Environmental Transformations and Interactions
Thawing Permafrost Reveals Complex Microbiome–Metabolite Interplay
This research examines microbiome–metabolite interactions in a thawing permafrost at Stordalen Mire, Sweden, revealing potential key regulators of greenhouse gas emissions in these rapidly changing ecosystems.
A multi-institutional study examined how microbes interact with small chemical compounds from microbes and surrounding plants from a field site in Northern Sweden, revealing changes in microbial communities and their environment. (Image courtesy of LOJ5407 | iStock)
The Science
Permafrost peatlands are frozen landscapes that hold a massive amount of carbon. As the Earth warms, these areas are thawing, leading to potential releases of stored carbon. The form of this carbon release (whether as carbon dioxide [CO₂] or methane [CH₄]) likely depends on the complex interactions between microbial communities and their environment, though the specific mechanisms controlling these processes remain poorly understood. A multi-institutional study based on a field site in Northern Sweden examined how microbes interact with small chemical compounds (metabolites) from microbes and the surrounding plants, revealing changes in microbial communities and their environment. The study found that microbes interact with sulfur- and nitrogen-rich compounds, possibly from mosses in bogs. This interaction appears to contribute to greenhouse gas production. Tracking microbes and metabolites is key to understanding greenhouse gas emissions and predicting the impact of thawing permafrost, revealing complex interactions between plants, soil chemistry, and microbial activity.
The Impact
The team’s approach of studying both metabolites and microbes provides a more complete picture of permafrost ecosystems than ever before. The chemical fingerprinting of metabolites allows for greater understanding of not just the current state of the Stordalen Mire, but also enables the prediction of future responses to thawing permafrost. By studying the complex connections between microbes, metabolites, and greenhouse gas emissions, researchers are addressing a critical gap in understanding the impacts of permafrost thaw. While the team’s findings confirm the potential for increased greenhouse gas release from thawing permafrost, they also open new avenues for developing targeted approaches to mitigate these impacts, guiding future research and policy decisions.
Summary
The roles of microbiome–metabolite interactions in environmental functioning are still not fully understood. A multi-institutional team of researchers analyzed shifts in both the microbial and the metabolite compositions across a permafrost thaw gradient in Stordalen Mire, Sweden. The microbiome was characterized using genome-resolved metagenomics collected at the Joint Genome Institute (JGI). The metabolome was characterized using high-resolution Fourier transform ion cyclotron resonance mass spectrometry (12 Tesla Bruker FTICR mass spectrometer) at the Environmental Molecular Sciences Laboratory (EMSL). Both JGI and EMSL are Department of Energy Office of Science user facilities. In addition, the team leveraged community assembly theory, supported through an Early Career Award for Pacific Northwest National Laboratory Earth scientist James Stegen, to test whether microorganisms and metabolites show concordant responses to changing drivers. Analyses of the data and theory showed that microbes and metabolites respond differently to the same environmental pressures, challenging assumptions in microbial models and suggesting that an understanding of microbes and metabolites might elucidate how ecosystems function. By looking closely at the links between specific microbes, metabolites, and greenhouse gas changes (CO₂ and CH₄), the team pinpointed key interactions between microbial species and lignin-like metabolites rich in sulfur and nitrogen that could be driving greenhouse gas emissions. The study demonstrates how examining these fine-scale interactions can provide a deeper understanding of the processes driving greenhouse gas emissions as permafrost thaws.
Contacts
Viviana Freire-Zapata, University of Arizona, vfreirezapata@arizona.edu
Malak M. Tfaily, University of Arizona, tfaily@arizona.edu
Funding
This study was supported, in part, by the Department of Energy, Office of Science, Biological and Environmental Research program. This research is a contribution of the EMERGE Biology Integration Institute funded by the NSF Biology Integration Institutes Program. Portions of this work were supported by awards from JGI and EMSL, both DOE Office of Science user facilities sponsored by the Biological and Environmental Research program. Additional support was provided by an Early Career Award for PNNL Earth scientist James Stegen, the Swedish Polar Research Secretariat, and Swedish Infrastructure for Ecosystem Science (SITES) for work done at the Abisko Scientific Research Station. This was made possible by data provided by Abisko Scientific Research Station and SITES. SITES is supported by the Swedish Research Council.
Publication
V. Freire-Zapata, et al. “Microbiome–metabolite linkages drive greenhouse gas dynamics over a permafrost thaw gradient.” Nature Microbiology 9, 2892–2908 (2024). [DOI: 10.1038/s41564-024-01800-z]