Multi-omics reveals how distinct microbial groups hand off nitrogen control during the critical transition from winter snowpack to spring melt
Figure 1. (Left) Soil nitrogen pools shift dramatically during snowmelt. (Right) Metabolic reconstruction of winter-adapted Bradyrhizobium reveals how they recycle biomass and oxidize amino acids under the snowpack, fueling the spring microbial bloom. Image courtesy of Image courtesy of Nature Microbiology / Patrick O. Sorensen et al.
The Science
Mountain snowpacks act as “water towers,” releasing massive pulses of water and nutrients when they melt. A multi-institutional team of scientists used advanced genetic and chemical tools and DOE user facility capabilities to reveal that soil microbes control the fate of this nitrogen through a melt-season “baton-pass.” “Winter-adapted” bacteria first recycle biomass under the snow, building up a nitrogen pool in their cells. As the snow melts, these bacteria die but hand off control of their nitrogen pool to “spring-adapted” microbes that convert this nitrogen into nitrate. Crucially, the study found that this handover isn’t just a release; the ecosystem has a built-in “brake” – mechanisms to retain nitrogen – that competes with pathways that lead to loss, determining how much nitrogen enters a stream.
The Impact
Mountain watersheds provide essential freshwater to millions, but declining snowpacks are altering hydrological, biogeochemical and ecological processes in mountain regions. This research shows that the nitrogen cycle relies on a synchronized handover between distinct microbial groups. If snow melts too early or too fast, this “baton-pass” could fail, potentially tipping the balance from nitrogen retention to loss. Understanding these specific microbial “gears” improves the ability to predict water quality and ecosystem health in vital watershed systems like the Colorado River Basin as winter snowpacks decline.
Summary
A multi-institutional team of researchers integrated genome-resolved metagenomics, metatranscriptomics, and metabolomics to track nitrogen cycling in the East River Watershed, Colorado. The team characterized the metabolic engines driving soil activity, revealing that the nitrogen cycle is a continuous, year-round process regulated by sequential microbial groups. They found that “winter-adapted” bacteria, particularly Bradyrhizobium species, are highly active under the snowpack, oxidizing amino acids and recycling biomass to fuel growth despite the cold. This winter activity primes the soil for a microbial bloom during snowmelt. As this biomass eventually crashes, a distinct group of “spring-adapted” archaea (Nitrososphaerales) takes over, driving a pulse of nitrate production. However, gene expression analysis revealed that this is not a one-way path to nutrient loss; the ecosystem retains significant capacity to recycle this nitrate back to ammonia (via dissimilatory nitrate reduction to ammonia, or DNRA). These findings demonstrate that soil nitrogen fate is determined by the successful handover between ecologically distinct microbial groups linked across the snowmelt period.
Contact
Patrick Sorensen, Assistant Professor
University of Rhode Island
Eoin L. Brodie, Watershed Function SFA LRM
Lawrence Berkeley National Laboratory
Funding
This material is based on work supported as part of the Watershed Function Scientific Focus Area at Lawrence Berkeley National Laboratory funded by the U.S. Department of Energy (DOE), Office of Science, Office of Biological and Environmental Research (BER). A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program and used resources at the DOE Joint Genome Institute (JGI) and the Environmental Molecular Sciences Laboratory (EMSL), which are DOE Office of Science User Facilities.
Publications
Sorensen, P. O., Karaoz, U., Beller, H. R., Bill, M., Bouskill, N. J., Banfield, J. F., Chu, R. K., Hoyt, D. W., Eder, E., Eloe-Fadrosh, E., Sharrar, A., Tfaily, M. M., Toyoda, J., Tolic, N., Wang, S., Wong, A. R., Williams, K. H., Zhong, Y., & Brodie, E. L. (2026). Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt. Nature Microbiology. https://doi.org/10.1038/s41564-025-02213-2