Genetic Divergence of Bradyrhizobium Strains Nodulating Soybeans as Revealed by Multilocus Sequence Analysis of Genes Inside and Outside the Symbiosis Island

Abstract

The genus Bradyrhizobium has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among Bradyrhizobium strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019, thrA, and truA). This was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA). However, seven genes inside the symbiosis island ("island" genes; nifA, nifH, nodC, nodV, fixA, trpD, and rhcC2) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored by Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, Bradyrhizobium huanghuaihaiense, Bradyrhizobium liaoningense, Bradyrhizobium daqingense, Bradyrhizobium sp. I, Bradyrhizobium sp. III, and Bradyrhizobium sp. IV) was not found in Bradyrhizobium yuanmingense, Bradyrhizobium sp. II, or Bradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes. Soybeans (Glycine max L.) were first domesticated in China and then introduced into different parts of the planet (1), now with an annual harvest area of 100 million hectares around the world (FAO, 2011). Ninety percent of their production comes from the United States, Brazil, Argentina, China, and India (FAO, 2007(FAO, to 2011. One of the key features of soybean is its ability to form symbiotic nitrogen-fixing nodules with diverse rhizobial species (2, 3), implying its important role in sustainable agriculture. It has been recurrently reported that Bradyrhizobium japonicum, Bradyrhizobium elkanii, Bradyrhizobium liaoningense, Bradyrhizobium yuanmingense, and Sinorhizobium fredii could nodulate soybeans (2-5). Recently, Bradyrhizobium huanghuaihaiense, Bradyrhizobium daqingense, Sinorhizobium sojae, and several unnamed species were also found to be effective microsymbionts of soybeans (2, 3, 6-8). Strain USDA110 represents a widely distributed type formerly known as B. japonicum Ia, but it has recently been proposed as a member of the new species Bradyrhizobium diazoefficiens (9).Recent studies not only suggested differences in the biogeographic distribution of rhizobial species nodulating soybeans but also demonstrated a biased selection of rhizobial species by different genotypes of soybeans (2,4,10,11). Consistent with these findings, comparative genomics of rhizobia revealed that the phyletic distribution of rhizobial functional genes involved in environmental adaptations and symbiotic interactions generally agrees with the phylogeny of rhizobial species (7). Therefore, it is important to distinguish different rhizobial species and even subdivis...

A novel symbiovar (aegeanense) of the genus Ensifer nodulates Vigna unguiculata

“…Aligned sequences from the selected genes were concatenated and 3120 bp positions were obtained (Table S5). The housekeeping genes gyrB , recA and glnII have been used widely in phylogenetic studies of Ensifer strains, while, recently, the core genes truA , thrA and SMc00019 were demonstrated to produce phylogenies congruent with the reference species tree of rhizobia . The discriminatory power of the selected gene sequences used for the Ensifer taxa was estimated by the number of parsimony‐informative sites contained in each gene (Table S5).…”

“…The housekeeping genes gyrB, recA and glnII have been used widely in phylogenetic studies of Ensifer strains, 49 -52 while, recently, the core genes truA, thrA and SMc00019 were demonstrated to produce phylogenies congruent with the reference species tree of rhizobia. 31,53,54 The discriminatory power of the selected gene sequences used for the Ensifer taxa was estimated by the number of parsimony-informative sites contained in each gene (Table S5). In our analysis, SMc00019 had the greatest percentage of parsimony-informative characters (31.5%), of the positions used, followed by truA (31.5%), gyrB (30.3%), glnII (29.2%), thrA (26.7%) and recA (23.5%).…”

“…Currently, rhizobia are grouped into symbiovars based mainly on nodC gene phylogenetic analyses and on symbiotic characteristics . The rchRST genes encoding conserved components of the type III secretion system (T3SS) have also been used in phylogenetic analyses of rhizobia as well as other core type III secretion genes, like rhcC2 and rhcJ . The rhizobial T3SSs contribute in nodulation in a manner depending on the host legume though they are not present in all rhizobia .…”

“…26,28 The rchRST genes encoding conserved components of the type III secretion system (T3SS) have also been used in phylogenetic analyses of rhizobia 29 as well as other core type III secretion genes, like rhcC2 and rhcJ. 30,31 The rhizobial T3SSs contribute in nodulation in a manner depending on the host legume though they are not present in all rhizobia. 32 Genes for rhizobial T3SS are found in symbiotic islands located either on the chromosome or on symbiotic plasmids (pSym).…”

Rhizobia Indigenous to the Okavango Region in Sub-Saharan Africa: Diversity, Adaptations, and Host Specificity

“…As several studies reported a congruent phylogeny among nodulation genes and nifH (45)(46)(47), the latter was regarded to be representative. The final alignment consisted of 286 nucleotides, and the Tamura 3-parameter model with gammadistributed evolutionary rates among sites (T92 ϩG) was the bestfit model according to MODELTEST analysis.…”