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Volume 145, Issue 11

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.

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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 four-base-specific restriction enzymes (I, I and III). 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 >848% similarity to rDNA sequences retrieved from the DNA databases. Sequenced clones fell into five major lineages of the domain : the gamma, delta and epsilon , Gram-positive bacteria and the division . At SA, the and the three subclasses of the were found. Most clone sequences belonged to the gamma . The high-GC Gram-positive bacteria and the gamma subclass of the 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 and high-GC Gram-positive bacteria were dominant.

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Keyword(s): 16S rDNA , amplified rDNA restriction analysis (ARDRA) , ARDRA, amplified rDNA restriction analysis , marine sediment , microbial diversity , NJ, neighbour-joining , RDP, Ribosomal Database Project and RFLP
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1999-11-01
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Microbial diversity in marine sediments from Sagami Bay and Tokyo Bay, Japan, as determined by 16S rRNA gene analysisThe DDBJ accession numbers for the sequences reported in this paper are AB022607–AB022642.
Microbiology 145, 3305 (1999); https://doi.org/10.1099/00221287-145-11-3305
/content/journal/micro/10.1099/00221287-145-11-3305
/content/journal/micro/10.1099/00221287-145-11-3305
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