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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 play a major role in life on
earth, yet only ~ 1% of all species have
been cultured, identified, and studied
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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
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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
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Figure 27.1
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Table 27.1
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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
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Carbon Cycle
Figure 27.2
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Degradation of organic matter
• Influenced by several factors
– nutrients present in environment
– abiotic conditions
– microbial community present
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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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Figure 27.3
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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?
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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)
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Figure 27.16
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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
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Figure 27.17
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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
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Understanding physical
structure
• Direct observation
– classical staining procedures
– fluorescent stains
– fluorescent molecular probes
• Often coupled with molecular
techniques
– specific molecular probes
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Figure 27.18
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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
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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
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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)
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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
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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
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