Describes the microbiology of fresh water ecosystems especially lentic environments such as lakes and wetlands.

1. AQUATIC
MICROBIOLOGY
H.G.D.A.P. Jayasinghe – BSc. (undergraduate)
Department of Microbiology
University of Kelaniya, Sri Lanka

2. What is aquatic microbiology?
• Is the science that deals with microscopic living organisms in fresh or salt
water systems.
• Aquatic environments are considered as microbial habitats.
• Fresh water habitats
• Salt water/marine habitats
• Estuarine habitats

3. 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

4. Neuston layer
• 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

5. LENTIC ENVIRONMENTS
• 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.

6. 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
littoral zone.

7. Littoral zone
• 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)

8. Limnetic zone
• Contains all the waters beyond the littoral zone and down the light
compensation level.
• 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

9. Profundal zone
• The bottom and deep water area of the lake
• Beyond the depth of effective light penetration
• Contains;
• 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??

10. • 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
salts.
• Hence, this zone provides rejuvenated nutrients and such nutrients are carried by
swimming animals or water currents to other zones.
Light
compensation
level

11. Benthic zone
• Is the ecological region at the lowest level of a body of water
• Includes;
• 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.)

12. Stratifications
• 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
halocline.
• 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”!!

13. Thermal Stratification
• 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

14. • 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???

15. Epilimnion
• 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
• But…
• Mineral nutrients gradually depletes….
Due to rapid
photosynthesis
…..

16. Hypolimnion
• Bottom, most dense layer with colder and deep water of a thermally
stratified lake
• Not affected by wind-mixing
• Too dark for oxygenic plant photosynthesis to occur. Hence, anaerobic
conditions prevail
• But still, bacterial photosynthesis can occur…

17. Thermocline
• 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
occurs

18. 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..

19. 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
• Climate
• Shape of the lake basin or morphometry

20. Oligotrophic lakes
• 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
phosphorous readings
• 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…

21. • Generally, these oligotrophic environments are free of weeds and large algal
bloom
• 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
environments

23. Eutrophic lakes
• 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

24. • Due to developing anaerobic
conditions in deeper waters;
• Aerobic waste digestion and water
purification halts..
• Water quality decreases gradually
• Anaerobic decomposition of aquatic
sludge will emanate gases with
offensive odors
• Oxygen depletion may lead to fish
death and winter kill situations
• Eutrophication may be either
natural or artificial.

26. Mesotrophic lakes
• 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
the surface
• Able to support a wide variety of fish.. Good for fishing…!!!

28. 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

29. 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
• Biofilms

30. Planktonic community
• 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

31. • 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

32. 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

33. 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)

34. Diatoms
• 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
• How???

35. 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

36. Detritus
• 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??

37. Microbial Loop
• Microbial loop is a trophic pathway in aquatic environments where DOC is
re-introduced in to the food web through the incorporation in to
microorganisms
• 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.

38. • 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

39. Microbial Loop: Importance

40. Microbial Mats
• 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
• Habitats??
• Mainly grow on submerged or moist surfaces
• Few can survive in deserts
• Few are endosymbionts

41. • Can colonize environments at -40 to 120 Celsius
• Usually held together by slimy Matrix substances created by inhabitant
microbes
• Some inhabitants form tangled web of filaments which makes the mat
tougher
• Mats are usually vertically stratified. Aerobic zone on the top is separated
from bottom anaerobic zone by a layer of oxidized iron

42. • 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

43. • 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
relationships.
• 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
mat
• One or two groups may remain on top of the food chain as their by-products are not
utilized by others

44. Biofilms
• 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
• Polysaccharides
• proteins

45. • Habitats;
• Found commonly on submerged solid substrates or substrates exposed to an aqueous
solution
• 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
conditions
• Social structure within a particular biofilm (i.e. interactions within organisms present
such as competition and cooperation) is highly dependent on types of organisms
present

46. • 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

47. Life cycle of a biofilm
• Biofilm lifecycle can be summarized in to three important steps;
1. Attachment
2. Growth and development
3. Detachment

48. 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
• Hydrophobicity
• When considered, hydrophobicity is the most important of the above three

49. • Hydrophobicity determines the ability of microbes to form biofilms
• Increased hydrophobicity means less repulsion between the EPS matrix and the
bacterium
• 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
adhesion sites
• 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

50. • When a single bacterium joins a biofilm,
• Expression of approximately 800 genes have reported to be altered and differentially
regulated
• As a result, cell undergoes a phenotypic shift in behavior
• This impart different physiological characteristics to the joined bacterium than its
planktonic members
• During colonization cells within the biofilm are able to communicate via
Quorum Sensing

51. 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

52. • 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