Microbiome-based applications for sustainable food production and waste-streams valorization

Natural microbiomes represent an untapped source of functionalities to be used as eco-friendly biofertilizers/pesticides, as well as for the biotransformation of biomasses into platform chemicals and bioactive compounds. In this view, we focused on two main research topics. First, we used Next Generation Sequencing and metagenomics to characterize the microbiome of Vitis vinifera roots – and surrounding soil – across two worldwide famous Italian viticultural sites. We focused on microbial communities at the soil-root interface as a determinant of the wine terroir, with particular emphasis on microbial Plant Growth-Promoting (PGP) functions, as decades of research have demonstrated the role of microbial communities in providing beneficial functions for plant nutrition, growth, and stress tolerance, making them a strategic player for the transition to sustainable agriculture. PGP functions include drought resistance, nitrogen fixation, phosphorus solubilization, exudation of bacterial siderophores, production of antimicrobials, phytohormones, and competition with pathogens and pests. Our results shed light on PGP microorganisms in Italian wine-producing sites, paving the way for implementing new microbiome-based inoculants for wine production aimed to increase product quality and sustainability. The second part of the thesis investigates microbiome-based biotransformation of lignocellulose (LC) into useful molecules. Lignocellulose is the most abundant polymer on Earth and is composed of carbohydrates (cellulose, hemicellulose, and pectin) and aromatic compounds (lignin), holding the potential to be deconstructed for several biotechnological applications, but recalcitrant to hydrolysis. We structurally and functionally explored the gut microbiome (GM) of the Alpine ibex (Capra ibex L.), a wild herbivore from Stelvio National Park, for the metagenomic biodiscovery of microbial species, hubs, and pathways involved in LC biotransformation. We provided glimpses of fecal bacterial strains as a possible solution for the bioconversion of lignocellulose to high-value compounds, such as volatile fatty acids and alcohols, with also a preliminary investigation of their biosynthetic potential.