Comparative genomic analysis of native Bradyrhizobium spp. nodulating Retama dasycarpa in Moroccan semi-arid ecosystems: insights into symbiotic diversity and environmental adaptation.

BACKGROUND: Retama dasycarpa, a drought-resistant legume endemic to Morocco's High Atlas Mountains, thrives in harsh conditions due to its association with nitrogen-fixing Bradyrhizobium strains. Despite the ecological significance of this symbiosis, the genetic diversity, symbiotic mechanisms, and stress adaptation strategies of these microsymbionts remain poorly understood. In this study we employed a comparative genomic approach to elucidate the genomic and functional traits of five strains isolated from R. dasycarpa nodules, with a focus on their symbiotic and stress-responsive gene repertoires. RESULTS: Phylogenomic analysis revealed that four of the five strains likely represent novel Bradyrhizobium species, as indicated by average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values below species delineation thresholds. Genomic comparisons identified core symbiotic genes, including nod, nif, and fix genes, essential for nodulation and nitrogen fixation. Interestingly, strain RDT46 lacked canonical nod genes but retained a minimal Type III Secretion System (T3SS), suggesting alternative symbiotic pathways. Pangenome analysis of 56 Bradyrhizobium genomes highlighted an open pangenome with extensive accessory gene content, reflecting adaptive versatility. Stress adaptation genes, such as those involved in osmoprotectant synthesis, oxidative stress response, and heat shock, were conserved across the five strains, underscoring their resilience to semi-arid conditions. CONCLUSIONS: This study uncovers previously unknown genomic diversity in R. dasycarpa-associated Bradyrhizobim spp., including evidence for non-canonical symbiosis mechanisms. The strains' genetic toolkit for stress tolerance highlights their potential as inoculants for revegetation of degraded semi-arid lands.