title: A deeply branched novel phylotype found in Japanese paddy soils.
abstract: Novel 16S rDNA clones which possibly constitute a sister clade from the two known archaeal lineages, Crenarchaeota and Euryarchaeota, were found in paddy soil environments. Overall signature sequences showed that the clone sequences shared a majority of signature sequence features with the Archaea and Eukarya. However, there were at least nine nucleotides which distinguished the novel clones from the domains Archaea and Eukarya. Phylogenetic trees, drawn by maximum-parsimony, neighbour-joining and maximum-likelihood methods, also supported the unique phylogenetic position of the clones. Both signature sequence and phylogenetic analyses strongly suggest that the novel organisms constitute a new group and their phylogenetic positions are distant from the Crenarchaeota and Euryarchaeota. A specific primer set was designed to detect the presence of the novel group of organisms in terrestrial environments. Specific DNA fragments were amplified from all paddy soil DNAs, suggesting that the novel organisms are widely distributed in rice paddy fields in Japan.
authors.affiliation: Microbial Resources and Chemotaxonomy Research Group, National Institute of Bioscience and Human-technology, Agency of Industrial Science and Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan3.|Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan.
authors.forename: Hongik
authors.initials: H
authors.lastname: Kim
authors.affiliation: Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan.
authors.forename: Daiske
authors.initials: D
authors.lastname: Honda
authors.affiliation: Microbial Resources and Chemotaxonomy Research Group, National Institute of Bioscience and Human-technology, Agency of Industrial Science and Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan3.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Hanada
authors.affiliation: Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan.
authors.forename: Norihiro
authors.initials: N
authors.lastname: Kanamori
authors.affiliation: Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Shibata
authors.affiliation: Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan.
authors.forename: Taro
authors.initials: T
authors.lastname: Miyaki
authors.affiliation: Microbial Resources and Chemotaxonomy Research Group, National Institute of Bioscience and Human-technology, Agency of Industrial Science and Technology, 1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan3.
authors.forename: Kazunori
authors.initials: K
authors.lastname: Nakamura
authors.affiliation: Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences1, and Institute of Molecular and Cellular Biosciences2, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Oyaizu
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D001482:Base Composition; D001483:Base Sequence; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D007564:Japan; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012275:Oryza; D010802:Phylogeny; D019642:RNA, Archaeal / Q000737:chemistry / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics; D017422:Sequence Analysis, DNA; D012988:Soil Microbiology
chemical_list: D019641:DNA, Archaeal; D004275:DNA, Ribosomal; D019642:RNA, Archaeal; D012336:RNA, Ribosomal, 16S