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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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• 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.

Table 27.2

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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