Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis

16S rDNA clone libraries were analysed to investigate the microbial diversi ty in marine sediments from Sagami Bay (stations SA, water depth of 1159 m, and SE, 1516 m) and Tokyo Bay (station TK, 43 m). A total of 197 clones wa s examined by amplified rDNA restriction analysis (ARDRA) using three four- base-specific restriction enzymes (HhaI, RsaI and HaeIII). In SA, 57 RFLP t ypes were detected from 77 clones. In SE, 17 RFLP types were detected from 62 clones. In TK, 21 RFLP types were detected from 58 clones. The genotypic diversity among the three sampling sites was 0.958, 0.636 and 0.821, respe ctively, indicating that the microbial diversity of SA was higher than at t he other two stations. At SA, the most abundant RFLP type constituted 10% o f all clones. The samples from SE and TK had dominant RFLP types which cons tituted 60% and 38% of the total clone libraries, respectively. The communi ty structure of SA included many single-type clones, which were found only once in the clone libraries. This structure contrasted with that of the oth er two stations. Thirty-seven clones were selected and sequenced according to dendrograms derived from ARDRA, to cover most of the microbial diversity in the clone libraries. No clones were identical to any of the known 16S r RNA sequences or to each other. All sequences had >84.8% similarity to rDNA sequences retrieved from the DNA databases. Sequenced clones fell into fiv e major lineages of the domain Bacteria: the gamma, delta and epsilon Prote obacteria, Gram-positive bacteria and the division Verrucomicrobia. At SA, the Verrucomicrobia and the three subclasses of the Proteobacteria were fou nd. Most clone sequences belonged to the gamma Proteobacteria. The high-GC Gram-positive bacteria and the gamma subclass of the Proteobacteria were co mmon at both SE and TK. Although the depths of SE and TK were very differen t, the community diversity inferred from ARDRA and the taxonomic position o f the dominant clones were similar. All clones belonging to the high-GC Gra m-positive bacteria collected from both SE and TK fell into the same cluste r and are regarded as members of an unknown actinomycete group. The clone c ompositions were different at each sampling site, and clones of the gamma P roteobacteria and high-GC Cram-positive bacteria were dominant.