Sinorhizobium prairiense sp. nov., a nitrogen-fixing symbiont of Phaseolus vulgaris isolated from Canadian prairie soil

TL;DR

Scientists discovered a new species of nitrogen-fixing bacteria that helps beans grow in Canadian prairie soil.

Contribution

A new species of Sinorhizobium, Sinorhizobium prairiense, is proposed based on genomic and phenotypic analysis.

Findings

The isolates form a distinct group within the Sinorhizobium clade and are closely related to Sinorhizobium meliloti.

The isolates contain four replicons and are capable of symbiotic nitrogen fixation with Phaseolus vulgaris.

The nodulation genes suggest a close relationship with the mediterranensis symbiovar and Sinorhizobium americanum.

Abstract

Three symbiotic bacteria (K101T, C101 and M103) were obtained from nodule-trapping experiments using Phaseolus vulgaris, which was inoculated with soil samples from three distinct field sites in Manitoba, Canada. Here, we provide a phenotypic characterization and genomic analysis of these bacteria. Based on a core phylogeny (424 core genes), digital DNA–DNA hybridization and average nucleotide alignment, these isolates group within the Sinorhizobium clade and are closely related to Sinorhizobium meliloti. Each strain contains four replicons that include a chromosome (3.5 Mb), a putative chromid (1.7 Mb) and two plasmids (plasmid A, 0.56 Mb; plasmid B, 0.77 Mb). The chromosome, chromid and plasmid B are closely related to the replicons found in S. meliloti, as shown by phylogenies constructed from the concatenation of either the parAB genes for the chromosome or the repABC genes for the chromid and plasmid B. The remaining plasmid was found to group with a plasmid from Sinorhizobium americanum. Consistent with this, the nodulation genes on this plasmid were also more similar to those in S. americanum, as seen in a phylogeny generated from the concatenation of the nodABC genes. Examination of the nodC phylogeny suggests a close association with the mediterranensis symbiovar. All three isolates were capable of symbiotic nitrogen fixation with P. vulgaris. Based on genomic and phenotypic data, we propose these isolates as a novel species within the Sinorhizobium clade, named Sinorhizobium prairiense sp. nov., for which the type strain is K101T (=LMG 33767T=DSM 118657T).

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