1. General Microbiology (Micr300)
Lecture 12
Environmental Microbiology
(Text Chapters: ; ; 19.22)

2. Populations, Guilds and Communities
In nature, individual microbial cells grow to form populations.
Metabolically related populations are called guilds
Set of guilds interact in microbial communities
Microbial communities in turn interact with communities of macroorganisms and the environment to define the entire ecosystem

4. Biogeochemical Cycles
Microorganisms play major roles in energy transformations and biogeochemical processes that result in the recycling of elements essential to living systems. The study of these chemical transformations is called biogeochemistry.

5. Environments and Microenvironments
Microorganisms are very small, and their habitats are likewise small. The microenvironment is the place where the microorganism actually lives.
For example, the outer zones of a small soil particle may be fully oxic, meaning that O2 is present, whereas the center, only a very short distance away, can remain completely anoxic (O2-free)

6. Competition and Cooperation
Microorganisms in nature often live a feast-or-famine existence such that only the best-adapted species thrive in a given niche. Cooperation among micro-organisms is also important in many microbial interrelationships.

7. Microbial Growth on Surfaces and Biofilms
Biofilms are bacterial assemblages, encased in slime, that form on surfaces.
Biofilms can lead to the destruction of inert and living surfaces as a result of the products excreted by the bacterial cells. Biofilm formation is a complex process involving cell-to-cell communication (Figure 19.5).

10. Microbial Habitats

11. Terrestrial Environments
The soil is a complex habitat with numerous microenvironments and niches (Figure 19.6).
Microorganisms are present in the soil primarily attached to soil particles. The most important factor influencing microbial activity in surface soil is the availability of water, whereas in deep soil (the subsurface environment), nutrient availability plays a major role.

13. Diagram of a Soil Aggregate

14. Freshwater Environments
In aquatic ecosystems, the main primary producers are usually phototrophic microorganisms.
Bacteria consume most of the organic matter produced, which can lead to depletion of oxygen in the environment. The biochemical oxygen demand (BOD) is a measure of the oxygen-consuming properties of a water sample.

15. Freshwater Environments
In many lakes in temperate climates, the water mass becomes stratified during the summer, with the warmer and less dense surface layers separated from the colder and denser bottom layers (Figure 19.9).
Even though a river may be well mixed because of rapid water flow and turbulence, large amounts of added organic matter can lead to a marked oxygen deficit from bacterial respiration (Figure 19.10).

19. Marine Habitats
Marine waters have less nutrients than many freshwaters, yet substantial numbers of microorganisms exist there. Many of these use light to drive ATP synthesis.
The form of rhodopsin (called proteorhodopsin) found in open ocean prokaryotes is very similar to bacteriorhodopsin but is present in cells that are phylogenetically Bacteria, not Archaea.

20. Marine Habitats
In terms of prokaryotes, species of the domain Bacteria tend to predominate in oceanic surface waters, whereas Archaea are more prevalent in deeper waters

21. Deep-Sea Microbiology
The deep sea is a cold, dark habitat where high hydrostatic pressure and low nutrient availability prevail.
Barophiles grow best under pressure; barotolerants can grow under elevated pressures but grow best at atmospheric pressures; and extreme barophiles, obtained from the greatest depths, require high pressure for growth (Figure 19.14).

23. Hydrothermal Vents
Hydrothermal vents are deep-sea hot springs where volcanic activity generates fluids containing large amounts of inorganic energy sources that can be used by chemolithotrophic bacteria (Figure 19.16).
These bacteria fix CO2 into organic carbon, some of which is then used by the deep-sea animals.

25. Hydrothermal Vents
There are two major types of vents, hot vents, or black smokers, and warm vents.
Deep-sea hydrothermal vents are habitats where the primary producers are chemolithotrophic rather than phototrophic

26. Biotransformation
A major toxic form of mercury is methylmercury. This form of mercury can yield Hg2+, which bacteria reduce to Hg0.
The ability of bacteria to resist the toxicity of heavy metals often results from the presence of specific plasmids that encode enzymes capable of detoxifying or pumping out the metals (Figure 19.41).

28. Petroleum Biodegradation
Hydrocarbons are subject to microbial attack. Hydrocarbon-oxidizing microorganisms are used for bioremediation of spilled oil, and their activities are assisted by addition of inorganic nutrients to balance the influx of carbon from the oil.
A wide variety of bacteria, several molds and yeasts, and certain cyanobacteria and green algae can oxidize petroleum products aerobically.

30. Biodegradation of Xenobiotics
Many chemically synthesized compounds—such as insecticides, herbicides, and plastics (collectively called xenobiotics)—are completely foreign to microorganisms.
Nonetheless, xenobiotics can often be degraded by one or another prokaryote. Both aerobic and anaerobic mechanisms are known.

31. Biodegradation of Xenobiotics
Although the aerobic breakdown of chlorinated xenobiotics is undoubtedly of ecological importance, reductive dechlorination is of particular environmental interest because of how rapidly anoxic conditions can develop in polluted microbial habitats in nature.
Some compounds may be degraded either partially or totally provided that some other organic material is present as the primary energy source. This phenomenon is called cometabolism.

32. Microbial Interactions with Plants
Key microbial habitats on plants include the rhizoplane/rhizosphere and the phyllosphere.
Lichens are symbiotic associations between a fungus and an alga or cyanobacterium.
Mycorrhizae are formed from fungi that associate with plant roots and improve their ability to absorb nutrients. Mycorrhizae have a great beneficial effect on plant health and competitiveness.

33. Root Nodule Bacteria and Symbiosis with Legumes
One of the most widespread and important plant-microbial symbioses is that between legumes and certain nitrogen-fixing bacteria. The plant provides the energy source needed by the root nodule bacteria, and the bacteria provide fixed nitrogen for the growth of the plant.
The bacteria induce the formation of root nodules within which the nitrogen-fixing process occurs. In the nodule, precise levels are controlled by the O2-binding protein leghemoglobin.

34. Stages in the infection and development
of root nodules