Antifungal Activity of Streptomyces sp. F204 Against Rhizoctonia Solani and Whole-Genome Sequencing and Metabolomic Analysis

Rhizoctonia solani Kühn is a destructive phytopathogenic fungus with an exceptionally broad host range, infecting over 32 plant families and 188 genera. In this study, we evaluated the antifungal activity of compound 1 from Streptomyces sp. F204 against R. solani, and characterized its genomic features and metabolomic responses under different culture conditions. Based on whole-genome sequences, the highest average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between strain F204 and its closest related type strain, Streptomyces puniciscabiei S77, were 91.64% and 45.00%, respectively. Compound 1, the active metabolite isolated from the fermentation broth of Streptomyces sp. F204, was evaluated using the mycelial growth rate method. Genome annotation predicted 8022 genes in strain F204, including protein-coding genes, rRNA genes, and tRNA genes, covering 86.72% of the total genome length. Additionally, antiSMASH 6.0.0 analysis identified 23 biosynthetic gene clusters putatively involved in secondary metabolite production. Comparative metabolomics revealed significantly enriched pathways across different media, including nicotinate and nicotinamide metabolism in Medium No. 2 (B) versus Gause’s synthetic medium (A), and pyrimidine metabolism as well as alanine, aspartate, and glutamate metabolism in ISP4 medium (C) versus Gause’s synthetic medium (A). On the basis of NMR and mass spectrometry (MS) data, compound 1 is proposed to be a structural analog of daptomycin. It exhibited strong concentration-dependent inhibition of R. solani mycelial growth, achieving 93.07 ± 0.49% inhibition at 200 μg/mL, with an IC50 value of 14.9 μg/mL. These findings indicate that Streptomyces sp. F204 represents a promising source of antifungal metabolites with considerable biosynthetic potential.