Genetic variation in symbiotic islands of natural variant strains of soybean Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens differing in competitiveness and in the efficiency of nitrogen fixation

Abstract

Soybean is the most important legume cropped worldwide and can highly benefit from the biological nitrogen fixation (BNF) process. Brazil is recognized for its leadership in the use of inoculants and two strains, Bradyrhizobium japonicum CPAC 15 (=SEMIA 5079) and Bradyrhizobium diazoefficiens CPAC 7 (=SEMIA 5080) compose the majority of the 70 million doses of soybean inoculants commercialized yearly in the country. We studied a collection of natural variants of these two strains, differing in properties of competitiveness and efficiency of BNF. We sequenced the genomes of the parental strain SEMIA 566 of B. japonicum , of three natural variants of this strain (S 204, S 340 and S 370), and compared with another variant of this group, strain CPAC 15. We also sequenced the genome of the parental strain SEMIA 586 of B. diazoefficiens , of three natural variants of this strain (CPAC 390, CPAC 392 and CPAC 394) and compared with the genome of another natural variant, strain CPAC 7. As the main genes responsible for nodulation (nod, noe, nol) and BNF (nif, fix) in soybean Bradyrhizobium are located in symbiotic islands, our objective was to identify genetic variations located in this region, including single nucleotide polymorphisms (SNPs) and insertions and deletions (indels), that could be potentially related to their different symbiotic phenotypes. We detected 44 genetic variations in the B. japonicum strains and three in B. diazoefficiens . As the B. japonicum strains have gone through a longer period of adaptation to the soil, the higher number of genetic variations could be explained by survival strategies under the harsh environmental conditions of the Brazilian Cerrado biome. Genetic variations were detected in genes enconding proteins such as a dephospho-CoA kinase, related to the CoA biosynthesis; a glucosamine-fructose-6-phosphate aminotransferase, key regulator of the hexosamine biosynthetic pathway; a LysR family transcriptional regulator related to nodulation genes; and NifE and NifS proteins, directly related to the BNF process. We suggest potential genetic variations related to differences in the symbiotic phenotypes.

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

“…In addition to examining variation in gene presence/absence, we compared the genomes of the variant and parental strains to identify nucleotide sequence variations potentially associated with differences in BNF efficiency or competitiveness for nodule occupancy. Recently, Bender et al (2022) analyzed SNPs in the SI A of some of the same strains used in our study; while some SNPs were detected in both studies, others were not, likely as we included more strains, used complete genomes, and used different annotation and analysis tools.…”

“…A high-quality draft genome of CPAC 15 was previously sequenced by Siqueira et al (2014) and was retrieved from the National Center of Biotechnology Information (NCBI; GenBank accession CP007569). Draft genomes of strains CNPSo 17, CNPSo 22, CNPSo 23, CNPSo 38, CNPSo 10, CNPSo 104, CNPSo 105, and CNPSo 107 were previously reported by Bender et al, (2022) and their raw Illumina data was used in the process of completing their genomes in this study. All other strains were sequenced as part of this study.…”

“…NifE participates in the Fe-Mo-co metallocluster synthesis of the MoFe-protein of nitrogenase, along with the nifB, nifH, nifN, nifQ, and nifV genes (Kennedy and Dean, 1992). These two SNPs were also detected in CNPSo 22 and CNPSo 38 by Bender et al (2022) and could impact the BNF efficiency of these variant strains.…”

Comparative genome analysis of Sesbania cannabina-nodulating Rhizobium spp. revealing the symbiotic and transferrable characteristics of symbiosis plasmids

“…Among them, the strains within different Rhizobium species presented extraordinarily highly conserved symbiosis genes [17], indicating that they might have acquired the symbiosis genes through HGT in a short evolutionary history. The symbiosis genes are usually located on pSyms [4,[37][38][39] or chromosomal symbiotic islands [40][41][42][43][44]. As for other fast-growing rhizobia, the symbiosis genes of S. cannabina-nodulating rhizobia A. pusense IRBG74 and Sinorhizobium alkalisoli YIC4027 were also located in a pSym [24,45].…”

Effects of Co-Inoculating Saccharomyces spp. with Bradyrhizobium japonicum on Atmospheric Nitrogen Fixation in Soybeans (Glycine max (L.))

“…Although the relevance of biological nitrogen nutrition of soybeans [ Glycine max (L.) Merr.] is recognized worldwide, inoculation with B. japonicum shows variable results and requires supplementation by other synergistic microbes to offer further support to the crop under production [ 22 , 23 ]. The measurement of BNF in legumes is essential for deriving a profound knowledge of their contributions to the N economies of agricultural systems and for N management in agricultural systems [ 24 ], and so is the measurement of the effect of soil yeast on N 2 -fixation and plant productivity.…”