Comparative genomic analysis ofBradyrhizobiumstrains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions

Abstract

ABSTRACTBradyrhizobiumis known for its ability to fix atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight putative natural variants ofB. japonicumSEMIA 586 (=CNPSo 17) orB. diazoefficiensSEMIA 566 (=CNPSo 10), previously used as commercial inoculants for soybean crops in Brazil. We aimed to detect genetic variations that might be related to biological nitrogen fixation, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains and used for comparative genomic analyses. The core genome phylogeny revealed that strains of each group are closely related, confirmed by high average nucleotide identity (ANI) values. However, variants accumulated divergences resulting from horizontal gene transfer (HGT), genomic rearrangements, and nucleotide polymorphisms. TheB. japonicumgroup presented a larger pangenome and a higher number of nucleotide polymorphisms than theB. diazoefficiensgroup, probably due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of theB. japonicumgroup carry two plasmids. The genetic variability found in both groups is discussed in light of the observed differences in their nitrogen fixation capacity, competitiveness for nodule occupancy, and environmental adaptation.SIGNIFICANCEThe two main reference strains for soybean inoculation in Brazil,B. japonicumCPAC 15 (=SEMIA 5079) andB. diazoefficiensCPAC 7 (=SEMIA 5080), have been considered highly competitive and highly efficient in nitrogen fixation, respectively. In this study, we obtained and analyzed the genomes of the parental and variant strains. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into evolution ofBradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.