A framework for integrating genomics, microbial traits, and ecosystem biogeochemistry
Microbes drive the biogeochemical cycles of earth systems, yet the long-standing goal of linking emerging genomic information, microbial traits, mechanistic ecosystem models, and projections under climate change has remained elusive despite a wealth of emerging genomic information. Here we developed a general genome-to-ecosystem (G2E) framework for integrating genome-inferred microbial kinetic traits into mechanistic models of terrestrial ecosystems and applied it at a well-studied Arctic wetland by benchmarking predictions against observed greenhouse gas emissions. We found variation in genome-inferred microbial kinetic traits resulted in large differences in simulated annual methane emissions, quantitatively demonstrating that the genomically observable variations in microbial capacity are consequential for ecosystem functioning. Applying microbial community-aggregated traits via genome relative-abundance-weighting gave better methane emissions predictions (i.e., up to 54% decrease in bias) compared to ignoring the observed abundances, highlighting the value of combined trait inferences and abundances. This work provides an example of integrating microbial functional trait-based genomics, mechanistic and pragmatic trait parameterizations of diverse microbial metabolisms, and mechanistic ecosystem modeling. The generalizable G2E framework will enable the use of abundant microbial metagenomics data to improve predictions of microbial interactions in many complex systems, including oceanic microbiomes.
Authors
- W. J. Riley (ORCID: https://orcid.org/0000-0002-4615-2304)
- Matthew B. Sullivan (ORCID: https://orcid.org/0000-0001-8398-8234)
- Kuang‐Yu Chang (ORCID: https://orcid.org/0000-0002-7859-5871)
- Jinyun Tang (ORCID: https://orcid.org/0000-0002-4792-1259)
- R. K. Varner (ORCID: https://orcid.org/0000-0002-3571-6629)
- Nicholas Bouskill (ORCID: https://orcid.org/0000-0002-6577-8724)
- R. F. Grant (ORCID: https://orcid.org/0000-0002-8890-6231)
- Ben J. Woodcroft (ORCID: https://orcid.org/0000-0003-0670-7480)
- Eoin Brodie (ORCID: https://orcid.org/0000-0002-8453-8435)
- Gianna L. Marschmann (ORCID: https://orcid.org/0000-0002-9065-2023)
- Ulaş Karaöz (ORCID: https://orcid.org/0000-0002-8238-6757)
- Zhen Li (ORCID: https://orcid.org/0000-0001-9511-3670)
- Kelly C. Wrighton (ORCID: https://orcid.org/0000-0003-0434-4217)
- S. R. Saleska (ORCID: https://orcid.org/0000-0002-4974-3628)
- Ian Shirley (ORCID: https://orcid.org/0000-0002-2229-1414)
- Eric King
- Patrick Crill (ORCID: https://orcid.org/0000-0003-1110-3059)
- Qiong Wu
Institutions
- Cosumnes River College (US)
- Lawrence Livermore National Laboratory (US)
- Translational Research Institute (AU)
- University of Arizona (US)
- Lawrence Berkeley National Laboratory (US)
- University of Alberta (CA)
- Queensland University of Technology (AU)
- University of New Hampshire (US)
- Stockholm University (SE)
- Bolin Centre for Climate Research (SE)
- The Ohio State University (US)
- Colorado State University (US)
- University of California, Berkeley (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-03-04
- DOI
- https://doi.org/10.1038/s41467-025-57386-5
- Citations
- 22
- Primary Topic
- Microbial Community Ecology and Physiology
- Type
- article
- Field-Weighted Citation Impact
- 36.04
Funders
- National Science Foundation
- U.S. Department of Energy
- Polarforskningssekretariatet
- National Energy Research Scientific Computing Center
- Vetenskapsrådet
- Office of Science
- Basic Energy Sciences
- Biological and Environmental Research
- Lawrence Livermore National Laboratory
- Lawrence Berkeley National Laboratory