DYNAMIC
AQUARIA
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DYNAMIC
  AQUARIA
BUILDING AND RESTORING LIVING
         ECOSYSTEMS

                     Third Edition

                 ...
Academic Press is an imprint of Elsevier
84 Theobald’s Road, London WC1X 8RR, UK
30 Corporate Drive, Suite 400, Burlington...
Contents




Preface  xi
Acknowledgments and Dedication         xv


                    C H A P T E R


                 ...
vi                                              Contents


                    C H A P T E R                              ...
Contents                                              vii

                   C H A P T E R                      Food Webs...
viii                                                 Contents


                    C H A P T E R                         ...
Contents                                               ix

                   C H A P T E R                        Nutrien...
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Preface


By the mid-20th century, widespread concerns were being               top priority of all human society. It seem...
xii                                                      Preface


our relationship to our biosphere. As we explain in thi...
Preface                                                    xiii

very few large public aquaria built during the past 20   ...
xiv                                                       Preface


   In Part II, on the biochemical environment, we dis-...
Acknowledgments and Dedication

It has been nearly 30 years since we initiated the develop-        have been many and thei...
xvi                                        Acknowledgments and Dedication


ongoing, stimulating interchanges and discussi...
C H A P T E R



                                                                 1

                                     ...
2                                                        1. Introduction


   We start our discussion by demonstrating tha...
The Origin of Life: Microcosm Earth                                                 3




          FIGURE 1.1 Relative ab...
4                                                            1. Introduction


                  TABLE 1.1 Biomonomers, Bi...
Microcosms and Mesocosms of Aquatic Ecosystems                                      5

    Such RNA in the ammonia, carbon...
6                                                       1. Introduction


“controlled ecologies” was reviewed by Adey (198...
Microcosms and Mesocosms of Aquatic Ecosystems                                      7

resources including carbon and nutr...
8                                                      1. Introduction


relevant in the real world, where efficiency coun...
References                                                                   9




               FIGURE 1.2 Family tree o...
10                                                                    1. Introduction


Hendal, J. (2006) Advanced Marine ...
P A R T



          I
PHYSICAL ENVIRONMENT
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  1. 1. DYNAMIC AQUARIA
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  3. 3. DYNAMIC AQUARIA BUILDING AND RESTORING LIVING ECOSYSTEMS Third Edition Walter H. Adey Karen Loveland National Museum of Natural History Smithsonian Institution Washington, D.C. AMSTERDAM • BOSTON • HEIDELBERG • LONDON • NEW YORK • OXFORD PARIS • SAN DIEGO • SAN FRANCISCO • SINGAPORE • SYDNEY • TOKYO Academic Press is an imprint of Elsevier
  4. 4. Academic Press is an imprint of Elsevier 84 Theobald’s Road, London WC1X 8RR, UK 30 Corporate Drive, Suite 400, Burlington, MA 01803, USA 525 B Street, Suite 1900, San Diego, California 92101-4495, USA First edition 1991 Second edition 1998 Third edition 2007 Copyright © 2007 Walter H. Adey and Karen Loveland. Published by Elsevier Inc. All rights reserved The right of Walter H. Adey and Karen Loveland to be identified as the authors of this work has been asserted in accordance with the Copyright, Designs and Patents Act 1988 No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means electronic, mechanical, photocopying, recording or otherwise, without the prior written permission of the publisher Permissions may be sought directly from Elsevier’s Science and Technology Rights Department in Oxford, UK; phone: (+44) (0) 1865 843830; fax: (+44) (0) 1865 853333; e-mail: permissions@elsevier.co.uk. You may also complete your request on-line via the Elsevier homepage (http://www.elsevier.com), by selecting “Customer Support” and then “Obtaining Permissions” British Library Cataloguing in Publication Data A catalogue record for this book is available from the British Library Library of Congress Cataloging in Publication Data A catalog record for this title is available from the Library of Congress ISBN-13: 978-0-12-370641-6 ISBN-10: 0-12-370641-6 For information on all Academic Press publications visit our web site at http://books.elsevier.com Typeset in 10/12pt Palatino by Charon Tec Ltd (A Macmillan Company), Chennai, India www.charontec.com Printed and bound in the USA 07 08 09 10 11 10 9 8 7 6 5 4 3 2 1
  5. 5. Contents Preface xi Acknowledgments and Dedication xv C H A P T E R 1 C H A P T E R Introduction 3 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 Ecosystems 50 Sediments and Model Ecosystems 51 P A R T Geological Storage 59 References 60 I PHYSICAL ENVIRONMENT C H A P T E R 4 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 v
  6. 6. vi Contents C H A P T E R C H A P T E R 5 8 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 Ecosystems 125 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 II 10 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
  7. 7. Contents vii 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 Denitrification 157 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 Ecosystems 165 Submerged Aquatic Vegetation 222 Summary 168 Marine SAV and Model Ecosystems 229 References 169 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 References 251 BIOLOGICAL STRUCTURE C H A P T E R C H A P T E R 12 15 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 Herbivores 257 The Magnitude of Biodiversity 183 Herbivores and Model Ecosystems 263 Community Structure and Ecological Models 186 References 265 Scaling and Reproduction 186 Model Diversity 187 Summary 189 References 189 C H A P T E R 16 C H A P T E R Carnivores: Predators of Animals 13 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
  8. 8. viii Contents C H A P T E R P A R T 17 IV Plankton and Planktivores: Floating Plants ECOLOGICAL SYSTEMS IN and Animals and Their Predators MICROCOSMS, MESOCOSMS, AND AQUARIA 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 References 302 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 References 368 The Deep Ocean 307 Bacteria 307 Fungi 307 C H A P T E R Protozoa 309 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 Aquaria 335 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
  9. 9. Contents ix 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 References 452 P A R T P A R T VI V SUMMARY THE ENVIRONMENT AND ECOLOGICAL ENGINEERING C H A P T E R 26 C H A P T E R Microcosms, Mesocosms, and Macrocosms: 24 Building and Restoring Ecosystems, a Synthesis 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 References 463 C H A P T E R Index 501 25 Large Scale: Water Quality Management with Solar Energy Capture The Quality of US Surface and Ground Waters 467 Nutrient Removal from Domestic Wastewaters 468
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  11. 11. Preface 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 xi
  12. 12. xii Preface 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,
  13. 13. Preface xiii 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.
  14. 14. xiv Preface 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.
  15. 15. 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 xv
  16. 16. 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.
  17. 17. C H A P T E R 1 Introduction 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. 1
  18. 18. 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
  19. 19. 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.
  20. 20. 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).
  21. 21. 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
  22. 22. 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
  23. 23. 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
  24. 24. 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. SUMMARY 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.
  25. 25. References 9 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. References 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.
  26. 26. 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
  27. 27. P A R T I PHYSICAL ENVIRONMENT
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