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

Pangenome analysis indicates evolutionary origins and genetic diversity: emphasis on the role of nodulation in symbiotic Bradyrhizobium

The Bradyrhizobium genus is widely known for encompassing many species capable of forming nodules and establishing the biological nitrogen fixation process with several legumes, significantly contributing to agriculture and environmental sustainability. Despite its importance, questions about the evolution, pangenome, and symbiotic genes of Bradyrhizobium are still poorly understood. In this study, we analyzed the pangenome of a set of Bradyrhizobium symbiotic species using the Roary and GET_HOMOLOGUES tools in strains originated from the Northern and Southern Hemispheres. We also investigated the presence and correlation of the fix, nif, nod, Type III secretion system (T3SS) and their effector proteins, and T4SS genes, trying to find differences between clades, hosts, and biogeographic origin. Pangenome analysis of Bradyrhizobium species from the Northern and Southern Hemispheres provided valuable insights into their diversity, biogeography, origin, and co-evolution with their legume host plants. The genus possesses a relatively small core genome compared to the expanded accessory genome, a key feature that facilitates genetic exchange and acquisition of new genes, allowing adaptation to a variety of environments. Notably, the presence or absence of T3SS effector proteins varied significantly according to the geographic location, suggesting specific environmental adaptations, as well as a direct relationship with nodulation genes. Comparative analysis indicated that symbiotic Bradyrhizobium species originated in the Northern Hemisphere and present a greater diversity of orthologous groups than those from the Southern Hemisphere. These results contribute to our understanding of the evolutionary history of these symbiotic bacteria.

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

Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s-1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation.IMPORTANCEToday, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops. As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. 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 the evolution of Bradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.

Nodulation Experiment by Cross-Inoculation of Nitrogen-Fixing Bacteria Isolated from Root Nodules of Several Leguminous Plants

Root-nodule nitrogen-fixing bacteria are known for being specific to particular legumes. This study isolated the endophytic root-nodule bacteria from the nodules of legumes and examined them to determine whether they could be used to promote the formation of nodules in other legumes. Forty-six isolates were collected from five leguminous plants and screened for housekeeping (16S rRNA), nitrogen fixation (nifH), and nodulation (nodC) genes. Based on the 16S rRNA gene sequencing and phylogenetic analysis, the bacterial isolates WC15, WC16, WC24, and GM5 were identified as Rhizobium, Sphingomonas, Methylobacterium, and Bradyrhizobium, respectively. The four isolates were found to have the nifH gene, and the study confirmed that one isolate (GM5) had both the nifH and nodC genes. The Salkowski method was used to measure the isolated bacteria for their capacity to produce phytohormone indole acetic acid (IAA). Additional experiments were performed to examine the effect of the isolated bacteria on root morphology and nodulation. Among the four tested isolates, both WC24 and GM5 induced nodulation in Glycine max. The gene expression studies revealed that GM5 had a higher expression of the nifH gene. The existence and expression of the nitrogen-fixing genes implied that the tested strain had the ability to fix the atmospheric nitrogen. These findings demonstrated that a nitrogen-fixing bacterium, Methylobacterium (WC24), isolated from a Trifolium repens, induced the formation of root nodules in non-host leguminous plants (Glycine max). This suggested the potential application of these rhizobia as biofertilizer. Further studies are required to verify the N2-fixing efficiency of the isolates.

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

Symbiotic nitrogen fixation between legumes and rhizobia makes a great contribution to the terrestrial ecosystem. The successful symbiosis between the partners mainly depends on the nod and nif genes in rhizobia, while the specific symbiosis is mainly determined by the structure of Nod factors and the corresponding secretion systems (type III secretion system; T3SS), etc. These symbiosis genes are usually located on symbiotic plasmids or a chromosomal symbiotic island, both could be transferred interspecies. In our previous studies, Sesbania cannabina-nodulating rhizobia across the world were classified into 16 species of four genera and all the strains, especially those of Rhizobium spp., harboured extraordinarily highly conserved symbiosis genes, suggesting that horizontal transfer of symbiosis genes might have happened among them. In order to learn the genomic basis of diversification of rhizobia under the selection of host specificity, we performed this study to compare the complete genome sequences of four Rhizobium strains associated with S. cannabina, YTUBH007, YTUZZ027, YTUHZ044 and YTUHZ045. Their complete genomes were sequenced and assembled at the replicon level. Each strain represents a different species according to the average nucleotide identity (ANI) values calculated using the whole-genome sequences; furthermore, except for YTUBH007, which was classified as Rhizobium binae, the remaining three strains were identified as new candidate species. A single symbiotic plasmid sized 345-402 kb containing complete nod, nif, fix, T3SS and conjugal transfer genes was detected in each strain. The high ANI and amino acid identity (AAI) values, as well as the close phylogenetic relationships among the entire symbiotic plasmid sequences, indicate that they have the same origin and the entire plasmid has been transferred among different Rhizobium species. These results indicate that S. cannabina stringently selects a certain symbiosis gene background of the rhizobia for nodulation, which might have forced the symbiosis genes to transfer from some introduced rhizobia to the related native or local-condition-adapted bacteria. The existence of almost complete conjugal transfer related elements, but not the gene virD, indicated that the self-transfer of the symbiotic plasmid in these rhizobial strains may be realized via a virD-independent pathway or through another unidentified gene. This study provides insight for the better understanding of high-frequency symbiotic plasmid transfer, host-specific nodulation and the host shift for rhizobia.

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

Crop production encounters challenges due to the dearth of nitrogen (N) and phosphorus (P), while excessive chemical fertilizer use causes environmental hazards. The use of N-fixing microbes and P-solubilizing microbes (PSMs) can be a sustainable strategy to overcome these problems. Here, we conducted a greenhouse pot experiment following a completely randomized blocked design to elucidate the influence of co-inoculating N-fixing bacteria (Bradyrhizobium japonicum) and PSMs (Saccharomyces cerevisiae and Saccharomyces exiguus) on atmospheric N₂-fixation, growth, and yield. The results indicate a significant influence of interaction on Indole-3-acetic acid production, P solubilization, seedling germination, and growth. It was also found that atmospheric N₂-fixation, nodule number per plant, nodule dry weight, straw, and root dry weight per plant at different growth stages were significantly increased under dual inoculation treatments relative to single inoculation or no inoculation treatment. Increased seed yield and N and P accumulation were also noticed under co-inoculation treatments. Soil available N was highest under sole bacterial inoculation and lowest under the control treatment, while soil available P was highest under co-inoculation treatments and lowest under the control treatment. We demonstrated that the co-inoculation of N-fixing bacteria and PSMs enhances P bioavailability and atmospheric N₂-fixation in soybeans leading to improved soil fertility, raising crop yields, and promoting sustainable agriculture.