Genomic Science Program
U.S. Department of Energy | Office of Science | Biological and Environmental Research Program

Metagenomic Insights into Microbial Traits Influencing Community Dynamics and N Cycling Post-Fire


Amelia R. Nelson1* (, Michael J. Wilkins1, Steven D. Allison2, Joanne B. Emerson3, Peter M. Homyak4, and Sydney I. Glassman4


1Colorado State University; 2University of California–Irvine; 3University of California–Davis; and 4University of California–Riverside


Climate change coupled to shifting land use patterns have increased the frequency and size of wildfires across the globe. These wildfire disturbances deplete soil microbial biomass and alter the community composition of the soil microbiome, which drives critical terrestrial biogeochemical cycling across ecosystems. Through this project, the team aims to couple field-derived metagenomic datasets, biogeochemical data via experimental pyrocosms, and ecosystem models to evaluate the impact of wildfire on microbially mediated N cycling across ecosystems (Mediterranean grasslands, chaparral shrublands, coniferous forests).


Wildfires, which are increasing in both frequency and severity with climate change, reduce soil microbial biomass and alter the community composition of the soil microbiome, selecting for pyrophilous taxa with encoded traits that enable them to thrive in burned soil. The soil microbiome plays a vital role in biogeochemical cycling and ecosystem function and is an important player in terrestrial nitrogen (N) cycling, but it is poorly understood how the altered post-fire soil microbiome community composition influences microbially mediated soil N cycling and subsequent emissions of greenhouse gasses (GHGs) like nitrous oxide from post-fire ecosystems. Multiomics (i.e., metagenomics and metatranscriptomics) data allows researchers to infer lifestyle traits (i.e., Grimes’ C-S-R framework) and function of pyrophilous taxa in post-fire soils. Through this project, the team has compiled an extensive multiomic dataset including 108 metagenomes and 12 metatranscriptomes from fire-impacted Colorado coniferous forests representing different burn severities (low and high severity) and across time (60-year chronosequence to 1-year post-fire). These sequencing efforts, totaling nearly 9 Tb of data, have resulted in 1651 metagenome-assembled genomes that span the Actinobacteria (n = 861 MAGs), Proteobacteria (n = 315), Acidobacteria (n = 115), along with 17 other bacterial phyla. Further, putative pyrophilous taxa from previous studies are represented, including the Actinobacteria Arthrobacter (n = 14) and Blastococcus (n = 11), and Proteobacteria Massilia (n = 9). Data from 1 year post-fire (Nelson et al. 2022) revealed that pyrophilous traits (e.g., fast growth, heat resistance, ability to use pyrogenic carbon) were critical in the post-fire soil microbiome, with their importance increasing with increased burn severity. Further, the dominance of MAGs exhibiting these traits was coupled to the loss of N cycling functions, including the absence of evidence for the expression of the bacterial gene catalyzing N fixation (nifH) and loss of both nitrifying taxa (Nitrospira) and genes (amoA and nxrAB) in severely burned surface soils. Further analyses on MAGs derived from longer-term studies (3, 5, and 11 years post-fire to 6 decades post-fire) and other ecosystems (i.e., California grasslands and chaparral shrublands) will reveal whether these short-term influences on N cycling are unique to CO coniferous forests and if they recede with time following burning. Combined, these datasets will shed light on the impact of wildfire on ecosystem N losses and the emission of GHGs from wildfire-impacted landscapes.


Nelson, R., et al. 2022. “Wildfire-Dependent Changes in Soil Microbiome Diversity and Function.” Nature Microbiology 7, 1419–30.

Funding Information

This work is funded through Department of Energy (DOE) BER #DE-SC0023127 “Predicting post-fire N cycling through traits and cross-kingdom interactions.”