After completing the experimental analysis, the raw LC-MS data were imported into the metabolomics processing software Progenesis QI (Waters Corporation, Milford, USA) for baseline filtering, peak identification, peak integration, retention time correction, and peak alignment. This process yielded a data matrix containing retention time, mass-to-charge ratio, and peak intensity values. Additionally, MS and MS/MS mass spectrometry data were matched against the public metabolomics databases HMDB (http://www.hmdb.ca/) and Metlin (https://metlin.scripps.edu/), as well as Meiji's in-house database, to obtain metabolite information.
"],"repository":["MetaboLights"],"study_status":["Public"],"ptm_modification":[""],"instrument_platform":["Liquid Chromatography MS - negative - reverse-phase","Liquid Chromatography MS - positive - reverse-phase"],"chromatography_protocol":["A 3 μL sample was separated on an HSS T3 chromatography column (100 mm × 2.1 mm i.d., 1.8 µm) and then analyzed by mass spectrometry. Mobile phase A consisted of 95% water + 5% acetonitrile (containing 0.1% formic acid); mobile phase B consisted of 47.5% acetonitrile + 47.5% isopropanol + 5% water (containing 0.1% formic acid). The flow rate was 0.40 mL/min, and the column temperature was 40°C. Mass spectrometry conditions.
"],"publication":["Organic fertilizer amendments reshape soil microbial communities and metabolic functions in sweet cherry production."],"submitter_name":["B S"],"submitter_affiliation":["Zhejiang University of Technology"],"organism_part":["Rhizosphere soil"],"technology_type":["mass spectrometry assay"],"disease":[""],"extraction_protocol":["Transfer 50 mg of the solid sample into a 2 mL centrifuge tube and add one 6 mm diameter grinding bead. Use 400 μL of the extraction solution (methanol:water = 4:1 (v:v)) containing an internal standard (L-2-chlorophenylalanine) at a concentration of 0.02 mg/mL for metabolite extraction. Grind the sample solution using a freezing tissue grinder for 6 min (-10°C, 50 Hz), followed by low-temperature ultrasonication for 30 min (5°C, 40 kHz). Place the sample at-20°C for 30 min, then centrifuge for 15 min (4°C, 13,000 g); transfer the supernatant to an injection vial equipped with an insertion tube for analytical measurement.
"],"organism":["Prunus avium L."],"full_dataset_link":["https://www.ebi.ac.uk/metabolights/MTBLS15458"],"author":["Jing Ren. Institute of Forestry, Fruit and Flower Research, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, China. mailrenjing@163.com."],"data_transformation_protocol":["The data matrix obtained from the search operation is uploaded to the Meiji Cloud Platform (cloud.majorbio.com) for analysis. The data matrix is first subjected to preprocessing as follows: missing values are removed using the 80% rule—namely, only variables with more than 80% of non-zero values across at least one sample set are retained; then, missing values are imputed using the minimum value from the original matrix. To minimize errors arising from sample preparation variations or instrument instability, the response intensities of the sample mass spectrometry peaks are normalized using the sum normalization method, yielding the normalized data matrix. Additionally, variables with a relative standard deviation (RSD) greater than 30% for the QC samples are removed, and the data undergoes log10 transformation to obtain the final data matrix intended for subsequent analyses.
"],"study_factor":["Treatment"],"submitter_email":["253313593@qq.com"],"sample_collection_protocol":["Four treatments were established: a control (CK) receiving conventional fertilization (commercial N-P-K compound fertilizer, 15-15-15, 0.8 kg·tree-1, applied by ditch burial), and three treatment groups (T1, T2, T3) each receiving the same conventional fertilizer plus additional amendments as detailed in Table 1.
"],"omics_type":["Metabolomics"],"study_design":["Thermo Scientific Vanquish UHPLC System","correlation analysis","Metabolomics","rhizosphere microecology","microbial community","Prunus avium L.","untargeted analysis","Thermo Scientific Q Exactive HF-X","organic substrate","Rhizosphere soil","EM inoculant","experimental sample"],"curator_keywords":["Thermo Scientific Vanquish UHPLC System","correlation analysis","Metabolomics","rhizosphere microecology","microbial community","Prunus avium L.","untargeted analysis","Thermo Scientific Q Exactive HF-X","organic substrate","Rhizosphere soil","EM inoculant","experimental sample"],"mass_spectrometry_protocol":["The mass spectrometry signal acquisition was performed using a positive-and negative-ion scanning mode, with a mass scanning range of 70–1050 m/z. The sheath gas flow rate was set to 50 psi, the auxiliary gas flow rate to 13 psi, and the auxiliary gas heating temperature to 425 °C. The ion spray voltage for the positive mode was set to 3500 V, and for the negative mode to –3500 V; the ion transmission tube temperature was 325 °C; and the normalized collision energy ranged from 20–40–60 V (cyclic collision energy). The primary mass spectrometry resolution was 60,000, and the secondary mass spectrometry resolution was 7,500; data were acquired in DDA mode.
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Four treatment groups were established: a control group (CK, garden soil with conventional fertilization) and three amended groups (T1: sheep manure-biochar-EM inoculant; T2: chicken manure-biochar-EM inoculant; T3: biochar-EM inoculant). Soil physicochemical assays indicated fertilization boosted available N, P, K and organic matter but reduced pH, with T3 yielding the greatest nutrient accumulation. By integrating high-throughput sequencing and LC-MS-based non-targeted metabolomics, we characterized the structure and diversity of root-associated bacterial and fungal communities, identified differentially abundant metabolites, annotated enriched metabolic pathways, and elucidated correlations between microorganisms and metabolites. Sequencing yielded 1,862,937 valid bacterial tags and 1,757,276 valid fungal tags, which were clustered into 11,698 bacterial ASVs and 4,011 fungal ASVs. Fertilization regimes substantially altered microbial community composition, with Pseudomonadota and Ascomycota as the dominant bacterial and fungal phyla, respectively. A total of 355 known metabolites were identified, predominantly enriched in xenobiotic biodegradation and amino acid metabolism pathways. T3 exhibited the highest number of differentially abundant metabolites (206) compared to CK, with significant enrichment in pyrimidine and phenylalanine metabolism. Correlation analysis revealed significant treatment-specific associations between key rhizosphere bacterial genera and differentially abundant metabolites (e.g., pyrimidine- and phenylalanine-pathway intermediates), with positive correlations dominating in T3 and negative correlations dominating in T2. Structural equation modeling (SEM) confirmed that fertilization regulated the accumulation of differential metabolites by altering the relative abundance of core rhizosphere microbial taxa. Collectively, our findings demonstrate that fertilization exerts treatment-specific regulatory effects on root-associated microbial communities and reshapes the soil metabolome, thereby providing a theoretical basis for precision fertilization and sustainable soil management in sweet cherry orchards.","dates":{"publication":"2026-09-20","submission":"2026-08-25"},"accession":"MTBLS15458","cross_references":{"KEGG":["C06772","C03626","C00183","C00392","C00429","C01835","C01613","C14415","C00253","C00082","C01933","C00246","C00079","C00864","C00806","C11332","C06423","C01921","C00836","C05122","C05466","C05464","C15515","C04230","C14153","C12269","C01879","C15025","C02237","C01746","C11142","C00330","C00559","C00294","C00955","C02735","C02040","C01744","C01752","C10833","C06868","C05851","C10897","C20157","C07073","C11918","C00137","C11110","C00633","C01772","C09126","C07288","C19434","C09099","C10438","C10761","C00120","C00009","C00849","C16195","C00811","C01494","C09844","C14743","C09827","C10826","C07113","C10494","C16995","C06577","C18459","C04741","C01484","C19228","C16184","C08618","C16939","C07591","C14766","C13856","C19670","C13846","C14240","C11103","C00515","C02642","C01035","C06809","C19781","C02366","C00152","C00135","C20522","C16778","C12989","C01157","C12323","C00588","C05519","C19281","C02067","C00334","C18474","C10935","C02835","C02710","C20634","C13736","C00073","C03145","C06593","C10475","C01089","C02294","C07525","C00250","C00643","C11129","C02693","C00284","C06104","C01924","C10294","C06325","C00364","C06818","C21793","C19548","C01733","C01132","C07129","C02656","C01546","C07414","C00153","C07630","C16765","C00257","C01460","C04083","C06825","C07065","C01750","C06973","C11770","C10112","C00599","C13800","C07202","C16821","C00164","C01606","C01029","C17715","C07112","C05582","C08277","C00355","C03485","C12144","C08898","C17002","C06912","C00587","C00780","C02821","C07492","C03299","C05551","C18489","C17714","C08317","C00263","C00092","C02515","C00318","C03990","C01694","C07407","C14552","C01481","C08628","C02679","C01753","C03519","C16185","C01227","C07236","C11512","C20214","C05570","C14607","C01019","C02140","C00179","C16908","C09981","C11778","C06424","C04148","C07660","C05961","C00977","C03681","C16512","C07599","C00525","C01179","C05441","C06124","C00187","C00745","C02640","C05127","C06543","C05442","C00793","C16398","C02712","C00755","C06333","C00065","C00906","C00245","C00956","C02777","C01234","C00315","C01407","C07736","C05946","C05682","C18872","C13198","C13391","C05688","C08602","C05379","C02174","C07116","C14399","C13558","C13557","C18247","C06232","C16247","C18180","C18456","C06817","C18561","C06922","C08382","C14702","C11028","C00747","C07637","C07022","C16556","C02287","C04133","C12739","C00647","C00075","C00373","C01705","C03434","C07625","C16631","C10981","C14414","C11065","C19524","C03824","C01988","C14846","C01010","C06055","C05422","C16559","C02352","C00433","C14787","C18309","C18597","C00975","C06414","C04771","C00111","C03360","C18729","C19509","C06525","C12215","C00275","C18653","C20209","C13734","C07395","C03167","C04691","C00112","C07044","C03108","C01267","C09964","C14333","C05146","C14706","C00195","C00119","C07093","C00018","C03189","C11007","C18428","C05932","C12835","C15587","C20155","C01180","C06194","C01185","C06837","C11100","C14343","C07362","C14801","C00499","C12284","C06911","C07520","C11343","C06607","C01182","C01353","C19295","C02355","C11434","C14207","C07455","C01075","C02564","C03141","C05925","C00190","C18593","C07255","C00627","C14292","C19909","C22040","C03082","C08233","C18806","C05548","C00513","C01345","C07203","C07577","C18081","C01239","C08480","C16619","C13693","C00206","C01718","C14426","C11182","C20232","C00700","C11490","C00371","C10395","C06179","C16637","C03794","C01893","C16625","C20956","C15650","C14190","C13668","C13280","C11159","C05983","C18555","C11686","C18904","C06206","C00705","C07034","C19543","C00279","C06606","C14185","C03166","C16634","C08042","C06683","C04478","C02532","C04441","C11008","C07456","C19612","C02222","C00307","C19274","C05686","C14238","C08164","C16855","C01245","C00202","C00295","C10979","C11702","C07668","C07269","C07653","C04640","C10019","C08331","C07184","C18724","C09311","C02734","C09951","C00655","C08021","C17047","C18403","C14133","C00014","C08082","C16394","C03175","C08761","C14350","C00921","C01865","C05838","C19603","C03366","C21008","C10681","C08476","C03150","C10999","C17407","C11342","C19017","C20141","C03622","C18078","C15658","C10023","C04437","C11019","C21476","C06963","C05768","C00303","C07949","C12270","C18379","C05595","C11121","C05720","C05335","C04462","C00935","C05381","C03319","C14844","C08340","C20239","C16557","C00961","C18728","C10077","C02810","C16558","C02370","C08727","C04524","C04409","C06909","C07351","C06928","C19331","C10600","C19044","C07819","C10065","C00053","C18490","C18388","C12633","C14861","C11052","C01990","C00061","C08734","C07496","C03065","C16621","C10187","C18739","C00715","C01721","C18850","C10484","C08549","C18486","C08570","C03779","C11208","C16511","C18827","C11435","C01608","C16612","C10414","C08272","C08469","C08437","C05939","C18884","C17079","C03492","C00365","C10086","C13179","C18112","C00847","C09805","C06855","C18857","C18801","C11585","C16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