Summary of Study ST004499
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 PR002833. The data can be accessed directly via it's Project DOI: 10.21228/M8G85W This work is supported by NIH grant, U2C- DK119886. See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Study ID | ST004499 |
| Study Title | Compounded effects of warming and drought accelerate microbially mediated organic matter decomposition and suppress methanogenesis in peatlands |
| Study Summary | Northern peatlands hold large soil carbon stocks but are highly sensitive to warming and hydrologic change. To assess how these climate perturbations alter organic matter chemistry, we performed LC-MS/MS metabolomics on peat from the whole-ecosystem SPRUCE experiment in northern Minnesota, where a 2021 drought lowered water tables by ~30 cm and intensified redox shifts. Peat from 10–20 cm depth was collected across warming treatments (+0 to +9 °C) in 2020–2022, lyophilized, extracted with methanol–water, and analyzed using both reverse-phase and HILIC chromatography. Although complementary metagenomic and metatranscriptomic analyses were also conducted in the broader project, this dataset focuses specifically on metabolite-level changes. Warming stimulated aerobic bacteria that correlated with porewater CO2 and metabolized phenolic compounds. Drought amplified warming effects by deepening water tables, stimulating aerobic respiration while suppressing fermentation and methanogenesis. Methanogen activity increased with warming under anoxic conditions but declined with drought. Metabolite-informed network analysis revealed covariance between fatty acids, amino acids, methanogens, and warming-responsive facultatively anaerobic heterotrophs, suggesting that organic acid exchange links temperature-sensitive heterotrophic and methanogenic processes |
| Institute | University of Arizona |
| Department | Environmental Science |
| Laboratory | Tfaily Lab |
| Last Name | Makke |
| First Name | Ghiwa |
| Address | 1230 North Cherry Avenue |
| ghiwamakke@arizona.edu | |
| Phone | 5209106052 |
| Submit Date | 2025-12-02 |
| Raw Data Available | Yes |
| Raw Data File Type(s) | mzML, raw(Thermo) |
| Analysis Type Detail | LC-MS |
| Release Date | 2026-01-21 |
| Release Version | 1 |
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Project:
| Project ID: | PR002833 |
| Project DOI: | doi: 10.21228/M8G85W |
| Project Title: | Compounded effects of warming and drought accelerate microbially mediated organic matter decomposition and suppress methanogenesis in peatlands |
| Project Summary: | Northern peatlands store nearly one-third of global soil carbon. In these cold, anoxic environments, decomposition is regulated by microbial networks adapted to oxygen limitation, allowing carbon, including recalcitrant phenolic compounds, to accumulate. Climate warming and drought increase oxygen availability, altering microbial carbon access. We leverage the SPRUCE whole-ecosystem warming experiment and an extreme drought that lowered water tables by 30 cm to determine how these perturbations influence microbial carbon cycling. Warming stimulated aerobic bacteria that correlated with porewater CO2 and metabolized phenolic compounds. Drought amplified warming effects by deepening water tables, stimulating aerobic respiration while suppressing fermentation and methanogenesis. Methanogen activity increased with warming under anoxic conditions but declined with drought. Metabolite-informed network analysis revealed covariance between fatty acids, amino acids, methanogens, and warming-responsive facultatively anaerobic heterotrophs, suggesting that organic acid exchange links temperature-sensitive heterotrophic and methanogenic processes. |
| 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: | SU004676 |
| Subject Type: | Soil sample |
Factors:
Subject type: Soil sample; Subject species: - (Factor headings shown in green)
| mb_sample_id | local_sample_id | Sample source | Year | Temperature |
|---|---|---|---|---|
| SA534462 | P20_2020 | Soil | 2020 | 2.25 |
| SA534463 | P4_2020 | Soil | 2020 | 4.5 |
| SA534464 | P13_2020 | Soil | 2020 | 4.5 |
| SA534465 | P8_2020 | Soil | 2020 | 6.75 |
| SA534466 | P16_2020 | Soil | 2020 | 6.75 |
| SA534467 | P17_2020 | Soil | 2020 | 9 |
| SA534468 | P10_2020 | Soil | 2020 | 9 |
| SA534469 | P19_2021 | Soil | 2021 | 0 |
| SA534470 | P6_2021 | Soil | 2021 | 0 |
| SA534471 | P11_2021 | Soil | 2021 | 2.25 |
| SA534472 | P20_2021 | Soil | 2021 | 2.25 |
| SA534473 | P13_2021 | Soil | 2021 | 4.5 |
| SA534474 | P4_2021 | Soil | 2021 | 4.5 |
| SA534475 | P8_2021 | Soil | 2021 | 6.75 |
| SA534476 | P16_2021 | Soil | 2021 | 6.75 |
| SA534477 | P10_2021 | Soil | 2021 | 9 |
| SA534478 | P17_2021 | Soil | 2021 | 9 |
| SA534479 | P19_2022 | Soil | 2022 | 0 |
| SA534480 | P6_2022 | Soil | 2022 | 0 |
| SA534481 | P11_2022 | Soil | 2022 | 2.25 |
| SA534482 | P20_2022 | Soil | 2022 | 2.25 |
| SA534483 | P4_2022 | Soil | 2022 | 4.5 |
| SA534484 | P13_2022 | Soil | 2022 | 4.5 |
| SA534485 | P8_2022 | Soil | 2022 | 6.75 |
| SA534486 | P16_2022 | Soil | 2022 | 6.75 |
| SA534487 | P10_2022 | Soil | 2022 | 9 |
| SA534488 | P17_2022 | Soil | 2022 | 9 |
| Showing results 1 to 27 of 27 |
Collection:
| Collection ID: | CO004669 |
| Collection Summary: | Peat samples were collected in August of 2020, 2021, and 2022 from each of the ten whole-ecosystem warming enclosures at the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment in the S1 Bog of the Marcell Experimental Forest (near Grand Rapids, MN; 47.30°N, 93.29°W). Surface material was collected using a serrated knife, and deeper material was obtained with a Russian peat corer. Cores were sectioned into 0–10, 10–20, and 20–30 cm depth increments and homogenized. For metabolomics, subsamples from the 10–20 cm depth—corresponding to the same material used for metagenomic analyses—were processed for extraction and LC-MS/MS analysis. |
| Sample Type: | soil |
Treatment:
| Treatment ID: | TR004685 |
| 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). For the present study, peat samples were collected from 10 actively warmed enclosures spanning five temperature treatments (0, +2.25, +4.5, +6.75, and +9 °C) under both ambient- and elevated-CO₂ conditions. The sample set includes chambers representing all warming levels across three years (2020–2022), with each year containing a combination of ambient CO₂ and +500 ppm elevated-CO₂ treatments consistent with SPRUCE chamber assignments. |
Sample Preparation:
| Sampleprep ID: | SP004682 |
| 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℃ |
Combined analysis:
| Analysis ID | AN007545 | AN007546 |
|---|---|---|
| Chromatography ID | CH005724 | CH005725 |
| MS ID | MS007242 | MS007243 |
| Analysis type | MS | MS |
| Chromatography type | Reversed phase | HILIC |
| Chromatography system | Thermo Vanquish UHPLC | Thermo Vanquish UHPLC |
| Column | Waters ACQUITY UPLC HSS T3 (150 x 2.1mm,1.8um) | Waters ACQUITY UPLC BEH Amide (150 x 2.1mm,1.7um) |
| MS Type | ESI | ESI |
| MS instrument type | Orbitrap | Orbitrap |
| MS instrument name | Thermo Orbitrap Exploris 480 | Thermo Orbitrap Exploris 480 |
| Ion Mode | POSITIVE | NEGATIVE |
| Units | Peak Area | Peak Area |
Chromatography:
| Chromatography ID: | CH005724 |
| 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: | CH005725 |
| 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 |
MS:
| MS ID: | MS007242 |
| Analysis ID: | AN007545 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data analysis was conducted using the Compound Discoverer 3.3 software by Thermo Fisher Scientific, employing an untargeted metabolomics workflow |
| Ion Mode: | POSITIVE |
| MS ID: | MS007243 |
| Analysis ID: | AN007546 |
| Instrument Name: | Thermo Orbitrap Exploris 480 |
| Instrument Type: | Orbitrap |
| MS Type: | ESI |
| MS Comments: | Data analysis was conducted using the Compound Discoverer 3.3 software by Thermo Fisher Scientific, employing an untargeted metabolomics workflow |
| Ion Mode: | NEGATIVE |
