Genomic insights into ‘Candidatus Pseudomonas auctus’ JDE115, a soybean endophyte with expanded nutrient acquisition and biocontrol-related gene repertoires

Pseudomonas species are globally distributed bacteria that influence soil and plant health, functioning as both pathogens and plant growth-promoting rhizobacteria (PGPR). Genomic analyses have revealed the genetic basis for their ecological versatility, including the evolution of diverse nutrient acquisition and biocontrol traits. Here, we report the draft genome of ‘Candidatus Pseudomonas auctus’ JDE115, a novel soybean nodule–associated PGPR with biocontrol potential that may contribute to sustainable agriculture. The draft genome comprises 6.18 Mb with a GC content of 60.68%. Comparative genomic analyses with closely related Pseudomonas taxa revealed lineage-specific gene clusters associated with nutrient acquisition and biocontrol-related functions, including genes encoding extracellular serine proteases, siderophores, chitinases, hydrogen cyanide synthase, and non-ribosomal peptide synthetases. Functional annotation across KEGG, COG, Pfam, CAZy, and antiSMASH databases highlighted enriched pathways for phosphorus, sulfur, zinc, and potassium metabolism, as well as secondary metabolite biosynthesis. Several biosynthetic clusters, including arylpolyenes, cyclic lipopeptides, and β-lactones, appear to be expanded relative to other PGPR genomes, suggesting lineage-specific adaptations for rhizosphere persistence and pathogen suppression. Despite the agronomic importance of plant-associated Pseudomonas, the genomic basis of non-rhizobial soybean nodule endophytes with combined PGPR and biocontrol potential remains poorly understood. Draft genome of novel soybean endophyte ‘Candidatus Pseudomonas auctus’ JDE115. Comparative genomics reveals lineage-specific biosynthetic gene cluster expansion. Enriched cyclic lipopeptide, arylpolyene, and β-lactone clusters suggest biocontrol roles. Genome encodes versatile nutrient acquisition and stress adaptation pathways. Findings broaden PGPR genomic diversity and support sustainable agriculture potential.