BROAD-SCALE APPROACHES TO THE DETERMINATION OF SOIL MICROBIAL COMMUNITY STRUCTURE - APPLICATION OF THE COMMUNITY DNA HYBRIDIZATION TECHNIQUE

Broad-scale approaches seek to integrate information on whole microbia l communities, It is widely recognized that culture techniques are too selective and unrepresentative to allow a realistic assessment of the overall structure of microbial communities, Techniques based on fatty acid or metabolic profiles determine the phenotypic composition of th e community. Complementary information about the genotypic structure o f soil microbial communities necessitates analysis of community DNA. T o determine broad-scale differences in soil microbial community struct ure (i.e., differences at the whole community level, rather than speci fic differences in species composition), we have applied a community h ybridization technique to determine the similarity and relative divers ity of two samples by cross hybridization. In previous studies this as say failed with whole-soil community DNA. Usable hybridization signals were obtained using whole-soil DNA, in this study, by digesting the D NA with restriction enzymes before the labeling with a random-primer r eaction, The community hybridization technique was tested using a grad ed series of microbial fractions, increasing in complexity, all isolat ed from the same soil sample, This demonstrated that single bacterial species and a mixture of cultivable bacteria were less complex and onl y 5% similar to whole-community DNA or bacteria directly extracted fro m the soil. Extracted bacterial and whole-community DNA were 75% simil ar to each other and equally complex. When DNA was extracted from four different agricultural soils, their similarities ranged from 35 to 75 %. The potential usefulness of community hybridization applied to soil microbial communities is discussed.