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

2. 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 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
Populations
assemblages of similar organisms
Communities
mixtures of different populations
Ecosystems
self-regulating biological communities and their physical environment

4. 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. Figure 27.1

6. Table 27.1

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

8. Carbon Cycle
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

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

10. nutrient immobilization
Table 27.2
mineralization
decomposition of organic matter to simpler inorganic compounds (e.g., NH4)
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

12. Microbial Ecology and Its Methods: An Overview
Many methods available
Main use is to understand microbial communities
Initial questions asked include
How many organisms are present?
What genera and species are represented in the ecosystem?

13. Examination of microbial populations
Techniques
Examination of microbial populations
determination of numbers and types of microbes
direct viable counts
enrichment techniques
when organisms do not grow under test condition
they may be nonviable
they may be viable but nonculturable (VBNC)

14. Figure 27.16

15. Molecular Techniques
Small subunit (SSU) ribosomal RNA analysis is used to identify community populations
Denaturing gradient gel electrophoresis (DGGE)
uses gradient of DNA denaturing agents to separate DNA fragments
DNA reassociation used to determine the number of genomes present

16. Figure 27.17

17. Examination of Microbial Community Structure
The most direct way to assess microbial community structure is to directly observe communities in nature
Assessment can be done in situ using immersed slides

18. Understanding physical structure
Direct observation
classical staining procedures
fluorescent stains
fluorescent molecular probes
Often coupled with molecular techniques
specific molecular probes

19. Figure 27.18

20. Understanding constituents
Filtration can be used to collect microorganisms from habitat
Volume, dry weight, or chemical content can be measured
not useful for non-discrete microorganisms (e.g., filamentous fungi)
Molecular “fingerprinting” techniques identify members of community

21. Environmental Genomics
Also called metagenomics
Goal is to define the function of the community gene pool under a variety of conditions
Requires collaboration of biologists trained in microbiology, ecology, math, and bioinformatics

22. Microbial Activity and Turnover
Direct chemical measurements of specific processes (e.g., nitrification)
Microarrays to measure gene expression
Stable isotope measurements
Microbial growth rates measured two ways:
direct microscopic examination
incorporation of radiolabelled components (e.g., thymidine)

23. Recovery or Addition of Individual Microbes
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Recovery or Addition of Individual Microbes
isolation of individual cells provides insight into microbial community
e.g., phenotypic (population) heterogeneity
cells from genetically uniform population have different phenotypes
reporter microbes with specific characteristics can be added to microbial community to understand community structure and function better
reporter genes present in reporter microbes respond to environmental and physiological changes

24. Isolation of individual cells
Optical tweezers
laser beam used to drag microbe away from its neighbors
Micromanipulator
fine capillary used to separate microbe from its neighbors
Isolation can be followed by analysis of organism’s DNA