1. Biogeochemical Cycling and Introductory Microbial Ecology
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Chapter 27
Biogeochemical Cycling and Introductory Microbial Ecology

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Microbial Ecology
the study of community dynamics and the interaction of microbes with each other, with plants and animals, and with the environment in which they live
Microbes make life possible
microbes play a major role in life on earth, yet only ~ 1% of all species have been cultured, identified, and studied

3. Foundations of Microbial Ecology
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Foundations of Microbial Ecology
populations
assemblages of similar organisms
communities
mixtures of different populations
ecosystems
self-regulating biological communities and their physical environment

4. Biogeochemical Cycling
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Biogeochemical Cycling
biogeochemical cycling of nutrients
involves biological and chemical processes
often involves oxidation-reduction reactions that change chemical and physical characteristics of nutrients
all nutrient cycles are linked and make life on Earth possible

5. Carbon Cycle Carbon can be a variety of forms
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Carbon Cycle
Carbon can be a variety of forms
reduced e.g., methane (CH4) and organic matter
oxidized e.g., CO and CO2

6. Carbon Cycle
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Carbon fixation can occur through the activities of photoautotrophic and chemoautotrophic organisms. Methane can be produced from inorganic substrates (CO2 and H2) or from organic matter. Carbon monoxide, produced by sources such as automobiles and industry, is returned to the carbon cycle by CO-oxidizing bacteria. Aerobic processes are noted with blue arrows, and anaerobic processes are shown with red arrows.
Figure 27.2

7. Degradation of organic matter
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Degradation of organic matter
influenced by several factors
nutrients present in environment
abiotic conditions
microbial community present

8. nutrient immobilization
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Table 27.2
mineralization
decomposition of organic matter to simpler inorganic compounds (e.g., NH4) protein to ammonium ions
nutrient immobilization
the nutrients that are converted into biomass become temporarily unavailable for nutrient cycling.

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Microorganisms form different products when breaking down complex organic matter aerobically than they do under anaerobic conditions. Under aerobic conditions oxidized products accumulate, while reduced products accumulate anaerobically. These reactions also illustrate commensalistic transformation of a substrate, where the waste products of one group of microorganisms can be used by a second type of microorganism.
Figure 27.3

10. Nitrogen Cycle can be carried out by either autotrophs or heterotrophs
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Nitrogen Cycle
can be
carried out
by either autotrophs or heterotrophs
Flows that occur predominantly under aerobic conditions are noted with open arrows. Anaerobic processes are noted with solid bold arrows. Processes occurring under both aerobic and anaerobic conditions are marked with cross-barred arrows. The anammox reaction of NO2– and NH4+ to yield N2 is shown. Important genera contributing to the nitrogen cycle are given as examples.
Figure 27.4

11. Nitrogen Cycle nitrogen fixation reduction of N2organic nitrogen
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Nitrogen Cycle
nitrogen fixation
reduction of N2organic nitrogen
unique to procaryotes
requires an expenditure of energy, source of electrons, and anaerobic environment
carried out by aerobes or anaerobes
aerobes use a variety of strategies to protect nitrogenase from oxygen

12. Nitrogen Cycle product of nitrogen fixation is ammonium (NH4+)
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Nitrogen Cycle
product of nitrogen fixation is ammonium (NH4+)
immediately incorporated into organic matter as an amine
nitrification
deamination of amino acids
NH4+ NO2-
NO2-  NO3-

13. More on the Nitrogen Cycle
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More on the Nitrogen Cycle
fate of NO3-
assimilatory nitrate reduction
NO3- is reduced and incorporated into organic nitrogen
dissimilatory nitrate reduction
NO3- serves as a terminal electron acceptor during anaerobic respiration
NO3- removed from ecosystem and returned to atmosphere as dinitrogen gas (N2)

14. Phosphorous Cycle has no gaseous component
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Phosphorous Cycle
has no gaseous component
environmental phosphorus usually present in low concentrations; is often the growth limiting nutrient
phosphorus exists in both organic and inorganic forms
orthophosphate (+5 valence)complex forms of phosphorus, including polyphosphates

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Figure 27.5

16. Sulfur Cycle dissimilatory sulfate reduction
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Sulfur Cycle
dissimilatory sulfate reduction
the use of sulfate as a terminal electron acceptor
assimilatory sulfate reduction
the reduction of sulfate for use in amino acid and protein biosynthesis

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Sulfur Cycle
Photosynthetic and chemosynthetic microorganisms contribute to the environmental sulfur cycle. Sulfate and sulfite reductions carried out by Desulfovibrio and related organisms (purple arrows) are dissimilatory processes. Sulfate reduction also can occur in assimilatory reactions, resulting in organic sulfur forms. Elemental sulfur reduction to sulfide is carried out by Desulfuromonas, thermophilic archaea, or cyanobacteria in hypersaline sediments. Sulfur oxidation can be carried out by a wide range of aerobic chemotrophs and by aerobic and anaerobic phototrophs.
Figure 27.6

18. Interaction of Element Cycles
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Interaction of Element Cycles
in nature cycles do not occur independently
e.g., an autotroph that fixes CO2 also requires N, P and S for protein, nucleic acid and phospholipid synthesis

19. The Physical Environment
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The Physical Environment
influences interactions of microorganisms with each other and with other organisms

20. The Microenvironment and Niche
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The Microenvironment and Niche
microenvironment
specific physical location of microorganism
impacted by fluxes of nutrients and diffusion rates of waste products
niche
function of an organism in a complex system, including place of the organism, resources used in a given location, and time of use

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Creation of a niche from a microenvironment. As shown, 2 nearby particles create a physical microenvironment for possible use by microorganisms. Chemical gradients, as with oxygen from the aerobic region, and sulfide from the anaerobic region, create a unique niche. This niche thus is the physical environment and the resources available for use by specialized aerobic sulfide-oxidizing bacteria.
Figure 27.10

22. Biofilms and Microbial Mats
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Biofilms and Microbial Mats
biofilms
organized microbial systems consisting of layers of microbial cells associated with surfaces (layers of organisms of different types)
Catheters and dialysis units
formation of biofilms creates microenvironments and niches hospitable to different types of microbes
Antibiotic resistance, waste product - nutrient
microbial mats
thick biofilms having macroscopic dimensions
often found in aquatic environments
Photosynthetic zone (Cyanobacteria), sulfur reducing bacteria (Desulfovibrio), anoxygenic photosynthetic bacteria (Chromatium).

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Winogradsky column

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Figure 27.11

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Microbial mat
Figure 27.12

26. Microorganisms and Ecosystems
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Microorganisms and Ecosystems
ecosystems
communities of organisms and their physical and chemical environments that function as self-regulating units

27. Roles of organisms in ecosystems
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Roles of organisms in ecosystems
primary production
synthesis of organic matter from CO2 and other inorganic compounds
primary producers
organisms that carry out primary production
decomposers
decompose accumulated organic matter
the microbial loop describes the interactions of
microbial loop
the multiple and overlapping roles played by microorganisms in nutrient cycling