Novel lactic acid bacteria as biocontrol agents against tomato bacterial canker: genomic insights into biosynthetic gene clusters

Bacterial canker, caused by Clavibacter michiganensis subsp. michiganensis, remains one of the most devastating diseases affecting tomato production globally, necessitating sustainable biocontrol strategies. This study investigates the biocontrol potential and plant growth efficacy of indigenous lactic acid bacteria isolated from tomato tissues in the Izmir province of Türkiye. Six potent isolates, identified as Lacticaseibacillus paracasei and Lacticaseibacillus zeae, were evaluated through in vitro assays and in planta trials across two susceptible tomato cultivars, ‘SC2121’ and ‘Corvette’. While the isolates exhibited no direct antagonism against Clavibacter michiganensis subsp. michiganensis in dual culture assays, they demonstrated significant disease suppression in planta, with Lacticaseibacillus paracasei LBT2 (G1) achieving up to 45.71% efficacy. All isolates displayed robust plant growth promoting traits, including indole acetic acid production, siderophore activity, and phosphate solubilization, leading to substantial increases in root and shoot biomass. To elucidate the molecular mechanisms underlying these effects, the whole genome of the most effective strain, LBT2, was sequenced. Genomic mining revealed five distinct biosynthetic gene clusters, including an arylpolyene cluster (88% similarity) for oxidative stress protection and an aerobactin-like siderophore cluster (66% similarity). Notably, the presence of highly divergent NRPS (3% similarity) and thiopeptide (14% similarity) clusters suggests the potential for novel, cryptic antimicrobial metabolites that may be activated within the host environment. These findings position Lacticaseibacillus paracasei LBT2 as a multi-functional biocontrol agent that integrates direct growth promotion with genomic potential for pathogen suppression, offering a promising tool for integrated pest management in tomato cultivation.