Identification of Beneficial Bacterial Strains for Tomato Growth Promotion and Biocontrol of Bacterial Canker Caused by Clavibacter michiganensis

Abstract

Bacterial canker of tomato, caused by Clavibacter michiganensis (Cm), remains difficult to control due to lack of effective management options. In this study, a collection of over 500 bacterial isolates was screened in vitro for antagonistic activity against Cm and plant growth-promoting (PGP) traits. Based on these results, 32 candidates were evaluated in planta, leading to the identification of three highly effective strains: Pantoea agglomerans SO16PY and two Pseudomonas marginalis sensu lato strains, IRDA16 and SO16PC, which consistently enhanced tomato vegetative growth. Notably, P. agglomerans SO16PY delayed disease onset in Cm-inoculated plants by up to 7 days and significantly reduced wilting severity, lowering the disease severity score from 85% to 45%. Strains IRDA16 and SO16PC also restricted disease development, reducing severity scores to 67.5% and 57.5%, respectively. Whole-genome sequencing and comparative genomics revealed that strains IRDA16 and SO16PC form a distinct, specialized rhizosphere lineage within the Pseudomonas marginalis group, exhibiting average nucleotide identity (ANI {approx} 96%) and digital DNA-DNA hybridization (dDDH {approx} 69.5%) values near species delineation thresholds. Genome mining identified diverse biosynthetic gene clusters (BGCs) encoding non-ribosomal peptide synthetases (NRPS), the lipopeptide viscosin, and terpenes, which likely drive the biostimulant and antagonistic traits of this novel Pseudomonas lineage. Together, these findings characterize promising bacterial candidates with dual biostimulant and biocontrol capacities while uncovering a genomically distinct Pseudomonas lineage optimized for beneficial plant-microbe interactions in sustainable agriculture. IMPORTANCEClavibacter michiganensis (Cm) is a major bacterial pathogen of tomato and poses a significant economic threat to global production. It is classified as an A2 quarantine pathogen by the European and Mediterranean Plant Protection Organization (EPPO). Current management strategies rely largely on chemical control, including copper-based compounds (e.g., Bordeaux mixture, copper oxychloride), mancozeb, and antibiotics like streptomycin. However, these approaches raise increasing concerns related to environmental contamination, phytotoxicity, and the development of resistant pathogen populations. As a sustainable alternative, plant growth-promoting bacteria (PGPR) have emerged as promising biocontrol agents. In this study, we identified bacterial strains exhibiting antagonistic activity against Cm both in vitro and in planta. Notably, these strains also enhanced tomato growth parameters, demonstrating their dual functionality. Given the environmental drawbacks associated with chemical inputs, the use of such beneficial microorganisms represents a promising strategy for advancing sustainable and ecofriendly tomato production systems.