Genomic insights into the broad-spectrum antifungal activity of a novel Paenibacillus polymyxa strain X-11

The Paenibacillus polymyxa group is potentially useful for regulating plant growth and controlling plant diseases. We previously isolated a novel P. polymyxa strain (X-11) that can promote plant growth. However, its antagonistic effects on plant pathogenic fungi and the underlying mechanisms therein remain unclear. To promote its utility for controlling plant diseases, strain X-11 was characterized in terms of its antagonistic effects on plant pathogenic fungi, genome sequence, genes related to antimicrobial activities, and extracellular antifungal proteins. Strain X-11 had significant antagonistic effects on several plant pathogenic fungi: Fusarium fujikuroi, Fusarium oxysporum, Magnaporthe oryzae, Botrytis cinerea, and Exserohilum turcicum. Its genome was revealed to contain 5,014 protein-coding genes as well as 49 tRNA and 10 rRNA sequences. The genome was most similar to that of P. polymyxa SC2, with 68.80% of its unique genes homologous to sequences in strain SC2. Furthermore, 85 genes related to antimicrobial activities were identified in the strain X-11 genome, including glycosyl hydrolase genes (20), serine protease genes (8), metalloproteinase genes (23), lanthionine antibiotic biosynthesis-related genes (6), and non-lanthionine antibiotic biosynthesis-related genes (2). Additionally, 14 nonribosomal peptide synthetase genes and 12 polyketide synthase genes were detected. Proteins with antifungal activities were identified in the inhibition zone between strain X-11 and Fusarium proliferatum (rice pathogen), including serine protease, lysophospholipase, metalloproteinase, glycoside hydrolase, β-glucosidase, peptidase M24, and amidase. Notably, bacillopeptidase F and bacillolysin were the most abundant antifungal proteins, suggesting that they may be the main contributors to strain X-11’s antifungal effects. An adenylation domain-containing protein involved in non-ribosomal peptide synthesis was also identified. The genomic characterization of strain X-11, coupled with experimental confirmation of its broad-spectrum antifungal activity, provides a strong genetic and functional basis for its development as a promising biocontrol agent against plant fungal diseases.