TAILLEFER, B.; BRAULT, A.; SARNIGUET, A.

The type VI secretion system (T6SS) is a widespread antibacterial weapon whose evolutionary flexibility promotes bacterial survival in competitive environments. Here, we characterized the vgrG6 cluster of Stenotrophomonas rhizophila CFBP13503, which encodes a putative PAAR-Rhs-fused effector (Rhs-Ct, Tse6) along with a poly-immunity cluster. Comparative genomics across Stenotrophomonas genus revealed strong conservation of the vgrG6 core genes, contrasting with a striking variability in the downstream poly-immunity region, consistent with rapid diversification and niche-specific adaptation. In silico structural analysis of Rhs-Ct domains from 158 Stenotrophomonas strains identified 14 distinct effector families with diverse putative enzymatic activities, including nucleases and deaminases. The Rhs-Ct from strain CFBP13503, Tse6, harbors a domain of unknown function that is rare across the bacterial diversity. Its closest orthologs were found in Gram-positive Actinomycetes and halophilic Gram-negative Planctomycetia. Strikingly, saline conditions significantly enhanced both S. rhizophila growth and T6SS activity. Functional assays demonstrated that Tse6 is specifically active against the phytopathogen Clavibacter michiganensis and the plant beneficial strains Curtobacterium herbarum and Plantibacter flavus, abolishing their resistance to S. rhizophilaT6SS attacks. Furthermore, the immunity protein Tsi6 was predicted to interact with Tse6 orthologs from phylogenetically distant taxa, indicating a broad protective capacity. Taken together, our results establish the vgrG6 cluster as a flexible adaptive module that links effector innovation and immunity diversification to ecological specialization. This work highlights the previously unrecognized role for the S. rhizophilaT6SS in mediating bacterial competition in saline niches dominated by certain Gram-positive species.