title: High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes.
abstract: Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.
authors.affiliation: Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan.
authors.forename: Mikihiko
authors.initials: M
authors.lastname: Kawai
authors.affiliation: Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Department of Bioscience and Biotechnology, Kyushu University Fukuoka, Japan.
authors.forename: Taiki
authors.initials: T
authors.lastname: Futagami
authors.affiliation: Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics Mishima, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Takaki
authors.affiliation: Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan.
authors.forename: Shinro
authors.initials: S
authors.lastname: Nishi
authors.affiliation: Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan.
authors.forename: Sayaka
authors.initials: S
authors.lastname: Hori
authors.affiliation: Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Arai
authors.affiliation: Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan.
authors.forename: Taishi
authors.initials: T
authors.lastname: Tsubouchi
authors.affiliation: Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Geobio-Engineering and Technology Group, Submarine Resources Research Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Morono
authors.affiliation: National Institute for Basic Biology, National Institutes of Natural Sciences Okazaki, Japan ; Department of Basic Biology, School of Life Science, The Graduate University for Advanced Studies Okazaki, Japan.
authors.forename: Ikuo
authors.initials: I
authors.lastname: Uchiyama
authors.affiliation: Department of Biological Sciences, Tokyo Institute of Technology Yokohama, Japan.
authors.forename: Takehiko
authors.initials: T
authors.lastname: Ito
authors.affiliation: Comparative Genomics Laboratory, Center for Information Biology, National Institute of Genetics Mishima, Japan.
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.affiliation: Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan ; Geobio-Engineering and Technology Group, Submarine Resources Research Project, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Nankoku, Japan.
authors.forename: Fumio
authors.initials: F
authors.lastname: Inagaki
authors.affiliation: Microbial Genome Research Group, Institute of Biogeosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC) Yokosuka, Japan.
authors.forename: Hideto
authors.initials: H
authors.lastname: Takami
keywords: deep biosphere; dehalogenation; metagenome; rdhA; sedimentary habitat