Distribution and Evolution of Nitrogen Fixation Genes in the Phylum <i>Bacteroidetes</i>

DOI Web Site PubMed 4 Citations 37 References Open Access
  • Inoue Jun-ichi
    Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center Synaptech Co. Ltd.
  • Oshima Kenshiro
    Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo
  • Suda Wataru
    Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo
  • Sakamoto Mitsuo
    Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center
  • Iino Takao
    Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center
  • Noda Satoko
    Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi
  • Hongoh Yuichi
    Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center Department of Biological Sciences, Tokyo Institute of Technology
  • Hattori Masahira
    Center for Omics and Bioinformatics, Graduate School of Frontier Sciences, The University of Tokyo
  • Ohkuma Moriya
    Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center Biomass Research Platform Team, RIKEN Biomass Engineering Program Cooperation Division, RIKEN Center for Sustainable Resource Science

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  • Distribution and Evolution of Nitrogen Fixation Genes in the Phylum Bacteroidetes

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Diazotrophs had not previously been identified among bacterial species in the phylum Bacteroidetes until the rapid expansion of bacterial genome sequences, which revealed the presence of nitrogen fixation (nif) genes in this phylum. We herein determined the draft genome sequences of Bacteroides graminisolvens JCM 15093T and Geofilum rubicundum JCM 15548T. In addition to these and previously reported ‘Candidatus Azobacteroides pseudotrichonymphae’ and Paludibacter propionicigenes, an extensive survey of the genome sequences of diverse Bacteroidetes members revealed the presence of a set of nif genes (nifHDKENB) in strains of Dysgonomonas gadei, Dysgonomonas capnocytophagoides, Saccharicrinis fermentans, and Alkaliflexus imshenetskii. These eight species belonged to and were distributed sporadically within the order Bacteroidales. Acetylene reduction activity was detected in the five species examined, strongly suggesting their diazotrophic nature. Phylogenetic analyses showed monophyletic clustering of the six Nif protein sequences in the eight Bacteroidales species, implying that nitrogen fixation is ancestral to Bacteroidales and has been retained in these species, but lost in many other lineages. The identification of nif genes in Bacteroidales facilitates the prediction of the organismal origins of related sequences directly obtained from various environments.

Journal

  • Microbes and Environments

    Microbes and Environments 30 (1), 44-50, 2015

    Japanese Society of Microbial Ecology / Japanese Society of Soil Microbiology / Taiwan Society of Microbial Ecology / Japanese Society of Plant Microbe Interactions / Japanese Society for Extremophiles

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