Functional characterisation of salt marsh sediments through microbes, viruses, and metabolites

Tidal salt marshes, with their peaty soils, halophilic plants, and large physico-chemical fluctuations, function as biodiversity hotspots, carbon sinks and natural barriers between sea and land. Ongoing global losses driven by storm surges, rising sea levels and human activities, call for multidisciplinary research and new metrics to inform their conservation, restoration, and construction. Current knowledge overlooks key aspects of salt marsh sediment microbiomes and metagenomic data remain limited. In particular, it is not resolved which substrates prokaryotes preferentially utilise, nor which metabolic pathways dominate soil organic matter (SOM) transformation. Moreover, viruses in salt marsh ecosystems are poorly characterised, with scant information on their diversity, distribution, hosts range, and ecosystem functions. This thesis aims to investigate natural, restored, and constructed salt marshes in the Venice Lagoon and characterise the diversity and functional potential of prokaryotes and viruses in sediments, alongside metabolite composition and edaphic features. We developed an integrative framework combining genome-scale metabolic models (GEMs), metabolomics, and virus-host predictions to uncover how microbial metabolism and viral processes jointly mediate SOM turnover. The sediment communities were dominated by aerobic and facultatively anaerobic heterotrophs, capable of respiration and fermentation, as well as sulphur-oxidisers, sulphate reducers, methylotrophs and acetogens, with high metabolic plasticity and functional redundancy. Analysis of GEMs highlighted the utilisation of plant-derived substrates and high import rates of alcohols, carboxylic acids, saccharides and amino acids. Beyond the canonical viral shunt and viral shuttle, our results suggest that viral lysis in sediments can alter carbohydrate, Acetate, and Succinate fluxes associated with prokaryotic plant degraders and primary producers, as well as Butyrate, Ammonium, Ethanol, Methanethiol from chemoheterotrophs. Finally, the analysis of viral auxiliary genes within the GEMs framework further suggested that metabolic reprogramming preferentially targets abundant sugars and amino acids, thus fostering the production and turnover of microbial organic matter.