A deeply branched novel phylotype found in Japanese paddy soils

• Published in: Microbiology (Society for General Microbiology) 2000-09, Vol.146 (9), p.2309-2315
• Main Authors: Kim, Hongik, Honda, Daiske, Hanada, Satoshi, Kanamori, Norihiro, Shibata, Satoshi, Miyaki, Taro, Nakamura, Kazunori, Oyaizu, Hiroshi
• Format: Article
• Language: English
• Subjects: Agronomy. Soil science and plant productions; Archaea - classification; Archaea - genetics; Archaea - isolation & purification; Base Composition; Base Sequence; Biochemistry and biology; Biological and medical sciences; Chemical, physicochemical, biochemical and biological properties; Crenarchaeota; DNA, Archaeal - chemistry; DNA, Archaeal - genetics; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; Euryarchaeota; Fundamental and applied biological sciences. Psychology; Japan; Microbiology; Molecular Sequence Data; Nucleic Acid Conformation; Oryza; Phylogeny; Physics, chemistry, biochemistry and biology of agricultural and forest soils; RNA, Archaeal - chemistry; RNA, Archaeal - genetics; RNA, Ribosomal, 16S - chemistry; RNA, Ribosomal, 16S - genetics; rRNA 16S gene; Sequence Analysis, DNA; Soil Microbiology; Soil science
• ISSN: 1350-0872; 1465-2080
• DOI: 10.1099/00221287-146-9-2309

Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences 1 , and Institute of Molecular and Cellular Biosciences 2 , The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113, Japan 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, Japan 3 Author for correspondence: Hongik Kim (National Institute of Bioscience and Human-technology). Tel: [phone]. Fax: [phone]. e-mail: hongik{at}nibh.go.jp 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. Keywords: novel soil clones, unculturable micro-organisms, paddy soil, novel phylotype Abbreviations: ML, maximum-likelihood; MP, maximum-parsimony; NJ, neighbour-joining The GenBank/EMBL/DDBJ accession numbers for the sequences of the novel soil clones and their aligned data set are D88480 – D88489 and ds36901 , respectively.