Marine and Fresh Water
Microorganisms in Marine Ecosystems
Microorganisms in benthic marine environments
Hydrocarbon metabolism fuels microbial communities on continental margins; massive deposits of methane hydrates are found at the ocean floor below 500 meters
Microbes found not only on seafloor but to a depth of at least 0.6 km where pressures are high and the organisms must be piezophilic (barophilic)
Benthos—oceanic sediments and the seafloor including hydrothermal vents; mainly high pressure, low light, and cold (1 to 4 °C) environments
Aquatic viruses
Virioplankton are major agents of mortality in the sea, influence microbial loop, are involved in horizontal gene transfer, and influence microbial community diversity
Virioplankton are the most numerous members of marine ecosystems; counting viruslike particles (VLPs) can be challenging
Microorganisms in the open ocean
Proteorhodopsin may supplement ATP production for a variety of microorganisms in nutrient-poor waters; aerobic anoxygenic phototrophs do not fix carbon, but use light energy to generate ATP; lithoheterotrophs also do not fix carbon, but use inorganic chemicals as a source of energy
The most abundant monophyletic group of organisms is an -proteobacterial lineage called SAR11; these small bacteria have recently been isolated and have small, efficient genomes; they are responsible for about 50% of bacterial biomass production and DOM flux in some marine environments
Cyanobacteria (including Trichodesmium) are important in fixing nitrogen in the pelagic zone; some bacteria can perform the anammox reaction wherein ammonia is oxidized to nitrogen gas anaerobically below the photic zone, and lost from the seas
Organic matter found in the photic zone (upper 200–300 meters) where light penetrates falls as marine snow into lower depths; much of the marine snow is not easily degraded; it is colonized by microbes that consume it, such that only about 1% reaches the seafloor; the collection of organic matter on the seafloor is important in moderating the effects of global warming; the addition of iron may increase draw down of carbon dioxide in high-nutrient low-chlorophyll (HNLC) ocean areas
The open ocean regions (pelagic) account for half of the world's photosynthesis; it is an oligotrophic environment (very low nutrient levels) that supports a diverse microbial community
Winogradsky columns can be used to model salt marshes and illustrate the interactions and gradients that occur in aquatic environments
At the top are oxygenic photosynthetic organisms such as diatoms and cyanobacteria
Further up in the column, chemolithotrophic and mixotrophic organisms may use hydrogen sulfide as an energy source and oxygen as the electron acceptor
Sulfide diffuses upward, creating an anaerobic, sulfide-rich zone where anoxygenic photosynthetic bacteria reside
Other anaerobic microorganisms use the fermentation products to carry out anaerobic respiration using sulfate as the electron acceptor and producing sulfide
In the bottom, anaerobic conditions foster the activity of fermentative microorganisms, which leads to the accumulation of fermentation products
Made by mixing together mud, water, and sources of nutrients (e.g., cellulose and other materials), then incubating the column in light
Microorganisms in estuaries and salt marshes
These nutrient-rich waters are often polluted and this can create dead zones or greatly increase microbial growth; harmful algal blooms (HABs), including red tides caused by dinoflagellates, occur when algae grow to high numbers and then release toxic compounds
The salinity varies in the estuary in time and space; microbial inhabitants need to be halotolerant (withstands salinity changes)
In estuaries, tidal mixing of freshwater and saltwater creates a salinity profile characterized by salt wedges, where heavier saltwater forms a layer below freshwater
Marine environments represent the major portion of biosphere; contain 96% of the Earth’s water; vital to global biogeochemical cycles
Microorganisms in Freshwater Ecosystems
Microorganisms in lakes
Lakes can be thermally stratified; stratified waters undergo seasonal turnovers because of temperature and specific gravity changes
Oligotrophic lakes remain oxic and do not exhibit oxygen stratification; eutrophic lakes usually have bottoms rich in organic matter; cyanobacterial and heterotrophic bacterial blooms can degrade eutrophic waters
Hypolimnion—cold, often anaerobic (particularly in nutrient-rich lakes) lower layer
Thermocline—region of rapid temperature decrease that spans the metalimnion; acts as a barrier to mixing
Epilimnion—warm, aerobic, upper layer
Deep lakes have a littoral zone where light penetrates and a lower pelagic zone, each with distinct nutrient cycles
Lakes vary in nutrient status
Eutrophic lakes are nutrient-rich; typically anoxic at the bottom
Oligotrophic lakes are nutrient-poor; typically oxic throughout
Microorganisms in streams and rivers
Ability to process organic matter is limited
If the amount of organic material is not excessive, algae will grow, which leads to oxygen production in the daytime and respiration at night (diurnal oxygen shifts)
If the amount of organic material is excessive (eutrophic), oxygen is used faster than it can be replenished, which causes the water to become anaerobic
Nonpoint sources of pollution include field and feedlot runoffs
Point sources of pollution include inadequately treated municipal wastes and other materials from specific locations
Nutrients available in streams and rivers can be from in-stream production (autochthonous) or from out-stream sources (allochthonous) such as leaves, and runoff from riparian areas; under most conditions, such added organic material does not exceed the oxidative capacity of the stream and it remains productive and aesthetically pleasing
Support benthic communities including biofilms of diverse microorganisms including photosynthetic primary producers; phytoplankton also are supported by dissolved and particulate organic carbon
Differ from lakes in that horizontal movement minimizes vertical stratification and most of the functional biomass is attached to surfaces (not planktonic); can be lotic (free running) or lentic (free standing)
Microorganisms in glaciers and permanently frozen lakes
Metabolically active environments that support a variety of microbes; frozen lakes may have thick ice caps that block solar radiation, leading to chemosynthetic communities
These ancient deposits hold microorganisms that may provide information about the biogeographic distribution of microorganisms and life on icy, extraterrestrial worlds (e.g., Europa)
Water as a Microbial Habitat
Nutrient cycling in marine and freshwater environments
The microbial loop recycles much of the organic matter produced by phytoplankton (photosynthate in the form of dissolved organic matter); the chemoheterotrophic bacteria that function in the microbial loop (thought of as particulate organic matter) are consumed by a series of larger predators (protists)
Redfield ratio—ratio of carbon-nitrogen-phosphorus (C:N:P) in phytoplankton; is important for following nutrient dynamics and for studying factors that limit microbial growth
Major source of organic matter in illuminated water is phytoplankton (including tiny picoplankton), consisting of photoautotrophic organisms that acquire needed nitrogen and phosphorous from surrounding water; microplankton include diatoms and dinoflagellates
Light is critical for primary production by autotrophs in marine and freshwater ecosystems; the zone where light penetrates is the photoic zone; solar radiation can warm surface waters and create a thermocline where warm waters float on cooler waters
Gases in aquatic environments
Methane
Hydrogen
Nitrogen
Carbon Dioxide
This equilibrium is impacted by the activity of aquatic microorganisms
The carbonate equilibrium system buffers the pH of water, with seawater highly buffered by the interplay of carbon dioxide, bicarbonate, and carbonate
Important in many chemical and biological processes
Oxygen
Aquatic environments are low-oxygen diffusion environments; this can lead to the formation of hypoxic or anoxic zones, which are inhabited by anaerobic microbes
At higher temperatures and with lower pressure the solubility of oxygen in water is further decreased
