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Understanding Wildfire Recovery, Starting in Soil

A metagenomic look at the soil microbes present a year after a wildfire.

 

A photograph of the forest floor, covered in pine needles, with burned trees in the background.

A burned field site at the Colorado-Wyoming border, where researchers collected soil samples for this study. (Image courtesy of Mike Wilkins)

The Science

After a wildfire burns, recovery begins at the forest floor. Within the soil, a microbiome of bacteria, viruses and fungi process carbon and nitrogen, paving the way for future plants and trees to grow. However, fire changes the microbes within the soil. To get a clearer picture of how burned ecosystems return to health, researchers have taken a look at microbial genomes across a spectrum of burned soils. By connecting microbial genes with functions useful for forest recovery, this study sheds light on how microbes contribute as a forest recovers after a wildfire.

The Impact

Healthy forests store carbon, filter water, and support all kinds of plants and animals, but with climate change driving more extreme wildfires, more and more forests are under threat. Understanding which microbes in the soil persist after a wildfire — and why they thrive — gives forest managers more avenues to bring forests back to full function. Foresters can transplant trees and soils, targeting helpful bacteria, viruses and fungi. Overall, better understanding of a recovering soil microbiome provides a window into how to model and track the forest recovery process. 

A burned tree stump, as the photo on the cover of nature microbiology.

Cover of Nature Microbiology (Image courtesy of Mike Wilkins, Nature Microbiology)

Summary

Most studies on post-wildfire soil microbiomes have focused on marker gene analyses, which take inventory of which microbes are present. This study, published in Nature Microbiology, went a step further, using both DNA and messenger RNA (mRNA) sequencing to identify those traits that have helped fungi, bacteria and viruses survive. With this metagenomic analysis, it was possible to identify specific attributes — such as heat resistance, fast growth rates, and an ability to metabolize burned material — that many microbes in burned soils had in common. 

To complete this analysis, a multi-institutional team of researchers collected soil samples from a wildfire that burned at the Colorado-Wyoming border, about a year after the fire. They sampled soil across a variety of conditions: unburned, low, moderate and high-burn severity sites. From those samples, they reconstructed and examined over six hundred bacterial genomes — mainly actinobacteria, as well as proteobacteria, bacteroidata, and patescibacteria. A major strength of this kind of analysis is the ability to see how microbial communities interact; beyond bacteria, these samples harbored fungal genomes, including a novel Leotiomycetes species and Coniochaeata lignaria, and both DNA and RNA viruses. One trait that stood out in both bacteria and fungi identified in this study was the ability of these organisms to degrade aromatic compounds from burned material. This study also sheds light on helpful microbes that had not returned to the forest within this timeframe, namely, ectomycorrhizal fungi species that can promote tree establishment and growth. 

This study builds on the pyrophilous fungi the JGI has previously sequenced, and provides a powerful snapshot of what soils across different burn severities look like a year after a fire. It also opens questions about what the soil microbiome looks like over longer times post-fire, and how long it takes a forest to return to pre-burn health.

This work brought together researchers from Colorado State University, the US Forest Service, New Mexico State University, the Environmental Molecular Sciences Laboratory and the U.S. Department of Energy (DOE) Joint Genome Institute (JGI). EMSL and the JGI are DOE Office of Science User Facilities located at Pacific Northwest National Laboratory and Lawrence Berkeley National Laboratory, respectively. The team’s research at both the JGI and EMSL was enabled by the Facilities Integrating Collaborations for User Science (FICUS) initiative. In this program, researchers leverage the capabilities of more than one DOE Office of Science National User Facilities in a single project.

Contacts

BER Contacts

Ramana Madupu, Ph.D.
Program Manager
Biological Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
[email protected] 

Paul Bayer
Program Manager, EMSL
Earth and Environmental Systems Sciences Division
Office of Biological and Environmental Research
Office of Science
US Department of Energy
[email protected] 

PI Contact
Michael J. Wilkins
Colorado State University 
[email protected]

Funding

This work was supported through a USDA NIFA award (2021-67019-34608) to M.J.W. FTICR-MS analyses were performed under the Facilities Integrating Collaborations for User Science (FICUS) initiative and used resources at the Environmental Molecular Sciences Laboratory (proposal ID 49615), which is a DOE Office of Science User Facility. This facility is sponsored by the Office of Biological and Environmental Research and operated under contract number DE-AC05-76RL01830. Metagenomic and metatranscriptomic sequencing was performed at the University of Colorado Cancer Center’s Genomics Shared Resource, which is supported by the Cancer Center Support Grant P30CA046934. This work utilized resources from the University of Colorado Boulder Research Computing Group, which is supported by the National Science Foundation (awards ACI-1532235 and ACI-1532236), the University of Colorado Boulder and Colorado State University. The work conducted by the US Department of Energy Joint Genome Institute, a DOE Office of Science User Facility, is supported by the Office of Science of the US Department of Energy under Contract No. DE-AC02-05CH11231.

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