The Mesorhizobium huakuii transcriptional regulator AbiEi plays a critical role in nodulation and is important for bacterial stress response

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.

Application of cotton straw biochar and compound Bacillus biofertilizer decrease the bioavailability of soil cd through impacting soil bacteria

Background

Cd seriously threatens soil environment, remedying Cd in farmland and clearing the response of soil environment to modifiers in Cd-contaminated soils is necessary. In this study, the effects of cotton straw biochar and compound Bacillus biofertilizer used as modifiers on the biochemical properties, enzyme activity, and microbial diversity in Cd-contaminated soils (1, 2, and 4 mg·kg⁻¹) were investigated.

Results

The results showed that both cotton straw biochar and compound Bacillus biofertilizer could improve the soil chemical characteristics, including the increase of soil C/N ratio, electrical conductance (EC) and pH, and the most important decrease of soil available Cd content by 60.24% and 74.34%, respectively (P < 0.05). On the other hand, adding cotton straw biochar and compound Bacillus biofertilizer in Cd stressed soil also improved soil biological characteristics. Among them, cotton straw biochar mainly through increasing soil alkaline phosphatase activity and improve bacteria abundance, compound Bacillus biofertilizer by increasing soil invertase, alkaline phosphatase, catalase, and urease activity increased bacterial community diversity. On the whole, the decrease of soil available Cd was mainly caused by the increase of soil pH, C/N, urease and alkaline phosphatase activities, and the relative abundance of Acidobacteria and Proteobacteria.

Conclusions

In summary, the applications of cotton straw biochar and compound Bacillus biofertilizer could decrease soil available Cd concentration, increase soil bacterial community diversity and functions metabolism, and reduce the damage of Cd stress, compared with cotton straw biochar, compound Bacillus biofertilizer was more effective in immobilizing Cd and improving soil environmental quality.