Viral lysis and host reprogramming impact carbohydrate, amino acid, and osmolyte cycling in salt marsh tidal creek sediments

ABSTRACT:

Salt marshes are highly productive ecosystems where microbial communities drive key

transformations of organic matter at rates often exceeding those of oceanic and inland

environments. Viruses are recognised as important drivers and regulators of global

biogeochemical cycling, yet their diversity, host range, and functional roles in salt

marsh ecosystems remain largely unresolved. To address these gaps, we investigated

how viral lysis and host reprogramming can affect microbe-mediated organic matter

transformations in a salt marsh of the Venice lagoon (Italy). Focusing on tidal creek

surface sediments, we reconstructed 311 metagenome-assembled genomes (MAGs),

built corresponding genome-scale metabolic models (GEMs) individually constrained

with 121 metabolites detected in the sediments, and identified 3,537 viral populations

(vOTUs) across 10 samples. To assess the impact of viral lysis, we inferred prokaryotic

hosts for 243 vOTUs and analysed host metabolism through MAG pathway analysis

and GEM flux modelling across 13 bacterial orders, thus highlighting a negative impact

on polysaccharide degradation, organic nitrogen mineralisation, and organosulphur

mineralisation/volatilisation processes. For host metabolic reprogramming, we

characterised a subset of 50 auxiliary viral genes (AVGs) by mapping them to GEM

reactions and analysing their stoichiometry, directionality, and pathway context,

outlining two dominant strategies: resource scavenging through nucleotide-sugar

biosynthesis, amino acid utilisation, and sulphate assimilation; functional host

maintenance through cofactor biosynthesis, electron transport, and energy production

through carbonyl-compound utilisation. Our findings provide a mechanistic view of the

viral influence on organic matter transformations in salt marsh sediments and confirm

viruses as key players in salt marsh biogeochemistry.

INSTRUMENT(S): Liquid Chromatography MS - positive - HILIC, Gas Chromatography MS - positive, Liquid Chromatography MS - negative - HILIC

PROVIDER: MTBLS12630 | MetaboLights | 2026-06-26

REPOSITORIES: MetaboLights