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Aquatic microbiology

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

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Aquatic microbiology

  1. 1. AQUATIC MICROBIOLOGY H.G.D.A.P. Jayasinghe – BSc. (undergraduate) Department of Microbiology University of Kelaniya, Sri Lanka
  2. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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
  22. 22. 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
  23. 23. • 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.
  24. 24. 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…!!!
  25. 25. 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
  26. 26. 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
  27. 27. 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
  28. 28. • 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
  29. 29. 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
  30. 30. 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)
  31. 31. 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???
  32. 32. 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
  33. 33. 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??
  34. 34. 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.
  35. 35. • 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
  36. 36. Microbial Loop: Importance
  37. 37. 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
  38. 38. • 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
  39. 39. • 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
  40. 40. • 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
  41. 41. 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
  42. 42. • 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
  43. 43. • 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
  44. 44. Life cycle of a biofilm • Biofilm lifecycle can be summarized in to three important steps; 1. Attachment 2. Growth and development 3. Detachment
  45. 45. 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
  46. 46. • 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
  47. 47. • 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
  48. 48. 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
  49. 49. • 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