Microbiology: Microbial Habitats

Marine Environments

• Phaeophyta (brown algae) are found in the upper littoral zone to sublittoral zone, up to 220 m in clear tropical water.
• Marine plankton (Chlorophyta and Chrysophyta) are found in the upper region of the ocean, 0-50 m deep.
• Green algae are found above 30 m deep.
• Marine protozoa are also present in marine environments.

Viruses in the Marine Environment

• Viruses are important members of marine and aquatic microbial communities.
• Virioplankton are the most numerous members of marine ecosystems.
• Virus-like particles (VLPs) are viruses that have been enumerated by transmission electron microscopy.
• The average VLP density in seawater is 10^6 to 10^7 per milliliter.
• Phage particles are recognized as the most abundant life form on Earth.

Benthic Marine Environments

• The largest microbial biomass is found under the sea.
• Recent studies on ocean sediments have revealed important information on microbial communities.
• The total subsurface biomass equals that of all terrestrial and marine plants.
• Some microbes are barophilic and can tolerate atmospheric pressures up to 1,100 atm.

Microbial Habitats

• There are three major habitats: aquatic, terrestrial, and atmospheric.
• Hydrosphere is an important habitat for microorganisms.

Water as a Microbial Habitat

• Important physical factors in aquatic environments include dissolved oxygen content, temperature, pH, and light penetration.
• Microorganisms can be autochthonous (indigenous) or allochthonous (foreign) in aquatic environments.

General Influencing Factors in Aquatic Environments

• Light determines the rate of photosynthesis and is dependent on the clarity of water, season, and latitude.
• Temperature is determined by latitude and weather condition, and affects the distribution of heat in water bodies.
• Pressure increases with depth, affecting the metabolism of organisms and the dissociation of carbonic acids, leading to a decrease in pH.
• Nutrient availability varies greatly in aquatic environments.
• Dissolved gases, including oxygen, carbon dioxide, and nitrogen, are important in aquatic environments.

Freshwater Habitats

• Lotic systems include free-running waters, such as rivers, streams, and canals.
• Lentic systems include free-standing waters, such as ponds, lakes, marshes, and slow-moving rivers.
• The neuston layer of freshwater habitats is a habitat for microorganisms, with a higher density of microorganisms than underlying water.

Zones in Freshwater Habitats

• The littoral zone has full light penetration and is dominated by submerged or partially submerged higher plants, algae, and cyanobacteria.
• The limnetic zone is open water away from shore, with full light penetration and dominated by algae and cyanobacteria.
• The light compensation point is the lowest level with effective light penetration, where photosynthetic activity equals respiratory activity.
• The profundal zone has very low light penetration, high in organic nutrients, and is dominated by anaerobic heterotrophs.

Zonation of Lakes

• The epilimnion is the warm and oxygen-rich surface layer.
• The thermocline is the zone of rapid temperature decrease.
• The hypolimnion is the cold and oxygen-poor bottom layer.

Stratification and Productivity in Lakes

• Phytoplankton are confined to the epilimnion during summer stratification.
• Productivity is dependent on nutrient inputs to the lake and nutrient recycling in the epilimnion.

Factors Affecting Growth of Microorganisms in Ponds and Lakes

• Temperature, pH, oxygen, sunlight penetration, and nutrient availability affect the growth of microorganisms.

Eutrophication

• Eutrophication is the process of nutrient enrichment, stimulating the growth of plants, algae, and bacteria.
• Effects of eutrophication include reduced submerged aquatic vegetation, increased turbidity, and decreased oxygen levels.

Microbial Communities in Lakes and Ponds

• Surface waters have autochthonous photoautotrophic bacteria, such as cyanobacteria.
• Deeper waters have heterotrophic bacteria, anaerobic photoautotrophic bacteria, and sulfate-reducing organisms.
• Sediments have anaerobic bacteria, including methanogenic bacteria and Desulfovibrio spp.

Nutrient Cycles in Lakes and Ponds

• Phytoplankton grow and fix CO2 to form organic matter, acquiring N and P from water.
• Biomass of phytoplankton enters the microbial loop, releasing dissolved organic matter that is used by heterotrophic bacteria.
• Heterotrophic bacteria transform dissolved organic matter into particulate organic matter, which is consumed and digested by large predators, releasing C as CO2 and other nutrients that are recycled to phytoplankton.

Ecological Functions of Microorganisms in Fresh Water Environments

• Decompose dead organic matter
• Assimilate and reintroduce dissolved organic matter
• Perform mineral cycling activities
• Contribute to primary production
• Serve as a food source for grazers### Microorganisms in Streams and Rivers
• Microorganisms in streams and rivers are influenced by nutrient sources, which can be autochthonous (in-stream production based on photosynthetic organisms) or allochthonous (from outside the stream, e.g., runoff from urban, industrial, or agricultural sites).
• Benthic microbial loops are important in most rivers and streams, with biofilms consisting primarily of heterotrophic microbes that are sources of degradation and mineralization.
• Eutrophic systems can occur in streams and rivers, characterized by a high rate of respiration that exceeds photosynthesis, leading to anoxic conditions, and are often caused by runoff from agricultural and urban areas.
• These eutrophic conditions can produce distinct, predictable changes in the microbial community, creating an oxygen sag curve.

Microorganisms in Lakes

• Lakes are lentic systems, dominated by planktonic microbes and invertebrates.
• Eutrophic lakes are nutrient-rich, with bottom sediments rich in organic matter, while oligotrophic lakes are nutrient-poor, remaining aerobic, and having a low microbial population.
• Deep lakes are divided into two main regions: the littoral zone (shoreline) and the pelagic zone (central region).
• The pelagic zone can be further divided into two layers: the epilimnion (warm upper layer) and the hypolimnion (deeper, cooler, bottom layer), which can be anaerobic, especially under nutrient-rich conditions.
• The two layers are separated by a zone of rapid temperature decrease called a thermocline.

Microorganisms in Estuaries and Salt Marshes

• Estuaries are semi-enclosed coastal regions where a river meets the sea, characterized by a salt wedge (salinity profile due to denser salt water).
• Microorganisms in estuaries are often halotolerant, able to withstand large changes in salinity.
• Estuarine waters are calm and nutrient-rich, but can also be prone to pollution, leading to loss of macroscopic life and harmful algal blooms.
• Salt marshes are unlike estuaries, lacking freshwater input from a single river, and can be modeled in Winogradsky columns.

Microorganisms in Marine Environments

• Marine environments encompass 97% of the Earth's water, with high pressure, high salinity (approximately 35%), and a pH range of 8.3-8.5.
• Barophiles are microbes that thrive under high pressure.
• Microorganisms in marine environments are adapted to survive in low-nutrient concentrations, are motile, and can exhibit unusual shapes.
• Marine environments can be divided into freshwater habitats and marine habitats.

Horizontal and Vertical Stratification of Marine Habitats

• Horizontal stratification includes the intertidal zone, neritic zone, continental slope, and oceanic zone.
• Vertical stratification includes the euphotic zone, epipelagic zone, mesopelagic zone, bathypelagic zone, and benthic zone.
• The euphotic zone is the area with effective light penetration, while the aphotic zone is below the euphotic zone.

Factors Affecting Microbial Growth in Marine Environments

• Hydrostatic pressure, light, temperature, and nutrients are factors that affect microbial growth in marine environments.
• Light absorption increases with depth, with only the euphotic zone (top 100 m) supporting primary productivity.
• Nutrients are usually low at the surface and increase beneath the euphotic zone, with surface nutrient levels improving only during upwelling processes.

Microorganisms in the Open Ocean

• Photosynthetic microbes that fix half of the world's carbon inhabit the upper 200-300 meters of the open ocean.
• The open ocean is an oligotrophic environment, with low nutrient levels.
• Microorganisms in the open ocean are adapted to survive in low-nutrient concentrations, and include SAR11, which are the most numerous organisms on Earth.

Ocean Photic Zone and Carbon Cycling

• The ocean photic zone is the area where photosynthesis occurs, with a constant exchange of CO2 at the surface.
• Dead organisms from the euphotic zone fall through the depths as marine snow, releasing nutrients that can be recycled back to the surface.
• Nutrient-rich deep waters lack light energy for photosynthetic primary production, but can be fertilized with iron to trigger diatom blooms.

Nitrogen Cycling in the Open Ocean

• The open ocean is limited by nitrogen, and recent studies have led to a new examination of the nitrogen cycle and amount of nitrogen fixed by various populations.
• Bacterial consortia capable of anammox reaction (anaerobic reduction of NH4 to N2) cause the loss of nitrogen that would otherwise support life.

Abundance of Microbes in the Open Ocean

• SAR11 are the most numerous organisms on Earth, making up 25% to 50% of the total bacteria and archaea in nearshore and open ocean surface waters.
• SAR11 and Silicobacter demonstrate unique adaptations to living in the oligotrophic open ocean, including the production of photeorhodopsin proton pump.

Marine Microbial Community

• The marine microbial community is composed of mostly gram-negative bacteria, such as Pseudomonas, Vibrio, and Flavobacterium, as well as gram-positive bacteria, such as Bacillus, in marine sediments.
• Desulfovibrio and methanogens are found in sediments, while chemolithotropic bacteria, such as Nitrosococcus, Nitrosomonas, Nitrospina, and Nitrobacter, are involved in nitrogen cycling.
• Marine algae of various divisions are also present in the marine microbial community.