Microflorae on the edges of global biosphere (deep seafloor and deep subsurface) : phylogenetic and ecological approaches

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This study aimed at the phylogenetic analyses of microorganisms inhabiting deep-sea and deep subsurface based on the DNA sequences of the 16S rRNA gene (165 rDNA) and the genes for ecologically relevant enzymes such as RuBisCO and dissimilatory sulfite reductase (DSR) Samples were collected from deep seafloor sediment by manned/unmanned submersibles and from 1000 m-deep boreholes in Tono area, central Japan.Bulk DNA was extracted from the deep-sea samples and used for PCR-amplification of 16S rRNA, FuBisCO and DSR genes. First, 16S rDNA from the deep-sea methane-rich seep sediment showed a diversified bacterial flora including sulfur-oxidizing bacteria (thiotrophs) and methane-oxidizing bacteria (methanotrophs). The occurrence of these thio-autotrophic and methanotrophic bacteria confirmed the idea that dense biological communities at methane-rich seeps are supported by microbial thiotrophic and methanotrophic production.Various types of RuBisCO genes were recovered from different deep … More -sea samples and analyzed ohy-ogenetically. The RuBisCO-based phylogenetic tree showed different cluster patterns from those of the 16S rDNA-based tree, which was ascribed to horizontal transfer of RuBisCO genes. Anaerobic RuBisCO genes were shown to distribute widely among the deep-sea samples, and their importance in the deep-sea autotrophic production was suggested.The genes of the DSR enzyme playing a major role in sulfate reduction were recovered from a deep-sea methane-rich seep. Phylogenetic analysis of the seep DSR genes showed the previously unknown DSR clusters presumably belonging to Archaea and Bacteria. Diversity of the DSR genes was greater than that of sulfate-reducing bacteria detected by the 16S rDNA-based analysis.Similar analyses were conducted with the samples collected from deep subsurface, and occurrence of diverse chemoautotrophs and anaerobes was demonstrated. Additionally, certain subsurface bacterial strains were isolated and cultured successfully. Taxonomic, phylogenetic and physiological characteristics are being studied. Less