Analysis of bacterial communities in the niche compartment of tomato plant.

For investigation of microbial communities present in the tomato compartment, we conducted a microbiome analysis on Hawaii 7996, a bacterial wilt-resistant tomato variety. Since the microbiome composition varies significantly among different plant compartments, we collected samples from seven compartments, including bulk soil, rhizosphere, root, stem, flower, gel, and seed. We aimed to identify shared and compartment-specific operational taxonomic units (OTUs) to gain insights into the potential functional roles of these microbiota. We performed cluster analysis on each sample using the qiime2 and R pipeline and found that the microbial community composition varied significantly among tomato compartments. These findings suggest that the microbiota associated with each compartment of the tomato plant could have different functional roles in the plant's growth and defense against pathogens. Further studies are needed to investigate the functional significance of these microbiota in different plant compartments.