Temporal Dynamics of the Tomato Rhizosphere Microbiome in Response to Synthetic Communities of Plant Growth-Promoting Rhizobacteria

Abstract

In sustainable agriculture, the application of microorganisms to soil is a widely adopted strategy aimed at enhancing soil microbiome functionality, restoring fertility, and recovering biodiversity diminished by intensive farming. While introducing individual beneficial microbes often encounters issues with establishment and persistence, multispecies microbial consortia offer a more robust alternative, providing complementary functions that enhance both their resilience and effectiveness. To test this approach, we designed three synthetic bacterial communities (SynComs), each composed of varying combinations of ten bacterial endophytes previously shown to promote plant growth and exert biocontrol effects. The SynComs were designed with ascending levels of richness (4, 6, and 10 members) and diversity (ranging from 3 to 6 bacterial genera). In growth chamber trials with tomatoes, the SynComs not only promoted plant growth but also induced significant shifts in the rhizosphere bacterial communities, primarily affecting less abundant taxa. The SynComs MIX2 and MIX3, which included Pseudomonas species, exhibited the greatest impact on both plant growth enhancement and shifts within the resident microbial community. Monitoring of the introduced strains over time demonstrated that most bioinoculants successfully established although at very low concentration in the rhizosphere.