Genomic and functional characterization of the Pantoea ananatis nfd35 strain, a potential biocontrol agent of anthracnose disease in Trichosanthes kirilowii Maxim

Abstract

Anthracnose, caused by Colletotrichum gloeosporioides, is a major fungal disease affecting Trichosanthes kirilowii Maxim. Long-term use of chemical fungicides has negative impacts on the environment and humans, and application of biological agents has been considered as a potential plant disease management strategy. To assess the potential of these endophytes for biological control, 36 endophytic bacterial strains were isolated from T. kirilowii fruits and evaluated for their ability to combat C. gloeosporioides through in vitro assays and greenhouse tests. The bacterial community with Shannon diversity index (1.62), Simpson's index (0.76), and Pielou's evenness index (0.78) was predominantly composed of Pseudomonas and Pantoea. Among these, Pseudomonas sp. nfd15, Pantoea sp. nfd22, and Pantoea sp. nfd35 exhibited biocontrol potential by significantly inhibiting the growth of C. gloeosporioides and reducing the leaf lesions of anthracnose. Greenhouse trials confirmed the efficacies of nfd35 in reducing anthracnose symptoms on detached fruits and potted plants, with the control rate of 57.90 % and 31.54 %, respectively. Biosafety assessments confirmed its suitability for tissue - cultured plantlets and field-grown seedlings. Strain nfd35 was further identified as Pantoea ananatis based on phenotypic and biochemical characteristics, 16S rRNA sequencing, and whole-genome analysis using average nucleotide identity (ANI) and average amino acid identity (AAI). The genome of nfd35 comprises a 4.42 Mb circular chromosome and two plasmids. Nine gene clusters were identified, and siderophore may play a major role in controlling anthracnose. These findings indicate that P. ananatis nfd35 is a promising biocontrol agent for the management of anthracnose in T. kirilowii.