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Lennon JT, Abramoff RZ, Allison SD, Burckhardt RM, DeAngelis KM, Dunne JP, Frey SD, Friedlingstein P, Hawkes CV, Hungate BA, Khurana S, Kivlin SN, Levine NM, Manzoni S, Martiny AC, Martiny JBH, Nguyen NK, Rawat M, Talmy D, Todd-Brown K, Vogt M, Wieder WR, Zakem EJ. Priorities, opportunities, and challenges for integrating microorganisms into Earth system models for climate change prediction. mBio 2024; 15:e0045524. [PMID: 38526088 PMCID: PMC11078004 DOI: 10.1128/mbio.00455-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024] Open
Abstract
Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a "top 10" list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs. We discuss the need for coarse-graining microbial information into functionally relevant categories, as well as the capacity for microorganisms to rapidly evolve in response to climate-change drivers. Microbiologists are uniquely positioned to collect novel and valuable information necessary for next-generation ESMs, but this requires data harmonization and transdisciplinary collaboration to effectively guide adaptation strategies and mitigation policy.
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Affiliation(s)
- J. T. Lennon
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - R. Z. Abramoff
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Ronin Institute, Montclair, New Jersey, USA
| | - S. D. Allison
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
- Department of Earth System Science, University of California Irvine, Irvine, California, USA
| | | | - K. M. DeAngelis
- Department of Microbiology, University of Massachusetts, Amherst, Massachusetts, USA
| | - J. P. Dunne
- NOAA/OAR Geophysical Fluid Dynamics Laboratory, Princeton, New Jersey, USA
| | - S. D. Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, USA
| | - P. Friedlingstein
- College of Engineering, Mathematics, and Physical Sciences, University of Exeter, Exeter, United Kingdom
| | - C. V. Hawkes
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - B. A. Hungate
- Department of Biological Sciences, Center for Ecosystem Science, Northern Arizona University, Flagstaff, Arizona, USA
| | - S. Khurana
- Department of Physical Geography, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - S. N. Kivlin
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - N. M. Levine
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - S. Manzoni
- Department of Physical Geography, Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - A. C. Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - J. B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, USA
| | - N. K. Nguyen
- American Society for Microbiology, Washington, DC, USA
| | - M. Rawat
- National Science Foundation, Washington, DC, USA
| | - D. Talmy
- Department of Microbiology, University of Tennessee, Knoxville, Tennessee, USA
| | - K. Todd-Brown
- Department of Environmental Engineering Sciences, University of Florida, Gainesville, Florida, USA
| | - M. Vogt
- Institute for Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - W. R. Wieder
- National Center for Atmospheric Research, Boulder, Colorado, USA
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, USA
| | - E. J. Zakem
- Department of Global Ecology, Carnegie Institution for Science, Stanford, California, USA
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Affiliation(s)
- A L Romero-Olivares
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA.
- Department of Biology, New Mexico State University, Las Cruces, NM, 88001, USA.
| | - E W Morrison
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
| | - A Pringle
- Department of Botany and Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - S D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
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Abstract
Fungi are mediators of the nitrogen and carbon cycles in terrestrial ecosystems. Examining how nitrogen uptake and organic matter decomposition potential differs in fungi can provide insight into the underlying mechanisms driving fungal ecological processes and ecosystem functioning. In this study, we assessed the frequency of genes encoding for specific enzymes that facilitate nitrogen uptake and organic matter decomposition in 879 fungal genomes with fungal taxa grouped into trait-based categories. Our linked gene-trait data approach revealed that gene frequencies vary across and within trait-based groups and that trait-based categories differ in trait space. We present two examples of how this linked gene-trait approach can be used to address ecological questions. First, we show that this type of approach can help us better understand, and potentially predict, how fungi will respond to environmental stress. Specifically, we found that trait-based categories with high nitrogen uptake gene frequency increased in relative abundance when exposed to high soil nitrogen enrichment. Second, by comparing frequencies of nitrogen uptake and organic matter decomposition genes, we found that most ectomycorrhizal fungi in our dataset have similar gene frequencies to brown rot fungi. This demonstrates that gene-trait data approaches can shed light on potential evolutionary trajectories of life history traits in fungi. We present a framework for exploring nitrogen uptake and organic matter decomposition gene frequencies in fungal trait-based groups and provide two concise examples on how to use our framework to address ecological questions from a mechanistic perspective.
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Affiliation(s)
- A L Romero-Olivares
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA.
- Department of Biology, New Mexico State University, Las Cruces, NM, 88001, USA.
| | - E W Morrison
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
| | - A Pringle
- Department of Botany and Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - S D Frey
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, NH, 03824, USA
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Stinson KA, Frey SD, Jackson MR, Coates-Connor E, Anthony M, Martinez K. Responses of non-native earthworms to experimental eradication of garlic mustard and implications for native vegetation. Ecosphere 2018. [DOI: 10.1002/ecs2.2353] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- K. A. Stinson
- Department of Environmental Conservation; University of Massachusetts; 160 Holdsworth Way Amherst Massachusetts 01002 USA
| | - S. D. Frey
- Department of Natural Resources and the Environment; University of New Hampshire; 56 College Road Durham New Hampshire 03824 USA
| | - M. R. Jackson
- Department of Environmental Conservation; University of Massachusetts; 160 Holdsworth Way Amherst Massachusetts 01002 USA
| | - E. Coates-Connor
- Department of Environmental Conservation; University of Massachusetts; 160 Holdsworth Way Amherst Massachusetts 01002 USA
| | - M. Anthony
- Department of Natural Resources and the Environment; University of New Hampshire; 56 College Road Durham New Hampshire 03824 USA
| | - K. Martinez
- Department of Biology; California State University Dominguez Hills; NSM A-143 1000 East Victoria Street Carson California 90747 USA
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Melillo JM, Frey SD, DeAngelis KM, Werner WJ, Bernard MJ, Bowles FP, Pold G, Knorr MA, Grandy AS. Long-term pattern and magnitude of soil carbon feedback to the climate system in a warming world. Science 2017; 358:101-105. [DOI: 10.1126/science.aan2874] [Citation(s) in RCA: 350] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/23/2017] [Indexed: 11/02/2022]
Abstract
In a 26-year soil warming experiment in a mid-latitude hardwood forest, we documented changes in soil carbon cycling to investigate the potential consequences for the climate system. We found that soil warming results in a four-phase pattern of soil organic matter decay and carbon dioxide fluxes to the atmosphere, with phases of substantial soil carbon loss alternating with phases of no detectable loss. Several factors combine to affect the timing, magnitude, and thermal acclimation of soil carbon loss. These include depletion of microbially accessible carbon pools, reductions in microbial biomass, a shift in microbial carbon use efficiency, and changes in microbial community composition. Our results support projections of a long-term, self-reinforcing carbon feedback from mid-latitude forests to the climate system as the world warms.
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Giasson MA, Ellison AM, Bowden RD, Crill PM, Davidson EA, Drake JE, Frey SD, Hadley JL, Lavine M, Melillo JM, Munger JW, Nadelhoffer KJ, Nicoll L, Ollinger SV, Savage KE, Steudler PA, Tang J, Varner RK, Wofsy SC, Foster DR, Finzi AC. Soil respiration in a northeastern US temperate forest: a 22-year synthesis. Ecosphere 2013. [DOI: 10.1890/es13.00183.1] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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