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

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 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.

Genome Evolution and Nitrogen Fixation in Bacterial Ectosymbionts of a Protist Inhabiting Wood-Feeding Cockroaches

“…Notably, the NifH from Prevotella bryantii B 1 4 did not cluster with the majority of the Bacteroidales NifH proteins, suggesting that P. bryantii B 1 4 nifH has a different origin and that the occurrence of nifH genes in the Bacteroidales is not entirely due to common ancestry. Deviations from a strict vertical evolution of nitrogenase genes in the Bacteroidales have also been noted previously (66).…”

“…Bacteroidales are often associated within the guts of animals and are typically known as degraders of polymeric carbohydrates (80), but recent genome sequencing has revealed the potential for nitrogen fixation in several members (66). It is also becoming increasingly clear that most Bacteroidales endo-and ectosymbionts of protists in the hindguts of termites and cockroaches are likely diazotrophs (16,37).…”

“…4 and 5), suggesting that their nitrogenase genes are ancestral and have generally evolved vertically but were lost in many Bacteroidales (66). The diversity of nifH homologues and associated nitrogenase genes in the Barbulanympha ectosymbiont suggests that a common ancestor possessed a diversity of nitrogenases that were subsequently lost or transferred among the Bacteroidales.…”

“…To generate a NifH phylogeny, the amino acids of ORFs annotated as "nitrogenase iron protein" or nifH were aligned using MAFFT with amino acid sequences from GenBank representing the known diversity of NifH, including those from recently sequenced Bacteroidales genomes (66). The alignment was trimmed using GBlocks.…”

The Gut Microbiota of Termites: Digesting the Diversity in the Light of Ecology and Evolution

“…The diversity of homologs of the nifH gene, a functional marker for nitrogen fixation, indicates broad diazotrophic potential in termite gut communities (e.g., 48,124). In lower termites, symbionts of flagellates seem to play an important role in the fixation and/or upgrading of nitrogen (20,42,43) (Figure 4b).…”