Abstract
Vigna minima is a climbing annual plant widely distributed in barren wilderness, grass land, and shrub bush of China and other countries such as Japan. However, the rhizobia nodulating with this plant has never been systematically studied. In order to reveal the biodiversity of nodulating rhizobia symbiosis with V. minima, a total of 874 rhizobium isolates were obtained from root nodules of the plant spread in 11 sampling sites of Shandong Peninsula, China, and they were designated as 41 haplotypes in the genus Bradyrhizobium based upon recA sequence analyses. By multilocus sequence analysis (MLSA) of five housekeeping genes (dnaK, glnII, gyrB, recA, and rpoB), the 41 strains representing different recA haplotypes were classified into nine defined species and nine novel genospecies. Bradyrhizobium elkanii, Bradyrhizobium ferriligni, and Bradyrhizobium pachyrhizi were the predominant and universally distributed groups. The phylogeny of symbiotic genes of nodC and nifH showed similar topology and phylogenetic relationships, in which all the representative strains were classified into two clades grouped with strains nodulating with Vigna spp., demonstrating that Vigna spp. shared common nodulating groups in the natural environment. All the representative strains formed nodules with V. minima in a nodulation test performed in green house conditions. The correlation between V. minima nodulating rhizobia and soil characteristics analyzed by CANOCO indicates that available nitrogen, total nitrogen, and organic carbon in the soil samples were the main factors affecting the distribution of rhizobia isolated in this study. This study systematically uncovered the biodiversity and distribution characteristics of V. minima nodulating rhizobia for the first time, which provided novel information for the formation of the corresponding rhizobium community.
Highlights
The genus Vigna is a member of the legume family, consisting of more than 100 species, which widely spread all over the world, mainly in warm temperate and tropical regions (Sakai et al, 2015)
Forty-one recA haplotypes, in which nine covered only one strain and H30 covered 238 strains, were classified according to the recA sequence analysis, and one randomly selected representative for each haplotype was used for the subsequent phylogenetic analyses (Supplementary Table 1)
According to the phylogenetic tree based on recA sequences, all the representative strains were classified into the genus of Bradyrhizobium
Summary
The genus Vigna is a member of the legume family, consisting of more than 100 species, which widely spread all over the world, mainly in warm temperate and tropical regions (Sakai et al, 2015). A number of wild species, such as Vigna minima (Roxb.), were included in this genus that were found to possess some valuable phenotypic characteristics, such as high tolerance to severe conditions including high salinity, acidic or alkaline soil, drought and flooding, and other excellent phenotypes such as resistance to pest and disease and crosscompatibility (Chankaew et al, 2014; Tomooka et al, 2014; Sakai et al, 2015; Yoshida et al, 2016). Rhizobia encompass more than 180 species in 21 genera of two classes (Alphaproteobacteria and Betaproteobacteria), and the genera Bradyrhizobium, Rhizobium, Mesorhizobium, and Ensifer harbored the most common and the majority of the rhizobial species; nodulation was thought to arose from Bradyrhizobium (Ormeño-Orrillo and Martínez-Romero, 2019; Chen et al, 2020)
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