Composition, function and manipulation of the spinach microbiome

A lab-in-the-field approach was developed to sample spinach across 4 sites in Italy across multiple harvest periods. Microbial communities associated to organs of the plants, as well as unplanted soil controls, were subjected to 16S rRNA gene amplicon sequencing, ITS amplicon sequencing and metagenomics. We analysed microbiome composition, putative function and dynamics at three distinct yet interconnected levels. (i) Within individual plants, from unplanted soil to individual organs both below and above ground, (ii) within the same lab-in-the field across harvest seasons and (iii) between lab-in-the fields across a pedogreographic gradient. Sequence data was analysed to identify diagnostic features of the plant microbiome associated to plant performance and environmental co-variates to identify Smart Microbiome Modulators (SMMs) aimed at manipulating microbiome composition in the field. We used existing microbial collection to design ad-hoc inoculants for in-farm applications. Upon treatments, microbial communities associated to plant's organs of the plants, as well as unplanted soil controls, were subjected to high-throughput sequencing investigations. Macroscopic and sequencing data were analysed to identify SMMs-responsive features in the plant food chain and propose mechanistic insights into SMMs mode of action and their wider impact.