Marine and Fresh Water

Gases in aquatic environments

Oxygen

At higher temperatures and with lower pressure the solubility of oxygen in water is further decreased

Aquatic environments are low-oxygen diffusion environments; this can lead to the formation of hypoxic or anoxic zones, which are inhabited by anaerobic microbes

Carbon Dioxide

Important in many chemical and biological processes

The carbonate equilibrium system buffers the pH of water, with seawater highly buffered by the interplay of carbon dioxide, bicarbonate, and carbonate

This equilibrium is impacted by the activity of aquatic microorganisms

Nitrogen

Hydrogen

Methane

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

Nutrient cycling in marine and freshwater environments

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

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

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)

Microorganisms in glaciers and permanently frozen lakes

These ancient deposits hold microorganisms that may provide information about the biogeographic distribution of microorganisms and life on icy, extraterrestrial worlds (e.g., Europa)

Metabolically active environments that support a variety of microbes; frozen lakes may have thick ice caps that block solar radiation, leading to chemosynthetic communities

Microorganisms in streams and rivers

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)

Support benthic communities including biofilms of diverse microorganisms including photosynthetic primary producers; phytoplankton also are supported by dissolved and particulate organic carbon

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

Ability to process organic matter is limited

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

Point sources of pollution include inadequately treated municipal wastes and other materials from specific locations

Nonpoint sources of pollution include field and feedlot runoffs

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)

Microorganisms in lakes

Lakes vary in nutrient status

Oligotrophic lakes are nutrient-poor; typically oxic throughout

Eutrophic lakes are nutrient-rich; typically anoxic at the bottom

Deep lakes have a littoral zone where light penetrates and a lower pelagic zone, each with distinct nutrient cycles

Lakes can be thermally stratified; stratified waters undergo seasonal turnovers because of temperature and specific gravity changes

Epilimnion—warm, aerobic, upper layer

Thermocline—region of rapid temperature decrease that spans the metalimnion; acts as a barrier to mixing

Hypolimnion—cold, often anaerobic (particularly in nutrient-rich lakes) lower layer

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

Marine environments represent the major portion of biosphere; contain 96% of the Earth’s water; vital to global biogeochemical cycles

Microorganisms in estuaries and salt marshes

In estuaries, tidal mixing of freshwater and saltwater creates a salinity profile characterized by salt wedges, where heavier saltwater forms a layer below freshwater

The salinity varies in the estuary in time and space; microbial inhabitants need to be halotolerant (withstands salinity changes)

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

Winogradsky columns can be used to model salt marshes and illustrate the interactions and gradients that occur in aquatic environments

Made by mixing together mud, water, and sources of nutrients (e.g., cellulose and other materials), then incubating the column in light

In the bottom, anaerobic conditions foster the activity of fermentative microorganisms, which leads to the accumulation of fermentation products

Other anaerobic microorganisms use the fermentation products to carry out anaerobic respiration using sulfate as the electron acceptor and producing sulfide

Sulfide diffuses upward, creating an anaerobic, sulfide-rich zone where anoxygenic photosynthetic bacteria reside

Further up in the column, chemolithotrophic and mixotrophic organisms may use hydrogen sulfide as an energy source and oxygen as the electron acceptor

At the top are oxygenic photosynthetic organisms such as diatoms and cyanobacteria

Microorganisms in the open ocean

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

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

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

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

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

Aquatic viruses

Virioplankton are the most numerous members of marine ecosystems; counting viruslike particles (VLPs) can be challenging

Virioplankton are major agents of mortality in the sea, influence microbial loop, are involved in horizontal gene transfer, and influence microbial community diversity

Microorganisms in benthic marine environments

Benthos—oceanic sediments and the seafloor including hydrothermal vents; mainly high pressure, low light, and cold (1 to 4 °C) environments

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)

Hydrocarbon metabolism fuels microbial communities on continental margins; massive deposits of methane hydrates are found at the ocean floor below 500 meters