Inoculation with plant growth-promoting bacteria alters the rhizosphere functioning of tomato plants

Inoculation with plant growth-promoting bacteria (PGPB) represents an efficient method in sustainable agriculture to improve nutrients availability and crop production in diverse environmental conditions. In the present work, untargeted metabolomics and community-level physiological profiles (CLPP) approaches were employed to investigate the shaping of tomato rhizosphere functioning and potential metabolic activity imposed by rhizosphere-associated microbiome, following inoculation with two different PGPB (Enterobacter sp. 15S and Pseudomonas sp. 16S). Significant increases in root and shoot dry biomass were observed in both inoculated treatments, when compared to uninoculated plants (p < 0.05). The untargeted metabolomics allowed discriminating the metabolic profiles of tomato rhizosphere, with distinct modulations imposed by either Enterobacter 15S or Pseudomonas 16S. Flavonoids and other phenolics were among the most frequently identified differential metabolites in the rhizosphere from both Enterobacter 15S and Pseudomonas 16S inoculated plants. Nevertheless, other metabolites like phytohormones and amino acids were also decisive to this specific modulation. The metabolic activity profile rhizosphere-associated microbiome of tomato plants unveiled by the CLPP analysis was congruent with the metabolomic data and reinforced the influence exerted by the bacterial inoculation on modulating the rhizosphere microbiome functioning. In particular, the microbiome associated with control and 16S-treated plants showed a higher functional diversity than those treated with Enterobacter 15S. Carbohydrates, carboxylic acids, amino acids, and polymers were the main classes of substrates which contributed to such differences.