Survey of the host associated and environmental microbiome of field-grown tomato plants

A lab-in-the-field approach was developed to sample two Italian grown tomato cultivars within the EU H2020 funded project CIRCLES. Microbial communities associated to four microhabitats of the plants, as well as unplanted soil controls, and farming machinery were subjected to amplicon sequencing and metagenomics. We analysed microbiome composition, function, and dynamics from 251 sequencing profiles. This revealed that microbial signatures conserved between cultivars, differentiating between plant-associated specimens and unplanted soil, and, within individual plants, between individual organs both below and above ground. Furthermore, our analysis suggest that the tomato microbiome is minimally perturbed by “cross-contaminations” from farming machinery. We used network analyses to identify diagnostic features of the plant microbiome associated to plant performance and environmental co-variates to identify Smart Microbiome Modulators (SMMs) for use downstream in the intervention phase of the. Our results show a distinct, conserved, microhabitat-dependent core tomato microbiota segregating leaf microbiome from the microbiome of that of the roots and rhizosphere. Intriguingly, leaf core enriched taxa display a taxonomic relatedness with previously reported pathogens. Conversely, the below ground associated conserved microbiota is enriched in genera encompassing plant-growth promoting rhizobacteria (PGPRs).