Data were then validated, aligned and filtered using the BinBase algorithm (rtx 5) with the following settings: validity of chromatogram (<10 peaks with intensity > 107 counts s−1), unbiased retention index marker detection (MS similarity > 800, validity of intensity range for high m/z marker ions), and retention index calculation by 5th order polynomial regression, as described in Fiehn et al. (2008) and Fiehn (2016). Further curation of the data was carried out as described in Fiehn (2016). Final curated results were reported as peak heights. Internal standards were included; however, these were for quality control and peak correction purposes. Data presented are therefore qualitative and compounds are tentatively identified, as commonly accepted for untargeted analysis (Gertsman and Barshop, 2018).
Peaks are annotated in manual comparison of MS/MS spectra and accurate masses of the precursor ion to spectra given in the Fiehn laboratory's LipidBlast spectral library (Kind et al., 2013). MassHunter Quant software was then used to verify peak candidates based on peak shape, peak height reproducibility and retention time reproducibility in replicate samples. Valid and reproducible peaks were analysed by targeted MS/MS with the aim of increasing overall peak annotations. Final curated results were reported as peak heights. Internal standards were included; however, these were for quality control and peak correction purposes only. Hence, data presented are therefore qualitative and compounds are tentatively identified, as is the common with untargeted analysis (Gertsman and Barshop, 2018).
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Gas Chromatography MS -"],"chromatography_protocol":["Metabolomic analysis was performed on a 6890 GC (Agilent Technologies) coupled to a Pegasus IV TOF MS (Leco Corp. St. Joseph, MI, USA), injected via a Gerstel CIS4 with dual MPS Injector (Gerstel, Muehlheim, Germany) using the chromatographic parameters described in Fiehn et al. (2008).
Sample analysis was performed using an Agilent 1290 Infinity LC system (G4220A binary pump, G4226A autosampler, and G1316C Column Thermostat) coupled to an Agilent 6530 MS in positive ion mode. Lipids were separated on an Acquity UPLC CSH C18 column (100 × 2.1 mm; 1.7 μm). For full instrument parameters see Table S2.
"],"publication":["Impacts of Plant Exclusion on Soil Lignocellulolytic Microbial Community Composition and Function. PMID:10.2139/ssrn.4499267"],"submitter_name":["David Fidler"],"submitter_affiliation":["Bangor University"],"organism_part":["soil metagenome"],"technology_type":["mass spectrometry"],"disease":[""],"extraction_protocol":["Samples were then shipped on dry ice (−78.5 °C) to the West Coast Metabolomics Center (UC Davis Genome Center, Davis, CA, USA) for untargeted primary metabolites by automated liner exchange cold injection system gas chromatography time of flight mass spectrometry (ALEX-CIS GCTOF MS) and complex lipid analysis by charged surface hybrid column electrospray ionization quadrupole time of flight tandem mass spectrometry (CSH-ESI QTOF MS/MS).
Untargeted primary metabolite extraction consisted of vortexing a 1:0.025 (w/v) soil-to-3:3:2 (v/v/v) MeCN/IPA/H2O solution, before shaking for 5 min at 4 °C, centrifuging and an aliquot of the supernatant recovered for analysis. Complex lipid extraction was performed using a modified bi-phasic method of Matyash et al. (2008). The main advantage of Matyash method over the Bligh and Dyer methods is that the lipids are contained in the upper extraction phase (as the Methyl tertiary-butyl ether (MTBE) solvent used in the Matyash method has a lower density than water, compared to the chloroform (CHCl3) solvent used in the Bligh and Dyer methods, which is more dense than water). Thus, the organic phase can be withdrawn directly without risk of contamination from the aqueous phase or the interphase. However, we note that the different methods can reveal different lipid yields (Sostare et al., 2018). Briefly, 225 μl of MeOH (containing internal standards) was added to 40 mg soil sample and vortexed for 20 s, followed by the addition of 750 μl MTBE and vortexed for a further 10 min. Samples were then placed in a bead grinder for 30 s. Subsequently, samples were shaken for 6 min at 4 °C, before the addition of 188 μl of MS-grade water and centrifugation (2 min). An aliquot of the supernatant was then removed and evaporated to dryness using a SpeedVac. Dried extracts were re-suspended using a mixture of 9:1 MeOH/toluene (v/v) (containing an internal standard).
"],"organism":["soil metagenome"],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS12728"],"author":["Griffiths Rob.","David Fidler. Bangor University. d.fidler@bangor.ac.uk.","McDonald James.","LeBrun Lucas.","Davey Jones. d.jones@bangor.ac.uk.","George Paul."],"data_transformation_protocol":["Briefly, data pre-processing was performed in ChromaTOF vs. 2.32, without smoothing, using; 3 s peak width, baseline subtraction just above the noise level, and automatic mass spectral deconvolution and peak detection at signal/noise levels of 5:1 throughout the chromatogram.
This was followed by data clean up using the mass spectral feature list optimizer (MS-FLO), as described in DeFelice et al. (2017).
"],"study_factor":["Treatment"],"submitter_email":["d.fidler@bangor.ac.uk"],"sample_collection_protocol":["Soil samples were collected and were immediately (within 30 s) frozen in the field by placement in liquid N2 to quench metabolic and lipid turnover. Samples were then lyophilised using a Modulyo Freeze Dryer with RV pump (Edwards Ltd. Crawley, UK) and the samples stored again at −80 °C. Samples were then shipped on dry ice (−78.5 °C) to Microbial ID Inc. (Newark, DE, USA) and extracted, fractionated, and transesterified according to the method of Buyer and Sasser (2012). Subsequently, samples were analysed using a 6890 gas chromatograph (GC) (Agilent Technologies, Wilmington, DE, USA) equipped with autosampler, split–splitless inlet, and flame ionization detector. The system was controlled with MIS Sherlock® (MIDI, Inc. Newark, DE, USA) and Agilent ChemStation software. GC-FID specification, analysis parameters and standards are as described in Buyer and Sasser (2012).
"],"omics_type":["Metabolomics"],"study_design":["untargeted metabolites","concentration of carbon atom in soil","soil metagenome"],"curator_keywords":["untargeted metabolites","concentration of carbon atom in soil","soil metagenome"],"mass_spectrometry_protocol":["The general workflow for data processing followed the mass spectrometry-data independent analysis (MS-DIAL) software method described in Tsugawa et al. (2015).
"],"metabolite_name":["17288","tagatose","pentadecanoic acid","21664","4-hydroxybenzoic acid","17044","glycocyamine","beta-mannosylglycerate","ferulic acid","glutaric acid","213019","93947","glucose-1-phosphate","gluconic acid","110018","377405","18022","18386","isoheptadecanoic acid","349293","377766","22885","adenosine","377770","pyruvic acid","glucoheptulose","21763","3781","113510","378763","17140","2691","melezitose","6-deoxyglucitol","146242","ornithine","2684","378531","376594","glyceric acid","183508","250544","119066","91421","18488","hydrocinnamic acid","glucose","3,6-anhydro-D-galactose","229977","377308","pimelic acid","oleamide","124996","2575","204582","89252","135763","1-kestose","sophorose","379636","cerotinic acid","21623","124346","377341","ribitol","4766","4526","133590","132267","leucine","135777","216584","365122","330511","palatinitol","146430","3208","3206","168799","methionine","124454","2233","326263","isothreonic acid","nicotinic acid","326249","5-aminovaleric acid","4550","133244","125784","palmitoleic acid","heptadecanoic acid","pyrrole-2-carboxylic acid","125897","341992","xylitol","341990","3-(4-hydroxyphenyl)propionic acid","17589","nonadecanoic acid","fumaric acid","217691","capric acid","trehalose","1173","379527","phenylethylamine","127704","3465","1-monostearin","379411","380511","377232","89145","26717","glutamic acid","62250","4-hydroxybutyric acid","105630","oleic acid","3122","1064","378468","146068","127661","hypoxanthine","glycine","136146","367449","3-hydroxybenzoic acid","104312","107941","360827","22363","379787","359832","2039","lyxitol","3247","360825","succinic acid","102248","360824","84181","1-hexadecanol","127640","207444","22334","3-(3-hydroxyphenyl)propionic acid","98101","1,5-anhydroglucitol","phytanic acid","366259","377041","106936","linoleic acid","2065","124484","342919","22227","behenic acid","104404","360846","pinitol","14724","377271","360842","serine","deoxycholic acid","127343","146259","beta sitosterol","380100","42161","360852","fucose","84193","oxoproline","octadecanol","127696","127451","proline","guanine","threose","lyxose","85168","7408","381429","conduritol-beta-epoxide","66311","4-aminobutyric acid","2-deoxytetronic acid","5244","126350","378294","378176","346248","120802","mannose","209671","2-hydroxyvaleric acid","240031","6104","346242","346241","azelaic acid","127676","209675","126343","209677","23635","methylmalonic acid","pentose","threonine","228","345265","1-monopalmitin","107891","370223","phosphoethanolamine","lignoceric acid","41836","473","87834","378198","linolenic acid","168800","479","379168","thymidine","87951","346225","46281","104395","49426","97743","104398","378059","41821","malic acid","myristic acid","380254","357024","xylose","arachidic acid","13139","210313","47358","16850","191801","371571","41811","2,4-diaminobutyric acid","379063","134","257","381497","alanine","210327","379060","16857","1912","105209","17830","72488","14682","130465","citraconic acid","ribose","3-hydroxybutyric acid","41924","371566","isomaltose","xanthine","22064","210697","parabanic acid","104126","46131","17833","16747","14689","53737","110985","lactic acid","109997","48427","6278","210231","88847","16833","210342","1815","347755","54","347514","342183","arachidonic acid","108312","22045","33282","160","glycerol","203820","379197","168","34135","84116","tyrosine","1704","inositol-4-monophosphate","360226","324863","46346","129225","210373","8598","33395","110604","118693","ethanolamine","88501","348828","UDP-N-acetylglucosamine","120526","6-hydroxynicotinic acid","pentitol","4',5-dihydroxy-7-glucosyloxyflavanone","phenylalanine","phosphate","fructose","glycerol-alpha-phosphate","33387","33386","17913","uracil","39801","1725","379095","thymine","16594","112601","adipic acid","209167","salicylic acid","21704","levoglucosan","43734","isoleucine","myo-inositol","2821","xylulose","aspartic acid","2706","99","110411","107143","371262","134642","tyramine","376958","2-hydroxyhexanoic acid","2-ketoisocaproic acid","allantoic acid","citric acid","191799","250732","18305","100865","hydroxycarbamate","106387","106385","4-hydroxycinnamic acid","376622","pantothenic acid","376621","hexuronic acid","glutamine","palmitic acid","1996","benzoic acid","376854","22902","377949","132248","41882","3-aminoisobutyric acid","aconitic acid","204862","beta-alanine","acetophenone","galactinol","raffinose","376647","2-ketoadipic acid","110343","2-monoolein","121473","365741","376631","N-acetylmannosamine","dodecanol","110573","1790","sucrose","189794","n-acetyl-d-hexosamine","threitol","glycerol-3-galactoside","16567","131101","378606","112501","34085","shikimic acid","110328","urea","119025","2403","124844","4709","erythrose","vanillic acid","16777","51865","160903","cytosin","hydroquinone","6-deoxyglucose","133778","114918","342561","pipecolinic acid","daidzein","1684","adenine","365772","valine","215667","erythritol"],"additional_accession":[]},"is_claimable":false,"name":"Soil microbial adaptation to carbon deprivation: Shifts in lignocellulolytic gene profiles following long-term plant exclusion","description":"Background:
Lignocellulose represents a primary input of organic carbon (C) into soils, yet the identity of specific microorganisms and genes which drive lignocellulose turnover in soils remain poorly understood. To address this knowledge gap, we used a 10-year grassland plant-exclusion experiment to investigate how reduced plant C inputs affects microbial communities and their lignocellulolytic potential using a combination of metagenomic sequencing and untargeted metabolomics. We specifically tested the hypothesis that microbial community function in bare fallow plots would transition towards microbiota with genes for recalcitrant biomass degradation (i.e., lignocellulose), when compared to grassland plots with high labile C inputs.
Results:
Long term plant exclusion lowered soil C and N and reduced cellulose content, whilst hemicellulose and lignin were unchanged. Similarly soil microbiomes were highly distinct in long-term bare soils, along with soil extracellular enzyme profiles, though short term plant-removal effects were less apparent. Plant exclusion resulted in a general enrichment of Firmicutes, Thaumarchaeota, Acidobacteria, Fusobacteria, and Ascomycota, with a general reduction in Actinobacteria. However, changes in bare soil lignocellulose degradation genes were more associated with discrete taxa from diverse lineages, particularly the Proteobacteria. Grouping of lignocellulose-degrading genes into broad substrate classes (cellulases, hemicellulases and lignases) revealed a possible increase in lignin degradation genes under plant exclusion confirming our hypothesis, although all other changes were at the level of the CAZy family. Intriguingly, untargeted metabolome profiles were highly responsive to plant exclusion, even after only one year. Bare soils were depleted in oligosaccharides and enriched in monosaccharides, fatty and carboxylic acids, supporting emerging evidence of long-term persistent C being within simple compounds.
Conclusions:
Together our data show that extracellular lignin degrading enzymes increase under long term plant exclusion. There is now a need for increased focus on the microbial metabolic mechanisms which regulate the processing and persistence of enzymatically released compounds, particularly in energy limited soils.
","dates":{"publication":"2025-07-16","submission":"2025-07-16"},"accession":"MTBLS12728","cross_references":{"pubmed":["10.2139/ssrn.4499267"]}}