Soybeans inoculated with root zone soils of Canadian native legumes harbour diverse and novel Bradyrhizobium spp. that possess agricultural potential

Abstract

An assessment was made of the evolutionary relationships of soybean nodulating bacteria associated with legumes native to eastern Canada to identify potential new sources of soybean inoculant strains. Short season soybeans were used to selectively trap bacteria from root zone soils of four native legume species. Screening of more than 800 bacterial isolates from soybean root nodules by analysis of recA gene sequences followed by analyses of selected genotypes using six core and two symbiosis (nodC and nifH) gene sequences permitted identification of diverse taxa that included eight novel and four named Bradyrhizobium species as well as lineages attributed to the genera Afipia and Tardiphaga. Plant tests showed that symbionts related to four named species as well as a novel Bradyrhizobium lineage were highly efficient with regard to nitrogen fixation on soybeans relative to an inoculant strain. A new symbiovar (sv. septentrionalis) is proposed based on a group of four novel Bradyrhizobium spp. that possess distinctive nodC and nifH gene sequences and symbiotic characteristics. Evidence is provided for horizontal transfer of sv. septentrionalis symbiosis genes between novel Bradyrhizobium spp., a process that rendered recipient bacteria ineffective on soybeans. Diverse lineages of non-symbiotic and symbiotic Bradyrhizobium spp. co-occured within monophyletic clusters in a phylogenetic tree of concatenated core genes, suggesting that loss and/or gain of symbiosis genes has occurred in the evolutionary history of the bacterial genus. Our data suggest that symbiont populations associated with legumes native to eastern Canada harbour elite strains of Bradyrhizobium for soybean inoculation.

Strains of Bradyrhizobium cosmicum sp. nov., isolated from contrasting habitats in Japan and Canada possess photosynthesis gene clusters with the hallmark of genomic islands

“…In a previous study [2], bacteria were isolated from root nodules of soybean plants that had been inoculated with root-zone soils from legumes native to Canada. Bacterial isolates were characterized by multiple locus sequence analysis (MLSA) of five protein-encoding core genes and several novel lineages in the genus Bradyrhizobium were identified.…”

“…Novel strain 58S1 T was isolated from a root nodule of a soybean plant that had been inoculated with a suspension of root-zone soil of Amphicarpaea bracteata (hog peanut) plants growing in deciduous woodland in Gatineau, Quebec, Canada [2]. Strain 58S1 T was deposited in the BCCM/LMG Bacteria Collection, University of Ghent, Belgium (LMG collection no.…”

“…betae PL7HG1 T [4] isolated from a tumour on the roots of sugar beet [3], B. amphicarpaeae 39S1MB T [37] isolated from a root nodule of soybean [2] and to Rhodopseudomonas palustris CGA009 [38]. In contrast, the arrangement of the genes in the PGC of strains 58S1 T and S23321 differs from B.…”

Diversity of bacteria associated with corn roots inoculated with Canadian woodland soils, and description of Pseudomonas aylmerense sp. nov.

“…Two corn cultivars, early Golden Bantam (E) and Bt4223 (Bt) were used as trap plants. The experimental set-up was done as reported previously [19] with modifications. Corn seeds were surface disinfected in 95% ethanol (Sigma-Aldrich, Canada) for 30 seconds followed by commercial bleach (Clorox; 5.25% NaOCl) for the same time.…”

“…As such, we initiated a prospective study to collect soil samples from a woodland in Aylmer, Québec, Canada. The rhizosphere soils of Canadian native legumes were targeted because previous studies show that they harbor unique and novel Bradyrhizobium genotypes [19, 20] using soybean as trap hosts. This article reports the characterization of bacteria isolated from rhizosphere soils of a Canadian woodland, and the description of a novel species, Pseudomonas alymerense sp.…”