Antimicrobial Secondary Metabolites From Rhizosphere‐Associated Streptomyces Species in Northern Nigerian Agricultural Soils: Genomic Mining and Bioactivity Assessment

Abstract

Streptomyces species are prolific producers of secondary metabolites with significant pharmaceutical potential, particularly in tropical agricultural ecosystems. This study characterised rhizosphere-associated Streptomyces species from agricultural soils around Prince Abubakar Audu University, Anyigba, Nigeria, and evaluated their antimicrobial secondary metabolite production capacity through combined genomic mining and bioactivity screening. Soil samples from maize and soybean rhizospheres across five sites were analysed using 16S rRNA gene sequencing, multilocus sequence typing, and whole-genome sequencing. Biosynthetic gene clusters (BGCs) were identified using antiSMASH and PRISM, and crude extracts were evaluated for antimicrobial activity against multidrug-resistant clinical isolates via LC-MS/MS analysis. Twenty-three Streptomyces isolates representing eight species were recovered. Genomic mining revealed 187 putative BGCs, including polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and hybrid PKS-NRPS clusters. Streptomyces sp. PAU-7 and Streptomyces griseoflavus PAU-15 demonstrated significant activity against methicillin-resistant Staphylococcus aureus (MRSA) and carbapenem-resistant Enterobacteriaceae (CRE). LC-MS/MS analysis identified twelve putatively novel secondary metabolites including three polyketide derivatives and four peptide-based compounds. Nigerian agricultural soils harbour diverse Streptomyces populations with substantial biosynthetic potential for putatively novel antimicrobial compounds.