Current Research


Photo from the air of boreal forest, meadow, and stream

Linking terrestrial-aquatic fluxes and stream carbon cycling to inform meta-ecosystem carbon balance

The movement of carbon (C) across land-water boundaries is a critical factor for metabolism in freshwater ecosystems and the net C balance of watersheds. Because streams are a primary interface between terrestrial and freshwater ecosystems, they are ideal test beds to advance understanding of land-water C transfers and meta-ecosystem ecology (i.e., the study of multiple ecosystems linked by energy and material transfers). Our research seeks to answer: (1) What is the magnitude and variability of land-to-water C transfers and stream C emissions? (2) How does meta-ecosystem C cycling vary within and among paired terrestrial-aquatic National Ecological Observatory Network (NEON) research sites across the United States? (3) What controls C form, cycling, and fate in meta-ecosystems? Our research will advance a predictive understanding of the daily, seasonal, and annual processes controlling watershed C cycling through measurements and models that cross land-water boundaries and approaches that integrate biology, geology, and chemistry across space and time. Collaborators: D Butman (University of Washington), W Wollheim (University of New Hampshire), J Jones (University of Alaska Fairbanks), K Cawley & K Goodman (NEON). "Collaborative Proposal: MRA: Linking land-to-water transport and stream carbon cycling to inform macrosystem carbon balance" - funded by NSF DEB. Funding period: 2020-2023.

Hydrologic connectivity and carbon fluxes in wetland-dominated catchments

Worldwide, low-lying areas once rich in forested wetlands have been converted to agricultural production after draining and filling. Prior to their loss, the wetlands reduced flooding through water storage, provided downstream environments with an important energy source in the form of dissolved organic carbon, and played a critical role in regional carbon budgets. This research will test how spatiotemporal changes in surface and subsurface hydrology govern carbon dynamics in wetland-rich landscapes. Using coupled empirical and modeling components, we will quantify: (1) dynamics of surface water connections and surface-subsurface exchange at wetland and catchment scales; and (2) consequent hydrologic influences on wetland- and catchment-scale carbon dynamics. The study sites are on the Delmarva Peninsula of Maryland. Our research will integrate hydrologic sciences, ecosystem ecology, biogeochemistry, and restoration science; and ultimately, help inform wetland restoration and land management across the coastal plain region. Collaborators: DL McLaughlin, ER Hotchkiss, & DT Scott (Virginia Tech); CN Jones (University of Alabama); MA Palmer (University of Maryland College Park). "Collaborative Research - Hydrologic Connectivity and Water Storage as Drivers of Carbon Export and Emissions from Wetland-Dominated Catchments" - funded by NSF DEB. Funding period: 2019-2022.

A mountain stream in Montana

Mechanisms of organic carbon removal in running waters

What processes drive organic carbon removal in streams? How does dissolved organic carbon removal regulate the degree to which running waters are biological reactors versus exporters of carbon? This project will address these unresolved questions by (1) integrating carbon spiraling metrics with more common stream carbon cycling measurements and (2) developing a proof-of-concept approach to test the degree to which non-additive effects of mixed organic matter sources (i.e., priming) control organic carbon removal in streams. PIs: MA Baker (Utah State), RO Hall (Montana), ER Hotchkiss (Virginia Tech). "Collaborative Research - Rivers and the carbon cycle: A mechanistic basis for dissolved organic carbon removal" - funded by NSF DEB. Funding period: 2018-2020.


Plont, S., B.M. O'Donnell, M.T. Gallagher, & E.R. Hotchkiss. 2020. Linking Carbon and Nitrogen Spiraling in Streams. Freshwater Science. doi: 10.1086/707810.
A forested stream in Coweeta, NC

Headwater stream networks in a warming world

We are testing the effects of temperature on organic matter breakdown at the stream reach and stream network scales. We will use data from temperature manipulations at multiple spatial and temporal scales at Coweeta Hydrologic Laboratory, NC to (1) inform ecological theory that uses basic principles to understand how the effects of temperature scale from individual organisms to entire ecosystems, and (2) build a model that simulates the effects of temperature on organic matter processing at the stream network scale. PIs: JP Benstead (University of Alabama), V Gulis (Coastal Carolina University), AM Helton (University of Connecticut), AD Rosemond (University of Georgia), ER Hotchkiss (Virginia Tech). "Collaborative Research - Headwater stream networks in a warming world: Predicting heterotrophic ecosystem function using theory, multi-scale temperature manipulations and modeling" - funded by NSF DEB. Funding period: 2017-2020.

An arctic river near Abisko, Sweden

Metabolic signatures of Swedish streams and rivers

This project will (1) determine how rates of ecosystem metabolism in Swedish rivers are shaped by regional climatic and anthropogenic gradients from hemi-boreal to the arctic, (2) quantify the extent to which streams in the Swedish landscape degrade terrestrial organic carbon and contribute to greenhouse gas evasion, and (3) advance the use of metabolism as a tool for environmental monitoring programs. PIs: R Sponseller, J Karlsson (Umeå University), ER Hotchkiss (Virginia Tech), H Laudon (Swedish University of Agricultural Sciences). "Taking the pulse of Swedish rivers: Using metabolism to monitor ecosystem responses to environmental change" - funded by Swedish Research Council Formas. Funding period: 2017-2019.

Google Earth image of interconnected streams, forests, wetlands, ponds, and river that make up a boreal river discontinuum

Biogeochemical consequences of river network discontinuities

While flow discontinuities within river networks (e.g., wetlands, reservoirs, confluences, intermittent surface waters) are ubiquitous, we rarely account for ecosystem heterogeneity in network-scale measurements or simulations of water quality and ecosystem processes (e.g., carbon metabolism, nutrient uptake). Indeed, much of our current understanding of freshwater ecosystem function is still informed by predicted physical, chemical, and biological shifts from upstream to downstream ecosystems along a simplified stream-river continuum (i.e., the river continuum concept). Ongoing research is measuring biogeochemical consequences of discontinuities within river networks. A recently funded working group is interested in "Ecosystem Mosaics and Broad-Scale Biogeochemistry". Collaborators K Bretz, S Plont (Virginia Tech), AM Helton (University of Connecticut), CT Solomon (Cary IES), SE Jones (Notre Dame), et al.


Hotchkiss, E.R., S.Sadro, & P.C. Hanson. 2018. Towards a more integrative perspective on carbon metabolism across lentic and lotic inland waters. Limnology & Oceanography Letters 3: 57-63. doi: 10.1002/lol2.10081
Forested creek in VA

Dynamics of carbon and nutrient transport and fate

Time series of water chemistry, climate, hydrology, and ecosystem processes (carbon metabolism, nutrient cycling, food web dynamics) can identify changing patterns and controls of carbon and nutrient variability, transport, and fates within and among ecosystems. Considering the spatial and temporal dynamics of linked nutrient, carbon, and water cycles will help us better understand how the efficiency of ecosystem- and catchment-scale carbon and nutrient transformations may respond to environmental change. Ongoing research with S Plont, B O'Donnell, M Gallagher (Virginia Tech). Additional collaborations with members of the Stream Resiliency RCN Working Group & Heterotrophic Regimes working group.


Mineau, M.M., W.M. Wollheim, I.D. Buffam, S.E.G. Findlay, R.O. Hall, E.R. Hotchkiss, L.E. Koenig, W.H. McDowell, & T.B. Parr. 2016. Dissolved organic carbon uptake in streams: A review and assessment of reach-scale measurements. Journal of Geophysical Research - Biogeosciences 121: 2019-2029.
O'Donnell, B. & E.R. Hotchkiss. 2019. Coupling Concentration- and Process-Discharge Relationships Integrates Water Chemistry and Metabolism in Streams. Water Resources Research 55: 10179-10190. doi: 10.2029/2019WR025025.
Plont, S., B.M. O'Donnell, M.T. Gallagher, & E.R. Hotchkiss. 2020. Linking Carbon and Nitrogen Spiraling in Streams. Freshwater Science. doi: 10.1086/707810.
O'Donnell, B. & E.R. Hotchkiss. In Prep. Resistance and resilience of stream metabolism to high flow disturbances.
Drone image of Stroubles Creek during flooding

Advancing real-time monitoring of stream corridor function

Stream ecosystem processes respond rapidly to physical changes in channels and corridors; quantifying process rates requires good estimates of time- and space-varying physical parameters such as inundated surface area and turbulence at the air-water interface. Uncertainties in channel morphology and gas exchange at time scales compatible with water quality sensor data currently limit our ability to produce high-quality estimates of ecosystem processes (e.g., ecosystem metabolism). Ongoing collaborations are using new applications of remote sensing and acoustic tools to enhance real-time monitoring of stream corridor health. Collaborators from different projects include: WC Hession (Virginia Tech), M Klaus (Umeå University).


Klaus, M., E. Geibrink, E.R. Hotchkiss, & J. Karlsson. 2019. Listening to air-water gas exchange in running waters. Limnology & Oceanography: Methods 17: 395-414. doi:10.1002/lom3.10321.
Arial image of experimental ponds with low/high organic matter treatments near Umeå, Sweden

Ecology and environmental change

Widespread changes in land use, climate, hydrology, and species composition are rapidly altering the structure and function of ecosystems. In addition to the whole-stream warming project described above, ongoing research collaborations related to environmental change include:

  • non-native beavers and stream metabolism
  • the science and policy of biological invasions
  • freshwater salinization and ecosystem function
  • using experimental ponds and whole-lake manipulations to identify how changes in temperature, ice cover, nutrients, organic carbon, and/or fish harvest alter ecosystem productivity, food web dynamics, and carbon cycling

See past research for other examples of environmental change research (e.g., damming rivers, invasive species, and land use change).


Jonsson, M., P. Hedström, K. Stenroth, E.R. Hotchkiss, F. Vasconcelos, J. Karlsson, & P. Byström. 2015. Climate change modifies the size structure of assemblages of emerging aquatic insects. Freshwater Biology 60: 78-88.
Hamdan, M., P. Byström, E.R. Hotchkiss, M.J. Al-Haidarey, J. Ask, & J. Karlsson. 2018. Carbon dioxide stimulates lake primary production. Scientific Reports 8: 10878.
Creed, I.F., A.K. Bergström, C.G. Trick, N.B. Grimm, D.O. Hessen, J. Karlsson, K.A. Kidd, E. Kritzberg, D.M. McKnight, E.C. Freeman, O.E. Senar, A. Andersson, J. Ask, M. Berggren, M. Cherif, R. Giesler, E.R. Hotchkiss, P. Kortelainen, M.M. Palta, T. Vrede, & G.A. Weyhenmeyer. 2018. Global change-driven effects on dissolved organic matter composition: Implications for food webs of northern lakes. Global Change Biology 24: 3692-3714.
Barney, J., T. Schenk, D. Haak, S. Salom, B. Brown, & E.R. Hotchkiss. 2019. Building Partnerships and Bridging Science and Policy to Address the Biological Invasions Crisis. Invasive Plant Science and Management.
García, V.J., E.R. Hotchkiss, & P. Rodríguez. Ecosystem metabolism as an indicator of beaver activity: sub-Antarctic streams and rivers impacted by beaver dams. In Preparation.
Klaus, M., S. MacIntyre, E.R. Hotchkiss, A.-K. Bergström, & J. Karlsson. Depth-integrated metabolism in clear and brown boreal lakes: the importance of accounting for vertical oxygen fluxes. In Preparation.
Byström, P., P. Hedström, E.R. Hotchkiss, P. Rodríguez, F. Vasconcelos, & J. Karlsson. Warming decreases fish population densities and biomass. In Preparation.
Plots of high-frequency sensor conductivity and stage data from Little Stony and Stroubles Creeks in Virginia

Preparing undergraduates for data science using high-frequency data

This collaborative project aims to improve undergraduate understanding of data science in biology, computer science, engineering, and environmental science. We will develop, implement, and assess new learning modules based on high-frequency, real-time data from water and traffic monitoring systems. Collaborators: V. Lohani, R. Dymond, & K. Xia (Virginia Tech); G. Biswas, A. Dubey, & C. Vanags (Vanderbilt); M.K. Jha, N. Aryal, & E.H. Park (North Carolina Agricultural & Technical State University). "Collaborative Research: An Interdisciplinary Approach to Prepare Undergraduates for Data Science Using Real-World Data from High Frequency Monitoring Systems" - funded by NSF DUE. Funding period: 2019-2023.