Use of 16S rRNA-targeted oligonucleotide probes to investigate the occurrence and selection of sulfate-reducing bacteria in response to nutrient addition to sediment slurry microcosms from a Japanese estuary

Abstract

The structures of prokaryotic communities are difficult to elucidate because of the apparent inability to culture most of the indigenous microorganisms. Here we report the use of 16S rRNA-targeted oligonucleotide probes to study changes in and the identities of sulfate-reducing bacterial populations present in enriched slurry microcosms from a predominantly freshwater and a predominantly marine site from the River Tama, Tokyo, Japan. Significant enrichment of signals from different oligonucleotide probes, designed to target cultured members of several SRB genera, were observed in amended slurries. Signal from a probe designed to detect Desulfobulbus spp. gave an increased response on propionate addition to slurries from both sites. The response to a probe designed to detect Desulfobacter was increased by acetate addition to slurries from the marine site. Response to a wide specificity probe also increased suggesting that uncharacterised groups were also enriched at the marine site. Our data suggest that Desulfobulbus may be an important propionate utiliser in the estuary, while Desulfobacter is responsible for acetate utilisation at the marine site. These results are compatible with the known physiology of Desulfobulbus and Desulfobacter and provide strong support for the use of oligonucleotide probes in the study of microbial communities.