Bradyrhizobium vignae sp. nov., a nitrogen-fixing symbiont isolated from effective nodules of Vigna and Arachis

Abstract

Twenty one strains of symbiotic bacteria from root nodules of local races of cowpea (Vigna unguiculata), Bambara groundnut (Vigna subterranea) and peanuts (Arachis hypogaea) grown on subsistence farmers' fields in the Kavango region of Namibia, were previously characterized as a novel group within the genus Bradyrhizobium. To verify their taxonomic position, the strains were further analysed using a polyphasic approach. 16S rRNA gene sequences were most similar to Bradyrhizobium manausense BR 3351 T , with Bradyrhizobium ganzhouense RITF806 T being the most closely related type strain in the phylogenetic analysis, and Bradyrhizobium yuanmingense CCBAU 10071 T in the ITS sequence analysis. Phylogenetic analysis of concatenated glnII-recA-rpoB-dnaK placed the strains in a highly supported lineage distinct from species of the genus Bradyrhizobium with validly published names; they were most closely related to Bradyrhizobium subterraneum 58 2-1 T . The status of the species was validated by results of DNA-DNA hybridization. The combination of phenotypic characteristics from several tests, including carbon source utilization and antibiotic resistance, could be used to differentiate representative strains of species of the genus Bradyrhizobium with validly published names. Novel strain 7-2 T induced effective nodules on Vigna subterranea, Vigna unguiculata, Arachis hypogaea and on Lablab purpureus. The DNA G+C content of strain 7-2 T was 65.4 mol% (Tm). Based on the data presented, we conclude that these strains represent a novel species for which the name Bradyrhizobium vignae sp. nov. is proposed, with strain 7-2 T [LMG 28791 T , DSMZ 100297 T , NTCCM0018 T (Windhoek)] as the type strain.In the Kavango region of Namibia, agriculture is largely dominated by smallholder farms, without irrigation or agrochemical inputs. Local farmers are confronted with low yields and decreasing soil fertility (Pröpper et al., 2010). The intercropping of grain legumes is common practice with local cereals interspersed in an irregular pattern (Grönemeyer et al., 2013). Cowpea (Vigna unguiculata (L.) Walp., local name in Kavango: makunde) is the main grain legume grown by farmers, but also Bambara groundnut [Vigna subterranea (L.) Verdc., local name: nongomene ] and peanuts (Arachis hypogaea L.) are planted, albeit to a lesser extent (Grönemeyer et al., 2013). Inoculants adapted to the crops and the harsh environmental conditions (long dry seasons and high temperatures) may help to increase yields for local smallholders.In a previous study (Grönemeyer et al., 2014), populations of symbiotic bacteria from nodules of pulses collected in the Kavango region of Namibia and in the Angolan province Bié were sampled. Pure cultures of Bradyrhizobium were isolated and characterized. On the basis of multilocus sequence analysis (MLSA) of concatemers of three protein-coding genes (glnII-recA-rpoB) and intergenic spacer (ITS) sequences, several novel lineages within the genus Bradyrhizobium were suggested by phylogenetic analyses (Gröne-meyer et al....

Bradyrhizobium archetypum sp. nov., Bradyrhizobium australiense sp. nov. and Bradyrhizobium murdochi sp. nov., isolated from nodules of legumes indigenous to Western Australia

“…Nowadays, the suggested threshold for species delineation for the genus Bradyrhizobium using five concatenated genes is 97 % NI [22]. Several phylogenetic studies have suggested a minimum of four [6, 12], or even three [8] concatenated housekeeping genes in the MLSA, and a considerable number of Bradyrhizobium species have been described using four genes and an NI value of 97 % as the threshold for species delineation [2, 13, 33, 35, 36]. In our study, both sets of genes on the MLSA presented NI for the new groups compared with the most related species far below 97 %; the only exception was of group GII.III, which shared from 97 to 97.3 % NI with B.…”

African origin of Bradyrhizobium populations nodulating Bambara groundnut (Vigna subterranea L. Verdc) in Ghanaian and South African soils

“…Consistent with the results obtained with the 16S rDNA gene sequence analysis in this study, the sequence data of nifH and three housekeeping genes ( atpD , recA and glnII ) of the nodule occupants of the five Bambara groundnut landraces also aligned with diverse species of Bradyrhizobium . Single gene phylogenetic analysis showed that some of the nodule bacteria in this study were related to Bradyrhizobium vignae , which nodulates Vigna subterranea , Vigna unguiculata , Arachis hypogaea and Lablab purpureus [ 45 ]. In the phylogenetic trees constructed from sequences of atpD , recA and glnII genes, some monophyletic groups were identified which showed no close relationship with any reference strains.…”

“…Recently, Gronemeyer et al . [ 45 , 51 – 52 ] showed that Bradyrhizobium subterraneum , Bradyrhizobium kavangense and Bradyrhizobium vignae (all of African origin) are responsible for the nodulation of Bambara groundnut. However, from the phylogenetic analysis of individual and concatenated genes in this study, there were many unknown Bradyrhizobium species from Ghanaian and South African soils that nodulated Bambara groundnut, and are still waiting to be properly described.…”

Molecular Basis of Root Nodule Symbiosis between Bradyrhizobium and ‘Crack-Entry’ Legume Groundnut (Arachis hypogaea L.)

“…Phylogenetic analysis also revealed the presence of a new subgroup of Bradyrhizobium, forming a symbiotic association with groundnut. Recent studies identified novel genospecies of Bradyrhizobium involved in nodulation [21,25]. Well-supported groups, obtained based on the intergenic spacer (IGS) sequences, were also retrieved using the nodC gene, suggesting nodC and IGS regions are generally transmitted vertically.…”