Comparative analysis of rhizosphere bacterial communities in tomato (Solanum lycopersicum L.) through 16S rRNA amplicon-based taxonomic and functional profiling

Microorganisms in the soil play essential roles in the growth and development of plants. However, there is limited understanding of how the health status of plants influences the functions of these microorganisms. This study aims to analyze the composition of bacterial communities in the rhizosphere soil of tomato plants (Solanum lycopersicum L.) from the Beggli micro-watershed in Kolar, Karnataka using high throughput 16S rRNA amplicon sequencing. Four different rhizosphere soil samples of tomato were taken and subjected to microbial diversity analysis. Analysis of the soil showed differences in pH, Electrical conductivity (EC), percent organic carbon and macronutrients (N, P, K) that affected microbial composition. DNA sequencing, bioinformatic analysis and amplicon sequencing detected 350 amplicon sequence variants (ASVs) in all the rhizosphere soil samples. Among them, TSB2 showed the highest ASVs (210). Proteobacteria were the phylum with the highest abundance in all the samples, followed by Firmicutes, Actinobacteria, Acidobacteriota and Chloroflexi. Taxonomic analysis showed Gammaproteobacteria, Alphaproteobacteria and Bacilli to be the most dominant classes of bacteria while Bacillus, Acinetobacter, Sphingomonas and Flavobacterium were the most predominant genera. Alpha diversity indices showed remarkable diversity in microbial richness with the Shannon Index ranging from 8.25 to 9.11. Beta diversity analysis revealed a clear clustering of microbial communities based on soil characteristics. Functional annotation by Kyoto Encyclopedia of Genes and Genomes (KEGG) and Clusters of Orthologous Groups of Proteins (COG) analysis revealed genes involved in nutrient cycling, oxidative stress response and plant-microbe interactions. These findings enhance our understanding of tomato rhizosphere bacterial community structure and guide sustainable soil management practices.