Comparative Analysis Reveals Host Species-Dependent Diversity Among 16 Virulent Bacteriophages Isolated Against Soybean Bradyrhizobium spp.

Phages play a role in shaping ecosystems by controlling host abundance via cell lysis, driving host evolution via horizontal gene transfer, and promoting nutrient cycling. The genus Bradyrhizobium includes bacteria able to symbiotically nodulate the roots of soybean (Glycine max), providing the plant with a direct source of biologically fixed nitrogen. Optimizing this symbiosis can minimize the use of nitrogen fertilizers and make soybean production more sustainable. Phages targeting Bradyrhizobium may modify their hosts’ genotype, alter phenotypic traits such as symbiotic effectiveness, and mediate competition among strains for nodulation sites. Sixteen phages were isolated against B. diazoefficiens strain USDA110 and B. elkanii strains USDA94 and USDA31. Comparative analyses revealed host species-dependent diversity in morphology, host range, and genome composition, leading to the identification of three previously undescribed phage species. Remarkably, all B. elkanii phages shared a siphophage morphology and formed a single species with >97% nucleotide identity, even when isolated from farms separated by up to ~70 km, suggesting genomic stability across geographic scales. In contrast, phages isolated against B. diazoefficiens had a podophage-like morphology, exhibited greater genetic diversity, and divided into two distinct species. Although no phages were recovered against the B. japonicum strains or native Delaware Bradyrhizobium isolates tested, some Delaware Bradyrhizobium isolates showed susceptibility in a host range assay. The phage genomes demonstrated features predicting phenotypes. The phage terminase genes predicted headful packaging which promotes generalized transduction. The B. elkanii phages all carried tmRNA genes capable of rescuing stalled ribosomes, and all but one of the phages isolated against the two host species carried DNA polymerase A indicating greater phage control of genome replication. State-of-the-art structural annotation of a hypothetical gene shared by the B. diazoefficiens phages, having a mean amino acid identity of ~25% and similarity of ~35%, predicted a putative tail fiber function. Together this work expands the limited knowledge available on soybean Bradyrhizobium phage ecology and genomics.