described. Development of gfp mutants with a series of different excitation and emission wavelengths makes it possible to identify multiple bacterial populations simultaneously. The gfp gene has been introduced into Sinorhizobium metitoti, Pseudomonas putida, and Pseudomonas sp., among other common soil bacteria, and used in soil ecology studies. Marked strains can be visualized in infection threads, root nodules, and colonized roots and even inside digestive vacuoles of protozoa (Fig. 4.5). If the gfp gene is cloned along with specific promoters, such as the met A (a-galactosidase) promoter, then they can be used as biosensors to report back to the observer if the inducers, in this case galactosides, are present and at what relative concentration in the surrounding environment (Bringhurst et at., 2002).

Marker gene approaches are restricted to use in organisms that can be manipulated in culture. While considerable information can be gained about how marked microbes interact with soil colloids and other soil organisms, and can be used as biosensors for detecting environmental concentrations of various compounds, they do not yield information about the vast, unknown majority of soil microbes for which cultured representatives have yet to be obtained.

extraction of nucleic acids (dna/rna)

Both whole-community nucleic acid analyses and those based on PCR amplification of target genes require that the nucleic acids contained in a soil sample be separated from the solid phase. A variety of methods used to extract nucleic acids


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