Dynamic succession of chickpea rhizobia over years and sampling sites in Xinjiang, China

Aims To investigate the succession of chickpea rhizobia over years and sampling sites. Methods Rhizobia were sampled four times from nodules of chickpea grown in four sites of Mulei County and Qitai County in Xinjiang, China during 2009-2016. The recA genes of rhizobia representing different populations were phylogenetically compared for their genotypic differentiation. Soil properties were examined to explore their hypothetical incidence on the rhizobial succession. Results The 628 isolates were all identified as Mesorhizobium muleiense, belonging to 28 genotypes distinguished by recA phylogeny. For each site, 15, 17, 10 and 7 genotypes were detected during the whole sampling period; while 4, 15, 12 and 17 genotypes were evidenced in each of the 4 sampling years (2009, 2013, 2015 and 2016) from all the four sites. Four major genotypes (T12 through T15) were found throughout the four years in the four sites at various frequencies. While the other genotypes were site and/or year specific. Both increased genetic diversity as revealed by Shannon-Weaver index and shifts in the population composition as revealed by genotyping were detected in the chickpea rhizobial populations during the study period. Nitrogen content, available phosphorus and potassium, and pH were the main factors correlated to the genotype distribution of chickpea rhizobia in the soil over years. Conclusions The genetic diversity of M. muleiense increased and the population composition shifted over years and at different sampling sites. The recA gene is an adequate molecular marker to estimate the intraspecific variation and succession of M. muleiense genotypes. The rhizobial genotype succession/evolution in the fields might be driven by the fluctuations of soil characteristics like nitrogen content, available phosphorus and potassium, and pH.