Multilocus Sequence Analysis for Assessment of the Biogeography and Evolutionary Genetics of Four Bradyrhizobium Species That Nodulate Soybeans on the Asiatic Continent

Abstract

A highly supported maximum-likelihood species phylogeny for the genus Bradyrhizobium was inferred from a supermatrix obtained from the concatenation of partial atpD, recA, glnII, and rpoB sequences corresponding to 33 reference strains and 76 bradyrhizobia isolated from the nodules of Glycine max (soybean) trap plants inoculated with soil samples from Myanmar, India, Nepal, and Vietnam. The power of the multigene approach using multiple strains per species was evaluated in terms of overall tree resolution and phylogenetic congruence, representing a practical and portable option for bacterial molecular systematics. Potential pitfalls of the approach are highlighted. Seventy-five of the isolates could be classified as B. japonicum type Ia (USDA110/ USDA122-like), B. liaoningense, B. yuanmingense, or B. elkanii, whereas one represented a novel Bradyrhizobium lineage. Most Nepalese B. japonicum Ia isolates belong to a highly epidemic clone closely related to strain USDA110. Significant phylogenetic evidence against the monophyly of the of B. japonicum I and Ia lineages was found. Analysis of their DNA polymorphisms revealed high population distances, significant genetic differentiation, and contrasting population genetic structures, suggesting that the strains in the Ia lineage are misclassified as B. japonicum. The DNA polymorphism patterns of all species conformed to the expectations of the neutral mutation and population equilibrium models and, excluding the B. japonicum Ia lineage, were consistent with intermediate recombination levels. All species displayed epidemic clones and had broad geographic and environmental distribution ranges, as revealed by mapping climate types and geographic origins of the isolates on the species tree.Soybean (Glycine max) is the most important grain legume in the world, with an annual production of around 180 million tons and a market value of more than 36 billion euros. This crop is planted on 5.7 million, 8.3 million, 29 million, and 30 million hectares in India, China, South America, and North America, respectively (66). It is a major cash crop for small farmers in Asia, in South America, and also in some African countries. The diversity of soybeans today is the result of more than 5,000 years of cultivation, which started in China, where more than 20,000 land races were selected and later globally distributed and further domesticated by modern breeding programs (4). Soybeans were introduced in India around 1000 CE via the silk route from China (26).Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium liaoningense, Ensifer (Sinorhizobium) fredii, Ensifer xinjiangense, and Mesorhizobium tianshanense are the microsymbionts currently known to nodulate soybeans naturally under field conditions (19,23,36,45,46,57,68). Soybean-nodulating B. japonicum strains have been isolated from different continents and climatic zones. Recently, two B. japonicum biovars (symbiotic ecotypes) were described (61). The B. japonicum bv. glycinearum isolates nodulate soybeans, whereas the B. ...

Ensifer alkalisoli sp. nov. isolated from root nodules of Sesbania cannabina grown in saline–alkaline soils

“…Similar to the previous reports (Martens et al, 2008;Vinuesa et al, 2008), MLSA with concatenated sequences (1312 bp) of the housekeeping genes recA, atpD and glnII in the present study (Fig. 2) presented greater discriminatory ability than 16S rRNA gene.…”

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

“…Branch support was estimated using the fast approximate likelihood ratio test (aLRT) and the ShimodairaHasegawa-like (SH-like) procedure [48]. To be consistent with other studies, Bradyrhizobium species were defined as the monophyletic clades including no more than one type strain with branch support ≥0.90 [49] and attempting to adhere to past species demarcations that utilized some of the same loci [35]. We analyzed inter-species variation using the ratio of fixed to shared polymorphisms using DnaSP [50].…”

“…Bradyrhizobium is the most cosmopolitan rhizobial lineage and is found free-living in soils and in aquatic environments as well as in symbiotic association with plant and animal hosts, including humans [29][30][31][32][33][34][35][36][37]. Recent work suggests that there are~19 species of Bradyrhizobium that form symbiotic associations with legumes [36], although non-symbiotic strains are also common in soils [37].…”

“…(e.g., BTAi1 and ORS278) lack a symbiosis island and use a different mechanism to nodulate hosts [41]. Previous studies have revealed that Bradyrhizobium populations can exhibit patterns consistent with epidemics such as a few genotypes existing at high frequency at a single site [33] or genotypes isolated at multiple locations [34,35,37]. But these patterns remain poorly understood, and it is unclear what role the symbiosis island might play as a driver of increased abundance and epidemic spread.…”

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

“…For further analyses, the following sequences were amplified from test or reference strains and aligned for phylogenetic analyses: 16S rRNA, 1228 bp with primers Bac8uf and Univ1492r, according to Grönemeyer et al (2012); ITS, with primers FGPS1490 and FGPS132 (Laguerre et al, 1996), with phylogenetic analysis according to Willems et al (2003) with 627 positions; nodC, 441 bp with primers NodCfor540 and NodCrev1160 (Sarita et al, 2005); glnII, 504 bp with primers glnII 12F and glnII 689R (Vinuesa et al, 2005); recA, 381 bp with primers recA 41F and recA 640R (Vinuesa et al, 2005); rpoB, 416 bp with primers rpoB-454F and rpoB-1364R (Vinuesa et al, 2008); dnaK, 239 bp with primers TSdnaK2 and TSdnaK4 (Stepkowski et al, 2005;Stepkowski et al, 2007) under conditions described previously (Grönemeyer et al, 2014). Concatemers of glnII-recA-rpoB-dnaK contained 1540 positions.…”