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9 – Community Structure
K. Alef, G. Sparling
Published 1995 · Chemistry, Biology
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Publisher Summary The quantification of the microbial community in soil is complicated because microorganisms are commonly attached to soil minerals and organic matter, and they occur in consortia usually containing different physiological and morphological types. One way to study microbial community structure in soil is to inhibit selectively the metabolic activity of different microbial groups. Fungi play an important role in the decomposition of organic matter such as cellulose and lignin in soil. Most traditional methods developed for the detection of microorganisms in soil suffer from the lack of specificity or sensitivity, or require the isolation of the target organisms. Methods based on isolation and identification of the nucleic acids of target organisms overcome these problems. The chapter describes three methods based on direct extraction of DNA in soil. The method represents three different approaches aiming at the same goal: the highest yield of extracted DNA sufficiently pure to allow the identification of its genetic origin. All methods aim at getting a high yield of DNA that is pure enough for molecular analysis by the DNA–DNA hybridization, the restriction fragment length polymorphism analysis, or the amplification by the polymerase chain reaction. Before the characterization of the isolated soil DNA is started, its concentration should be evaluated. Soil DNA samples can be tested by dot blotting and Southern blotting, as is done in other DNA samples. Serological assays for the detection of target microorganisms are based on a reaction of one or more antigenic determinants, present on molecules of the target, with antibodies directed against these determinants.
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