Summary of Study ST003907

This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR002445. The data can be accessed directly via it's Project DOI: 10.21228/M8KZ63 This work is supported by NIH grant, U2C- DK119886.

See: https://www.metabolomicsworkbench.org/about/howtocite.php

This study contains a large results data set and is not available in the mwTab file. It is only available for download via FTP as data file(s) here.

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Study IDST003907
Study TitleNorthern peatland microbial networks exhibit resilience to warming and acquire electron acceptor from soil organic matter
Study SummaryPeatlands store vast amounts of carbon, but how their microbial and chemical processes respond to climate change remains unclear. In this study, we investigated how soil microbial communities and organic matter chemistry in a northern Minnesota peatland respond to long-term experimental warming. Peat samples were collected from four depths (10–175 cm) across 10 whole-ecosystem warming enclosures at the SPRUCE (Spruce and Peatland Responses Under Changing Environments) site in the Marcell Experimental Forest. We used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to analyze the chemical composition of peat at different depths, alongside metagenomic sequencing to reconstruct nearly 700 microbial genomes. Despite sustained warming for three years, microbial community structure remained stable, indicating resilience to temperature stress. However, functional gene analysis and metabolomics revealed shifts in carbon processing pathways, with sulfate reduction, denitrification, and acetogenesis emerging as key decomposition processes. Genome-resolved metagenomics further revealed methanogen metabolic flexibility, including potential for hydrogenotrophic, acetoclastic, and methylotrophic methanogenesis pathways. Supporting this, integration of metabolomic and genomic data highlighted a key mechanism by which microbial metabolism may access alternative electron acceptors: the ratio of choline-O-sulfate to choline was strongly correlated with the abundance of the betC gene, which encodes choline sulfatase. This enzyme cleaves choline-O-sulfate to release sulfate, potentially fueling anaerobic respiration via sulfate-reducing microbes. These findings suggest that microbial metabolic flexibility, coupled with changes in peat chemistry, plays a critical role in maintaining peatland carbon cycling under warming conditions.
Institute
University of Arizona
DepartmentEnvironmental Science
LaboratoryTfaily Lab
Last NameMakke
First NameGhiwa
Address1230 North Cherry Avenue
Emailghiwamakke@arizona.edu
Phone5209106052
Submit Date2025-03-31
Raw Data AvailableYes
Raw Data File Type(s)mzML, raw(Thermo)
Analysis Type DetailLC-MS
Release Date2025-05-29
Release Version1
Ghiwa Makke Ghiwa Makke
https://dx.doi.org/10.21228/M8KZ63
ftp://www.metabolomicsworkbench.org/Studies/ application/zip

Select appropriate tab below to view additional metadata details:

Project:

Project ID:PR002445
Project DOI:doi: 10.21228/M8KZ63
Project Title:Northern peatland microbial communities exhibit resistance to warming and acquire electron acceptors from soil organic matter
Project Summary:The microbial networks that regulate belowground carbon turnover and respond to climate change drivers in peatlands are poorly understood. Here, we leverage a whole ecosystem warming experiment to elucidate the key processes of terminal carbon decomposition and community responses to temperature rise. Our dataset of 697 metagenome-assembled genomes (MAGs) extends from surface (10 cm) to 2 m deep into the peat column, with only 3.7% of genomes overlapping with other well-studied peatlands. Unexpectedly, community composition has yet to show a significant response to warming after 3 years, suggesting that metabolically diverse soil microbial networks are resilient to climate change. Surprisingly, the dominant methanogens showed the potential for both acetoclastic and hydrogenotrophic methanogenesis. Nonetheless, the predominant pathways for anaerobic carbon decomposition include sulfate/sulfite reduction, denitrification, and acetogenesis, rather than methanogenesis based on gene abundances. Multi-omics data suggest that organic matter cleavage provides terminal electron acceptors, which together with methanogen metabolic flexibility, may explain peat microbiome resilience to warming.
Institute:University of Arizona
Department:Environmental Science
Laboratory:Tfaily Lab
Last Name:Makke
First Name:Ghiwa
Address:1230 North Cherry Avenue, Tucson, AZ, 85721, USA
Email:ghiwamakke@arizona.edu
Phone:520-626-3650

Subject:

Subject ID:SU004042
Subject Type:Soil sample

Factors:

Subject type: Soil sample; Subject species: - (Factor headings shown in green)

mb_sample_id local_sample_id Depth Temperature
SA429984P6-100-2018D100 0
SA429985P19-100-2018D100 0
SA429986P11-100-2018D100 2.25
SA429987P20-100-2018D100 2.25
SA429988P4-100-2018D100 4.5
SA429989P13-100-2018D100 4.5
SA429990P16-100-2018D100 6.75
SA429991P8-100-2018D100 6.75
SA429992P17-100-2018D100 9
SA429993P10-100-2018D100 9
SA429994P19-150-2018D150 0
SA429995P6-150-2018D150 0
SA429996P20-150-2018D150 2.25
SA429997P11-150-2018D150 2.25
SA429998P4-150-2018D150 4.5
SA429999P13-150-2018D150 4.5
SA430000P8-150-2018D150 6.75
SA430001P16-150-2018D150 6.75
SA430002P10-150-2018D150 9
SA430003P17-150-2018D150 9
SA430004P19-20-2018D20 0
SA430005P6-20-2018D20 0
SA430006P20-20-2018D20 2.25
SA430007P11-20-2018D20 2.25
SA430008P4-20-2018D20 4.5
SA430009P13-20-2018D20 4.5
SA430010P8-20-2018D20 6.75
SA430011P16-20-2018D20 6.75
SA430012P17-20-2018D20 9
SA430013P10-20-2018D20 9
SA430014P19-40-2018D40 0
SA430015P6-40-2018D40 0
SA430016P11-40-2018D40 2.25
SA430017P20-40-2018D40 2.25
SA430018P13-40-2018D40 4.5
SA430019P4-40-2018D40 4.5
SA430020P16-40-2018D40 6.75
SA430021P8-40-2018D40 6.75
SA430022P17-40-2018D40 9
SA430023P10-40-2018D40 9
Showing results 1 to 40 of 40

Collection:

Collection ID:CO004035
Collection Summary:Peat samples were collected in August of 2018 from the hollows of each of the 10 whole-ecosystem warming chambers of the Spruce and Peatland Responses Under Changing Environments (SPRUCE) warming experiment located in the ombrotrophic, acidic S1 Bog of the Marcell Experimental Forest, north of Grand Rapids, MN with a serrated knife at the surface and a Russian corer at depth. The samples were separated into depth increments and six 0.35-g subsamples of homogenized peat from the 10-20 cm, 40-50 cm, 100-125 cm, and 150-175 cm depth increments.
Sample Type:soil

Treatment:

Treatment ID:TR004051
Treatment Summary:The SPRUCE experiment where the samples were collected consists of 17 open-top chambers that control the peat and air temperature (ambient, +0, +2.25, +4.5, +6.75 and +9°C) as well as atmospheric CO2 concentration (ambient and 900 ppm).

Sample Preparation:

Sampleprep ID:SP004048
Sampleprep Summary:To dry samples and ensure uniform starting weight for extraction, peat samples were first lyophilized using a Labconco FreeZone, Benchtop freeze dryer for 48 hr. The freeze-dried peat samples (0.2 g) were extracted by adding 20 mL of an 80:20 solution of MeOH: sterile MilliQ water. Samples were briefly vortexed and sonicated in a water bath for 2 hr at 20 °C (FisherBrand CPX3800). The supernatant was filtered through a 0.45 um filter to remove cellular debris and plant material. Of this extract, 7 mL was transferred to two glass autosampler vials (3.5 mL each), dried in a vacuum centrifuge (Eppendorf Vacufuge plus), and stored at −80 °C. Prior to CL-MS/MS analysis, samples were reconstituted in 80:20 water: methanol for reverse phase (RP), and 50:50 water: acetonitrile for hydrophilic interaction liquid chromatography (HILIC).
Extract Storage:-20℃

Chromatography:

Chromatography ID:CH004863
Instrument Name:Thermo Vanquish UHPLC
Column Name:Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um)
Column Temperature:45
Flow Gradient:0–3 min held at 1% B; 3–19 min 1% B – 95% B; 19–20 min 95% B
Flow Rate:300 uL/minute
Solvent A:100% water; 0.1% formic acid
Solvent B:100% Methanol; 0.1% formic acid
Chromatography Type:Reversed phase
  
Chromatography ID:CH004864
Instrument Name:Thermo Vanquish UHPLC
Column Name:Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um)
Column Temperature:45
Flow Gradient:0–3 min held at 1% B; 3–19 min 1% B – 95% B; 19–20 min 95% B
Flow Rate:300 uL/minute
Solvent A:90% acetonitrile/10% water; 0.1% formic acid; 10 mM ammonium acetate
Solvent B:50% acetonitrile/50% water; 0.1% formic acid; 10 mM ammonium acetate,
Chromatography Type:HILIC

Analysis:

Analysis ID:AN006412
Laboratory Name:Analytical & Biological Mass Spectrometry Core Facility (University of Arizona)
Analysis Type:MS
Chromatography ID:CH004863
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003907_AN006412_Results.txt
Units:Peak Area
  
Analysis ID:AN006413
Laboratory Name:Analytical & Biological Mass Spectrometry Core Facility (University of Arizona)
Analysis Type:MS
Chromatography ID:CH004864
Has Mz:1
Has Rt:1
Rt Units:Minutes
Results File:ST003907_AN006413_Results.txt
Units:Peak Area
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