Tiedje, J. M., S. Asuming-Brempong, K. Nuesslein, T. L. Marsh, and S. J. Flynn. 1999. Opening the black box of soil microbial diversity. Applied Soil Ecology 13:109-122.
Soil probably harbours most of our planet’s undiscovered biodiversity. Recent results from both, culturing and nucleic acid-based approaches indicate that soil microbial diversity is even higher than previously imagined. One reason for the high diversity is that much of the diversity can be found at very small scales. If the same genotypes are not repeated at other locations, the large-scale diversity is greatly multiplied. It remains to be seen to what extent this large genotypic diversity actually affects functional diversity, microbial ecology, or biotechnological significance. Here we present a framework of methods for opening the soil black box that provides different levels of resolution of both microbial community structure and activity. The rationale for and examples of use of three of these methods are presented: guanine plus cytosine content of total soil DNA (G+C), terminal restriction fragment length polymorphism (T-RFLP) of 16S rRNA genes amplified from soil DNA, and amplified ribosomal DNA restriction analysis (ARDRA) of rRNA genes from soil DNA and from isolates. These methods give coarse and moderate scale resolution of the soil community. The G+C method, which is one of the few comprehensive coarse scale methods, is also quantitative and can be used to separate DNA into G+C fractions for a second level of composition or activity analysis. The example of the ARDRA method used here illustrates that the same populations of 2,4-D degraders became dominant in three soils of very different land use history and that several of the 2,4-D degrading isolates from these sites had the same ARDRA pattern found from the soil DNA indicating that the isolates represent the dominant populations in the 2,4-D treated soil.
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