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Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes.

Inoue J, Oshima K, Suda W, Sakamoto M, Iino T, Noda S, Hongoh Y, Hattori M, Ohkuma M - Microbes Environ. (2015)

Bottom Line: 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.The identification of nif genes in Bacteroidales facilitates the prediction of the organismal origins of related sequences directly obtained from various environments.

View Article: PubMed Central - PubMed

Affiliation: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Koyadai 3–1–1, Tsukuba, Ibaraki 305–0074, Japan; Synaptech Co. Ltd., Ohte 1–2–37–C–105, Kofu, Yamanashi 400–0015, Japan.

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 15093(T) 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.

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Structure of the nif gene cluster in genomes of Bacteroidales species. The genes indicated by H, D, K, E, N, B, and A are nifH, nifD, nifK, nifE, nifN, nifB, and nifA, respectively. Genes indicated by P are glnB-like putative regulators for nitrogen fixation, those indicated by F are ferredoxin-encoding genes, and those indicated by Ma, Mb, and Mc are modA, modB, and modC homologous genes, respectively, for molybdenum availability. In P. propionicigenes, anfH, anfK, anfG, and anfD are indicated by Ha, Ka, Ga, and Da, respectively. When the genes are located in separate genome regions, the distance between genes are indicated.
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f1-30_44: Structure of the nif gene cluster in genomes of Bacteroidales species. The genes indicated by H, D, K, E, N, B, and A are nifH, nifD, nifK, nifE, nifN, nifB, and nifA, respectively. Genes indicated by P are glnB-like putative regulators for nitrogen fixation, those indicated by F are ferredoxin-encoding genes, and those indicated by Ma, Mb, and Mc are modA, modB, and modC homologous genes, respectively, for molybdenum availability. In P. propionicigenes, anfH, anfK, anfG, and anfD are indicated by Ha, Ka, Ga, and Da, respectively. When the genes are located in separate genome regions, the distance between genes are indicated.

Mentions: Annotations of the genome sequences revealed the presence of nifH, nifD, nifK, nifE, nifN, and nifB in the eight Bacteroidales genomes. These six genes (nifHDKENB) were clustered in this gene order in the seven genomes, except for A. imshenetskii DSM 15055T (Fig. 1). In A. imshenetskii, nifHDK and nifENB were separated by a distance of 29 kb. These six genes corresponded to the minimum nif gene set proposed as a criterion for predicting nitrogen fixation based on genome sequences (9).


Distribution and evolution of nitrogen fixation genes in the phylum Bacteroidetes.

Inoue J, Oshima K, Suda W, Sakamoto M, Iino T, Noda S, Hongoh Y, Hattori M, Ohkuma M - Microbes Environ. (2015)

Structure of the nif gene cluster in genomes of Bacteroidales species. The genes indicated by H, D, K, E, N, B, and A are nifH, nifD, nifK, nifE, nifN, nifB, and nifA, respectively. Genes indicated by P are glnB-like putative regulators for nitrogen fixation, those indicated by F are ferredoxin-encoding genes, and those indicated by Ma, Mb, and Mc are modA, modB, and modC homologous genes, respectively, for molybdenum availability. In P. propionicigenes, anfH, anfK, anfG, and anfD are indicated by Ha, Ka, Ga, and Da, respectively. When the genes are located in separate genome regions, the distance between genes are indicated.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4356463&req=5

f1-30_44: Structure of the nif gene cluster in genomes of Bacteroidales species. The genes indicated by H, D, K, E, N, B, and A are nifH, nifD, nifK, nifE, nifN, nifB, and nifA, respectively. Genes indicated by P are glnB-like putative regulators for nitrogen fixation, those indicated by F are ferredoxin-encoding genes, and those indicated by Ma, Mb, and Mc are modA, modB, and modC homologous genes, respectively, for molybdenum availability. In P. propionicigenes, anfH, anfK, anfG, and anfD are indicated by Ha, Ka, Ga, and Da, respectively. When the genes are located in separate genome regions, the distance between genes are indicated.
Mentions: Annotations of the genome sequences revealed the presence of nifH, nifD, nifK, nifE, nifN, and nifB in the eight Bacteroidales genomes. These six genes (nifHDKENB) were clustered in this gene order in the seven genomes, except for A. imshenetskii DSM 15055T (Fig. 1). In A. imshenetskii, nifHDK and nifENB were separated by a distance of 29 kb. These six genes corresponded to the minimum nif gene set proposed as a criterion for predicting nitrogen fixation based on genome sequences (9).

Bottom Line: 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.The identification of nif genes in Bacteroidales facilitates the prediction of the organismal origins of related sequences directly obtained from various environments.

View Article: PubMed Central - PubMed

Affiliation: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Koyadai 3–1–1, Tsukuba, Ibaraki 305–0074, Japan; Synaptech Co. Ltd., Ohte 1–2–37–C–105, Kofu, Yamanashi 400–0015, Japan.

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 15093(T) 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.

Show MeSH
Related in: MedlinePlus