Diversity and vertical distribution of cultured and uncultured Deltaproteobacteria in an intertidal mud flat of the Wadden Sea

The diversity and distribution of Deltaproteobacteria in an intertidal mud flat of the German Wadden Sea was characterized by molecular biological techniques and cultivation. A 16S rRNA gene library generated with general primers (303 clones) suggested that sulfate-reducing bacteria (SRB) related to Desulfobulbaceae and Desulfosarcina were abundant. Fluorescence in situ hybridization (FISH) with probes targeting these groups was used to characterize their vertical distribution. The combination of FISH with catalysed reporter deposition (CARD-FISH) significantly enhanced the detection of selected subgroups of Deltaproteobacteria, particularly in deeper sediment layers. Up to 11% of all cells were assigned to SRB. Organisms related to Desulfosarcina and Desulfobulbaceae were the dominant SRB in the surface sediments. Two abundant subpopulations of Desulfosarcina-related bacteria were identified by FISH. The SRB community differed between the sampling site and a sandy intertidal flat chosen as a reference. Enrichments and MPN cultures inoculated with surface sediment were monitored by FISH. Nine strains of Deltaproteobacteria were isolated. Four strains were related to Desulfobulbaceae, such as Desulfobacterium catecholicum and Desulfocapsa spp. A subgroup including clone sequences and strains related to D. catecholicum could be detected in situ by a specific FISH probe. The first physiological experiments suggested specific functional roles for the isolates. Two strains utilized environmentally relevant compounds in coastal areas such as catechol and nitrate. One strain related to Desulfocapsa spp. disproportionated thiosulfate and might thus contribute to the sulfur isotope fractionation at the study site. A Fe(III)-reducing strain was obtained that affiliated with the Pelobacter-Desulphuromonas group. This group accounted for up to 6% of total cell numbers and even exceeded SRB numbers in upper sediment layers. These bacteria might substantially contribute to carbon mineralization via dissimilatory reduction of, e.g. Fe(III).