THE CARBONATE SYSTEM AND
space can be totally surrounded by organic material
THE FORMATION OF CALCITE
or it can be created against a substrate or an already
formed mineral base.
2. The capability of bounding cellular membranes
The construction of hard parts of silica and phosphate
to pump ions (typically Mg2 , Ca2 , Si4 , CO3 , 2
2 is very important to biosphere function. However, they
PO4 , H , etc.).
do not begin to compare in magnitude to the importance
The enclosure of the mineralization space allows of calcium carbonate. The direct or indirect formation of
the membrane-pumping function to build up high con- calcite and aragonite by organisms has massively
centrations, generally greatly supersaturated, of the altered the Earth’s atmosphere, hydrosphere, and lithos-
appropriate mineral components. The ion pumping phere and moved about 70 000 gigatons of carbon from
capabilities of phospholipid membranes are well known the original atmosphere primarily to the oceans and
(Figure 10.1) and are typically the subject of whole thence to the lithosphere. Limestones and lime-rich rocks
chapters in modern biochemical texts (e.g. Mathews and are among the principal elements of the Earth’s crust.
van Holde, 1996). Typically, the pore of an ion-channel Yet, they were virtually absent before the activities and
is formed by a protein, embedded in the phospholipid numbers of organisms became significant on a global
membrane, and, especially in plants, the structure and biochemical basis.
rapid function of these channels have been extensively The reason for this tremendous biogeochemical pro-
studied (Heldt, 2005). Some ion-channels pump ions to cessing is more or less obvious: the carbonate ion is
create an electrical gradient (e.g. the strong pH gradient oxidized carbon, the basic building block of living
between stroma and thylakoid in photosynthesis; see organisms. Through carbon dioxide, the basic respiratory
Chapter 5); however, generally the electrical gradient is product of most of Earth’s organisms, and the primary
avoided by exchanging ions of equivalent valence and substrate for the building of biomass in photosynthe-
this is likely critical in coral calcification (see below). sis, carbonate mineralization is directly linked to the
Other components of greater sophistication may or core chemistry of living organisms. Furthermore, as we
may not be present. The most common of these are discussed in Chapter 8, carbon dioxide does not simply
nucleation sites created by organic molecules (often dissolve in water, remaining in its gaseous state (e.g.
acidic glycoproteins) that attract and hold the cation like nitrogen); it also reacts with water to develop a
(e.g. Ca2 ) from which mineralization can initiate. series of ions linked directly to the acidity/basicity of
Another component that can provide more control to the aqueous environment, a key element in organism
biomineralization is an organic matrix that provides function. Finally, although there are other biological
144 10. Biomineralization and Calcification
FIGURE 10.1 Generalized cell membranes showing pumping organelles and function. (A) Typical cell and membrane; (B) bicarbonate
pumping; (C) sodium–potassium pumping. The and refer to the specific protein that form the pore (in channel) and with adenosine triphos-
phate (ATP) energy drive the pumping process. From Mathews and van Holde (1996). Reprinted by permission of Addison Wesley Longman.
carbonates, calcium is abundant in the Earth’s crust and with a saturated aqueous solution. Particularly in
oceans and forms several key crystalline minerals that, warm, tropical seas where the surface waters are highly
under the physical/chemical conditions at the surface supersaturated with calcium carbonate, calcification
of the Earth today, are approximately in equilibrium would be expected to happen massively sometimes
Halimeda: Photosynthesis-Induced Calcification 145
incidentally to the normal functioning of many organ-
isms and their ecosystems.
Oolitic (aragonite) sands are abundant on shallow,
tropical banks and can be important rock-formers where
the environmental conditions are too extreme for corals
and calcifying algae. While many attempts have been
made to implicate algae (as cyanobacteria) directly in this
process, the consensus today is that the warm, calcium-
saturated, very high pH conditions of the water over
these banks (probably due to phytoplankton) results in
aragonite crystallization out of solution without direct
Because an understanding of the calcium carbonate
biomineralization process is crucial to the design and
operation of many microcosms, mesocosms, and aquaria,
we examine two key calcifying organisms of coral reefs:
the green alga Halimeda and scleractinian, hermatypic
corals in general. Halimeda calcifies almost incidentally
to the photosynthesis processes. Stony corals have more
direct biotic control over mineralization. However, they
also rely not only on their internal symbiotic photosyn-
thetic system with zooxanthellae but also on the reef
community of algae in general to provide conditions
that are favorable for competitive calcification. Adey
(1998) reviews, in depth, the role of algae in coral reef
Halimeda is a well-known tropical benthic genus of
green algae. Fairly large, of centimeter to several decime-
ter dimensions, species of this genus consist of strings FIGURE 10.2 Halimeda favulosa, drawn from a 10-inch-high plant
of flattened or sometimes crinkled, calcified discs con- collected in the Bahamas. This green alga is constructed of filaments
nected by flexible joints. They are abundant in shallow without cross walls (coenocytic). In the segments, the filaments branch
and end in swelled-tip utricles that lay down a matrix of aragonite.
seas around the tropics especially on “coral” reefs and in
Between the segments, the filaments are not calcified, giving the plant
their lagoons, although some species range down reef the flexibility and the capability of withstanding moderate water
drop-offs to great depths. During the 1950s when large motion. From Taylor (1960).
numbers of deep boreholes were drilled into Pacific
atolls, geologists found that the dominant element of
the carbonate structure of these atolls was not stony
coral but rather a lithified sand made up of the lobes of swollen to form a continuous surface as a kind of cellular
Halimeda. The members of this genus rank as one of the pavement. Just below the surface of the lobe, there are
most important calcifiers of the biosphere; it is likely considerable spaces between the utricles (Figure 10.3).
that their CaCO3 production over all tropical seas is The calcification, mostly of aragonite needles, occurs
considerably greater than that of the stony corals. almost entirely in these interutricular spaces. Thus, as
Halimeda (Figure 10.2) is a member of the green algal we described above, through the anatomy of their utri-
order Siphonales and is further described in Chapter 14. cles, these algae have provided one of the basic require-
In brief, anatomically, members of this genus are con- ments for biomineralization, confined spaces in which
structed of tubules, with very few cross walls. Thus, critical supersaturation can occur.
individual cells are extremely long and narrow. At the When a Halimeda disc is sectioned (some are soft
surface of the discs or lobes, the “bat-like” surface enough to be cut with a razor blade), it is possible to see
expression of these tubules (called utricles) is slightly under a dissecting microscope that the chloroplasts are
146 10. Biomineralization and Calcification
environment, mineralization proceeds rapidly. A strong
demonstration of this process can be provided by plac-
ing Halimeda discs in sea water buffered to a low pH. The
discs will photosynthesize normally but will not calcify.
Also, extracts of dead Halimeda utricles dropped into
supersaturated but otherwise stable solutions of calcium
carbonate will cause initiation and rapid growth of arag-
onite crystals. Readers interested in the details of this
process can consult the article by Borowitzka (1989).
An interesting question at this point is, Why is it that
all tropical algae do not calcify as they rapidly photosyn-
thesize in tropical sunlight? Many do, in fact, develop a
coating of loose aragonite crystals. However, most lack
the appropriate intercellular spaces, and the outer cor-
tex where chloroplasts and photosynthesis are concen-
trated is densely packed with cells. In many cases,
where apparently appropriate spaces are present, the
initiating (or nucleating) molecules are not present.
Finally, many species may even develop chemistry that
is inhibitory to calcification. Calcification is only one
strategy for life by tropical algae. Another, such as that
used by algal turfs, is to grow and reproduce very rap-
idly. Grazing only removes the larger, slower growing
In general, in shallow, warm, calcium carbonate-
saturated tropical seas, algae induce considerable calci-
fication simply as a result of photosynthesis. Some of
this calcium carbonate (aragonite or calcite) does dis-
solve at night, as algal respiration releases CO2 taken
up earlier in photosynthesis (algal biomass does not
continually build up despite the high level of photo-
synthesis because of grazing and loss of fragments to
FIGURE 10.3 Movement of calcium and carbon dioxide and the lagoon and ocean). Eventually, much of the algal cap-
carbonate cycle in the green alga Halimeda. The calcification is prima- tured carbon, after being grazed, is respired by ani-
rily extracellular and does not involve ion pumping by membranes. It mals, but a good part of this released CO2 is removed
is “incidental” to the process of photosynthesis as the small molecule up into the water column, above the algal surface, or
of CO2 is “sucked” out of the interutricular spaces. Modified after
off in the adjacent lagoon.
Borowitzka (1989). Reprinted with permission of Springer-Verlag.
crowded into the outer parts of the utricles. Most of the CALCIFICATION IN STONY CORALS
cellular remainder of the lobes and joints is colorless or
nearly so. Thus, when photosynthesis is proceeding Calcification in the stony corals is somewhat differ-
rapidly, CO2 diffuses from the water immediately exte- ent from that in Halimeda, in that it occurs under the
rior to the plant and, particularly because this is the basal disc of each polyp. This biomineralization zone
largest surface of each utricle, from the interutricular is well removed, on the scale of a millimeter to a centi-
spaces. This strongly raises the pH and the concentra- meter, from the photosynthetic region occupied by the
tion of carbonate ion (CO2 ) in the interutricular spaces.
3 zooxanthellae, which is typically located in the upper
As long as calcium is available to diffuse through the part of the polyp. It seems highly unlikely that carbon
porous cell wall from the exterior, calcium carbonate dioxide removal and subsequent pH elevation is a
becomes highly supersaturated in these largely enclosed direct driving force in coral calcification, although it is
spaces. The cell membranes lining the utricular wall almost certainly an important factor.
have macromolecules probably with attached exposed In recent years, models have been developed
calcium ions that initiate aragonite crystal growth. Once (Figure 10.4), particularly by McConnaughey (1989;
started, with the elevated pH and elevated carbonate 1995), that fit what is now known of the physiological
Calcification in Stony Corals 147
FIGURE 10.4 Model of calcification in the generalized stony coral. The key elements for calcification
are the pumping of calcium and hydrogen ions by the calcifying cells, the reaction of hydrogen ions with
ambient bicarbonate, and the uptake of CO2 by zooxanthellae and external algae (see text for details).
performance of many stony corals rather closely. Unlike bearing macromolecules with projecting and charged
in Halimeda, it seems that membrane pumping of calcium calcium ions are probably also a factor in initiating
ions to, and hydrogen ions from, the mostly enclosed calcification and providing appropriate morphology.
spaces between the basal disc of the polyps and the However, if hydrogen ions are pumped higher up
aragonite skeleton is the key to control of calcification in the polyps, in the process of raising pH against
by the animal. The carbon dioxide molecules, being small the aragonite skeleton, these ions begin to create an
and uncharged, diffuse through membranes and cells acidified zone. On the other hand, these ions react with
easily to the calcification site as a result of respiratory the abundant bicarbonate ion in the water column and
processes of the cells making up the base of the polyp. the gastroenteron of each polyp to produce CO2. As the
The removal of hydrogen ions greatly raises pH in the equations show, for every one molecule of CO2 taken
calcification area beneath the polyp, causing the equi- up and calcium carbonate laid down, two ions of bicar-
librium in the reaction between water and carbon bonate are used and two molecules of CO2 are produced.
dioxide to shift to dominance and supersaturation by Since the buildup of acidic conditions and excess carbon
carbonate ion (CO2 ). With calcium being pumped in,
3 dioxide would soon slow the calcification process, if
once aragonite crystallization has started, calcification allowed to continue, the removal of carbon dioxide by
occurs rapidly. Tissues having cells with membranes the coral zooxanthellae (for photosynthesis) is critical
148 10. Biomineralization and Calcification
an algal cell can pump bicarbonate ion (which is highly
abundant) and can provide enzymes to assist conver-
sion to CO2 for use in photosynthesis. However, this
requires energy. By symbiotically associating with the
coral animal, the algae get CO2 (and nutrients in gen-
eral) in some abundance at low energy cost. Likewise,
corals (and most molluscs) could simply expend energy
and pump the required ions to calcify, and indeed some
genera lack zooxanthellae. However, genera that lack
zooxanthellae calcify quite slowly. By associating with
symbiotic algae, the corals receive not only some of the
sugars produced by the algae, but also an enhanced
production of calcium carbonate skeleta. On a global
scale, this is seen in the massive calcium carbonate pro-
duction of many reef corals, which far outweighs that of
On the ecosystem scale, the photosynthesis of free-
FIGURE 10.5 Diurnal uptake of calcium and bicarbonate ions in living algae in a coral reef community typically greatly
a 130-gallon coral reef system, based on eight sets of data points, exceeds that of the coral zooxanthellae. This is instru-
taken from 11/96 to 5/97. Note, concentrations are set high, as mental in driving the calcification rate of reef ecosystems,
described in the text, to avoid depletion during a run. Note that and is a critical element of the coral reef calcification
removal of both ions is parallel, tending to decrease slightly in rate process to which we return below (Adey, 1998).
during the day. There is little or no uptake of the ions at night. See
Figure 20.9 for diurnal pH values. These dictate a free carbon dioxide
In the calcification model we have presented, bicar-
concentration ranging from roughly 2 mg/liter in the morning to bonate and carbonate ions are removed in some quantity
1 mg/liter late in the day. from the water column as substrate for the entire calcifi-
cation process. At normal seawater pH, bicarbonate ion
is abundant, and with the typical continuous input of
to continued rapid calcification. While corals and other oceanic seawater across wild, well-developed reefs, sig-
calcifiers do calcify in the dark, the rates are much nificant depletion of bicarbonate seems highly unlikely.
slower than when the zooxanthellae are able to photo- On the other hand, the depletion of total alkalinity across
synthesize (Figure 10.5). calcifying reefs has been determined and has been used
Thus, calcification by the described process supports as a direct measure of total calcification (see e.g. Kinsey,
photosynthesis, providing the preferred low energy 1978; Smith, 1978; Barnes and Devereaux, 1984). Alkali-
carbon substrate CO2, which is in very short supply nity depletion (principally as bicarbonate and carbonate)
under typical reef conditions of pH. Photosynthesis, in in closed or semiclosed systems thus can be an issue in
turn, supports calcification, locally removing the acidi- depressing stony coral calcification, as we discuss in
fying CO2 conditions that would soon greatly slow cal- some depth below.
cification. Thus, the symbiosis between the animal part
of the coral and the zooxanthellae is far more than just
an exchange of nutrients and CO2 for sugars; it is likely CALCIFICATION, STONY CORALS, CORAL
a key to the rapid calcification that is the dominating REEFS, AND GLOBAL WARMING
factor of life for many corals. Almost certainly species of
different genera utilize these elements in a variety of Considerable discussion has centered around the
ways (see Chapter 19). growth of stony corals in reef aquaria. Much of it,
More recent work on dissolved inorganic carbon uti- unfortunately, is unrelated to the reality of calcium car-
lization by stony corals (Al-Moghrabi et al., 1996; Goiran bonate construction in wild ecosystems. While there is
et al., 1996) generally supports the model described certainly some value in centering attention on the tip
above. While these articles demonstrate that under rate of extension of scleractinian corals in culture sys-
some conditions coral zooxanthellae can also directly tems (Chapter 24), and we discuss these matters below
uptake HCO3 (rather than CO2), and this is likely true and in Chapter 20, the principal purpose of this book
for algae in general (see Chapter 8), the overriding rule is to develop the parameters for the creation of model
is that most corals, as well as all organisms, do not reefs and other ecosystems. Thus, some discussion of
live in a laboratory flask; they live in a highly competi- the larger-scale process, that is, bioherm or coral reef
tive world where efficiency matters. It may well be that formation, in general, is necessary.
Calcification, Stony Corals, Coral Reefs, and Global Warming 149
TABLE 10.2 Net Calcification Rates for Various Coral Reef Communities
Location Biotopes or communities Rate (kg CaCO3/m2/year)
Houtman Abrolhos Island Coral bank 12
Johnston Atoll Back reef, heavy coral 9.6
Central Kaneohe Bay Coral zone 8.8
Rangiroa Atoll Encrusting coralline pavement 7.5
Johnston Atoll Lagoon, heavy coral cover 6.4
One Tree Island Reef flat, coral zone 4.6
Johnston Atoll Coral/algal pavement 4.4
One Tree Island Algal pavement 4.0
Enewetak Atoll Reef flat, coral/algal community 4
Enewetak Atoll Reef flat, algal turf 4
Lizard Island Lagoon reef flat 3.1
Lizard Island Seaward reef flat 2.7
Kaneohe Bay Coral/algal ocean reef 2.6
Enewetak Atoll Windward fore reef 1–2
Tulear Barrier Reef Coral/algal reef flat 1.9
Johnston Atoll Lagoon, reticulated reefs 1.5
One Tree Island Reef flat, sand/rubble 0.4
Note. All results obtained by alkalinity depression. Modified from Pichon (1996).
There are many kinds of tropical, calcium carbonate Some very rapidly growing branching species (Acropora
reef structures or bioherms (Adey, 1978). Some are spp.) range up to almost 19 mm/month of tip extension,
created primarily by calcifying algae (algal ridges, although the average rate is closer to 10–11 mm/month.
corallines, atolls, Halimeda). Even nonalgal bioherms, If these values are placed in the context of branch cross
mostly coral reefs, are not areally or physiologically section, this would be the equivalent of about 0.1 mean
dominated by stony corals (Adey and Steneck, 1985; (0.2 max) mm/month, less than the rate of accretion of
Kinsey, 1992). Stony corals play an important role in the massive species, 0.8 mean (1.6 max) mm/month. If
the construction of many reefs by forming an arago- an entire reef surface were to be made of coral growing
nitic framework, the interstices of which are then filled at the known mean rates, yearly accretion would be less
by the activities of other calcifying organisms. As we than 1.0 mm/year. Thus, stony coral accretion could
mentioned above, Halimeda (a green alga) is probably nearly account for whole reef calcification, but since
the most important bulk calcifier in reefs worldwide, stony corals account for only about 20% of reef surfaces
although coralline red algae, other calcifying greens, (Adey, 1998; Kinsey, 1992) then numerous other calci-
molluscs, foraminifera, and numerous other inverte- fiers must be producing infill carbonate at about the
brate groups are significant contributors. same rate as the stony corals.
Extensive investigations of average calcification As we discuss at some length in Chapter 20, species
rates in coral reefs in the Indo-Pacific (based on alka- diversity per unit area is higher in coral reefs in general
linity depletion) have shown that while calcium car- than in any other biological community on Earth
bonate accretion rates at reef surfaces can range up to (including rain forests). A major factor in this diversity
12 kg/m2/year in some isolated reef segments, mean is the spatial heterogeneity or surface complexity cre-
rates for whole reefs are closer to 1.5 kg/m2/year ated primarily by branching stony corals. Thus, while
(Table 10.2). This amounts to a mean whole reef accre- corals cannot be responsible for more than about
tion rate of less than 1 mm/year, with a maximum local 20–30% of total reef calcification (and primary produc-
rate of about 7 mm/year. Yet, in the Caribbean, rates of tion, see Chapters 5 and 20), they are primarily respon-
reef accretion over the past 5000 years as documented sible for the framework and multiplicity of surfaces
by extensive drilling have exceeded 10 mm/year that give rise to high diversity.
(Adey, 1978; MacIntyre, 1988). The latter situations As is clear from the above discussion of the calcium
were so-called bank barrier reefs with extensive carbonate deposition process, and that in Chapter 8,
Acropora frameworks, but in situations where currents concerning CO2 and pH, there is a strong link between
probably were able to maximize the framework infill calcification and pH. The calcification process in part
from broader carbonate banks. results from CO2 removal and pH elevation. While, in
The growth rates of coral surfaces and branches general, calcification is driven by photosynthetic activ-
(Table 10.3) provide an entirely different perspective. ity and energy-driven ion pumping, these processes
150 10. Biomineralization and Calcification
TABLE 10.3 Growth Rates of Scleractinian Corals in Coral Reef Communities
Species Location Growth rate (cm/year) Method
Porites lobata Great Barrier Reef 0.4–0.9 X-radiography
Porites lutea Enewetak 1.35 X-radiography
Porites lutea Enewetak 0.3–1.2 X-radiography
Porites lutea Enewetak 0.9–1.2 X-radiography
Favia speciosa Enewetak 0.5 X-radiography
Favia speciosa Moreton Bay 0.6 X-radiography
Favites flexuosa Bikini 0.8 X-radiography
Montastrea annularis Barbados 1.9 Real time
Montastrea annularis Jamaica 0.2–0.7 Real time (alizarin)
Montastrea annularis St. Croix 0.7–0.9 Real time (alizarin)
Montastrea annularis Florida 0.9–1.3 Real time (alizarin)
Montastrea annularis Florida 1.7 X-radiography
Pocillopora damicornis Hawaii 0.9–1.5 Real time (alizarin)
Pocillopora damicornis Panama 3.9 Real time (alizarin)
Pocillopora damicornis Samoa 2.3 Real time
Pocillopora damicornis Great Barrier Reef 2.5 Real time
Acropora palmata Curacao 8.8 Real time
Acropora palmata St. Croix 5.9–10.1 Real time (alizarin)
Acropora cervicornis Barbados 14.4 Real time
Acropora cervicornis Barbados and St. Croix 10.0 Real time
Acropora pulchra Philippines 18.1 Real time
Acropora pulchra Carolines 22.6 Real time
Acropora formosa Samoa 18.5 Real time
Acropora formosa Great Barrier Reef 8.0–16.6 Real time
Acropora formosa Phuket 8.5 Real time
Note. Modified from Pichon (1996).
effectively work against a pH gradient. The human CALCIFICATION IN MESOCOSMS
release of CO2 into the atmosphere is resulting in global AND AQUARIA
warming, which in itself is a danger to coral reefs.
However, 30–50% of this released CO2 is going into the Unless a specific and massive export mechanism is
ocean and has resulted in an average reduction of present in a semiclosed aquatic mesocosm or aquarium
oceanic pH by 0.1 units. This may be very small, but if used to simulate a wild ecosystem, it is unlikely that
CO2 release continues, by the end of the century it is any biomineralization, except for calcium carbonate,
likely to be on the order of 0.4 units (Kleypas et al., will be limited by lack of the necessary ions. In Chapter
1999; Tedesco et al., 2005). This will certainly reduce cal- 9, we briefly discussed a case where diatoms were rou-
cification in the oceans in general and cause significant tinely harvested and removed from the glass walls of a
changes in community structure, especially in those large reef microcosm for many years. Eventually, silicon
parts of the open ocean where coccolithophores are dom- depletion resulted. However, this is the exception that
inant. However, in coral reefs, where community exis- proves the rule. Even in the case of calcium carbonate
tence is connected to calcification, the results could be (or calcium phosphate), as long as an appropriate min-
disastrous indeed. As we describe in Chapter 25, using eral substrate, such as an oolite, for a reef system, or a
the techniques and understanding provided in this book, shelly sand, for a cold water rocky shore or an estuary,
major steps can be taking to help stop this process, is present, limitation by lack of the appropriate calcifi-
reverse CO2 accumulation, thus hopefully providing one cation ions for teeth, bone, or shells, in a system with a
of the key elements to restoring coral reef ecosystems reasonable community structure, has not been demon-
worldwide. However, this problem is much larger than strated. On the other hand, coral reef systems provide a
ecosystem restoration since it involves a global change in special case in which alkalinity and/or calcium limita-
the methodology of human energy acquisition. tion is not only possible but quite likely if such a system
Coral Reef Aquaria and Stony Coral Calcification 151
includes abundant coral reef calcifiers, including stony equivalent of carbonate) but little active tissue. Unlike
corals, and is performing at optimum levels. trees, coral colonies show an even starker contrast
Some authors have concluded that we do not know because they almost always show tissue die-back at the
enough about coral reef metabolism to rationally build base or sides, depending on morphology, while the tips
effective living system models (Atkinson and Falter, or upper surfaces continue to grow.
2003). Surely we have much to learn about calcification For any given coral colony, if it is “growing” well,
in coral reefs, especially with regard to variation among that is, adding carbonate, survival against continual pre-
species and between reefs. However, as we shall describe dation and competition with other corals, colonial inver-
below, and in greater depth in Chapter 20, the knowl- tebrates, and algae is greatly enhanced. As described
edge of coral reef calcification accumulated, especially in by Luckett et al. (1996), growth rates of Porites and
the last 20 years, allows us to achieve a truly remarkable Dichocoenia in the model system under discussion were
veracity in closed system modeling of coral reefs. typically 1–2 mm/month, appreciable but not maximal.
Other genera remained healthy for the entire period of
time, but did not grow significantly (e.g. Diploria spp.).
CORAL REEF AQUARIA AND STONY Species of a few genera (e.g. Mussa sp.) slowly shrank
CORAL CALCIFICATION and eventually died.
During the period under discussion, calcium concen-
The authors have operated a 130-gallon coral reef tration in the 130-gallon coral reef microcosm remained
ecosystem for 10 years with a diverse assemblage of at a mean level of 380–390 mg/liter. On the other hand,
stony corals, calcareous algae (Halimeda (Color Plate 13) as measured at the end of the period, alkalinity had
and corallines), molluscs, molting crustaceans, and cal- reduced from the normal level of 2.3–2.5 to about
cifying worms (see Chapter 20 for an extensive descrip- 1.6 meq/liter. During the 9th year, the concentration of
tion). For the first 8 of that 10 years, other than the calcium in the system was kept at about 420 mg/liter
presence of an oolite (aragonitic) sand in the base of the using kalkwasser. No effort was made to adjust alkalinity.
system, a small organic throughput (passed through to During the 10th year, the effects of maintaining cal-
harvested algal turf) and a less than 5% per month cium concentration at about 7% over normal at 450 mg/
water change (to avoid salt drift), no specific calcium or liter were examined (using the neutralized supernatant
alkalinity additions were made. Corallines and Halimeda of acidified oolite), and alkalinity was experimentally
grew abundantly in this system. Also, throughout this maintained at 2.6 meq/liter using potassium or sodium
8-year period, several genera of stony corals reproduced bicarbonate. Additional coral colonies of Indo-Pacific
sexually, a Tridacna clam introduced in the 2nd year Acropora and Montipora, mounted on plastic cups, were
grew from about 5 cm in length to nearly 30 cm, and a added to the system to provide a comparison with infor-
rare reef lobster, introduced early in the 2nd year, con- mation from Pacific reefs. As shown in Figure 10.6,
tinued to molt regularly. None of this activity suggests growth rates were considerably higher than those found
any significant limitation for calcium, carbonate, or in earlier studies.
phosphate ions. Over many months, total calcification rates of this
As described by Small and Adey (2001), the stony reef community, based on both calcium and bicarbon-
corals in this microcosm had a pattern of growth that ate removal (which are approximately equal), ranged
was apparently limiting for some species and genera from 5 to 7 kg/m2/year of calcium carbonate. This is
and not for others (Color Plates 2, 13–15, and 18). considerably higher than the mean rate for Indo-Pacific
Clearly, stony coral survival, whether in the wild or in reefs of 1.2 kg CaCO3/m2/year noted above and falls
a model, is dependent in part on the balancing of pre- within the range of about the upper 2% of tabulated
dation and other damage against growth. A rapidly reef surfaces (Pichon, 1996). Thus, this reef microcosm
growing individual coral colony may or may not add is operating on the high side for calcification. This is
significant biomass over time. It is clear that in a wild not due to the elevated calcium and bicarbonate con-
reef as a whole, unless it is a very young reef or one centrations, as demonstrated by Small and Adey (2001).
recovering from significant damage, such as a hurri- Only part of this total system calcification is due to
cane, continuous addition of biomass cannot occur. corals, Halimeda, and coralline algal and molluscs also
Thus, while “growth” over time occurs as calcification, being present (Color Plates 12, 18, 19, and 22). However,
equivalent biomass increase cannot occur. In some ways the stony corals occupy 15–20% of the surface of this
many forest trees are similar. After reaching maturity model reef, about average for wild systems. When
only a small amount of active photosynthesizing, repro- individual coral colonies are separated into closed
ductive, or transport tissue is added. For the majority chambers for short periods their uptake rates are such
of its life, the tree adds major biomass as cellulose (the as to provide for the total level of calcification in the
152 10. Biomineralization and Calcification
principle, no ecosystem stands alone. Matching inputs
with exports is a key to operating microcosms and
mesocosms of those ecosystems. In this case, input of
alkalinity as sodium or potassium bicarbonate matches
that input in the wild ecosystem.
In a coral reef microcosm or mesocosm with moder-
ate stony coral coverage and minimum predation, cal-
cium depletion can be prevented by the daily addition
of fresh oolitic (aragonitic) sand. Where extensive cov-
erage of calcifiers, including stony corals, and/or exces-
sive coral predation is present, or if rapid growth rates
are desired, oolitic sand can be dissolved with reagent-
grade hydrochloric acid (HCl), to provide a calcium-
rich additive. The supernatant of this process should
be allowed to nearly neutralize (pH 6.5–6.7) with excess
oolite, and should have a concentration of about
30 000 mg/liter. Sufficient supernatant can be added
daily to a model system to balance out the calcification
that is occurring. This process is equivalent to open ocean
input in the wild, where coral colonies remove calcium
from overflowing waters to build their structures.
FIGURE 10.6 Growth of the stony coral Porites astreoides in the The same basic process applies to alkalinity. Wild reefs
130-gallon reef system from the time of its larval settlement in late are scrubbers of carbonate from overflowing ocean
1992 or early 1993 until present. Note that this coral has a head mor-
waters, as many studies have shown. The addition of
phology, typically being hemispherical at maturity; thus, mean
diameter represents only a small part of total calcification. Prior to bicarbonate provides a process that is close to that work-
mid-1994, growth was moderate based on only aragonite addition ing in wild reefs. Unfortunately, that addition must
and resulting in slightly depressed calcium concentrations (see text). come with a cation. Either sodium or potassium bicar-
The addition of trace elements and Ca(OH)2 apparently gradually bonate will suffice, but the sodium will have less long-
caused a reduction in growth rate, perhaps due to elevated strontium
term effect on the water chemistry. The combination of
levels (to 14 mg/liter) and interference with calcification. The remo-
val of all trace element additions and the management of calcium HCl/oolite and NaHCO3 that we have described will
and total alkalinity approximately 5–15% above seawater concentra- add excess sodium chloride to a system. Since these are
tions greatly increased growth rate. the most abundant ions in sea water, the effects are likely
minimal. For a typical microcosm or mesocosm, water-
exchange rates of about 12% per month will keep NaCl
entire system at 100% coverage (Color Plates 13–15). concentration at less than 10% over normal. This
This is very much in agreement with the information exchange rate will prevent the drift of conservative salts
presented above and from many sources for wild reefs. due to evaporative losses (see Chapter 4). An appropri-
If pieces of reef carbonate with their typical surface ately designed sea salt mix could greatly reduce the
coverage of algal turf are placed in a similar closed magnitude of exchange water required.
chamber, significant alkalinity depletion (and therefore Recent research (Small and Adey, 2001) using the
calcification) occurs. This is not of the magnitude of 130-gallon aquarium microcosm described in detail in
stony corals or Halimeda (it is about 50% of whole sys- Chapter 20, has shown the McConnaughey (1995) model
tem levels), but it is certainly significant. While some of of bicarbonate uptake and calcification by stony corals
this background calcification is due to small inverte- to be correct. Thus, removal of the CO2 produced by
brates and corallines, much of it results from precipita- coral calcification is critical to efficient continued calci-
tion in small cavities (micritization), due to removal of fication. That same research has shown that, at least in
CO2 by the highly productive algal turf. the fastest of reef calcifiers (Acropora), colony zooxan-
A purist aquarist operating a coral microcosm as a thellae are unable to keep up with CO2 production and
closed system might be concerned about the “artificial” that the presence of enough free-living algae to raise
need to add alkalinity as bicarbonate. However, in a pH to the typical daytime levels of reef ecosystems
wild reef this alkalinity is “sucked out” of overflowing increases coral calcification by over 60% (Figure 10.7).
ocean waters. Most of the alkalinity is emplaced in those Thus, the optimally calcifying coral reef ecosystem is one
ocean waters far from the reef in localized deep anaero- in which algae occupy 50–75% of the surface. Similarly,
bic waters (such as the Black Sea). To repeat a general with at least 25% of the surface occupied by calcifying
Coral Reef Aquaria and Stony Coral Calcification 153
FIGURE 10.7 The effects of free-living, independent algae on coral calcification as indicated by pH, oxygen, and
alkalinity depletion in test chamber subsets of a coral reef microcosm. (A, B) The corals alone have little effect on pH
during a day run showing the compensation of calcification for photosynthesis, while coral and Chondria (free-living)
and Chondria alone rapidly elevate pH; (C, D) Photosynthesis, as demonstrated by O2 release, occurs in all combina-
tions, but is minimal in coral-alone runs; (E, F) Chondria alone does not show alkalinity depletion (thus no calcifica-
tion); coral samples alone show alkalinity depletion (thus calcification); the combination of corals and free-living,
noncalcifying algae provides maximum alkalinity depletion and thus calcification. From Small and Adey (2001).
154 10. Biomineralization and Calcification
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Marine Systems. K. Black, and G. Shimmield (Eds). Blackwell
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on a coral reef; a survey using pH and oxygen electrode tech-
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C H A P T E R
Control of the Biochemical Environment
Filters, Bacteria, and the Algal Turf Scrubber
As a beginning to the modeling and restoring of drugs, and recreation, when disruption of adjacent
aquatic ecosystems, in the first set of chapters in this wild environments (or human environments) will
book, we have introduced the role of physical/chemical result from the organism concentration that culture
factors “allowing” life to develop, and in circumscribing requires.
the biosphere and its ecosystems. We have also repeat- The larger human issue of disruption of environments
edly emphasized that organism metabolism, since the by the concentration of people is different mostly as a
dawn of life, has radically altered the Earth’s chemical matter of scale. In concentrating a human population in a
and physical environment. The biosphere today is quite city, and then delivering a steady stream of food with its
stable, as compared to that in the early eons following nutrients to that city, the local stream or river becomes
the origin of life, and no doubt in the eras following the sink, usually with disastrous consequences. The
major meteorite or comet impacts. Nevertheless, many “nutrient” carbon is a little different in that it goes into
species have the potential to quickly develop population the atmosphere as CO2 (even if a sewage plant is added
explosions, significantly disrupting their environments, to the loop). As we discussed in Chapter 8, excess CO2 in
even to the extent of multiple population crashes and water environments drives down pH and can be a sig-
ecosystem death. The balance of nature generally refers nificant negative factor for many species. However, as
to limits placed on population explosion, and therefore long as it was only food that we were dealing with in this
chemical disruption, by resource limitations. As we will context, carbon mattered little, it was mostly cycled
discuss in later chapters, the balance can also be in food through the atmosphere to plants and algae outside the
webs. In the ecosystem context, the nutrients (N, P, C, Fe, city and in the oceans. However, once the carbon began
etc.) that provide that limitation have long ago been to be released en masse from geologically stored hydro-
locked up, in the Earth or the deep ocean, providing a carbons, to provide additional energy (beyond food
natural brake, albeit with fluctuations. In modeling and energy) for human heat and transportation, and this
restoring ecosystems, and in building a display aquar- release became in excess of the capabilities of the bios-
ium, we constantly deal with that basic balance between phere’s photosynthesizers to take it up and restore it, it
environmental chemistry and organic potential. began to build up in the atmosphere. This CO2 buildup
In this chapter, we entertain the question of how to is causing the Earth to retain more solar heat, with the
solve the chemical problems