Past Research

Archived Project Descriptions & Related Publications

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: KX Pérez Rivera, K Xia, V Lohani,  & L Marston (Virginia Tech); G Biswas, A Dubey, & C.Vanags (Vanderbilt); MK Jha, N Aryal, & EH 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.

Snyder, C., D.M. Asamen, M.Y. Naseri, N. Aryal, G. Biswas, A. Dubey, E. Henrick, E.R. Hotchkiss, M.K. Jha, S.X. Jiang, E.C. Kern, V.K. Lohani, L.T. Marston, C.P. Vanags, & K. Xia. Understanding data science instruction in multiple STEM domains. 2021. American Society for Engineering Education Conference Proceedings.
Naseri, M.Y., C. Snyder, B. McLoughlin, S. Bhandari, N. Aryal, G. Biswas, E. Henrick, E.R. Hotchkiss, M.K. Jha, S.X. Jiang, E.C. Kern, V.K. Lohani, L.T. Marston, C.P. Vanags, & K. Xia. 2022. A modular approach for integrating data science concepts into multiple undergraduate STEM+C courses. American Society for Engineering Education Conference Proceedings. 
Naseri, M.Y., C. Snyder, K.X. Pérez Rivera, S. Bhandari, H.A. Workneh, N. Aryal, G. Biswas, E.C. Henrick, E.R. Hotchkiss, M.K. Jha, S.X. Jiang, E. Kern, V.K. Lohani, L.T. Marston, C. Vanags, & K. Zia. A modular approach for integrating data science concepts into multiple undergraduate science and engineering courses. Revision Submitted.
A forested stream in Coweeta, NC

Headwater stream networks in a warming world

We tested the effects of temperature on organic matter breakdown at the stream reach and stream network scales. We used 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: 2017-2022.

Bretz, K.A., A.R. Jackson, S. Rahman, J.M. Monroe, & E.R. Hotchkiss. In Press. Integrating ecosystem patch contributions to stream corridor carbon dioxide and methane fluxes. Journal of Geophysical Research – Biogeosciences.
Bretz, K.A., N.M. Murphy, & E.R. Hotchkiss. Carbon biogeochemistry and export governed by flow in a non-perennial stream. In Revision.
Hare, D.K., A.M. Helton, C.S. Cummins, P.M. Bumpers, N.J. TomczykG, P.A. Rogers, S.J. Wenger, E.R. Hotchkiss, A.D. Rosemond, & J.P. Benstead. Leaf litter breakdown phenology in headwater stream networks is modulated by groundwater thermal inputs and litter type. Revision Submitted.
Bretz, K.A., J.P. Gannon, & E.R. Hotchkiss. Metabolic patterns of non-perennial stream pools. In Preparation. 
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 addressed 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: 2018-2022.

Plont, S., B.M. O'Donnell, M.T. Gallagher, & E.R. Hotchkiss. 2020. Linking Carbon and Nitrogen Spiraling in Streams. Freshwater Science 39: 126-136. doi: 10.1086/707810.
Plont, S., J. Riney, & E.R. Hotchkiss. 2022. Integrating perspectives on dissolved organic carbon removal and whole-stream metabolism. Journal of Geophysical Research – Biogeosciences 127: e2021JG006610.
Plont, S., D. Scott, & E.R. Hotchkiss. Biogeochemical processes are altered by non-conservative mixing at stream confluences. Revisions Submitted. Preprint DOI: 10.1002/essoar.10512986.1. 
Monroe, J.M., K.A. Bretz, & E.R. Hotchkiss. Stream intermittency and fragmentation alters microbial metabolic potential. In Preparation.
Hotchkiss, E.R., K.A. Bretz, C. López Lloreda, K. Pérez Rivera, S. Plont, A. Gray, C. Braswell, L. Morris, N. Murphy, & B. Onozuka. A global assessment of organic carbon metabolism and spiraling in running waters. In Preparation.
Plont. S., C. Hemphill, J.E. Riney, & E.R. Hotchkiss. Carbon and nutrient cycling are suppressed downstream of a stream confluence. In Preparation.
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). Our collaborations used novel 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.

Metabolic signatures of Swedish streams and rivers

This project tested (1) how rates of ecosystem metabolism in Swedish rivers are shaped by regional climatic and anthropogenic gradients from hemi-boreal to the arctic, (2) the extent to which streams in the Swedish landscape degrade terrestrial organic carbon and contribute to greenhouse gas evasion, and (3) 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.

Carbon cycling and microbial assemblage structure along boreal stream-river-reservoir transitions

We measured the sources, transformations, and fluxes of dissolved organic matter, greenhouse gases, and microbial assemblages in a large boreal river network, from soils to the sea. The Romaine River was dammed for hydropower, so we also had the opportunity to identify distinct contributions of river/reservoir sections at varying stages of pre- and post-dam to network- and landscape-scale biogeochemistry. With P del Giorgio, M Gérardin (Université du Québec à Montréal), et al.

Hotchkiss, E.R. & P.A. del Giorgio. Integrating gas exchange rates and carbon emissions along a boreal river discontinuum. In Preparation.
Gérardin, M.L., E.R. Hotchkiss, & P.A. del Giorgio. Identifying the factors controlling the pCO2 decline along a riverine continuum. In Preparation.
Ruiz González, C., M. Stadler, J.P. Niño-García, T. Vick-Majors, E.R. Hotchkiss, & P.A. del Giorgio. Dispersal across the landscape shapes the rare biosphere of freshwater bacterioplankton communities. In Preparation. 

Sources of CO2 in running waters

The proportions of carbon dioxide (CO2) emitted from streams and rivers that come from terrestrially-derived CO2 or from CO2 produced within freshwaters through aquatic metabolism are not well quantified. We compared stream and river metabolism, groundwater-streamwater exchange, fluvial organic C export, and freshwater CO2 emissions to place in-stream biological processes in the context of network-scale C budgets.

Hotchkiss, E.R., R.O. Hall, R.A. Sponseller, D. Butman, J. Klaminder, H. Laudon, M. Rosvall, & J. Karlsson. 2015. Sources of and processes controlling CO2 emissions change with the size of streams and rivers. Nature Geoscience 8: 696-699.
Hotchkiss, E.R., et al. Metabolism and carbon fate in a boreal network. In Preparation.

Nutrient limitation in boreal streams

We explored interactions between nutrient and carbon availability, metabolism, and microbial assemblages in boreal streams with varying water chemistry and landscape characteristics. 

Burrows, R.M., E.R. Hotchkiss, M. Jonsson, H. Laudon, B.G. McKie, & R.A. Sponseller. 2015. Nitrogen limitation of heterotrophic biofilms in boreal streams. Freshwater Biology 60: 1237-1251.
Burrows, R.M., E.R. Hotchkiss, M. Blackburn, & R.A. Sponseller. Stream nitrate uptake dynamics in a nitrogen-limited region. In Preparation.

Tracing carbon sources in boreal stream food webs

Large subsidies of terrestrial organic matter support heterotrophic carbon (C) and nutrient demands in boreal streams, but the degree to which in-stream photosynthesis contributes to food web dynamics is not well known. We used stable isotopes to measure the contributions of terrestrial and aquatic C to invertebrate consumers. We also linked diet sources with ecosystem C pools and fluxes, including rates of whole-stream metabolism. 

Landström, E. (2015) Resource use by macroinvertebrates within boreal stream food webs. Master's Thesis, Umeå University, Sweden.

Fate of newly fixed carbon in a mountain stream (NSF DDIG)

Despite the longstanding appreciation that algal C can fuel stream food webs, we know little about how primary production contributes to C cycling in running waters (e.g., the capacity of primary producers to influence C dynamics; the time scales over which newly fixed C turns over in different stream C pools). Using a whole-stream 13CDIC (dissolved inorganic C) pulse-chase experiment, we applied a novel combination of an ecosystem-level tracer addition and modeling to trace 13CDIC assimilation by algae, short-term release as CO2 and dissolved organic C, and longer-term fate of newly fixed C. While biology governed short-term fluxes of algal C, hydrology likely controlled longer-term fates.

Hotchkiss, E.R. & R.O. Hall. 2015. Whole-stream 13C tracer addition reveals distinct fates of newly fixed carbon. Ecology 96: 403-416.

Nutrient and carbon cycling in rivers

We measured nitrogen, phosphorus, and carbon uptake and spiraling in rivers of the western and midwestern United States. My project employed a two-compartment Bayesian model and experimental microbial dissolved organic C (DOC) consumption assays to identify a positive priming effect in increasing microbial consumption of more refractory C. Biologically available DOC likely stimulates (i.e., primes) the consumption of more stable DOC by heterotrophic microbes in rivers.

Hotchkiss, E.R., R.O. Hall, M.A. Baker, E.J. Rosi-Marshall, & J.L. Tank. 2014. Modeling priming effects on microbial consumption of dissolved organic carbon in rivers. Journal of Geophysical Research - Biogeosciences 119: 982-995.
Hall, R.O., J.L. Tank, M.A. Baker, E.J. Rosi-Marshall, & E.R. Hotchkiss. 2016. Metabolism, gas exchange, and carbon spiraling in rivers. Ecosystems 19: 73-86.

Microbial assemblage structure and freshwater carbon cycling

We used microbial assemblage data and measurements of microbial carbon consumption from different freshwater ecosystems to test how microbes may respond to changes in carbon and nutrient sources.

Gregory, S.A., N.C. Berg-Mattson, A.L. Saville, R.O. Hall, & E.R. Hotchkiss. Microbial assemblage structure and carbon source control dissolved organic carbon consumption. 

Consequences of multiple species invasions in a productive spring stream

Four non-native fish species (convict cichlid, green swordtail, guppy, tadpole madtom) and one non-native snail species (red-rim melania) have established populations in Kelly Warm Springs, Grand Teton National Park, Wyoming. We used historical samples to compare densities and biomass of native invertebrate species before and after the red-rim melania invasion. To quantify how multiple species invasions may influence stream food webs, we also measured fish and invertebrate population densities and biomass as well as fish stomach contents along a natural temperature gradient. 

Hotchkiss, E.R., S. Laske, T. Niekum, R. Hays, & R.O. Hall. 2011. Status of native and invasive fish populations in Kelly Warm Springs, Grand Teton National Park, WY. Report to Wyoming Game & Fish.

Diel ecosystem respiration in streams

Most aquatic ecosystem metabolism calculations assume respiration is constant over 24-hours or that diel respiration can be estimated using changes in water temperature. These assumptions limit our knowledge of diel mechanisms governing freshwater ecosystem metabolism and C cycling, as biologically available organic C may also vary over 24-hours. We used diel δ18O2 and O2 data, coupled with a Bayesian process model, to estimate diel ecosystem metabolism in three Wyoming streams. We found that daytime respiration exceeded nighttime respiration and temperature-adjusted calculations of respiration did not account for the magnitude of diel respiration modeled with δ18O2.

Hotchkiss, E.R., & R.O. Hall. 2014. High rates of daytime respiration in three streams: Use of δ18O2 and O2 to model diel ecosystem metabolism. Limnology & Oceanography 59: 798-810.

Controls on nitrate uptake in a semi-arid stream 

We quantified the role of hydrology, geomorphology, and biology in governing water chemistry and nitrate uptake along three different reaches of Red Canyon Creek, Wyoming.

Hubbard, K.A., L.K. Lautz, M.J. Mitchell, B. Mayer, & E.R. Hotchkiss. 2010. Evaluating nitrate uptake in a Rocky Mountain stream using labelled 15N and ambient nitrate chemistry. Hydrological Processes 24: 3322-3336.

Carbon cycling by invasive snails

We measured rates of biomass and CO2 production during growth and calcification by the invasive freshwater snail, Melanoides tuberculata, in Kelly Warm Springs, Wyoming. We also compared Melanoides CO2 and secondary production with ecosystem metabolism and fluxes of CO2 from the stream to the atmosphere. While snail biomass and calcification rates were high, CO2 produced from calcification was small compared to net ecosystem CO2 production. High rates of primary production appears to buffer the impacts of high-density invasive snails on native invertebrates and stream C cycling.

Hotchkiss, E.R., & R.O. Hall. 2010. Linking calcification by exotic snails to stream inorganic carbon cycling. Oecologia 163: 235-245.

Denitrification in a tropical stream 

The loss of fish species may alter stream nitrogen (N) budgets. Land use changes and increased sedimentation also alter benthic substrate and N availability, and both are important factors in denitrification. We quantified denitrification in Rio Las Marías, Venezuela and compared denitrification to other rates of ecosystem N loss and cycling.

Solomon, C.T., E.R. Hotchkiss, J.M. Moslemi, A.J. Ulseth, E.H. Stanley, R.O. Hall, & A.S. Flecker. 2009. Sediment size and nutrients regulate denitrification in a tropical stream. Journal of the North American Benthological Society 28: 480-490. 

Land use and stream nitrogen cycling

Erin was a graduate research assistant for the last season of LINX2 research on nitrogen (N) transport and uptake in streams using 15N tracer additions in urban, agricultural, and reference streams in and around Grand Teton National Park, Wyoming.

Lotic Intersite Nutrient eXperiments (LINX)

Sea turtle population dynamics

As a seasonal research technician with the National Park Service, Erin collected data on nesting activities, body conditions, and hatch success of hawksbill, leatherback, and green sea turtles on Buck Island Reef National Monument. Erin also helped with exotic mammal removal and monitoring, juvenile hawksbill mark and recapture, and the creation of a plant ID database for Buck Island, St. Croix, U.S. Virgin Islands.

Buck Island Reef National Monument

Productivity of restored and managed wetlands

Erin worked as a seasonal research technician at Southern Illinois University-Carbondale on a project studying the density, diversity and productivity of aquatic plants and macroinvertebrates in a restored wetland, and their impact on waterfowl feeding behavior in Two Rivers National Wildlife Refuge, Illinois. 

Two Rivers National Wildlife Refuge

Conjunctivitis and house finch behavior

Erin's undergraduate research project at Emory University quantified changes in house finch feeding behavior and aggression when infected with Microplasma gallisepticum.

Hotchkiss, E.R., A.K. Davis, J.J. Cherry, & S. Altizer. 2005. Mycoplasmal conjunctivitis and the behavior of wild house finches (Carpodacus mexicanus) at bird feeders. Bird Behavior 17: 1-8.

Nutrient limitation in a tropical stream (OTS REU

Erin studied the role of limiting nutrients on chironomid larvae growth rates at La Selva Research Station, Costa Rica as a summer REU (research experience for undergraduates) Fellow with the Pringle Lab, University of Georgia. Erin also helped with a project measuring nutrient limitation of in-stream microbial respiration.

La Selva Research Station

Nitrogen cycling in Midwestern streams and reservoirs

Erin's independent project while working as a summer undergraduate research tech with the Tank Lab at the University of Notre Dame compared potential rates of nitrification and denitrification in streams surrounded by different land-use types (forested, urban, and agricultural). Erin also assisted with field and laboratory work for several projects studying the nitrogen dynamics in Michigan streams and a reservoir in Illinois. 

Tank Research Group

Genetic diversity of spatially isolated switchgrass

During a summer undergraduate research internship at the Oak Ridge National Laboratory, Erin quantified the genetic diversity of spatially isolated switchgrass populations from the eastern United States.

Plant Systems Biology