Rhizosphere Microbiome Influence on Tomato Growth under Low-Nutrient Settings

Studies have shown that reduced nutrient availability enhances microbial diversity around plant roots, positively impacting plant productivity. However, the specific contributions of rhizosphere microbiomes in nutrient-poor environments still need to be better understood. This study investigates the role of Plant Growth-Promoting Rhizobacteria (PGPR) in enhancing the growth of Solanum lycopersicum under hydroponic conditions. We hypothesised that nutrient limitation would increase the selection of beneficial bacterial communities, compensating for nutrient deficiencies. Our hydroponic system, with treatments consisting of 50% reduced fertiliser application supplemented with a soil-derived inoculum, exhibited greater bacterial diversity and biomass than controls, suggesting a successful enrichment of PGPR that compensates for nutrient deficiencies. Using 16S rRNA gene sequencing, we found a significant enrichment ( p ≤ 0.001) and correlation with beneficial plant traits ( p ≤ 0.05) of bacterial genera such as Luteolibacter , Sphingopyxis , and Kaistia . Shotgun metagenomics identified the critical role of Methyloversatilis in nitrogen fixation and other key taxa bacterial proteins in plant-bacteria interactions. Additionally, our findings identify core taxa across different cultivation systems. These results support the potential for microbiome engineering to enhance microbial diversity and plant productivity, offering a path to reduce fertiliser use in agriculture and improve sustainability.