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East River Catchment in Crested Butte, CO

Building from research at the Rifle site on subsurface biogeochemical processes over meter length scales, the Berkeley Lab Subsurface Biogeochemistry Watershed Function SFA is being conducted at a headwaters catchment (East River, CO) and aims to develop an understanding of biogeochemical processes at the watershed scale.

Microbially-mediated biogeochemical processes that occur at the micron-scale impact watershed function and ecosystem outputs at the tens of kilometers scale. Watershed functioning relies on complex interactions among vegetation, hydrology, topography, and geology that lead to distinct environmental compartments at the surface and in the subsurface. Our work will leverage the genome-resolved metagenomic bioinformatics methods developed through research at the Rifle site and will focus on six different aspects:

We hypothesize that detailed analysis of meanders, important riparian zone compartments, can generate insights about key biogeochemical processes that can be used to approximate the function of the larger system. Meanders were subdivided into the river channel, hyporheic zone (the region of sediment and porous space where river water and shallow groundwater mix), and the surface and subsurface vegetated soils and sediments, whose characteristics reflect past and present river flow dynamics. The objectives are to infer processes that contribute to C and N cycling based on the metabolic potential of the microbial communities and to identify hotspots and hot moments of microbial activity in the riparian zone and their impacts on nutrient cycling in the watershed.


Warming of mountainous watersheds, causing decreased snow cover and earlier snowmelt, is expected to reduce overland flow, increase early-season infiltration, and lead to deeper transport of solutes and increased production of CO2 within the vadose zone. As part of the SFA team led by Dr. Tetsu Tokunaga, we are studying the contribution of East River’s subsurface microbial communities to the carbon cycle. Temporal and spatial (along a hillslope gradient as well as depth-resolved) metagenomics and metatranscriptomic samples are interrogated to answer this question.


The vegetation of the Upper East River watershed is representative of the Western U.S., including upland meadows, stands of aspens and conifers, and patches of sagebrush.  We hypothesize there are differences in the soil metabolic potential between these vegetation types and along the longitudinal profile of the Upper East River watershed.  By using genome-resolved metagenomics we aim to link above ground vegetation types to below ground soil processes.  This information should enable watershed scale predictions of soil processes from the distribution of these vegetation types.

In collaboration with Dr. Michelle Newcomer (Lawrence Berkeley National Laboratory), we are studying microbial communities of the hyporheic zone. We are interested in understanding how the hydrology, geology, and water chemistry surrounding and within the hyporheic zone influence the microbial community and the metabolic capacities of the organisms present and, in turn, how microbial activity impacts nutrient exports via the river as well as trace gas emission. 


Wetlands are the largest natural source of methane emissions, responsible for approximately 20% - 30% of global emissions. Many wetlands have formed along the East River, and we are interested in understanding how microbes drive methane metabolism in these wetlands. Specifically, we are interested in what metabolic capacity these microbes possess and how their in situ activity varies spatially and temporally in the wetlands with respect to methane emissions. As part of the SFA watershed team, we are collaborating with Dr. Markus Bill and Dr. Mark Conrad (Lawrence Berkeley National Laboratory) to quantify methane gas and methane isotopes in the wetland ecosystem. 

In collaboration with Dr. Eoin Brodie (Lawrence Berkeley National Laboratory), our newest project investigates the droughts that are plaguing the Rocky Mountains and much of the Western US. Drought effects can place soil microbiomes in dysbiosis, changing microbial diversity and metabolisms, in turn altering nutrient cycling in the ecosystem and threatening core watershed functions. By linking changes in microbial life strategies (traits) to in situ biogeochemical cycling in simulated drought conditions (dry down from snowmelt), we can test our hypothesis that drought is driving changes in microbial carbon and nitrogen cycling. Consequently, this research will help predict future forest health and greenhouse gas emissions in mountainous watersheds struggling with drought.

Relevant publications

Adi Lavy et al. 

Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

Paula Matheus Carnevali et al. 

Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale

[1] Chacon et al., “Divergent Responses of Soil Microorganisms to Throughfall Exclusion across Tropical Forest Soils Driven by Soil Fertility and Climate History”; Bouskill et al., “Pre-Exposure to Drought Increases the Resistance of Tropical Forest Soil Bacterial Communities to Extended Drought.”

[2] Naylor and Coleman-Derr, “Drought Stress and Root-Associated Bacterial Communities.”

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