First report of a novel Paenibacillus strain JDF1 and its biocontrol potential against citrus bacterial canker

Citrus bacterial canker (CBC), caused by <i>Xanthomonas citri</i> subsp. <i>citri</i> (<i>Xcc</i>), causes severe annual yield losses on citrus crops worldwide. Current control strategies including quarantine, copper-based chemicals, and resistant varieties are limited by poor adaptability, pathogen resistance, and long breeding cycles. Herein, a novel endophytic <i>Paenibacillus</i> strain, designated JDF1, was isolated from <i>Veronica persica</i> (a common weed in citrus orchards). <i>In vitro</i> assays demonstrated that JDF1 inhibited <i>Xcc</i>. Greenhouse trials with "Eureka" lemon showed that low-concentration JDF1 (OD₆₀₀ = 0.2) and its cell-free supernatant eliminated CBC symptoms without inducing phytotoxicity. Notably, JDF1 retained over 60% of its activity following heat treatment at 50 °C for 6 h. Phylogenetic analyses revealed that JDF1 is closely related to <i>P. xylanexedens</i> (98.52% 16S rRNA gene similarity) and <i>P. polysaccharolyticus</i> (99.8% housekeeping gene similarity). Further average nucleotide identity (ANI) analysis confirmed that strain JDF1 belongs to the same species as <i>P. polysaccharolyticus</i>, with a sequence similarity of 97.31%. JDF1 tolerated CaCuSO₄ concentrations up to 600 mg/L and exhibited resistance to ampicillin and streptomycin. Genome sequencing of JDF1 predicted multiple genes associated with antibiotic biosynthesis, primarily including those involved in the production of polyketide, terpenoid, tyrocidin A, iturin A, lanthipeptide (class II), ranthipeptide, and lassopeptide. In a deeper investigation of the biocontrol mechanisms, a phospholipid antibiotic, bacilysocin, was identified in the JDF1 culture via LC-MS analysis. Collectively, these findings indicate that JDF1 is a promising novel biocontrol agent (BCA) against <i>Xcc</i>, with the dual advantages of high efficacy at low concentrations and thermostability, thereby enhancing its potential for agricultural application.