The Pseudomonas putida type VI secretion systems shape the tomato rhizosphere microbiota.

Bacterial competition mechanisms drive microbial community dynamics across diverse ecological niches. The type VI secretion system (T6SS) represents a sophisticated nanomachine used by Gram-negative bacteria for contact-dependent elimination of competitors through the delivery of toxic effectors. While the T6SS has been well-documented in mammalian gut microbiota development, its role in shaping plant rhizosphere communities remains poorly understood despite the ecological importance of rhizosphere microbiota. This study investigates how the three Pseudomonas putida KT2440 T6SS clusters influence the tomato rhizosphere microbiota in agricultural soil. Through comprehensive in vitro and in vivo analyses, we demonstrate that while the K2/K3-T6SSs remain inactive under standard laboratory conditions, they become specifically functional in the presence of plant pathogens, suggesting an adaptive response to competitive pressure. Our experiments with T6SS-deficient mutants reveal that the P. putida T6SSs are important for effective rhizosphere colonization, with mutant strains showing significantly reduced colonization capabilities compared to wildtype strain in competitive soil environments. Most importantly, our data establish that the P. putida T6SSs directly shape the taxonomic diversity and community structure of the rhizosphere microbiota of tomato plants. These results place the T6SS as a critical factor driving the evolution of complex polymicrobial communities within the plant rhizosphere, paralleling its established role in the gut microbiota. This research advances our understanding of the ecological functions of the different T6SSs in P. putida and the molecular mechanisms underlying microbial community assembly in the rhizosphere. Thus, it offers valuable insights for agricultural applications involving beneficial microbes and plant health management strategies.