Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes

Jun Ichi Inoue, Kenshiro Oshima, Wataru Suda, Mitsuo Sakamoto, Takao Iino, Satoko Noda, Yuichi Hongoh, Masahira Hattori, Moriya Ohkuma

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

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 15548 T. 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.

Original languageEnglish
Pages (from-to)44-50
Number of pages7
JournalMicrobes and Environments
Volume30
Issue number1
DOIs
Publication statusPublished - 2015
Externally publishedYes

Fingerprint

nitrogen fixation
Dysgonomonas
gene
genome
genes
Bacteroides
nitrogen-fixing bacteria
acetylene reduction
acetylene
amino acid sequences
prediction
Bacteroidetes
Bacteroidales
distribution
phylogeny
phylogenetics
protein

Keywords

  • Bacteroidales
  • Nif gene
  • Nitrogenase
  • Symbiosis
  • Termite

ASJC Scopus subject areas

  • Plant Science
  • Soil Science
  • Ecology, Evolution, Behavior and Systematics

Cite this

Inoue, J. I., Oshima, K., Suda, W., Sakamoto, M., Iino, T., Noda, S., ... Ohkuma, M. (2015). Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes. Microbes and Environments, 30(1), 44-50. https://doi.org/10.1264/jsme2.ME14142

Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes. / Inoue, Jun Ichi; Oshima, Kenshiro; Suda, Wataru; Sakamoto, Mitsuo; Iino, Takao; Noda, Satoko; Hongoh, Yuichi; Hattori, Masahira; Ohkuma, Moriya.

In: Microbes and Environments, Vol. 30, No. 1, 2015, p. 44-50.

Research output: Contribution to journalArticle

Inoue, JI, Oshima, K, Suda, W, Sakamoto, M, Iino, T, Noda, S, Hongoh, Y, Hattori, M & Ohkuma, M 2015, 'Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes', Microbes and Environments, vol. 30, no. 1, pp. 44-50. https://doi.org/10.1264/jsme2.ME14142
Inoue, Jun Ichi ; Oshima, Kenshiro ; Suda, Wataru ; Sakamoto, Mitsuo ; Iino, Takao ; Noda, Satoko ; Hongoh, Yuichi ; Hattori, Masahira ; Ohkuma, Moriya. / Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes. In: Microbes and Environments. 2015 ; Vol. 30, No. 1. pp. 44-50.
@article{d0e785149cb34b38bbcdb39769a53191,
title = "Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes",
abstract = "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 15548 T. 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.",
keywords = "Bacteroidales, Nif gene, Nitrogenase, Symbiosis, Termite",
author = "Inoue, {Jun Ichi} and Kenshiro Oshima and Wataru Suda and Mitsuo Sakamoto and Takao Iino and Satoko Noda and Yuichi Hongoh and Masahira Hattori and Moriya Ohkuma",
year = "2015",
doi = "10.1264/jsme2.ME14142",
language = "English",
volume = "30",
pages = "44--50",
journal = "Microbes and Environments",
issn = "1342-6311",
publisher = "Japanese Society Of Microbial Ecology",
number = "1",

}

TY - JOUR

T1 - Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes

AU - Inoue, Jun Ichi

AU - Oshima, Kenshiro

AU - Suda, Wataru

AU - Sakamoto, Mitsuo

AU - Iino, Takao

AU - Noda, Satoko

AU - Hongoh, Yuichi

AU - Hattori, Masahira

AU - Ohkuma, Moriya

PY - 2015

Y1 - 2015

N2 - 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 15548 T. 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.

AB - 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 15548 T. 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.

KW - Bacteroidales

KW - Nif gene

KW - Nitrogenase

KW - Symbiosis

KW - Termite

UR - http://www.scopus.com/inward/record.url?scp=84925456954&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84925456954&partnerID=8YFLogxK

U2 - 10.1264/jsme2.ME14142

DO - 10.1264/jsme2.ME14142

M3 - Article

VL - 30

SP - 44

EP - 50

JO - Microbes and Environments

JF - Microbes and Environments

SN - 1342-6311

IS - 1

ER -