The Nitrogen-Fixation Island Insertion Site Is Conserved in Diazotrophic Pseudomonas stutzeri and Pseudomonas sp. Isolated from Distal and Close Geographical Regions

Abstract

The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.

The novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501

“…Former reports suggested that an Hfq homolog, NrfA, was required for nifA expression in Azorhizobium caulinodans and Rhodobacter capsulatus although the involvement of an RNA molecule in this regulation was not shown (48)(49)(50). The nif islands in P. stutzeri isolated from diverse niches and geographical origin revealed relatively high degrees of conservation (18)(19)(20)(21), also implying that this ncRNA-based regulatory role is not limited to A1501 but can be extended to other nitrogen-fixing isolates, including the unique Pseudomonas azotifigens strain DSM17556 that is phylogenetically close to P. stutzeri (18,21,51).…”

“…A recent in silico analysis revealed that the island is also conserved in other available genomes of nitrogen-fixing P. stutzeri (ref. 21 and references therein). The regulation of nif gene transcription in most diazotrophs depends on the sigma factor RpoN/global nitrogen activator NtrC/nif-specific activator NifA regulatory cascade (22).…”

Ammonium excretion, auxin production and effects of maize inoculation with ethylenediamine-resistant mutants of Pseudomonas sp.

“…The ability to fix atmospheric nitrogen is not common in species of Pseudomonas genus, which comprises more than 140 species with a great metabolic diversity (Venieraki et al 2014). The diazotrophic capacity of Pseudomonas species seems to have been acquired through horizontal gene transfer, not being considered a determining taxonomic characteristic.…”

Identification and genomic analysis of temperate Pseudomonas bacteriophage PstS-1 from the Japan trench at a depth of 7000 m

“…In addition, it has been recently reported that culturable heterotrophs and environmental sequences related to P. stutzeri dominated in hadal zones [39]. Members of P. stutzeri display diverse metabolic capabilities, such as denitrification, nitrogen fixation and degradation of aromatic compounds [41,42]. In this study, we isolated a psychrotolerant P. stutzeri-related strain from hadopelagic water (depth of 7000 m) of the Japan Trench and characterized a novel inducible temperate phage from this organism.…”