MetaboLightsapplication/xmlftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12630/m_MTBLS12630_LC-MS_negative_hilic_metabolite_profiling-1_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12630/m_MTBLS12630_GC-MS_positive__metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12630/m_MTBLS12630_LC-MS_positive_hilic_metabolite_profiling_v2_maf.tsvftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12630/a_MTBLS12630_LC-MS_negative_hilic_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12630/a_MTBLS12630_LC-MS_positive_hilic_metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12630/i_Investigation.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12630/a_MTBLS12630_GC-MS_positive__metabolite_profiling.txtftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12630/s_MTBLS12630.txtprimary200OKftp://ftp.ebi.ac.uk/pub/databases/metabolights/studies/public/MTBLS12630<p>Metabolites were tentatively identified by comparing experimental mass spectra with MS-DIAL LC-MS reference libraries “ESI(+)-MS/MS from authentic standards (16,481 unique compounds)” and “ESI(-)-MS/MS from authentic standards (9,033 unique compounds)”. Volatile compounds were tentatively identified with MS-DIAL GC-MS reference libraries “All records with Kovats RI (9062 unique compounds)” and further confirmed by comparing mass spectra with the NIST reference library (NIST 08, National Institute of Standards and Technology, Gaithersburg, MD, 2008).</p>MetaboLightsPublicLiquid Chromatography MS - positive - HILICGas Chromatography MS - positiveLiquid Chromatography MS - negative - HILIC<p>For LC-MS, processed samples were analysed with an Ultimate 3000 UHPLC chromatograph coupled with a Q-Exactive™ hybrid quadrupole-Orbitrap™ mass spectrometer (Thermo Fisher Scientific, Waltham, Massachusetts, USA). A TSKgel Amide-80, 3 µm, 2.0×150 mm (LabService Analytica, Anzola dell’Emilia, Bologna, Italy) column stabilised at 30 °C was used in HILIC mode. Eluents were acetonitrile and 3 mM ammonium acetate at a flow rate of 0.2 mL/min. The gradient was 95% acetonitrile for 3 min, linear increasing to 70% ammonium acetate in 24 min, 70% constant ammonium acetate for 3 min and then 95%</p><p>acetonitrile in 2 min, equilibration for 8 min.</p><p><br></p><p>GC-MS conditions were: Restek Rxi- 624SIL MS capillary column (60 m x 250 μm x 1.4 μm, Restek S.R.L., Milano, Italy). Helium was used as a carrier with a flow rate of 1.2 mL/min. The analyses were carried out with a temperature ramp: the starting temperature (40 °C) was held constant for 5 minutes, followed by an increase of 5 °C/min until 320 °C held constant for 5 min with a total run time of 66 min.</p>Viral lysis and host reprogramming impact carbohydrate, amino acid, and osmolyte cycling in salt marsh tidal creek sediments.University of PadovaSilvia Pettenuzzosedimentmass spectrometry assay<p>For Liquid Chromatography–Mass Spectrometry (LC-MS), aliquots of 1 g of sediment (6 NAT, 6 RES) were centrifuged and, after water removal, re-weighed to determine the exact mass of the solid fraction (~0.3 g). The sediment was extracted with 800 µL of a methanol:ultrapure water (1:3) solution, containing 200 µg/L of phenylalanine-d 5 as internal standard, and 1.2 mL of chloroform. The extraction mixture was vortexed for 30 s before and after the addition of chloroform and then centrifuged for 5 min at 1000 rpm. The methanol:ultrapure water fraction was filtered on 0.2 µm Regenerate Cellulose membrane filters (Phenomenex, 4 mm syringe filters) before injection. Quality control (QC) samples were prepared as a pool of all sediment samples under analysis and extracted with the same protocol.</p><p><br></p><p>For Gas Chromatography–Mass Spectrometry (GC-MS), aliquots of 2 g of homogenised sediment samples (6 NAT, 6 RES), with the addition of 50 µL of n-decane (1 mg/L) as internal standard, were analysed with a Centri sample preparation platform (Markes International, Bridgend, United Kingdom). Volatile compounds were extracted and pre-concentrated with the HiSorb sorptive extraction, using a multi-phase standard DVB/CWR/PDMS fiber. Incubation was</p><p>performed for 60 min at 60 °C, with vial vortexed for 10 s at 400 rpm. Desorption was performed for 10 min at 250 °C. Desorb trap settings were: trap purge time 0.2 min, purge flow 50 mL/min, trap low and high temperature 5 °C and 280 °C, respectively, trap desorption time 3 min with a split flow of 15 mL/min.</p>marine salt marsh sedimentSolventhttps://www.ebi.ac.uk/metabolights/MTBLS12630Alessandro Vezzi.Riccardo Frizzo. Università degli Studi di Padova. riccardo.frizzo@phd.unipd.it.Sciamila Hemmati.Enrico Bortoletto. Università degli Studi di Padova.Sara Bogialli. Università degli Studi di Padova. sara.bogialli@unipd.it.Stefano Mammi.Mattia Panin.Paola Venier. Università degli Studi di Padova. paola.venier@unipd.it.Lorenzo Archetti.Silvia Pettenuzzo. Università degli Studi di Padova. silvia.pettenuzzo@unipd.it.Irene Gregori.<p>Raw data were converted to ABF format (Reyfics Analysis Base File Converter) and processed with MS-DIAL 4.9. Parameters for data extraction were selected on the basis of the chromatographic performances of the above-mentioned equipment. The feature’s areas were extracted from MS-DIAL, after alignment, identification and normalisation for QCs and internal standard, for further analysis. Curation of assignments, molecular classification,and statistical analyses were performed on LC-, GC-MS data with MetaboAnalyst 6.0: metabolites found with LC- and GC-MS were assigned to chemical sub-classes based on HMDB classification using the Enrichment analysis module. For LC-, GC-MS, all peak areas (PA) were normalised by sum and auto-scaled, then Two-sample Student’s t-test was applied to asses which metabolites differed between the NAT and RES areas, and PCoA analysis was used to evaluate the clustering pattern of the samples. Permutational Multivariate Analysis of Variance (PERMANOVA) was also performed to assess the significance of the composition differences between groups. </p>Salt marsh areasilvia.pettenuzzo@unipd.it<p>Surface sediment samples (0-2.5 cm depth) were collected on June 26 th , 2023, at 5:30 am, in low tide conditions, from the inner tidal creeks of one natural (NAT) and one restored (RES) area of the Boschettona salt marsh, located in the southern Venice lagoon, Italy (45,15°; 12,12°). Three sampling points per area were selected, each in two replicates and at a minimum distance of 2 m from one another. All sediment samples were collected with nitrile long cuff gloves, using aluminium spoons treated with alcohol and UV-irradiated. Sampling was performed by sinking the spoon into the sediment to a depth of 2.5 cm, and rotating it to collect the sediments. After collection, spoons were rinsed in the surrounding water and wiped with clean paper. For metagenomics, elemental composition, and metabolomics analyses, aliquots of 40 mL of wet sediments were collected, immediately frozen in dry ice, transported, and stored at -80 °C for 2 months.</p>MetabolomicsMetabolomicsMetagenomicsviral lysisAgilent 5977B GC/MSDpooled quality control samplehost reprogramminguntargeted analysissolvent blankviromicssaltmarshsedimentexperimental sampleGC-MSgenome-scale modelsLC-MSThermo Scientific Q ExactiveThermo Scientific Dionex Ultimate 3000 UHPLC systemmarine salt marsh sedimentauxiliary viral genesAgilent 8860 GC systemSolventpooled quality control sampleAgilent 5977B GC/MSDMetabolomicsMetagenomicsviral lysishost reprogramminguntargeted analysissolvent blankviromicssaltmarshsedimentexperimental sampleGC-MSgenome-scale modelsLC-MSThermo Scientific Q ExactiveThermo Scientific Dionex Ultimate 3000 UHPLC systemmarine salt marsh sedimentSolventauxiliary viral genesAgilent 8860 GC system<p>For LC-MS mass spectrometric conditions were: electrospray ionization (ESI) in both positive (+) and negative (-) mode, data dependent acquisition with resolution 35,000 in full MS and 17,500 in MS/MS, AGC target 1·10 6 in full MS and 1·10 5 in MS/MS, max injection time of 100 ms, m/z range 70-1000, isolation window 2.0 m/z, collision gas nitrogen, normalized collision energy 25 eV. Data dependent settings were: Minimum AGC target 9·10 3 and dynamic exclusion 20s. The capillary voltage was 4.0 kV (+)/ 2.8 kV (-), capillary temperature 300 °C (+)/280 °C (-), and auxiliary gas was nitrogen at 20 psi. The calibration was performed with a standard solution and the software Xcalibur 3.1 was used for instrument control (Thermo Fisher Scientific, Waltham, Massachusetts, USA). Sample measurement order was randomised to avoid experimental drifts.</p><p><br></p><p>For GC-MS the mass spectrometer, with an electron impact mode at 70 eV, was set to scan from m/z 40 to 500. Transfer line was set at 260 °C and MS source and quadrupole temperatures were set at 230 and 150 °C, respectively.</p>DEOXYCARNITINETaurineTryptamineNorleucineGuanosine5-MethylcytosineALPHA-AMINOADIPATEThymidineGlutamylphenylalanine2-Methylpyrrolidinegamma-GlutamyltyrosineIndolineCYTIDINEEctoineMETHYLTHIOADENOSINEdioctylamine4-HYDROXY-L-PROLINEDEOXYCYTIDINEMalic acidCytosinegamma-Glutamylleucinegamma-Glutamylmethionine5-O-methylvisammiosideThreonineN-METHYL-GLUTAMATENebularineMaltoseCitrullinePropionylcarnitineLotusineHomothreonineMelezitoseAlanine betaine2'-DeoxycytidineHomostachydrineErgothioneineGlutamic acidCARNITINEGabapentinSerineProline5-MethylcytidineN-AcetylarginineGuanineTributylamineOnoninConiinePyroglutamic acid4-AMINOBUTANOATEIsoleucineMETHIONINETHYMIDINETREHALOSEAdenosinePhenylalanineIndole-3-acetic acid5,6-DIHYDROURACILThymineAdenine3-Guanidinopropionic acidGUANOSINEDEOXYGUANOSINE2'-DeoxyguanosineValineGentiobioseALANINEAcetylcarnitineSUCROSEInosineAcetylcholinebetaineTRIGONELLINEUracilDimethylglycinePantothenic acidfalseViral lysis and host reprogramming impact carbohydrate, amino acid, and osmolyte cycling in salt marsh tidal creek sediments<p>Salt marshes are highly productive ecosystems where microbial communities drive key</p><p>transformations of organic matter at rates often exceeding those of oceanic and inland</p><p>environments. Viruses are recognised as important drivers and regulators of global</p><p>biogeochemical cycling, yet their diversity, host range, and functional roles in salt</p><p>marsh ecosystems remain largely unresolved. To address these gaps, we investigated</p><p>how viral lysis and host reprogramming can affect microbe-mediated organic matter</p><p>transformations in a salt marsh of the Venice lagoon (Italy). Focusing on tidal creek</p><p>surface sediments, we reconstructed 311 metagenome-assembled genomes (MAGs),</p><p>built corresponding genome-scale metabolic models (GEMs) individually constrained</p><p>with 121 metabolites detected in the sediments, and identified 3,537 viral populations</p><p>(vOTUs) across 10 samples. To assess the impact of viral lysis, we inferred prokaryotic</p><p>hosts for 243 vOTUs and analysed host metabolism through MAG pathway analysis</p><p>and GEM flux modelling across 13 bacterial orders, thus highlighting a negative impact</p><p>on polysaccharide degradation, organic nitrogen mineralisation, and organosulphur</p><p>mineralisation/volatilisation processes. For host metabolic reprogramming, we</p><p>characterised a subset of 50 auxiliary viral genes (AVGs) by mapping them to GEM</p><p>reactions and analysing their stoichiometry, directionality, and pathway context,</p><p>outlining two dominant strategies: resource scavenging through nucleotide-sugar</p><p>biosynthesis, amino acid utilisation, and sulphate assimilation; functional host</p><p>maintenance through cofactor biosynthesis, electron transport, and energy production</p><p>through carbonyl-compound utilisation. Our findings provide a mechanistic view of the</p><p>viral influence on organic matter transformations in salt marsh sediments and confirm</p><p>viruses as key players in salt marsh biogeochemistry.</p>2026-06-262025-06-23MTBLS12630MTBLC183886MTBLC72816MTBLC37023MTBLC30915MTBLC22605MTBLC22660MTBLC37084MTBLC21260MTBLC17562MTBLC27389MTBLC18012MTBLC133038MTBLC157877MTBLC82968MTBLC82969MTBLC18237MTBLC28300MTBLC16235MTBLC16750MTBLC17368MTBLC17596MTBLC6032MTBLC25017MTBLC6650MTBLC61993MTBLC29864MTBLC37684MTBLC47965MTBLC16440MTBLC18394MTBLC28716MTBLC28044MTBLC17964MTBLC17802MTBLC33951MTBLC17521MTBLC32111MTBLC15741MTBLC17992MTBLC15891MTBLC18095MTBLC35697MTBLC16551MTBLC18186MTBLC27226MTBLC16704MTBLC10017MTBLC15318MTBLC17151MTBLC43619MTBLC17847MTBLC35581MTBLC17437MTBLC87434MTBLC17169MTBLC87499MTBLC29021MTBLC28897MTBLC17907MTBLC77927MTBLC49000MTBLC17700MTBLC77929MTBLC45296MTBLC84268MTBLC4608MTBLC46202MTBLC5672MTBLC34276MTBLC15698MTBLC17172MTBLC145240MTBLC15968MTBLC16003MTBLC20392MTBLC15901MTBLC20607MTBLC27551MTBLC228843MTBLC57589MTBLC15355MTBLC16708MTBLC16335MTBLC16449MTBLC28825MTBLC22860MTBLC17126MTBLC18211MTBLC28322MTBLC16040MTBLC16244MTBLC17724MTBLC132284MTBLC27592MTBLC4828MTBLC42797MTBLC28066MTBLC82966MTBLC5757MTBLC229981MTBLC16411MTBLC43295MTBLC17191MTBLC81190MTBLC17306MTBLC6731MTBLC16811MTBLC17509MTBLC143241MTBLC18255MTBLC29083MTBLC18347MTBLC7775MTBLC7916MTBLC16227MTBLC28867MTBLC16924MTBLC17822MTBLC26986MTBLC17748MTBLC17821MTBLC28742MTBLC229203MTBLC16765MTBLC17568MTBLC27266CHEBI:183886CHEBI:72816CHEBI:37023CHEBI:30915CHEBI:22605CHEBI:22660CHEBI:37084CHEBI:21260CHEBI:17562CHEBI:27389CHEBI:18012CHEBI:133038CHEBI:157877CHEBI:82968CHEBI:82969CHEBI:18237CHEBI:28300CHEBI:16235CHEBI:16750CHEBI:17368CHEBI:17596CHEBI:6032CHEBI:25017CHEBI:6650CHEBI:61993CHEBI:29864CHEBI:37684CHEBI:47965CHEBI:16440CHEBI:18394CHEBI:28716CHEBI:28044CHEBI:17964CHEBI:17802CHEBI:33951CHEBI:17521CHEBI:32111CHEBI:15741CHEBI:17992CHEBI:15891CHEBI:18095CHEBI:35697CHEBI:16551CHEBI:18186CHEBI:27226CHEBI:16704CHEBI:10017CHEBI:15318CHEBI:17151CHEBI:43619CHEBI:17847CHEBI:35581CHEBI:17437CHEBI:87434CHEBI:17169CHEBI:87499CHEBI:29021CHEBI:28897CHEBI:17907CHEBI:77927CHEBI:49000CHEBI:17700CHEBI:77929CHEBI:45296CHEBI:84268CHEBI:4608CHEBI:46202CHEBI:5672CHEBI:34276CHEBI:15698CHEBI:17172CHEBI:145240CHEBI:15968CHEBI:16003CHEBI:20392CHEBI:15901CHEBI:20607CHEBI:27551CHEBI:228843CHEBI:57589CHEBI:15355CHEBI:16708CHEBI:16335CHEBI:16449CHEBI:28825CHEBI:22860CHEBI:17126CHEBI:18211CHEBI:28322CHEBI:16040CHEBI:16244CHEBI:17724CHEBI:132284CHEBI:27592CHEBI:4828CHEBI:42797CHEBI:28066CHEBI:82966CHEBI:5757CHEBI:229981CHEBI:16411CHEBI:43295CHEBI:17191CHEBI:81190CHEBI:17306CHEBI:6731CHEBI:16811CHEBI:17509CHEBI:143241CHEBI:18255CHEBI:29083CHEBI:18347CHEBI:7775CHEBI:7916CHEBI:16227CHEBI:28867CHEBI:16924CHEBI:17822CHEBI:26986CHEBI:17748CHEBI:17821CHEBI:28742CHEBI:229203CHEBI:16765CHEBI:17568CHEBI:27266