Bradyrhizobium ottawaense sp. nov., a symbiotic nitrogen fixing bacterium from root nodules of soybeans in Canada.

Xiumei Yu,Eden S. P. Bromfield,James T. Tambong,Sylvie Cloutier

doi:10.1099/ijs.0.065540-0

Abstract

Sixteen strains of symbiotic bacteria from root nodules of Glycine max grown in Ottawa, Canada, were previously characterized and placed in a novel group within the genus Bradyrhizobium. To verify their taxonomic status, these strains were further characterized using a polyphasic approach. All strains possessed identical 16S rRNA gene sequences that were 99.79 % similar to the closest relative, Bradyrhizobium liaoningense LMG 18230T. Phylogenetic analysis of concatenated atpD, glnII, recA, gyrB, rpoB and dnaK genes divided the 16 strains into three multilocus sequence types that were placed in a highly supported lineage distinct from named species of the genus Bradyrhizobium consistent with results of DNA–DNA hybridization. Based on analysis of symbiosis gene sequences (nodC and nifH), all novel strains were placed in a phylogenetic group with five species of the genus Bradyrhizobium that nodulate soybeans. The combination of phenotypic characteristics from several tests including carbon and nitrogen source utilization and antibiotic resistance could be used to differentiate representative strains from recognized species of the genus Bradyrhizobium. Novel strain OO99T elicits effective nodules on Glycine max, Glycine soja and Macroptilium atropurpureum, partially effective nodules on Desmodium canadense and Vigna unguiculata, and ineffective nodules on Amphicarpaea bracteata and Phaseolus vulgaris. Based on the data presented, we conclude that our strains represent a novel species for which the name Bradyrhizobium ottawaense sp. nov. is proposed, with OO99T ( = LMG 26739T = HAMBI 3284T) as the type strain. The DNA G+C content is 62.6 mol%.

Highlights

The GenBank/EMBL/DDBJ accession number for the 16S rRNA, atpD, glnII, recA, gyrB, rpoB, dnaK, nodC and nifH gene sequences of strain OO99T are JN186270, HQ455212, HQ587750, HQ587287, HQ873179, HQ587518, JF308816, HQ587980 and JN186287, respectively
Bacteria were grown on yeast-extract mannitol (YEM) agar medium (Vincent, 1970) and pure cultures maintained in 20 % (w/v) glycerol at 280 uC
Consistent with a previous report (Wang et al, 2013), two major groups of species of the genus Bradyrhizobium were evident in phylogenetic trees of 16S rRNA gene sequences: one represented by Bradyrhizobium japonicum and the other by Bradyrhizobium elkanii (Fig. S2)

Summary

Introduction

The GenBank/EMBL/DDBJ accession number for the 16S rRNA, atpD, glnII, recA, gyrB, rpoB, dnaK, nodC and nifH gene sequences of strain OO99T are JN186270, HQ455212, HQ587750, HQ587287, HQ873179, HQ587518, JF308816, HQ587980 and JN186287, respectively. We further characterize these strains using a variety of genotypic and phenotypic methods, and, based on the results, a novel species, Bradyrhizobium ottawaense sp.

Results

Conclusion