Comparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum

The genus Herbaspirillum gained the spotlight due to the several reports of diazotrophic strains and promising results in plant-growth field assays. However, as diversity exploration of Herbaspirillum species gained momentum, it became clearer that the plant beneficial lifestyle was not the only form of ecological interaction in this genus, due to reports of phytopathogenesis and nosocomial infections. Here we performed a deep search across all publicly available Herbaspirillum genomes. Using a robust core genome phylogeny, we have found that all described species are well delineated, being the only exception H. aquaticum and H. huttiense clade. We also uncovered that the nif genes are only highly prevalent in H. rubrisubalbicans; however, irrespective to the species, all nif genes share the same gene arrangement with high protein identity, and are present in only two main types, in inverted strands. By means of a NifHDKENB phylogenetic tree, we have further revealed that the Herbaspirillum nif sequences may have been acquired from the same last common ancestor belonging to the Nitrosomonadales order.

Automated summary

The genus Herbaspirillum has gained attention for its potential diazotrophic strains and beneficial effects on plant growth. However, further exploration revealed that this genus is not limited to plant beneficial interactions, but also involved in phytopathogenesis and nosocomial infections. Through genome analysis and phylogenetic study, we found that all described Herbaspirillum species are well defined, except for H. aquaticum and H. huttiense. We also discovered that the nif genes are highly prevalent in H. rubrisubalbicans, but share a similar gene arrangement and ancestral origin with other Herbaspirillum species.