Last revised:
Tuesday, February 29, 2000
Ch. 40 (pp. 832-844) in Prescott et al, Microbiology, 4th Ed.
Note:
These notes are provided as a guide to topics the instructor hopes to cover during lecture. Actual coverage will
always
differ somewhat from what is printed here. These notes are not a substitute for the actual lecture!
Copyright 2000. Thomas M. Terry
Ecological
Perspectives
- Ecology is the study of organisms and their environments. It asks
different questions, and uses different methods, than the study of individual
organisms and their internal machinery as we have been studying so far this
semester.
- Example: A microbial ecologist might be interested in soil, or a pond. Typical
questions might include:
- what varieties of organisms are present?
- How do they
interact?
- What happens to the population if environmental conditions change
(e.g. hotter, drier, more acidic, etc.).
- What changes occur if a new organism
is introduced?
- What happens if oil is spilled?
- Or heavy metal wastes added?
- The answers to these questions are often very difficult to come by. Even the
simplest sounding questions, e.g. "What organisms are present", is not easy to
answer. If we rely on counting only those organisms that will grow on an agar
plate in our laboratory conditions, we grossly underestimate many
microbes that can be found by microscopic or other analytical techniques, but
do not show up on a typical heterotrophic plate count.
- Microbes adsorb to surfaces, creating biofilms. Biofilms consist of microbes and surrounding polysaccharide matrix. Much of what we know about microbes comes from studies of pure cultures in vitro. How this extrapolates to the behavior of complex mixed cultures growing in biofilms that are commonplace in nature we do not know.
- Microbes in nature have evolved stratagems both for competition and cooperation. For example, many microbes produce toxic compounds targeted at other microbes (antibiotics, bacteriocins, etc.). Some microbes are dependent on the metabolic activities of others; e.g., methanogens require H2 produced by anaerobic fermentations.
- Rita Colwell (NIH) and others have discovered that some bacteria
in nature are viable but non-culturable (VNC). I.e., they can be seen
microscopically, and shown to be metabolically active (= viable, alive), but
they won't grow on the surface of plates (= non-culturable). Perhaps only 1% of
the number of cells of some species of bacteria will grow.
- What is the significance of this observation? It is not clear. Some would argue
that the VNC bacteria are dying but not yet dead; they may have lost some
critical gene(s) needed for replication. Perhaps they are of no great
significance. Perhaps they are enormously important. It is not immediately
clear how to answer such questions.
- The study of ecology begins by accounting for the features of environments and
the organisms found in them.
- What is an environment? It includes physical features (heat, wind);
chemical features (pH, presence or absence of water, nutrients and
minerals); and other organisms (which may be competitors, potential prey
or predators, potential mates, etc.). These are called abiotic and
biotic factors, respectively. Together, these factors comprise an
ecosystem, which might be as small as a tiny pond or as large as the
Coniferous forests that cover hundreds of thousands of square miles across
North America, Europe, and Asia.
- If you are a "naked" microbe living on a beach, the most important factors in
your survival may be the level of heat. If you are an E. coli bacterium
living in the gut, heat is not a major concern; your survival probably depends
more on your ability to compete successfully for the dregs of undigested food,
and to withstand the various phages, colicins, and other biotic threats to your
survival. And of course all this changes drastically the moment you are
excreted into a sewage pipe.
- We saw earlier in the course that all organisms require the
six elements CHNOPS in sizable quantities, and that these minerals may occur in
different forms.
- In fact, depending on whether the local environment is aerobic
or anaerobic, the exact chemical form of any of these elements may change
quickly and drastically.
- Example: If a soil becomes water logged and anaerobic, sulfate
may be converted into hydrogen sulfide and nitrate into nitrogen gas or ammonia
(via anaerobic respiration). As water recedes and the soil becomes aerobic
again, the remaining ammonia is oxidized back to nitrate in stages.
- All of this
(and many other processes) occur largely because of the activities of soil
microbes. Without these microbes, life as we know it would not occur, because
necessary elements would remain tied up in unusable chemical forms and
gradually be removed by sedimentation.
- cycling and transfer of nutrients among all living organisms
- biological and chemical processes involved
- rocks/soil -- atmosphere -- water
- cycling of C, N, S, Fe, P, Mn occurs on a global scale
- microorganisms crucial - profound effect on levels of different
compounds available in environment
- usually involves switching thru different redox states, and gaseous
versus solid states
- need to understand where substances produced, and where used (aerobic vs. anaerobic
zones, etc)
- See figure 40.7 in your text, and figure drawn in class. The major cycling of C
is from CO2 to organic matter (by autotrophs) and from organic matter back to
CO2 (by respiration, burning of fossil fuels, etc.)
- In addition, however, there is a significant removal of CO2 whenever hydrogen
gas is produced anaerobically to form methane (anaerobic respiration by
methanogens).
- This is not a trivial process; annual production of methane is
about 180 x 1012 grams of methane by biotic processes (belching from ruminants
being the single most important) and an additional 130 x 1012 grams by abiotic
processes (mostly from incomplete combustion during burning of biomass).
- Interestingly, more methane is produced in freshwater and terrestrial
environments than in saltwater, despite the fact that 2/3 of the earth's
surface is oceanic. This is probably due to the high concentrations of sulfate
in saltwater, which allows sulfate-reducing bacteria (which also need hydrogen
gas in order to grow) to compete with methanogens for the available hydrogen.
Nitrogen
Cycle
- This is the most
complex cycle. See Fig. 40.9 in your text.
- View animation of the Nitrogen Cycle
- Major reservoir = N2 gas in atmosphere (80% of atmosphere) - most stable form
- Several key reactions carried out only by microorganisms
- Key processes:
- Nitrogen fixation: N2 --> NH3
- only carried out by certain bacterial genera: Rhizobium (root nodule symbionts), Azotobacter (free-living soil bacteria), others.
- aerobic or anaerobic; ~ 60% on land; 40% in oceans
- Decomposition / ammonification: organic N --> NH4+
- carried out by chemoorganotrophs, both aerobes and
anaerobes
- some recycled into organic N in soil; some into atmosphere
- excretion of extra nitrogen is often in some compound
containing -NH2 groups, which quickly form ammonia (NH3) once they are
liberated into the environment. That's why a baby's diaper smells like ammonia.
- Nitrification: NH4+ --> nitrite, nitrate
- mostly chemolithotrophs; some chemoorganotrophs in acidic areas
- aerobic conditions; mostly well-drained soils at neutral pH
- nitrate leached from soil by rainfall; water runoff from fertilized areas can become rich in nitrites, dangerous for animal health
- inhibitors are sometimes added to fertilizers. E.g., nitrapyrin - inhibits NH3 --> nitrite (1st step); decreases pollution of waterways
- Denitrification: nitrate--> N2 or NH3
- chemoorganotrophs (anaerobic respiration)
- Assimilatory nitrate reduction: nitrate --> organic nitrogen
- many organisms can carry this out
- Be careful to distinguish nitrification, denitrification as separate processes, and the conditions under which each
occurs.
Table: Nitrification vs Denitrification
| Nitrification | Denitrification |
|---|
| Aerobic status |
Obligate Aerobes |
Facultative |
| Respiratory Classification |
Aerobic Respiration |
Anaerobic Respiration |
| Respiratory electron acceptor |
O2 |
NO3-, NO2-, others |
| C-source |
Autotroph |
Heterotroph |
| Energy source |
Chemolithotroph |
Chemoorganotroph |
| Taxonomic group |
Nitrosomonas, Nitrobacter |
Variable group; many different genera |
| Reversibility |
Reversible |
Not reversible |
- See Fig. 40.8 in your text, and animation below. Note that both
assimilatory and dissimilatory sulfate reduction can occur, as we have seen
with nitrate.
- View animation of the Sulfur Cycle
- Some major steps in the sulfur cycle include:
- Assimilative reduction of sulfate (SO4=) into -SH groups in proteins.
- Release of -SH to form H2S during excretion, decomposition, and desulfurylation.
- Oxidation of H2S by chemolithotrophs to form sulfur (So) and sulfate (SO4=)
- Dissimilative reduction of sulfate (SO4=) by anaerobic respiration of sulfate-reducing bacteria.
- carried out by mesophiles and hyperthermophiles
- often same environment as methanogens, compete for available electron donors
(e.g., H, acetate)
- when sulfate present, sulfate reducers will win
- only occurs when lots of organic C present (needed to generate electron donors)>
- process often limited by organic C levels in marine sediments
- pollution: sewage, garbage increase organic C, increase HS-, H2S production (both toxic to many organisms)
- Anaerobic oxidation of H2S and S by anoxygenic phototrophic bacteria (purple and green bacteria)
- The sulfur cycle includes more steps than are shown here. Sulfur compounds undergo some interconversions due to chemical and geologic processes (not shown here). In addition, a number of organic sulfur compounds accumulate in significant amounts, especially in marine environments.
- For example, about 45 tons of dimethyl sulfide are produced annually by degradation of dimethylsulfonium propionate, a chemical produced by marine algae for osmoregulation. This is gradually broken down by a variety of biotic and abiotic mechanisms.
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