Design of PCR Primers and Gene Probes for General Detection of Alkane-Degrading Bacteria

Abstract

For the extensive detection of alkane-degrading bacteria, three combinations of PCR primer sets and gene probes were designed based on homologous regions within a variety of alkane hydroxylase genes registered in GenBank and examined for their availability. PCR with the primers amplified DNA fragments of expected size from all the bacterial strains used for primer design, and all of the amplified fragments gave positive results on Southern hybridization with the newly designed probes. To evaluate the availability of these primers and probes, they were applied to 74 wild-type alkane-degrading bacteria newly isolated from various environments. The primers amplified DNA fragments of expected size from all the wild-type strains, while the probes gave positive results against amplified fragments from 59 strains. The results suggest that this primer and probe system can detect most alkane-degrading bacteria, and can be applied to evaluate alkane-degradation potential in the environment.