Seasonal changes in the relative abundance of uncultivated sulfate-reducing bacteria in a salt marsh sediment and in the rhizosphere of Spartina alterniflora.

Phylogenetic diversity and community composition of sulfate-reducing bacteria in a salt marsh sediment and in the rhizosphere of Spartina alterniflora were investigated. Uncultivated Desulfobacteriaceae family-related phylotypes were studied by selectively amplifying 16S rRNA gene fragments from DNA extracted from salt marsh rhizosphere samples. Two novel phylotypes were retrieved from rhizosphere samples, with A01 having 89.1% sequence similarity with Desulfococcus multivorans and 4D19 having 96.3% sequence similarity with Desulfosarcina variabilis. Additionally, six sequences that were extremely closely related to Desulfococcus multivorans (99% sequence similarity) were found. Reference RNAs containing sequences identical to corresponding cloned regions of A01 or 4D19 16S rRNA were synthesized via in vitro transcription and were used in subsequent quantitative membrane hybridization experiments. Oligonucleotide probes A01-183 and 4D19-189 were designed to specifically target these two novel phylotypes and were tested for target specificity against synthesized RNA and reference RNAs extracted from pure cultures. The newly designed probes were then used, together with eubacterial probes, to determine the relative abundances of the novel phylotypes in the salt marsh sediment and the rhizosphere. Mean relative abundances of A01-183 and 4D19-189 targets were 7.5 and 3.4%, respectively, suggesting that the target organisms of A01-183 and, to a lesser extent, of 4D19-189 play an important role in the salt marsh sediment and the Spartina rhizosphere. A seasonal trend of increased A01 relative abundance during the period of vegetative plant growth was evident, suggesting a close interaction between A01 and S. alterniflora.