University of Vermont

Rubenstein Ecosystem Science Laboratory

Rubenstein Lab REU projects National Science Foundation logo

Potential REU Projects:

Interdisciplinary Research on Human Impacts in the Lake Champlain Ecosystem

Our REU program focuses on the intersections of human activity and societal structure with the Lake Champlain ecosystem, how these intersections have impacted Lake Champlain, and how these impacts feed back to influence human behavior and society. The strength of this framework is the opportunities for students to work in teams to link interdisciplinary approaches within the natural sciences or between the natural and social sciences. By assisting each other, students will be exposed to and better understand the connection of their primary research area to a secondary discipline and its associated methods.

The combinations of human-induced alterations to Lake Champlain (e.g., invasive species, eutrophication, and habitat fragmentation) and Lake Champlain's highly heterogeneous habitats (e.g., warm, shallow and isolated bays to deep open waters of the main lake) provide a rich template on which students can pose research questions and test hypotheses across both natural and social sciences. Below is a list of possible summer projects in which students can participate, although we also encourage students to think about other or related research projects to explore.

Project Descriptions

Project 01: Identify and characterize the heterotrophic bacteria colonizing the cyanobacterium Microcystis aeruginosa in Lake Champlain

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Heterotrophic bacteria are known to grow in and on the colonies of the bloom forming cyanobacterium Mycrocystis aeruginosa and can play mutualistic, commensal, or parasitic roles (Paerl and Millie 1996). These bacteria impact nutrient release from Microcystis (Jiang et al. 2007) and some have predicted that these bacteria can influence bloom dynamics (Maruyama et al. 2003, Berg et al. 2009). An interesting observation is that the bacteria associated with Microcystis vary dramatically depending on the geographical, biological, and physiochemical conditions of the lake and are therefore specific for particular bodies of water. We would like to identify and characterize the heterotrophic bacteria associated with Microcystis in Lake Champlain and begin to explore the interactions between some of these specific bacteria and Microcystis. Our long term goal is to understand the role of this heterotrophic community in algal bloom dynamics. The project will use a combination of basic bacterial culture, microcosm studies, and molecular techniques to describe this community. This research project will be of particular interest to anyone interested in learning more about microbial ecology. This experience will combine extensive laboratory time, a little fieldwork to collect algal samples, and some computer work for molecular database analyses.

Project 02: Impaired hyporheic functioning in urban stream

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The hyporheic zone is the layer of surface sediments at the bottom of streams channels through which the stream water flows. Microbial processes in this hyporheic zone are critically important to recycle nutrients used to maintain primary production in stream ecosystems and may be important to detoxify pollutants that enter streams from developed areas (Stanford and Ward 1988, Boulten et al. 1998, Edwardson and Bowden 2003). Sediment delivered in run-off from urban areas, however, may plug the hyporheic zone and reduce its ability to process nutrients and pollutants. This project will employ a simple but novel way to record the spatial extent of the hyporheic zone in urban-impaired and reference streams to test the hypothesis that the spatial extent of the hyporheic zone is reduced in streams impacted by urban runoff. Results from this research could have important implications regarding the masses of nutrients that flow into Lake Champlain from tributaries. This experience is expected to be a combination of laboratory work (20% time), fieldwork (60%), and computer work (20%).

Project 03: Synoptic stream network sampling

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Most of the focus on tributary inputs to Lake Champlain has been based on the concentrations and discharge at the mouth of the major rivers that drain into the lake (e.g. Facey et al. 2010). In recent years we have begun to consider how tributaries contribute differently to river loading, based on varying land uses and land covers. For the most part, this finer-scale examination has been based on regular, intensive, automated, sampling methods (e.g., Rundel et al. 2009) that require expensive equipment and therefore can only be installed at a limited number of locations. An alternative and entirely complementary approach is to sample at a few carefully selected times, extensively, with a simple manual sampling approach. This so-called “synoptic” sampling approach (e.g. Hill et al. 2011) provides a “snap-shot” of the watershed under the prevailing conditions. In this project, the student will lead several synoptic sampling events that focus on base flow and storm flow periods in the Missisquoi and/or Winooski Rivers. Patterns of nutrient concentrations will be correlated with land use and land cover characteristics in the contributing watershed (Weigel et al. 2003). This information will provide a finer-grained picture of nutrient distributions and variability in these watersheds, which could be a valuable complement to the longer-term but more spatially-restricted sampling done by state monitoring and local research initiatives. This experience is expected to be a combination of laboratory work (25% time), fieldwork (50%), and computer work (25%).

Project 04: Biotic versus abiotic phosphate uptake in stream ecosystem

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Nutrient uptake is a key ecosystem function in any ecosystem (Stream Solute Workshop 1990). Over the last several years the stream ecology community has develop several related approaches to estimate nutrient update in streams with fairly simple methods. In most streams, it is possible to demonstrate phosphate “disappears” rapidly. It is not clear, however, whether this disappearance is due to biotic uptake or abiotic sorption on sediments. Both processes are known to be important, but the relative importance is unknown. The distinction is potentially critical because biotic uptake might be a less permanent repository for phosphorus than chemical sorption. At the very least, we might misinterpret the key processes governing phosphorus movement in streams if we do not know the relative importance of biotic versus abiotic processes that remove phosphorus from stream water. In this project, the student will use a simple modification of a widely-used method to assess nutrient uptake (Covino et al. 2010) to quantify the relative importance of biotic versus abiotic phosphate uptake in a suite of streams. This experience is expected to be a combination of laboratory work (50% time), fieldwork (30%), and computer work (20%).

Project 05: Numerical hydrodynamic modeling of Lake Champlain

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The physical environment of lakes is shaped by the hydrodynamic processes that impact the distribution of water temperature, nutrients, dissolved oxygen and sediments (Bouffard et al. 2013). In turn, the physical environment shapes the growth and survival of the lake biota, including algae (Leon et al. 2011). In this project we will focus on understanding the hydrodynamics and circulation in Missisquoi Bay, a shallow bay on Lake Champlain that is particularly susceptible to harmful algal blooms (HABs) (LCBP 2012). We will develop a three-dimensional numerical model of the entire domain of Lake Champlain using SUNTANS, a Reynolds-averaged Navier-Stokes solver written in C++ and Python (Fringer et al. 2006). The focus will be on what is driving circulation in Missisquoi Bay, a location of frequent HABs, investigating the relevance of local meteorological forcing and river inputs vs lakewide forcing such as internal waves (Dorostokar and Boegman 2013). We will compare model results to data collected in the bay in the previous two summers when the bay exhibited contrasting conditions in HABs. Coding experience in a programming language such as Matlab, Python and/or C++ will be extremely helpful, but knowledge of any particular language is not necessary. This project will involve extensive computer work, with little to no fieldwork and no laboratory work.

Project 06: Impacts of habitat fragmentation on the genetics of Lake Champlain fish populations

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Since the mid-1800s, ten major causeways have been constructed throughout Lake Champlain, effectively separating the lake into several distinct basins. Causeways could inhibit fish movement, leading to population fragmentation and depleted gene flow among basins (Templeton et al. 1990). Though there are small openings in the causeways, they are generally shallow and could lead to isolation of cold-water fish species. If causeways have effectively restricted the movement of fish to within basins, we would expect to see genetic sub-structuring by basin of fish that prefer deep and cold water (Marsden and Langdon 2012). To test this hypothesis, the student will use population genetics and molecular techniques (Sullivan and Stepien 2014) to assess the population fragmentation of slimy sculpin (Cottus cognatus), a cold-water fish species common to Lake Champlain (Huff et al. 2010; Adams and Schmetterling 2011). This experience will involve extensive laboratory time, a little fieldwork (e.g., seining, trawling, eletrofishing) to assist a graduate student with additional collections of other fish species, and some computer work.

Project 07: Effects of eutrophication on plankton diversity

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The frequency and intensity of summer cyanobacteria blooms have recently been increasing in Lake Champlain, largely in response to eutrophication of the watershed (Boyer 2008; Smeltzer et al. 2012). However, Lake Champlain has a very large and heterogeneous catchment area, and nutrient inputs and bloom occurrence vary across different regions of the lake (Facey et al. 2012). Complex interactions among plankton communities that may result in dominance by cyanobacteria are mediated by the environmental features of each sub-region, including nutrient concentrations as well as physical characteristics such as basin shape and water movements (Pearce et al. 2013). Using existing long-term data that includes phytoplankton and zooplankton abundance as well as nutrient concentrations and physical characteristics at 15 sites across the lake, students will have the opportunity to investigate relationships between physical parameters and plankton biodiversity and community dynamics across environmental gradients within Lake Champlain. Computer work (data analysis and modeling) will be extensive, with limited but possible opportunities to incorporate field and/or lab components. A willingness to learn the programming code R is required.

Project 08: Factors controlling sedimentary nutrients and trace elements input into water column: comparative research in biogeochemically different systems

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Phosphorus (P) is recognized as the key nutrient for developing and maintaining algal blooms in many freshwater lakes, including Lake Champlain. Although management efforts have reduced nutrients entering the lake from point sources, blooms are still prevalent due to non-point sources such as agricultural runoff and internal loadings from lake sediments. The mechanisms contributing to internal P loadings, however, are poorly understood in Lake Champlain. To test hypotheses about these processes, the student will conduct comparative research in two systems with and without major river inputs - Missisquoi Bay (Lake Champlain) and Shelburne Pond. The student will collect field samples of P, trace elements (Al, Ca, Fe, Mn), and other metrics of water quality that may affect P distribution in water and sediments. Data will be used to evaluate the relative importance of river inputs for internal P and trace element loadings using a combination of laboratory and modeling techniques. This experience will provide the student with extensive hands-on training in field collection techniques and laboratory analyses of water and sediment samples, and will involve moderate computer work.

Project 09: Pathways of nitrogen processing along a gradient from stream to lake

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Nitrogen cycling processes can alter the flux of nitrogen delivered to downstream ecosystems. For example, nitrogen can be assimilated by biota, removed from the system via bacterial denitrification, regenerated from organic forms, or it can change form via processes such as nitrification. Processing of nitrogen is generally known to be important in small, headwater streams. However, direct comparisons of nitrogen cycling rates across a gradient from stream to river to lake are rare. These measurements are critical to understand the flux of nitrogen entering a lake ecosystem, as we can identity hotspots of N removal or processes that may make N more mobile (such as nitrification). Using isotopic tracers, the student will measure key rates of nitrogen cycling in a sub-watershed of Lake Champlain from small streams to the lake, as well as in Lake Champlain. These data will be useful for watershed scale and lake management to improve water quality. This experience will include moderate fieldwork and computer work, and extensive laboratory work.

Project 10: Evaluating the effectiveness of presentation styles to communicate science to the general public

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Communicating science is becoming an increasingly important component of scientific “deliverables” for agencies, institutions, and individual scientists. Important advances in science can be lost on the public without effective translation and communication. For this project, the REU student will work with educators from UVM and ECHO Lake Aquarium and Science Center, located on Burlington’s waterfront, to develop a study that examines the effectiveness of different presentation styles for translating science to the general public at ECHO. The student will produce multiple styles of presentations on eutrophication, invasive species, or habitat fragmentation in Lake Champlain, and then quantitatively compare their effectiveness through surveys, interviews, or other assessment methods. This project has a lot of scope for creativity and the REU student can tap into other REU projects, including peers and mentors, for assistance and support. This experience will include extensive social science fieldwork, moderate to extensive computer work (depending on media used to produce presentations), and little to no lab work.

Project 11: Seasonality in fatty acid content of Lake Champlain fish fillets

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Vermont fishing regulations permit recreational anglers to sell their catch to food distributors. However, Lake Champlain experiences cyanobacteria blooms during summer. Cyanobacteria are extremely low in essential fatty acids, and hypothesized to short-circuit the transfer of fatty acids up the food web (Brett and Müller-Navarro 1997, Elser et al. 2000, Müller-Navarro et al. 2004), although demonstration of this effect to propagate up to fish has not been demonstrated. In this project, the REU student will test for seasonality in fatty acid content of yellow perch, white perch, and sunfish captured from Lake Champlain and sold by a local vendor for public consumption. Samples have been collected monthly since July 2014 and will continue into summer 2015. This experience will include extensive laboratory work in a lipid biochemistry lab, moderate computer work, and little fieldwork.

Project 12: Ecological and economic impacts of invasive species in the Lake Champlain Basin

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Are you interested in invasive species and their ecologic and economic impacts? Do you want experience working with a local NGO to understand and predict the economic, social and biophysical consequences of terrestrial and aquatic invasive species in the Lake Champlain Basin? An REU student is needed to research the life histories of potential aquatic invasive species, develop invasion (ecological and economic) risk assessments if an invasion were to occur, and work to identify cost effective prevention programs to help minimize the threats posed by these species. This project offers an opportunity for collaborative work with an established NGO with opportunities for cross-disciplinary work in an applied setting. While this research effort is primarily computer-based, collaboration with other REU projects and mentors should afford opportunities to engage in limited field work. For an example of the type of work this project will entail, see Yellow Wood Associates (2014). This experience will include extensive computer work, minimal field work, and no laboratory work.

Project 13: Investigating pharmaceutical contaminants in Lake Champlain: Levels, sources, and interventions

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Pharmaceutical contaminants in the aquatic environment pose a range of risks to ecosystems and public health (Jones et al. 2004). Recent work by the United States Geological Survey (USGS) has found chemical pollutants, including pharmaceuticals, in 80% of surface waters tested across the country, but only limited studies have investigated concentrations of pharmaceuticals in Lake Champlain. Students interested in partnering with this REU project will join a team working on four overlapping areas of research:

  • Determine the amounts and effects of pharmaceutical contaminants in Lake Champlain: this area of research will include natural science field and lab work. Primary duties may include water and biological sample collection and analysis and/or laboratory testing to determine pharmaceutical effects on aquatic species. Fieldwork and/or lab work will be extensive and computer work will be moderate.
  • Identify key sources of pharmaceutical contaminants in Lake Champlain: this focus area may include spatial analysis and/or social science fieldwork including interviews and surveys. Social science fieldwork will be moderate to extensive and computer work will be moderate.
  • Develop effective interventions for minimizing pharmaceutical contamination in the lake: work in this area may include the development and testing of social interventions (e.g. educational campaigns). Social science fieldwork will be moderate to extensive and computer work will be moderate.
  • Investigate the current status of policy related to pharmaceutical waste in Vermont and at the federal level; identify potential policy interventions that can support change in behaviors related to pharmaceutical waste. Social science fieldwork will be minimal to moderate and computer work will be moderate to extensive.

To succeed in this research endeavor, students should be willing to develop their skills to efficiently sort through a large amount of scientific writing, gathering key points from each and translating them into succinct literature reviews. Students will work independently and patiently without becoming easily distracted; and should be self-driven, organized, and inquisitive. Students should have an interest not only in science but in the sociological and policy implications of scientific research and their interplay. Student should be optimistic and enthusiastic about communicating all research findings to the public through oral and written presentations. This project is all about thinking holistically about interconnections between biology, chemistry, geographic, sociological, and political economy factors involved in the environmental challenges of pharmaceutical contamination. Most importantly, interested students should have a passion and curiosity for scientific endeavors.

Project 14: Habitat fragmentation and walleye movement in Lake Champlain: A comparison of time and technologies

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Starting in 1850, causeway construction fragmented Lake Champlain into five basins, with connectivity between basins limited to small openings through causeways (Marsden et al. 2010, Marsden and Langdon 2012). We do not know how the causeways have impacted fish population dynamics or how fish use the present-day arrangement of causeways and corridors to get from one basin to another, if at all (Marsden and Langdon 2012). For this project, the REU student will examine the movements of walleye in Lake Champlain to test the hypothesis that their movement is restricted among basins. The student will use a combination of traditional fish tagging data since the 1950s and contemporary acoustic telemetry tagging data (Adams et al. 2012) to address this hypothesis. The experience will provide the student opportunities to learn standard fisheries science techniques (e.g., analysis of mark-recapture data), cutting-edge acoustic technology techniques, apply a broad suite of data analysis tools, and interact with state biologists from the Vermont Fish & Wildlife Department. Fieldwork will be moderate and include such tasks as downloading data from acoustic receivers, sampling and tagging fish, building concrete anchors, and splicing mooring lines. Computer work will be extensive and will require a willingness to compile archived mark-recapture data and learn to use the freeware program “R” to manipulate and analyze telemetry data. Minimal laboratory work is expected.


Adams, N. S., J. W. Beeman, and J. Eiler. 2012. Telemetry techniques. American Fisheries Society, Bethesda, Maryland.

Adams, S. B. and D. A. Schmetterling. 2011. Freshwater sculpins: phylogenetics to ecology. Transactions of the American Fisheries Society 136:1736-1741.

Berg, K.A., et al. 2009. High diversity of cultivable heterotrophic bacteria in association with cyanobacterial water blooms. The ISME Journal 3:314-225.

Bouffard, D., Ackerman, J.D., and Boegman, L. 2013. Factors affecting the development and dynamics of hypoxia in a shallow large stratified lake: Hourly to seasonal patterns. Water Resour. Res.49:14 pp.

Boulton, A. J., S. Findlay, P. Marmonier, E. H. Stanley, and H. M. Valett. 1998. The functional significance of the hyporheic zone in streams and rivers. Annual Review of Ecology and Systematics 29:59-81.

Boyer, G.L. 2008.  Cyanobacterial Toxins in New York and the Lower Great Lakes Ecosystems.  In H.K. Hudnell (Editor), Cyanobacterial Harmful Algal Blooms: State of the Science and Research Needs.  New York: Springer, pp. 153-165.

Brett MT, Müller-Navarro DC (1997) The role of highly unsaturated fatty acids in aquatic food-web processes. Freshw Biol 38:483–499

Covino, T. P., B. L. McGlynn, and R. A. McNamara. 2010. Tracer additions for spiraling curve characterization (TASCC): quantifying stream nutrient uptake kinetics from ambient to saturation. Limnology and Oceanography-Methods 8:484-498.

Dorostkar, A., and Boegman, L. 2013. Internal hydraulic jumps in a long narrow lake. Limnol. Oceanogr. 58:153-172.

Elser JJ, Fagan WF, Denno RF, Dobberfuhl DR, Folarin A, Huberty A, Interlandi S, Kilham SS, McCauley E, Schulz KL, Siemann EH, Sterner RW (2000) Nutritional constraints in terrestrial and freshwater food webs. Nature 408:578–580

Facey, D.E., J.E. Marsden, T.B. Mihuc, and E.A. Howe.  2012. Lake Champlain 2010: A summary of recent research and monitoring initiatives. Journal of Great Lakes Research 38(Supplement 1):1-5.

Fringer, O. B., Gerritsen, M., and Street, R. L. 2006. An unstructured-grid, finite-volume, nonhydrostatic, parallel coastal ocean simulator. Ocean Modelling 14(3-4):139–173.

Greenwald, M. J., W. B. Bowden, M. N. Gooseff, J. P. Zarnetske, J. P. McNamara, J. H. Bradford, and T. R. Brosten. 2008. Hyporheic exchange and water chemistry of two arctic tundra streams of contrasting geomorphology. J. Geophysical Research (Biogeosciences) doi:10.1029/2007JG000549.

Hill, B., D. Bolgrien, A. Herlihy, T. Jicha, and T. Angradi. 2011. A synoptic survey of nitrogen and phosphorus in tributary streams and great rivers of the Upper Mississippi, Missouri, and Ohio River Basins. Water, Air, & Soil Pollution 216:605-619.

Huff, D. D., et al. 2010. Patterns of ancestry and genetic diversity in reintroduced populations of the slimy sculpin: implications for conservation. Conservation Genetics 11:2379-2391.

Jiang, L.J., et al. 2007. Quantitative studies on phosphorus transference occuring between Microcystis aeruginosa and its attached bacterium (Pseudomonas sp.). Hydrobiologia 581:161-165.

Jones, O.A.H., N. Voulvoulis, and J. N. Lester. 2004. Potential ecological and human health risks associated with the presence of pharmaceutically active compounds in the aquatic environment. Critical Reviews in Toxicology 34:335-350.

Lake Champlain Basin Program. 2012. State of the Lake (pp. 1–44). Retrieved from

Leon, L.F., Smith, R.E.H., Hipsey, M.R., Bocaniov, S.A., Higgins, S.N., Hecky, R.E., Antenucci, J.P. and Guildford, S.J. 2011. Application of a 3D hydrodynamic-biological model for seasonal and spatial dynamics of water quality and phytoplankton in Lake Erie. J. Great Lakes Res. 37:41-53.

Marsden, J. E. and R. W. Langdon. 2012. The history and future of Lake Champlain's fishes and fisheries. Journal of Great Lakes Research 38:19-34.

Marsden, J. E., B. D. Chipman, B. Pientka, W. F. Schoch, and B. A. Young. 2010. Strategic plan for Lake Champlain fisheries. Miscellaneous Publications. Great Lakes Fishery Commission (3).

Maruyama, T., et al. 2003. Dynamics of microcystin-degrading bacteria in mucilage of Microcystis. Microbial Ecology 46: 279-288.

Paerl, H.W. and D.F. Millie. 1996. Physiological ecology of toxic aquatic cyanobacteria. Phycologia 35(Suppl. 6):160-167.

Pearce, A.R., D.M. Rizzo, M.C. Watzin, and G.K. Druschel.  2013. Unraveling associations between cyanobacteria blooms and in-lake environmental conditions in Missisquoi Bay, Lake Champlain, USA, using a modified self-organizing map. Environmental Science and Technology47:14267–14274.

Ravet JL, Brett MT, Arhonditsis GB (2010) The effects of seston lipids on zooplankton fatty acid composition in Lake Washington, Washington, USA. Ecology 91:180-190

Rundel, P. W., E. A. Graham, M. F. Allen, J. C. Fisher, and T. C. Harmon. 2009. Environmental sensor networks in ecological research. New Phytologist 182:589-607.

Smeltzer, E., A. Shambaugh, and P. Stangel. 2012. Environmental change in Lake Champlain revealed by long-term monitoring. Journal of Great Lakes Research 38(Supplement 1):6–18.

Stanford, J. A., and J. V. Ward. 1988. The hyporheic habitat of river ecosystems. Nature 335:64-66.

Stream Solute Workshop. 1990. Concepts and methods for assessing solute dynamics in stream ecosystems. J. North Amer. Benthol. Soc. 9(2):95-119.

Sullivan, T. J. and C. A. Stepien. 2014. Genetic diversity and divergence of yellow perch spawning populations across the Huron-Erie Corridor, from Lake Huron through western Lake Erie. Journal of Great Lakes Research 40:101-109.

Templeton, A. R., et al. 1990. The genetic consequences of habitat fragmentation. Annals of the Missouri Botanical Garden 77:13-27.

Weigel, B. M., L. Z. Wang, P. W. Rasmussen, J. T. Butcher, P. M. Stewart, T. P. Simon, and M. J. Wiley. 2003. Relative influence of variables at multiple spatial scales on stream macroinvertebrates in the Northern Lakes and Forest ecoregion, USA. Freshwater Biology 48:1440-1461.

Yellow Wood Associates. 2014. The Actual and Potential Economic Impact of Invasive Species on the Adirondack Park: A Preliminary Assessment. A Report to the Adirondack Park Invasive Plant Program. 78 pages.

Last modified December 18 2014 09:42 AM