Soils of the Chinese Hubei Province Show a Very High Diversity of Sinorhizobium fredii Strains

Proc. Natl. Acad. Sci. U.S.A.

et al. 2012

203

173

The rhizobium–legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. Extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium–legume symbiosis. We sequenced 26 genomes of Sinorhizobium and Bradyrhizobium nodulating soybean to test this hypothesis. The Bradyrhizobium core genome is disproportionally enriched in lipid and secondary metabolism, whereas several gene clusters known to be involved in osmoprotection and adaptation to alkaline pH are specific to the Sinorhizobium core genome. These features are consistent with biogeographic patterns of these bacteria. Surprisingly, no genes are specifically shared by these soybean microsymbionts compared with other legume microsymbionts. On the other hand, phyletic patterns of 561 known symbiosis genes of rhizobia reflected the species phylogeny of these soybean microsymbionts and other rhizobia. Similar analyses with 887 known functional genes or the whole pan genome of rhizobia revealed that only the phyletic distribution of functional genes was consistent with the species tree of rhizobia. Further evolutionary genetics revealed that recombination dominated the evolution of core genome. Taken together, our results suggested that faithfully vertical genes were rare compared with those with history of recombination including lateral gene transfer, although rhizobial adaptations to symbiotic interactions and other environmental conditions extensively recruited lineage-specific shell genes under direct or indirect control through the speciation process.

Section: Resultsmentioning

confidence: 99%

Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations

Tian

Zhou

Proc. Natl. Acad. Sci. U.S.A.

et al. 2012

203

173

“…The soybean rhizobia in the North China Plain were characterized by the predominance of S. fredii (68.28%) followed by B. elkanii (7.12%) and the other eight genospecies (0.32 to 5.83%). In the subtropical and tropic regions of China, which has acidic soils in general, the most abundant soybean rhizobia was B. japonicum, followed by B. elkanii and several genospecies of Bradyrhizobium (23), while S. fredii was isolated only in some zones (4). In Xinjiang, which has saline alkaline soils, both S. fredii (45%) and B. liaoningense (43%) were the predominant soybean rhizobia, while B. yuanmingense, B. japonicum, and Rhizobium strains were the minor groups.…”

Section: Discussionmentioning

confidence: 99%

“…To date, rhizobia nodulating with soybean in Xinjiang (a geographically isolated region surrounded by deserts and high mountains) and in subtropical and tropic regions of China have been systematically studied (4,5,10,23,47,48), and diverse soybean rhizobia belonging to Bradyrhizobium, Mesorhizobium, and Sinorhizobium have been reported in these studies (4,5,10,23,47,48). In addition, biogeographic patterns have been observed in the soybean rhizobia (10,20,23).…”

mentioning

confidence: 99%

Biodiversity and Biogeography of Rhizobia Associated with Soybean Plants Grown in the North China Plain

Liu

Chen

et al. 2011

Appl Environ Microbiol

147

101

As the putative center of origin for soybean and the second largest region of soybean production in China, the North China Plain covers temperate and subtropical regions with diverse soil characteristics. However, the soybean rhizobia in this plain have not been sufficiently studied. To investigate the biodiversity and biogeography of soybean rhizobia in this plain, a total of 309 isolates of symbiotic bacteria from the soybean nodules collected from 16 sampling sites were studied by molecular characterization. These isolates were classified into 10 genospecies belonging to the genera Sinorhizobium and Bradyrhizobium, including four novel groups, with S. fredii (68.28%) as the dominant group. The phylogeny of symbiotic genes nodC and nifH defined four lineages among the isolates associated with Sinorhizobium fredii, Bradyrhizobium elkanii, B. japonicum, and B. yuanmingense, demonstrating the different origins of symbiotic genes and their coevolution with the chromosome. The possible lateral transfer of symbiotic genes was detected in several cases. The association between soil factors (available N, P, and K and pH) and the distribution of genospecies suggest clear biogeographic patterns: Sinorhizobium spp. were superdominant in sampling sites with alkaline-saline soils, while Bradyrhizobium spp. were more abundant in neutral soils. This study clarified the biodiversity and biogeography of soybean rhizobia in the North China Plain.

“…Bradyrhizobium and Sinorhizobium are recurrently reported as microsymbionts of soybeans (8)(9)(10)(11)(12)(13)(14). In contrast to the widely distributed Bradyrhizobium, Sinorhizobium strains nodulating soybeans were mainly found in Asia (9,10,(15)(16)(17)(18) and were reported as the dominant microsymbionts of soybeans in saline-alkaline soils (9,10,16,17). Moreover, Sinorhizobium strains have been demonstrated to be successful soybean inoculants under these soil conditions (19,20).…”

mentioning

confidence: 99%

Replicon-Dependent Differentiation of Symbiosis-Related Genes in Sinorhizobium Strains Nodulating Glycine max

Guo

Wang

et al. 2014

Appl Environ Microbiol

In order to investigate the genetic differentiation of Sinorhizobium strains nodulating Glycine max and related microevolutionary mechanisms, three housekeeping genes (SMc00019, truA, and thrA) and 16 symbiosis-related genes on the chromosome (7 genes), pSymA (6 genes), and pSymB (3 genes) were analyzed. Five distinct species were identified among the test strains by calculating the average nucleotide identity (ANI) of SMc00019-truA-thrA: Sinorhizobium fredii, Sinorhizobium sojae, Sinorhizobium sp. I, Sinorhizobium sp. II, and Sinorhizobium sp. III. These species assignments were also supported by population genetics and phylogenetic analyses of housekeeping genes and symbiosis-related genes on the chromosome and pSymB. Different levels of genetic differentiation were observed among these species or different replicons. S. sojae was the most divergent from the other test species and was characterized by its low intraspecies diversity and limited geographic distribution. Intergenic recombination dominated the evolution of 19 genes from different replicons. Intraspecies recombination happened frequently in housekeeping genes and symbiosis-related genes on the chromosome and pSymB, whereas pSymA genes showed a clear pattern of lateral-transfer events between different species. Moreover, pSymA genes were characterized by a lower level of polymorphism and recombination than those on the chromosome and pSymB. Taken together, genes from different replicons of rhizobia might be involved in the establishment of symbiosis with legumes, but these symbiosis-related genes might have evolved differently according to their corresponding replicons.