Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysis The DDBJ accession numbers for the sequences reported in this paper are AB022607–AB022642.

Abstract

16S rDNA clone libraries were analysed to investigate the microbial diversity in marine sediments from Sagami Bay (stations SA, water depth of 1159 m, and SB, 1516 m) and Tokyo Bay (station TK, 43 m). A total of 197 clones was examined by amplified rDNA restriction analysis (ARDRA) using three fourbase-specific restriction enzymes (HhaI, RsaI and HaeIII). In SA, 57 RFLP types were detected from 77 clones. In SB, 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 0958, 0636 and 0821, respectively, indicating that the microbial diversity of SA was higher than at the other two stations. At SA, the most abundant RFLP type constituted 10 % of all clones. The samples from SB and TK had dominant RFLP types which constituted 60 % and 38 % of the total clone libraries, respectively. The community structure of SA included many single-type clones, which were found only once in the clone libraries. This structure contrasted with that of the other 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 rRNA sequences or to each other. All sequences had S848 % similarity to rDNA sequences retrieved from the DNA databases. Sequenced clones fell into five major lineages of the domain Bacteria : the gamma, delta and epsilon Proteobacteria, Gram-positive bacteria and the division Verrucomicrobia. At SA, the Verrucomicrobia and the three subclasses of the Proteobacteria were found. Most clone sequences belonged to the gamma Proteobacteria. The high-GC Gram-positive bacteria and the gamma subclass of the Proteobacteria were common at both SB and TK. Although the depths of SB and TK were very different, the community diversity inferred from ARDRA and the taxonomic position of the dominant clones were similar. All clones belonging to the high-GC Gram-positive bacteria collected from both SB and TK fell into the same cluster and are regarded as members of an unknown actinomycete group. The clone compositions were different at each sampling site, and clones of the gamma Proteobacteria and high-GC Gram-positive bacteria were dominant.

Characterization of halophilic bacteria from environmental samples from the brackish water of Pulicat Lake, India

“…and could be a novel organism. When only cultivation-dependent approaches were utilized, the γ-Proteobacteria and Firmicutes did, indeed, predominate, as evidenced in the previous studies of marine sediment by Gray & Herwing (1996), Urakawa et al (1999) and in solar salterns by Yeon et al (2005). Microbial diversity analysis in water and sediment of Lake Chaka, a hypersaline lake on Tibetan plateau, also revealed the distribution of bacterial isolates into three groups: Firmicutes, γ-Proteobacteria and Actinobacteria ).…”

Bacterial diversity and biogeography in deep-sea surface sediments of the South Atlantic Ocean

“…Among Diversity and biogeography in deep-sea sediments R Schauer et al these phylotypes 11 OTUs (12 sequences) clustered with the NOR5/OM60 clade that includes 'Congregibacter litoralis' strain KT71, the first marine aerobic anoxygenic phototrophic Gammaproteobacteria in culture (Fuchs et al, 2007;Yan et al, 2009 (Figures 3a and b) and to Cret-1F, BD1-1, PWP and South Ionian groups (11 OUT, 27 sequences). These groups included only 16S rRNA gene sequences that originated from other deep-sea or permanent cold marine habitats Li et al, 1999;Ravenschlag et al, 1999;Urakawa et al, 1999;Bowman and McCuaig, 2003;Polymenakou et al, 2005;Xu et al, 2005;Zhao and Zeng, 2005). The Alpha-, Beta-and Deltaproteobacteria accounted together for 18 to 23% of all sequences in the libraries.…”

Characterization of microbial communities in marine surface sediments by terminal-restriction fragment length polymorphism (T-RFLP) analysis and quinone profiling

“…Today, new molecular techniques based on 16S rRNA enable us to analyze the microbial community without cultivation (Pace et al 1986). One important approach is 16S rDNA clone library analysis (Giovannoni et al 1990), and several studies have been carried out on marine sediment communities using this technique (Gray & Herwig 1996, Ravenschlag et al 1999, Urakawa et al 1999a However, this technique is not sufficient for comparative studies involving several sampling locations or for monitoring population shifts, since it is time-consuming and labor-intensive. For these reasons, there is currently great interest in molecular fingerprinting techniques, such as denaturing gradient gel electrophoresis (DGGE), as effective approaches for evaluating large numbers of samples or monitoring population shifts (Muyzer et al 1993).…”