Limits...
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.

Show MeSH

Related in: MedlinePlus

Phylogenetic relationships of NifH protein sequences of Bacteroidales species and related sequences from termite-gut microbial communities. The maximum likelihood trees of the Cluster III of NifH (a) and Cluster II of AnfH (b) were inferred based on 141 and 123 amino acid sites with the WAG+G+I model, respectively. Bootstrap values in percentages are indicated at the nodes when the values were over 50%. The scale bar corresponds to 0.1 substitutions per site.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4356463&req=5

f3-30_44: Phylogenetic relationships of NifH protein sequences of Bacteroidales species and related sequences from termite-gut microbial communities. The maximum likelihood trees of the Cluster III of NifH (a) and Cluster II of AnfH (b) were inferred based on 141 and 123 amino acid sites with the WAG+G+I model, respectively. Bootstrap values in percentages are indicated at the nodes when the values were over 50%. The scale bar corresponds to 0.1 substitutions per site.

Mentions: The presence of the set of nif genes related to conventional nitrogenase and acetylene reduction under nitrogen poor conditions were strong indications of nitrogen fixation ability in the Bacteroidales species identified in this study. The further expansion of potential diazotrophs is expected due to the great species diversity that has not yet been examined by genome sequencing. A related partial nifH gene sequence was recently identified in another Bacteroidales member, Mangrovibacterium diazotrophium (18) (see Fig. 3). As shown in this study for the gut symbiotic community of termites, the identification of nif genes in wider varieties of species will be very useful for predicting the more organismal origins of nif gene sequences in various environments, which is important for obtaining a clearer understanding of the ecology of diazotrophs and their roles in ecosystems.


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)

Phylogenetic relationships of NifH protein sequences of Bacteroidales species and related sequences from termite-gut microbial communities. The maximum likelihood trees of the Cluster III of NifH (a) and Cluster II of AnfH (b) were inferred based on 141 and 123 amino acid sites with the WAG+G+I model, respectively. Bootstrap values in percentages are indicated at the nodes when the values were over 50%. The scale bar corresponds to 0.1 substitutions per site.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3-30_44: Phylogenetic relationships of NifH protein sequences of Bacteroidales species and related sequences from termite-gut microbial communities. The maximum likelihood trees of the Cluster III of NifH (a) and Cluster II of AnfH (b) were inferred based on 141 and 123 amino acid sites with the WAG+G+I model, respectively. Bootstrap values in percentages are indicated at the nodes when the values were over 50%. The scale bar corresponds to 0.1 substitutions per site.
Mentions: The presence of the set of nif genes related to conventional nitrogenase and acetylene reduction under nitrogen poor conditions were strong indications of nitrogen fixation ability in the Bacteroidales species identified in this study. The further expansion of potential diazotrophs is expected due to the great species diversity that has not yet been examined by genome sequencing. A related partial nifH gene sequence was recently identified in another Bacteroidales member, Mangrovibacterium diazotrophium (18) (see Fig. 3). As shown in this study for the gut symbiotic community of termites, the identification of nif genes in wider varieties of species will be very useful for predicting the more organismal origins of nif gene sequences in various environments, which is important for obtaining a clearer understanding of the ecology of diazotrophs and their roles in ecosystems.

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