Fringing zone- areas that are subjected to irregular water covers Pelagic zone – the main water body Benthic zone – bottom sediments and rocks
Littoral zone is also home for a greater variety of consumers. Zooplanktons are rather characteristic and defers from other two zones in preponderance of less buoyant crustacea which often cling to plants or rest on the bottom when not actively moving (using there appendages)
H.G.D.A.P. Jayasinghe – BSc. (undergraduate)
Department of Microbiology
University of Kelaniya, Sri Lanka
What is aquatic microbiology?
• Is the science that deals with microscopic living organisms in fresh or salt
• Aquatic environments are considered as microbial habitats.
• Fresh water habitats
• Salt water/marine habitats
• Estuarine habitats
Fresh water microbial habitats
• Natural or man-made habitats that are permanently or periodically under water
• Two types
• Lentic environments - contains still water. (i.e. lakes, wet lands etc.)
• Lotic environments - contains flowing water (i.e. rivers, streams etc.)
• Both types can be divided in to three basic zones
• Fringing zone
• Pelagic zone
• Benthic zone
• Uppermost layer / surface microlayer of the hydrosphere
• Is the interface between the atmosphere and the hydrosphere
• An extreme environment
• Many adverse factors (i.e. exposure to radiation, temperature fluctuations) can occur
• Insoluble and less dense organic material accumulates in this layer and as a
result, is aligned with non-polar organic materials
• Therefore, is a thin gel-like structure where microbes can live
• Aquatic ecosystems in which;
• Water is still and not rapidly moving
• Some lakes have irregular mixing cycles and known as poly-mixing and;
some are mixed all around the year and known as homo-mixing
• Can be divided in to different zones based on;
• Light penetration
• Water density etc.
Zonation based on Light Penetration
• Based on light penetration, there are three basic zones or more accurately, sub-
habitats in lentic waters.
• Littoral zone
• Limnetic zone
• Pro-fundal zone
• None of the above three zones should essentially exist in all lentic waters
• A small pond may contain littoral zone only
• In contrast, a deep lake with abruptly sloping lake basin, may contain an extremely reducd
• Adjoins the shore
• Thus, is the home of rooted aquatic plants
• Extends down to the light compensation level
• Producers are of two main types
• Rooted or benthic plants
• Phytoplankton or floating green plants (algae)
• Contains all the waters beyond the littoral zone and down the light
• Derives its oxygen content from;
• Photosynthetic activity of phytoplankton
• The atmosphere immediately over lake surface
• Biotic components of limnetic zone includes;
• Plankton, nekton, and sometimes, Neuston
• The bottom and deep water area of the lake
• Beyond the depth of effective light penetration
• Warmest water in the winter (near 4 Celsius) and coldest water in the summer. (that is in
north-temperate latitudes of course. Not here…)
• Life in Profundal zone!! How would it be like??
• Life in the Profundal zone are adapted to withstand long low oxygen periods.
• Many of the bacteria are anaerobic.
• Many of them constantly perform anaerobic decomposition of organic matter that
accumulates in the bottom, may it be plant debris, animal excreta or remains.
• By the action of biological processes take place here, bottom organic sediments are
re-mineralized and nitrogen and phosphorous are put back to circulation as soluble
• Hence, this zone provides rejuvenated nutrients and such nutrients are carried by
swimming animals or water currents to other zones.
• Is the ecological region at the lowest level of a body of water
• Sediment surface and some sub-surface layers
• Benthic zone inhabitants (Benthos) include;
• Bacteria, of which mostly anaerobic decomposers
• Benthic invertebrates (i.e. crustaceans, polychaetes etc.)
• Separation of water bodies in to layers
• Takes place when a stable density differences are generated.
• May be due to;
• Surface heating with the establishment of a thermocline
• Differences in salt concentration of participating waters with the establishment of a
• Is this good??
Well, such stratifications, be it
a thermal or salinity, provides a
barrier to nutrient circulation.
So, could it be good in any
means?? I will stick to “NO”!!
• Is the existence of turbulently mixed layer of warm water (Epilimnion)
overlying a colder mass of relatively stagnant water (Hypolimnion) in a water
body with the establishment of a thermocline due to cold water being more
denser than warm water.
• Depends on;
• Shape and depth of the lake
• Amount of wind
• Orientation of the lake
• if the thermocline is located deep enough,
• Wind-induced turbulence may not be sufficient to penetrate it
• Hence, lower water mass will be stagnant and deoxygenated
• Mixing between productive surface (area where nutrient fixing occur) and bottom
(area where re-mineralization occur) will be reduced.
• If the thermocline persists for long enough,
• Upon depletion of oxygen, electron donors will be nitrates at first and then sulfates.
• What problems would it cause??
• Life below thermocline?? Any idea???
• Upper, warmer, and wind-mixed layer of a thermally stratified lake
• Water is turbulently mixed (at least for some portion of the day)
• Can freely exchange gasses with the atmosphere due to its exposure
• Mineral nutrients gradually depletes….
Due to rapid
• Bottom, most dense layer with colder and deep water of a thermally
• Not affected by wind-mixing
• Too dark for oxygenic plant photosynthesis to occur. Hence, anaerobic
• But still, bacterial photosynthesis can occur…
• Boundary between Epilimnion and Hypolimnion
• Temperature change for a unit depth (temperature gradient) is most rapid
• Establishment of a thermocline is arbitrary when thermal stratification
Ageing of lakes
• Lakes do grow old…
• It’s a simultaneous process
• Occurs along its trophic levels; which depends on nutrient level, depth and biological
composition of the lake.
• We can speed this up by allowing nutrients to accumulate in lakes..
• Nutrients from agriculture, fertilizers, streets, sewage and storm drains.
• That is for our own disadvantage though..
Trophic states of lakes
• Trophic state of a lake is an indication of its biological productivity
• That is, in other words, is an indication of the amount of living material
supported within them
• Trophic state of a lake is affected by;
• Rate of nutrient supply
• Shape of the lake basin or morphometry
• Contains clear, deep waters
• Clean and pristine lakes with very low primary production
• Food chains are very structured
• Are even capable of sustaining large game fish…
• Very high water clarity readings and very low chlorophyll and
• And of course, are aesthetically pleasing…..
Clear and cold blue water..
No weeds to disturb… clean
and pristine lake.. Who
doesn’t want to bath…
• Generally, these oligotrophic environments are free of weeds and large algal
• Rate of decomposition is much higher than rate of primary production
• Due to rapid decomposition, is low in dissolved organic material and also, low in
inorganic nutrients, especially nitrogen and phosphorus compounds
• Inhabitant microbes are called Oligotrophs or Oligotrophic microorganisms
• These have very low nutrient requirements and hence, can grow in low nutrient
• Most productive. Support a very large biomass
• Normally weedy. Subjected to frequent algal blooms
• Large amounts of bottom-accumulated organic matter
• Very low levels of dissolved oxygen. Highly stratified waters
• Susceptible for oxygen depletion in Hypolimnion
• Supports a large fish population
• Low water clarity readings, high chlorophyll and phosphorous readings
• Due to developing anaerobic
conditions in deeper waters;
• Aerobic waste digestion and water
• Water quality decreases gradually
• Anaerobic decomposition of aquatic
sludge will emanate gases with
• Oxygen depletion may lead to fish
death and winter kill situations
• Eutrophication may be either
natural or artificial.
• Are in the boundary between oligotrophic and eutrophic lakes
• Have more nutrients and production than oligotrophic lakes but not as much
as eutrophic lakes
• Moderate water clarity, chlorophyll and phosphorous readings
• Some accumulated organic matter on bottom and occasional algal bloom at
• Able to support a wide variety of fish.. Good for fishing…!!!
Adverse effects of nutrient pollution of lakes
• Aesthetics are destroyed
• Recreational values are destroyed
• Water quality is impaired by foul tastes and odors
• Gases that are emanate by rotting algae have foul odors
• Toxins from rotting algae cause gastric problems
• Decomposing algae at bottom give high BOD load
• Rooted weeds interfere with recreation
• Lake basins are gradually filled
Fresh water microbial communities
• Depending on composition, organization and functioning as communities,
fresh water microbial communities can be divided as follows;
• Planktonic community
• Sediment community
• Microbial mats
• Organisms that have little or no control over where they go – Plankton
• Plankton are not essentially needed to be microscopic. But mostly, they are..
• Fish are not plankton, they are nekton. Why???
• Plankton can be;
• Plant-type - Phytoplankton
• Bacteria-type - Bacterio-plankton
• Animal-type - Zooplankton
• Zoo plankton can be divided in to;
Permanente zoo plankton
Temporary zoo plankton (Example: Barnacle larvae: nauplii)
• Temporary zoo plankton are rare in fresh water ecosystems
Phytoplankton and Primary production
• Are producers and base of many food webs
• Are very productive
• The principle component is the diatom, a form of single celled alga
• These diatoms have diurnal rhythm in a water column
• And can quickly reproduce and are highly productive
Phytoplanktonic primary production
• Many phytoplankton are single-celled algae.
• Fix dissolved carbon dioxide and produce various organic compounds
• Primary production is dependent upon;
• Availability of essential nutrients
• Water temperature
• pH of the water
• Organic matter produced can be divided as;
• Particulate Organic Matter (POM)
• Dissolved Organic Matter (DOM)
• Principle component of phytoplankton community
• A form of single-celled algae with an outer wall made out of silica
• Have a diurnal rhythm in water columns
• At nights, sink to lower levels
• At day moves to upper levels to obtain solar energy
Phytoplanktonic primary production Cont..
• In marine environments, primary production is….
Very low… Due to lack of essential mineral nutrients
• In aquatic environments,
It is higher due to ample resources
• All dead organic matter distinguishable from living matter
• POM is about 10%, DOM is about 90%
• Includes bodies and body fragments of dead organisms as well as excreta
and fecal material
• Settling of detritus in aquatic environments??
• Colonized by?? And what do theses inhabitants do??
• Microbial loop is a trophic pathway in aquatic environments where DOC is
re-introduced in to the food web through the incorporation in to
• A sort of a micro-scale food web
• It is a mod of pathways of carbon and nutrient cycling through microbial
components and explains how microorganisms can be integrated in to
classical food chain.
• DOC is introduced to lentic environments via;
• Bacterial lysis
• Leakage or exudation of fixed carbon from phytoplankton
• Excretion of waste products by aquatic animals
• Sloppy feeding by zoo plankton etc.
• Over 95% of this DOC is high molecular weight compounds
• Hence, not readily utilizable for aquatic organisms at higher trophic levels
• But, bacteria can utilize these DOM and increase in numbers
• Heterotrophic bacteria will breakdown HMW compounds and utilize them for energy
• As other organisms such as protozoa can feed on such bacteria, this introduces DOC in
to food web
• This results in additional energy being available for higher trophic levels
• Together with biofilms, are defined as surface associated layers of microbial cells
embedded in Extracellular Polymeric Substances (EPS)
• Microbial mats are, multi-layered sheets of microorganisms that are mainly formed
by bacteria and archaea
• Mainly grow on submerged or moist surfaces
• Few can survive in deserts
• Few are endosymbionts
• Can colonize environments at -40 to 120 Celsius
• Usually held together by slimy Matrix substances created by inhabitant
• Some inhabitants form tangled web of filaments which makes the mat
• Mats are usually vertically stratified. Aerobic zone on the top is separated
from bottom anaerobic zone by a layer of oxidized iron
• Mats can grow to few cm of thickness at most. But still, creates a several layers
of different internal chemical environments
• Each layer is composed of microorganisms of the same or closely related
species that can tolerate or feed on dominant chemicals at their level
• In each layer, dominant microbes are decided upon their comparative advantage
or the ability o out perform other microbes to live and survive in that layer
• It is dependent upon their metabolic capabilities and conditions they can tolerate
• As metabolic capabilities decided by the phylogeny, several closely related microbes can
inhabit the same layer
• However, ecological relationship between microorganisms within the same mat
is a combination of both competition and cooperation.
• Hence, different layers are divided based on their individual metabolic
contribution to the microbial community within and also by their phylogenetic
• A microbial mat generally forms its’ own food chain where;
• By-products of one group serve as ‘food’ for another group of microbes within the
• One or two groups may remain on top of the food chain as their by-products are not
utilized by others
• An aggregate of microbes in which cells that are frequently embedded within
a self-produced matrix of EPS, adhere to each other and/or to a surface.
• Biofilm EPS is a polymeric conglomeration and may contain;
• Extracellular DNA
• Found commonly on submerged solid substrates or substrates exposed to an aqueous
• On mats floating on liquid surfaces
• On surfaces of leaves in high humidity
• A biofilm may contain many different types of microbes each of which perform
specialized metabolic function within the mat
• Some species are capable of forming single-species biofilms under certain
• Social structure within a particular biofilm (i.e. interactions within organisms present
such as competition and cooperation) is highly dependent on types of organisms
• However, microbial cells growing in a biofilm are physiologically distinct
from planktonic cells of the same organism
• A biofilm may grow very quickly, from microscopic to macroscopic when
sufficient resources are available
Life cycle of a biofilm
• Biofilm lifecycle can be summarized in to three important steps;
2. Growth and development
Step 1: Attachment
• Initial attachment of a free floating microbe to a surface is reversible
• Occur using weak Van Der Waal bonds
• Secondly it attaches more permanently using;
• Cell adhesion structures like pili
• Cell adhesion molecules such as extracellular proteins
• When considered, hydrophobicity is the most important of the above three
• Hydrophobicity determines the ability of microbes to form biofilms
• Increased hydrophobicity means less repulsion between the EPS matrix and the
• Bacteria pioneers who initially attaches to the surface starts building the EPS
matrix that holds the biofilm together
• In addition to matrix substances and bacterial cells, EPS matrix may also contain
materials from environment such as minerals, soil particles etc.
• This facilitate the arrival of other biofilm bacteria by providing more
• If there are species that are unable to attach to a surface on their own, they are often
able to anchor the matrix directly to earlier colonists
• When a single bacterium joins a biofilm,
• Expression of approximately 800 genes have reported to be altered and differentially
• As a result, cell undergoes a phenotypic shift in behavior
• This impart different physiological characteristics to the joined bacterium than its
• During colonization cells within the biofilm are able to communicate via
Step 2: Growth and Development
• Growth of a biofilm occurs through a combination of
• Division of existing cells
• Recruitment of new cells
• The next sub-step; is the development of the biofilm.
• At the development state;
• Biofilm gets well established
• May only change in size and shape
• Once the biofilm has fully formed,
• It contains channels in which nutrients and also, signaling molecules involved
in Quorum sensing can circulate.
• Cells in different regions exhibit different patterns of gene expression
• As a result of above, biofilms often develop their own metabolism