Identification and genomic insights into a plant probiotic Bacillus subtilis strain CF1 isolated from Protaetia brevitarsis frass.

Abstract

Background: Plant probiotic bacteria offer a sustainable strategy for enhancing crop health and productivity. Insect frass has emerged as a unique niche for isolating beneficial microorganisms with novel traits. In this study, we isolated a bacterial strain CF1 from the frass of Protaetia brevitarsis and characterized its biocontrol and plant growth‑promoting potential against Fusarium crown rot of wheat.

Results: Based on whole‑genome analysis, strain CF1 was identified as Bacillus subtilis. CF1 exhibited strong antagonistic activity against Fusarium graminearum and F. asiaticum, with inhibition rates of 34.67% and 33.95%, respectively. Its cell‑free filtrate showed dose‑dependent antifungal activity, reaching 43.70% inhibition against F. graminearum at a 5‑fold dilution. Phenotypic characterization confirmed its ability to produce IAA equivalents, siderophores, and solubilized phosphate. In pot experiments, CF1 effectively suppressed Fusarium crown rot, achieving a biocontrol efficacy of 43.47%, comparable to that of the well‑characterized strain B. velezensis SQR9 (44.07%). The inoculation of CF1 also promoted wheat growth, increasing plant height and plant biomass. Whole-genome sequencing revealed a 4.11 Mb genome encoding 4,277 genes, with 11 biosynthetic gene clusters for secondary metabolites, including bacillaene, fengycin, bacillibactin, surfactin, bacilysin, subtilomycin, subtilosin A, and pulcherriminic acid, along with three biosynthetic gene clusters of unknown function, suggesting potentially unique bioactivities. Genome mining further uncovered numerous genes associated with plant growth promotion, rhizosphere colonization, stress resistance, and volatile organic compound production.

Conclusions: B. subtilis CF1 is a promising microbial agent that combines strong antifungal activity, plant growth‑promoting traits, and a diverse set of genetic features that may confer unique properties, warranting further field validation for sustainable wheat production.