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Title: Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling

Abstract

Climate change is expected to have significant and uncertain impacts on methane (CH 4) emissions from northern peatlands. Biogeochemical models can extrapolate site-specific CH 4 measurements to larger scales and predict responses of CH 4 emissions to environmental changes. However, these models include considerable uncertainties and limitations in representing CH4 production, consumption, and transport processes. To improve predictions of CH 4 transformations, we incorporated acetate and stable carbon (C) isotopic dynamics associated with CH 4 cycling into a biogeochemistry model, DNDC. By including these new features, DNDC explicitly simulates acetate dynamics and the relative contribution of acetotrophic and hydrogenotrophic methanogenesis (AM and HM) to CH 4 production, and predicts the C isotopic signature (δ 13C) in soil C pools and emitted gases. When tested against biogeochemical and microbial community observations at two sites in a zone of thawing permafrost in a subarctic peatland in Sweden, the new formulation substantially improved agreement with CH 4 production pathways and δ 13C in emitted CH 413C-CH 4), a measure of the integrated effects of microbial production and consumption, and of physical transport. We also investigated the sensitivity of simulated δ 13C-CH 4 to C isotopic composition of substrates and, to fractionationmore » factors for CH4 production (α AM and α HM), CH 4 oxidation (α MO), and plant-mediated CH 4 transport (α TP). The sensitivity analysis indicated that the δ13C-CH 4 is highly sensitive to the factors associated with microbial metabolism (α AM, α HM, and α MO). The model framework simulating stable C isotopic dynamics provides a robust basis for better constraining and testing microbial mechanisms in predicting CH 4 cycling in peatlands.« less

Authors:
ORCiD logo [1]; ORCiD logo [2];  [1]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [5];  [6]; ORCiD logo [7];  [8];  [9];  [1]
  1. Univ. of New Hampshire, Durham, NH (United States). Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space
  2. Rochester Institute of Technology, NY (United States). Thomas H. Gosnell School of Life Sciences
  3. Florida State Univ., Tallahassee, FL (United States). Dept. of Earth, Ocean and Atmospheric Science
  4. Department of Geological Sciences, Stockholm University, Stockholm Sweden
  5. Univ. of New Hampshire, Durham, NH (United States). Earth Systems Research Center, Institute for the Study of Earth, Oceans and Space; Univ. of New Hampshire, Durham, NH (United States). Dept. of Earth Sciences
  6. Univ. of Queensland, Brisbane (Australia). Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences
  7. The Ohio State Univ., Columbus, OH (United States). Dept of Microbiology
  8. Univ. of Massachusetts, Lowell, MA (United States). Dept. of Biological Sciences
  9. Univ. of Arizona, Tucson, AZ (United States). Dept. of Ecology and Evolutionary Biology
Publication Date:
Research Org.:
Univ. of Arizona, Tucson, AZ (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1363819
Grant/Contract Number:
SC0004632; SC0010580
Resource Type:
Journal Article: Published Article
Journal Name:
Journal of Advances in Modeling Earth Systems
Additional Journal Information:
Journal Volume: 9; Journal Issue: 2; Journal ID: ISSN 1942-2466
Publisher:
American Geophysical Union (AGU)
Country of Publication:
United States
Language:
English
Subject:
54 ENVIRONMENTAL SCIENCES; 58 GEOSCIENCES

Citation Formats

Deng, Jia, McCalley, Carmody K., Frolking, Steve, Chanton, Jeff, Crill, Patrick, Varner, Ruth, Tyson, Gene, Rich, Virginia, Hines, Mark, Saleska, Scott R., and Li, Changsheng. Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling. United States: N. p., 2017. Web. doi:10.1002/2016MS000817.
Deng, Jia, McCalley, Carmody K., Frolking, Steve, Chanton, Jeff, Crill, Patrick, Varner, Ruth, Tyson, Gene, Rich, Virginia, Hines, Mark, Saleska, Scott R., & Li, Changsheng. Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling. United States. doi:10.1002/2016MS000817.
Deng, Jia, McCalley, Carmody K., Frolking, Steve, Chanton, Jeff, Crill, Patrick, Varner, Ruth, Tyson, Gene, Rich, Virginia, Hines, Mark, Saleska, Scott R., and Li, Changsheng. 2017. "Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling". United States. doi:10.1002/2016MS000817.
@article{osti_1363819,
title = {Adding stable carbon isotopes improves model representation of the role of microbial communities in peatland methane cycling},
author = {Deng, Jia and McCalley, Carmody K. and Frolking, Steve and Chanton, Jeff and Crill, Patrick and Varner, Ruth and Tyson, Gene and Rich, Virginia and Hines, Mark and Saleska, Scott R. and Li, Changsheng},
abstractNote = {Climate change is expected to have significant and uncertain impacts on methane (CH4) emissions from northern peatlands. Biogeochemical models can extrapolate site-specific CH4 measurements to larger scales and predict responses of CH4 emissions to environmental changes. However, these models include considerable uncertainties and limitations in representing CH4 production, consumption, and transport processes. To improve predictions of CH4 transformations, we incorporated acetate and stable carbon (C) isotopic dynamics associated with CH4 cycling into a biogeochemistry model, DNDC. By including these new features, DNDC explicitly simulates acetate dynamics and the relative contribution of acetotrophic and hydrogenotrophic methanogenesis (AM and HM) to CH4 production, and predicts the C isotopic signature (δ13C) in soil C pools and emitted gases. When tested against biogeochemical and microbial community observations at two sites in a zone of thawing permafrost in a subarctic peatland in Sweden, the new formulation substantially improved agreement with CH4 production pathways and δ13C in emitted CH4 (δ13C-CH4), a measure of the integrated effects of microbial production and consumption, and of physical transport. We also investigated the sensitivity of simulated δ13C-CH4 to C isotopic composition of substrates and, to fractionation factors for CH4 production (αAM and αHM), CH4 oxidation (αMO), and plant-mediated CH4 transport (αTP). The sensitivity analysis indicated that the δ13C-CH4 is highly sensitive to the factors associated with microbial metabolism (αAM, αHM, and αMO). The model framework simulating stable C isotopic dynamics provides a robust basis for better constraining and testing microbial mechanisms in predicting CH4 cycling in peatlands.},
doi = {10.1002/2016MS000817},
journal = {Journal of Advances in Modeling Earth Systems},
number = 2,
volume = 9,
place = {United States},
year = 2017,
month = 6
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1002/2016MS000817

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  • Climate change is expected to have significant and uncertain impacts on methane (CH 4) emissions from northern peatlands. Biogeochemical models can extrapolate site-specific CH 4 measurements to larger scales and predict responses of CH 4 emissions to environmental changes. However, these models include considerable uncertainties and limitations in representing CH4 production, consumption, and transport processes. To improve predictions of CH 4 transformations, we incorporated acetate and stable carbon (C) isotopic dynamics associated with CH 4 cycling into a biogeochemistry model, DNDC. By including these new features, DNDC explicitly simulates acetate dynamics and the relative contribution of acetotrophic and hydrogenotrophic methanogenesismore » (AM and HM) to CH 4 production, and predicts the C isotopic signature (δ 13C) in soil C pools and emitted gases. When tested against biogeochemical and microbial community observations at two sites in a zone of thawing permafrost in a subarctic peatland in Sweden, the new formulation substantially improved agreement with CH 4 production pathways and δ 13C in emitted CH 413C-CH 4), a measure of the integrated effects of microbial production and consumption, and of physical transport. We also investigated the sensitivity of simulated δ 13C-CH 4 to C isotopic composition of substrates and, to fractionation factors for CH4 production (α AM and α HM), CH 4 oxidation (α MO), and plant-mediated CH 4 transport (α TP). The sensitivity analysis indicated that the δ13C-CH 4 is highly sensitive to the factors associated with microbial metabolism (α AM, α HM, and α MO). The model framework simulating stable C isotopic dynamics provides a robust basis for better constraining and testing microbial mechanisms in predicting CH 4 cycling in peatlands.« less
  • Marine methane seep habitats represent an important control on the global flux of methane between the subsurface and water column reservoirs. Meta-omics studies have begun to outline community-wide metabolic potential, but expression patterns of proteins that enact sulfate-mediated anaerobic methane oxidation in seeps are poorly characterized. Proteomic stable isotope probing (proteomic SIP) offers an additional layer of information for characterizing phylogenetically specific, functionally relevant activity in mixed microbial communities. Here we applied proteomic SIP to 15NH4+ and CH4 amended seep sediment microcosms in an attempt to track the protein synthesis of slow-growing, low-energy microbial systems. Across all samples, 3495 proteinsmore » were identified, 21% of which were 15N-labeled. We observed active synthesis (15N enrichment) of all proteins believed to be involved in sulfate reduction and reverse methanogenesis including methylenetetrahydromethanopterin reductase (Mer). The abundance and phylogenetic range of methyl-coenzyme M reductase (Mcr) orthologs produced during incubation experiments suggests that seeps provide sufficient niches for multiple organisms performing analogous metabolisms. Twenty-eight previously unreported post-translational modifications of McrA were measured, indicating dynamic enzymatic machinery and offering a dimension of functional diversity beyond gene-dictated sequence. RNA polymerase associated with putative sulfur-oxidizing Epsilonproteobacteria and aerobic Gammaproteobacteria were more abundant among pre-incubation proteins, suggesting diminished metabolic activity in long-term anoxic, sulfidic experimental incubations. Twenty-six proteins of unknown function were detected in all proteomic experiments and actively expressed in labeled experiments, suggesting that they play important roles in methane seep ecosystems. The addition of stable isotope probing to environmental proteomics experiments provides a mechanism to begin to assess the degree to which diagnostic meatbolic proteins are long-lived or acively synthesized in complex, slow-growing microbial communities. Our work here demonstrates that sediment-hosted microbial assemblages in marine methane seeps are dynamic, heterogeneous systems with broad functional diversity.« less
  • Many studies have shown that changes in nitrogen (N) availability affect primary productivity in a variety of terrestrial systems, but less is known about the effects of the changing N cycle on soil organic matter (SOM) decomposition. We used a variety of techniques to examine the effects of chronic N amendments on SOM chemistry and microbial community structure and function in an alpine tundra soil. We collected surface soil (0-5 cm) samples from five control and five long-term N-amended plots established and maintained at the Niwot Ridge Long-term Ecological Research (LTER) site. Samples were bulked by treatment and all analysesmore » were conducted on composite samples. The fungal community shifted in response to N amendments, with a decrease in the relative abundance of basidiomycetes. Bacterial community composition also shifted in the fertilized soil, with increases in the relative abundance of sequences related to the Bacteroidetes and Gemmatimonadetes, and decreases in the relative abundance of the Verrucomicrobia. We did not uncover any bacterial sequences that were closely related to known nitrifiers in either soil, but sequences related to archaeal nitrifiers were found in control soils. The ratio of fungi to bacteria did not change in the N-amended soils, but the ratio of archaea to bacteria dropped from 20% to less than 1% in the N-amended plots. Comparisons of aliphatic and aromatic carbon compounds, two broad categories of soil carbon compounds, revealed no between treatment differences. However, G-lignins were found in higher relative abundance in the fertilized soils, while proteins were detected in lower relative abundance. Finally, the activities of two soil enzymes involved in N cycling changed in response to chronic N amendments. These results suggest that chronic N fertilization induces significant shifts in soil carbon dynamics that correspond to shifts in microbial community structure and function.« less