Polymerase chain reaction and hybridization on DNA extracted from soil as a tool for Frankia spp. population distribution studies in soil

The distribution of Frankia populations in soil is usuary studied by plant trapping in combination with genetic characterization. We compared this app roach with the evaluation of population distribution by polymerase chain re action (PCR) and hybridization. Seven populations of Frankia spp. strains, characterized by restriction by HaeIII of the nifD-nifK amplified fragments (nif-HaeIII profiles), were found to have different distribution in a soil column of 60 cm in depth. The nifD-nlfK intergenic spacer and the 5'-part of the nifK gene were sequenced for one representative of the seven nif-Hae III profiles to design specific oligonucleotide probes. The results on the distribution of Frankia populations by PCR amplification on DNA extracted d irectly from samples from three soil depths (10-20 cm; 30-40 cm; 50-60 cm) and hybridization with specific probes are congruent with the distribution observed by plant trapping.