Abstract
Simple Summary The problem of antimicrobial resistance represents a real danger to mankind. There is a crucial necessity to search for new antibiotics. The current advances in sequencing techniques and bioinformatics represent a critical tool for finding out the hidden biosynthetic capabilities within bacterial genomes and finding out novel active secondary metabolites. In this work, we managed to recover the Streptomyces vinaceusdrappus strain AC-40, a rhizobacterium with potent and broad-spectrum antimicrobial activity. We made whole genome sequencing and genome mining for the genes and gene clusters related to beneficial traits such as the production of secondary metabolites and plant growth promotion. Streptomyces are factories of antimicrobial secondary metabolites. We isolated a Streptomyces species associated with the Pelargonium graveolens rhizosphere. Its total metabolic extract exhibited potent antibacterial and antifungal properties against all the tested pathogenic microbes. Whole genome sequencing and genome analyses were performed to take a look at its main characteristics and to reconstruct the metabolic pathways that can be associated with biotechnologically useful traits. AntiSMASH was used to identify the secondary metabolite gene clusters. In addition, we searched for known genes associated with plant growth-promoting characteristics. Finally, a comparative and pan-genome analysis with three closely related genomes was conducted. It was identified as Streptomyces vinaceusdrappus strain AC-40. Genome mining indicated the presence of several secondary metabolite gene clusters. Some of them are identical or homologs to gene clusters of known metabolites with antimicrobial, antioxidant, and other bioactivities. It also showed the presence of several genes related to plant growth promotion traits. The comparative genome analysis indicated that at least five of these gene clusters are highly conserved through rochei group genomes. The genotypic and phenotypic characteristics of S. vinaceusdrappus strain AC-40 indicate that it is a promising source of beneficial secondary metabolites with pharmaceutical and biotechnological applications.