Molecular Evolution Of Soybean Nodulating Bradyrhizobium And Biogeography Of Indigenous Soybean Rhizobia Revealed By Amplicon Pyrosequencing

Rhizobia are soil bacteria that fix nitrogen after becoming established inside root nodules of appropriate legumes. Rhizobial inoculants could be outcompeted by indigenous rhizobia in certain soil conditions and the application of inoculants in agriculture is therefore severely affected. The soybean rhizobia belong to Bradyrhizobium were widely distributed in the world and as a principal inoculant for soybeans.This study which investigated genetic divergence levels among Bradyrhizobium strains nodulating soybeans in China using phylogenetics and evolutionary genetics, can lay a solid foundation for screening for effective inoculant for soybeans.(1) Based on three useful phylogenetic and taxonomic markers (SMc00019-thrA-truA),76representative Bradyrhizobium strains were identified as eleven genospecies:B. japonicum, B. diazoefficiens, B. daqingense, B. elkanii,B. huanghuaihaiense, B. liaoningense, B. yuanmingense, Bradyrhizobium sp. I, Bradyrhizobium sp. Ⅱ, Bradyrhizobium sp. Ⅲ and Bradyrhizobium sp. IV;(2) Seven genes inside the symbiosis island (island genes:nifA, nifH, nodC, nodV,fixA, trpD and rhcC2) showed contrasting lower level of nucleotide diversity and recombination rate than off_island genes (SMc00019, thrA, truA,fabB, glyA,phyR, exoN and hsfA). Moreover, eight genospecies (including B. japonicum, B. diazoefficiens, B. daqingense, B. huanghuaihaiense, B. liaoningense, Bradyrhizobium sp. I, Bradyrhizobium sp. Ⅲ and Bradyrhizobium sp. Ⅳ) formed a clade in the phylogeny of island genes.(3) There was a potential relationship between the gene flow of island genes and the divergence of off_island genes.On the other hand, we applied the pyrosequencing of rpoB amplicon to study biogeography and biodiversity of indigenous soybean rhizobia in three ecoregions of China (Northeast China, South China and HuangHuangHuai), which can offer theoretical guidance for selecting suitable strains as inoculant for soybeans.(1) The variation of bacterial diversity (a diversity) and community dissimilarities (β diversity) were attributable to spatial distribution.(2) a diversity of soil bacterial communities was significantly related to soil factors such as pH, N, Orc, K, Na+, HCO3-, Cl-, P, EC, and community dissimilarities was largely dependent of geographic distance, soil chemistry and aboveground plant.(3) soybean rhizobia, both in soil and root nodule, exhibit patterns of biogeography, the soybean rhizobia of most abundance in Northeast China was B. japonicum and Bradyrhizobium sp. Ⅲ in soil, whereas Bradyrhizobium sp. Ⅲ in root nodule; In South China, B. diazoefficiens was the dominant group both in soil and root nodule; The diversity of indigenous soybean rhizobia in soil of HuangHuaiHai was shown a high degree, including Bradyrhizobium sp.Ⅲ, B. japonicum, B. huanghuaihaiense, B. elkanii, S. sojae and S.fredii. B. japonicum and S.fredii were isolated from root nodule in HuangHuaiHai, and S.fredii was the main microsymbionts of soybean.(4) There were soil factors like N, P, K, Ore, and pH, that may affect the biogeographic distribution of indigenous soybean rhizobia, though the key factor may be different among three ecoregions.Taken together, these results could provide helpful guidance in selecting efficient rhizobial inoculants for different ecoregions. For example, Bradyrhizobium sp. Ⅲ and B. japonicum in Northeast China, and B. diazoefficiens in South China, these strains were dominant groups in each corresponding ecoregion, respectively and belong to the same epidemic clade in the phylogeny of island genes; S. fredii, the dominant group in HuangHuaiHai, can be a suitable inoculant strain in this ecoregion.