A deeply branched novel phylotype found in Japanese paddy soils.
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.
Kim
Hongik
H
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.
Honda
Daiske
D
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.
Hanada
Satoshi
S
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.
Kanamori
Norihiro
N
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.
Shibata
Satoshi
S
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.
Miyaki
Taro
T
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.
Nakamura
Kazunori
K
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.
Oyaizu
Hiroshi
H
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.
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
D019641:DNA, Archaeal; D004275:DNA, Ribosomal; D019642:RNA, Archaeal; D012336:RNA, Ribosomal, 16S