Objective Sclerotinia rot caused by S. sclerotiorum is an important disease of broccoli, and mining antagonistic bacteria is the foundation for Sclerotinia rot biological control. This study aimed to use the broccoli endophytic bacterium MQ-04 as the test material, clarify its antagonistic activity against S. sclerotiorum, and complete the sequencing, assembly, and analysis of its genome.

Method The antagonistic effect of strain MQ-04 against S. sclerotiorum was evaluated using the plate confrontation method, and its control effect against Sclerotinia rot was assessed using the detached leaf assay. The physiological and biochemical characteristics of strain MQ-04 were determined with the API 50 CH test kit. PCR was used to clone the gyrB gene sequence, and bioinformatics tools were employed for sequence alignment and phylogenetic analysis to clarify the taxonomic status of strain MQ-04. High-throughput sequencing was performed to generate second- and third-generation data, followed by genome assembly and analysis using relevant software and online tools.

Result The plate confrontation experiment showed that strain MQ-04 significantly inhibited the mycelial growth of S. sclerotiorum, with an inhibition rate of 64.5%. The detached leaf inoculation test indicated that strain MQ-04 treatment significantly reduced lesion diameter, with a lesion size of 0.98 cm at 3 days post-inoculation, and the control effect was 61.87%. Physiological and biochemical tests revealed that strain MQ-04 could metabolize 22 carbohydrates including D-glucose, D-fructose, and glycogen, but could not utilize 27 carbohydrates including glycerol, erythritol, or D-arabinose. A phylogenetic tree constructed based on the gyrB sequences of strain MQ-04 and related species showed that strain MQ-04 clustered with Bacillus inaquosorum with 100% support. Integrating the physiological, biochemical, and molecular biological results, the MQ-04 was identified as B. inaquosorum. The whole genome sequencing results showed that the complete genome of strain MQ-04 was 4 242 855 bp in length with a GC content of 44.03%. It contained 4 331 genes, including 4 121 protein-coding genes and 86 tRNA genes. Additionally, 8 secondary metabolite gene clusters were identified in the strain MQ-04 genome, involved in the synthesis of substances such as surfactin, zwittermicin A, and aurantinin.

Conclusion This study clarified the taxonomic status and antifungal potential of the antagonistic bacterium strain MQ-04 against S. sclerotiorum in broccoli through physiological and biochemical tests, molecular identification, and whole genome analysis, and provided a foundation for further research on its biocontrol potential and mechanisms.