The aim of the present study was to investigate the bacterial community structures of deep-sea water (DSW) and surface seawater (SSW) samples in Japan by molecular biological techniques. DGGE analyses and pyrosequencing analysis revealed that bacterial community structures of DSW were diverse and differed from those of SSW. This is the first report on the horizontal variation of bacterial community structures of DSW throughout Japan. In addition, pyrosequencing analysis revealed that the number of phyla in DSW was larger than that in SSW, and specific phyla, such as Firmicutes and Planctomycetes, were characterized by a higher proportion of the bacterial community structure in DSW than in SSW. Taken together, these results indicate that a variety of bacteria that are specifically adapted to the DSW environments can be expected to be found in DSW, and DSW would thus be a potential resource for novel or unique microorganisms and compounds.
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