Chapter 53 : Methods of Soil Microbial Community Analysis

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Soil microbial communities probably are the most complex of natural communities, and one study estimated that there may be as many as 1,000,000 “distinct genomes” per g of soil. This chapter is divided into two sections, the first covering approaches that require laboratory cultivation or incubation and the second addressing those based on analysis of indicator molecules that have been extracted directly from soil communities. A commonly used approach for identification of environmental isolates is based on growth on specific substrates and fermentative abilities. A more precise method of determining the phylogenetic affiliation of an isolate is by characterization of its rRNA. The technique is based on the concept that rRNA molecules, particularly the 16S and 23S rRNA molecules of prokaryotes, are highly conserved throughout evolution and are therefore useful as specific indicators of the phylogenetic affiliations of environmental isolates. A variety of DNA fingerprinting techniques can be used to rapidly differentiate closely related environmental strains. Regardless of the specific technique, the data obtained are DNA fragments that, when separated on agarose or polyacrylamide gels, yield a banding pattern specific to the genome under investigation. Rapid screening methods are of three categories that include: denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), and terminal restriction fragment length polymorphism (T-RFLP) analysis. The chapter talks about automated ribosomal intergenic spacer analysis (ARISA). An alternative approach to soil microbial community analysis is cloning of the soil “metagenome,” defined as the genomes of the total microbiota found in soils.

Citation: Ogram A, Castro H, Chauhan A. 2007. Methods of Soil Microbial Community Analysis, p 652-662. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch53
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