EXTRACTION OF RIBOSOMAL-RNA AND GENOMIC DNA FROM SOIL FOR STUDYING THE DIVERSITY OF THE INDIGENOUS BACTERIAL COMMUNITY

A method for the indirect (cell extraction followed by nucleic acid ex traction) isolation of bacterial ribosomal RNA (rRNA) and genomic DNA from soil was developed. The protocol allowed for the rapid parallel e xtraction of genomic DNA as well as small and large ribosomal subunit RNA from four soils of different texture. DNA and rRNA yields from the se soils were 15-30 and 0.25-1.0 mu g g(-1) soil, respectively. Follow ing different purification steps, the rRNA as well as genomic DNA extr acts obtained were sufficiently pure for either reverse transcription and polymerase chain reaction (PCR) amplification, or direct PCR ampli fication. Using a set of universal bacterial primers based on conserve d regions of the 16S rRNA sequence, both approaches yielded mixed targ et molecules for subsequent denaturing gradient gel electrophoresis fi ngerprinting of soil microbial diversity. The amplified rRNA-based bac terial diversity assessment was compared with diversity assessments ba sed on amplified DNA in one selected soil. Results showed similarities as well as differences between the profiles generated on the basis of rRNA and those based on genomic DNA, which suggested that the bacteri al communities defined on the basis of their genomic DNA contained var iable amounts of rRNA. (C) 1998 Elsevier Science B.V.