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

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

Foundations of Microbial Ecology Populations assemblages of similar organisms Communities mixtures of different populations Ecosystems self-regulating biological communities and their physical environment

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

Figure 27.1

Table 27.1

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

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

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

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.

Copyright © The McGraw-Hill companies, Inc Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. 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

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?

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)

Figure 27.16

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

Figure 27.17

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

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

Figure 27.18

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

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

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)

Recovery or Addition of Individual Microbes Copyright © The McGraw-Hill companies, Inc. Permission required for reproduction or display. 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

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