Geli mixing Crystal Lake

A GELI (gradual entrainment lake inverter) used to mix Crystal Lake.

Affliated Projects

Here we catalogue significant projects that have used the resources and facilities offered by the NTL-LTER program. These featured projects have all made substantial contributions to the ecological research of north-temperate lakes, and encompass a wide variety of limnological themes. These projects are characterized by their duration, often spanning multiple years or even decades, and have been made possible through external funding sources.

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Cascade Program of Whole-Lake Experiments (1981 – 2024)

The ‘Cascade Program’ of whole-lake experiments is named for the first whole-ecosystem experiment to test the trophic cascade hypothesis that shifts in apex predators cascade through the food web to affect phytoplankton biomass and production (Carpenter et al. 1987). Multiple PIs were involved in 7 whole-lake experiments to date.  Further experiments investigated trophic cascade effects on microbial processes (Pace and Funke 1991), gas exchange between lakes and the atmosphere (Schindler et al. 1997, Cole et al. 2000), interactions of nutrient enrichment with cascade effects (Carpenter et al. 2001), and contributions of terrestrial organic carbon to aquatic consumers (Cole et al. 2006). Modeling studies led to the hypotheses  that nonlinear dynamics of food-web shifts (Carpenter et al. 2008) and phytoplankton blooms (Carpenter and Brock 2006, Batt et al. 2013)  cause early warnings in time series data before the ecosystem changed.  Early warnings occurred in a trophic cascade experiment (Carpenter et al. 2011) a nutrient enrichment experiment (Wilkinson et al. 2018).  A ‘treat-and-halt’ experiment where enrichment ended as soon as warnings occurred showed that early warnings could be effective tools for water quality management (Pace et al. 2017).  Spatial patterns of pigments and metabolites in lake surface water also provided early warnings of phytoplankton blooms (Butitta et al. 2017, Buelo et al. 2022).  In 2024 a new experiment will begin to test the hypothesis that shading by dissolved organic matter counters effects of nutrient enrichment and maintains low phytoplankton biomass despite enrichment (Carpenter et al. 2022).

Years Motivation Selected Papers (Conceptual Motivating papers and presentations of Key Findings)
1981-1983 Could trophic cascades account for differences in phytoplankton and primary production that were unrelated to nutrients? (Carpenter and Kitchell 1984); (Carpenter et al. 1985); (Bergquist and Carpenter 1986)
1984-1986 Whole-lake food web reversal: experimental test of the Cascade hypothesis (Carpenter et al. 1987); (Elser et al. 1988)
As part of the project we investigated tools for long-term study of cascades using paleo data (Carpenter et al. 1986); (Kitchell and Carpenter 1987)
1987-1990 Does time-series variance of top predators’ biomass affect time-series variance of primary production? How does variance propagate through food webs? (Carpenter and Kitchell 1987); (Carpenter 1988b); (Leavitt et al. 1989)
1988 The Complex Interactions meeting was held at Notre Dame in 1987 and the book was completed during Carpenter’s sabbatical at CFL in 1987-1988. (Carpenter 1988a)
1987-1990 Mike Pace joined the Cascade Project with separate NSF support to investigate changes and effects of microbial processes before, during and after trophic cascades (Pace et al. 1990) ; (Pace and Funke 1991)
1993 Synthesis volume for Trophic Cascade Project 1984-1990 (Carpenter and Kitchell 1993)
1991-1997 As nutrients increase are trophic cascades stronger or weaker? In a nutshell, enrichment makes cascade effects stronger. Jon Cole joined the Cascade Project. (Carpenter et al. 2001); (Cole et al. 2000); and many more from this multi-investigator multi-university project.
1998-2005 What supports heterotrophy in lakes – limnetic OC or terrestrial OC? We added DI13C to whole lakes to measure the aquatic vs. terrestrial contributions of C to biomass of predators (Pace et al. 2004); (Carpenter et al. 2005); (Cole et al. 2006); (Pace et al. 2007); (Wilkinson et al. 2013)
1998-2005 Are trophic cascades critical transitions, and does it matter? (Walters and Kitchell 2001); (Carpenter 2003)
2007-2011 Do statistical changes in time series foreshadow trophic cascades? Can the statistics provide early warnings? (Carpenter et al. 2008); (Carpenter et al. 2011); (Seekell et al. 2012); (Batt et al. 2013b); (Pace et al. 2013); (Cline et al. 2014)
2013-2016 Can time-series statistics provide early warnings of Cyanobacteria blooms? (Carpenter and Brock 2006); (Carpenter et al. 2009); (Batt et al. 2013a); (Pace et al. 2017); (Wilkinson et al. 2018)
2017-2019 What did we learn from 33 years of whole-lake experiments? (Carpenter and Pace 2018); (Pace et al. 2019)
2018-2022 Can spatial statistics provide early warnings of Cyanobacteria blooms? (Butitta et al. 2017); (Buelo et al. 2018); (Buelo et al. 2022)
2023- Do increases of CDOM increase the resilience of pigment concentrations to nutrient enrichment? (Carpenter et al. 2022)

Select Publications:

  • Batt, R., W. Brock, S. Carpenter, J. Cole, M. Pace, and D. Seekell. 2013a. Asymmetric response of early warning indicators of phytoplankton transition to and from cycles. Theoretical Ecology 6.10.1007/s12080-013-0190-8
  • Batt, R. D., S. R. Carpenter, J. J. Cole, M. L. Pace, and R. A. Johnson. 2013b. Changes in ecosystem resilience detected in automated measures of ecosystem metabolism during a whole-lake manipulation. Proceedings of the National Academy of Sciences 110: 17398-17403.10.1073/pnas.1316721110
  • Bergquist, A. M., and S. R. Carpenter. 1986. Limnetic herbivory: Effects on phytoplankton populations and primary production. Ecology 67: 1351-1360
  • Buelo, C. D., S. R. Carpenter, and M. L. Pace. 2018. A modeling analysis of spatial statistical indicators of thresholds for algal blooms. Limnology and Oceanography Letters 3: 384-392.doi:10.1002/lol2.10091
  • Buelo, C. D., M. L. Pace, S. R. Carpenter, E. H. Stanley, D. A. Ortiz, and D. T. Ha. 2022. Evaluating the performance of temporal and spatial early warning statistics of algal blooms. Ecological Applications 32: e2616.
  • Butitta, V. L., S. R. Carpenter, L. C. Loken, M. L. Pace, and E. H. Stanley. 2017. Spatial early warning signals in a lake manipulation. Ecosphere 8: e01941-n/a.10.1002/ecs2.1941
  • Carpenter, S., W. Brock, J. Cole, and M. Pace. 2009. Leading indicators of phytoplankton transitions caused by resource competition. Theoretical Ecology 2: 139-148.10.1007/s12080-009-0038-4
  • Carpenter, S. R. [ed.]. 1988a. Complex Interactions in Lake Communities. Springer Verlag.
  • —. 1988b. Transmission of Variance through Lake Food Webs, p. 119-135. In S. R. Carpenter [ed.], Complex Interactions in Lake Communities. Springer New York.
  • Carpenter, S. R. 2003. Regime Shifts in Lake Ecosystems: Pattern and Variation. Ecology Institute.
  • Carpenter, S. R., and W. A. Brock. 2006. Rising variance: a leading indicator of ecological transition. Ecology Letters 9: 311-318.DOI 10.1111/j.1461-0248.2005.00877.x
  • Carpenter, S. R., W. A. Brock, J. J. Cole, J. F. Kitchell, and M. L. Pace. 2008. Leading indicators of trophic cascades. Ecology Letters 11: 128-138.DOI 10.1111/j.1461-0248.2007.01131.x
  • Carpenter, S. R. and others 2001. Trophic cascades, nutrients and lake productivity: Whole-lake experiments. Ecological Monographs 71: 163-186.doi:10.1890/0012-9615(2001)071[0163:TCNALP]2.0.CO;2
  • Carpenter, S. R. and others 2011. Early Warnings of Regime Shifts: A Whole-Ecosystem Experiment. Science 332: 1079-1082.10.1126/science.1203672
  • Carpenter, S. R. and others 2005. Ecosystem subsidies: Terrestrial support of aquatic food webs from 13C addition to contrasting lakes Ecology 86: 2737-2750.10.1890/04-1282
  • Carpenter, S. R., M. M. Elser, and J. J. Elser. 1986. Chlorophyll production, degradation, and sedimentation: Implications for paleolimnology1. Limnology and Oceanography 31: 112-124.
  • Carpenter, S. R., and J. F. Kitchell. 1984. Plankton Community Structure and Limnetic Primary Production. The American Naturalist 124: 159-172.10.1086/284261
  • —. 1987. The Temporal Scale of Variance in Limnetic Primary Production. The American Naturalist 129: 417-433.10.1086/284646
  • Carpenter, S. R., and J. F. Kitchell [eds.]. 1993. Trophic Cascades in Lakes. Cambridge University Press.
  • Carpenter, S. R., J. F. Kitchell, and J. R. Hodgson. 1985. Cascading trophic interactions and lake productivity. Bioscience 35: 634-639
  • Carpenter, S. R. and others 1987. Regulation of lake primary productivity by food web structure. Ecology 68: 1863-1876
  • Carpenter, S. R., and M. L. Pace. 2018. Synthesis of a 33-yr series of whole-lake experiments: Effects of nutrients, grazers, and precipitation-driven water color on chlorophyll. Limnology and Oceanography Letters 3: 419-427.doi:10.1002/lol2.10094
  • Carpenter, S. R., M. L. Pace, and G. M. Wilkinson. 2022. DOC, grazers, and resilience of phytoplankton to enrichment. Limnology and Oceanography Letters 7: 466-474.
  • Cline, T. J. and others 2014. Early warnings of regime shifts: evaluation of spatial indicators from a whole-ecosystem experiment. Ecosphere 5: 1-13.10.1890/ES13-00398.1
  • Cole, J. J., S. R. Carpenter, M. L. Pace, M. C. Van de Bogert, J. L. Kitchell, and J. R. Hodgson. 2006. Differential support of lake food webs by three types of terrestrial organic carbon. Ecology Letters 9: 558-568.10.1111/j.1461-0248.2006.00898.x
  • Cole, J. J., M. L. Pace, S. R. Carpenter, and J. F. Kitchell. 2000. Persistence of net heterotrophy in lakes during nutrient addition and food web manipulations. Limnology and Oceanography 45: 1718-1730.
  • Elser, J. J., M. M. Elser, N. A. MacKay, and S. R. Carpenter. 1988. Zooplankton-mediated transitions between N- and P-limited algal growth. Limnology and Oceanography 33: 1-14
  • Kitchell, J. F., and S. R. Carpenter. 1987. Piscivores, plankti¬vores, fossils, and phorbins. In W. C. Kerfoot and A. Sih [eds.], Predation:  Direct and Indirect Impacts on Aquatic Communities. University Press of New England.
  • Leavitt, P. R., S. R. Carpenter, and J. F. Kitchell. 1989. Whole-lake experiments: The annual record of fossil pigments and zooplankton. Limnology and Oceanography 34: 700-717.10.4319/lo.1989.34.4.0700
  • Pace, M. L. and others 2017. Reversal of a cyanobacterial bloom in response to early warnings. Proceedings of the National Academy of Sciences 114: 352-357.10.1073/pnas.1612424114
  • Pace, M. L. and others 2007. Does terrestrial organic carbon subsidize the planktonic food web in a clear-water lake? Limnology and Oceanography 52: 2177-2189.10.4319/lo.2007.52.5.2177
  • Pace, M. L., S. R. Carpenter, R. A. Johnson, and J. T. Kurzweil. 2013. Zooplankton provide early warnings of a regime shift in a whole-lake manipulation. Limnology and Oceanography 58: 525-532
  • Pace, M. L., S. R. Carpenter, and G. M. Wilkinson. 2019. Long-term studies and reproducibility: Lessons from whole-lake experiments. Limnology and Oceanography 64: S22-S33.doi:10.1002/lno.11012
  • Pace, M. L. and others 2004. Whole-lake carbon-13 additions reveal terrestrial support of aquatic food webs. Nature 427: 240.10.1038/nature02227
  • Pace, M. L., and E. Funke. 1991. Regulation of Planktonic Microbial Communities by Nutrients and Herbivores. Ecology 72: 904-914.10.2307/1940592
  • Pace, M. L., G. B. McManus, and S. E. G. Findlay. 1990. Planktonic community structure determines the fate of bacterial production in a temperate lake. Limnology and Oceanography 35: 795-808.
  • Seekell, D. A., S. R. Carpenter, and M. L. Pace. 2012. Conditional heteroskedasticity as a leading indicator of ecological regime shifts. The American Naturalist 178: 442-451
  • Walters, C. J., and J. F. Kitchell. 2001. Cultivation/depensation effects on juvenile survival and recruitment: implications for the theory of fishing. Canadian Journal of Fisheries and Aquatic Sciences 58: 39-50
  • Wilkinson, G. M. and others 2018. Early warning signals precede cyanobacterial blooms in multiple whole-lake experiments. Ecological Monographs 88: 188-203.doi:10.1002/ecm.1286
  • Wilkinson, G. M., M. L. Pace, and J. J. Cole. 2013. Terrestrial dominance of organic matter in north temperate lakes. Global Biogeochemical Cycles 27: 43-51.10.1029/2012gb004453


External EDI link

Principal Investigators:

Stephen R. Carpenter (U. Notre Dame, U. Wisconsin-Madison) 1981 – present
Jonathan J. Cole (Cary Institute) 1991 – 2016
James R. Hodgson (St. Norbert College) 1981 – 2012
James F. Kitchell (U. Wisconsin-Madison) 1981 – 2012
David M. Lodge (U. Notre Dame) 1991 — 1997
Michael L. Pace (Cary, U. Virginia 1988 – present
Craig D. Sandgren (U. Wisconsin-Milwaukee) 1991 – 1997
Emily H. Stanley (U. Wisconsin-Madison) 2018 – 2022
Grace M. Wilkinson (U. Wisconsin-Madison) 2022 — present

Little Rock Acidification Experiment (1983-1999)

The Little Rock Acidification Experiment was a joint project involving the USEPA (Duluth Lab), University of Minnesota-Twin Cities, University of Wisconsin-Superior, University of Wisconsin-Madison, and the Wisconsin Department of Natural Resources.  Little Rock Lake is a bi-lobed lake in Vilas County, Wisconsin, USA.  In 1983 the lake was divided in half by an impermeable curtain and from 1984-1989 the northern basin of the lake was acidified with sulfuric acid in three two-year stages.  The target pHs for 1984-5, 1986-7, and 1988-9 were 5.7, 5.2, and 4.7, respectively.  Starting in 1990 the lake was allowed to recover naturally with the curtain still in place.  The main objective was to understand the population, community, and ecosystem responses to whole-lake acidification.  Funding for this project was provided by the USEPA and NSF.

Select Publications:

  • Bloom, N. S., Watras, C. J., & Hurley, J. P. (1991). Impact of acidification on the methylmercury cycle of remote seepage lakes. Water Air & Soil Pollution56, 477-491.
  • Brezonik, P. L., Mach, C. E., Downing, G., Richardson, N., & Brigham, M. (1990). Effects of acidification on minor and trace metal chemistry in Little Rock Lake, Wisconsin. Environmental Toxicology and Chemistry: An International Journal9(7), 871-885.
  • Brezonik, P. L., Baker, L. A., Eaton, J. R., Frost, T. M., Garrison, P., Kratz, T. K., … & Webster, K. E. (1987). Experimental acidification of Little Rock Lake, Wisconsin. In Acidic Precipitation: Proceedings of the International Symposium on Acidic Precipitation Muskoka, Ontario, September 15–20, 1985 (pp. 1169-1175). Springer Netherlands.
  • Brezonik, P. L., Eaton, J. G., Frost, T. M., Garrison, P. J., Kratz, T. K., Mach, C. E., … & Webster, K. E. (1993). Experimental acidification of Little Rock Lake, Wisconsin: chemical and biological changes over the pH range 6.1 to 4.7. Canadian Journal of Fisheries and Aquatic Sciences50(5), 1101-1121.
  • Fischer, J. M., Klug, J. L., Ives, A. R., & Frost, T. M. (2001). Ecological history affects zooplankton community responses to acidification. Ecology82(11), 2984-3000.
  • Fischer, J. M., Frost, T. M., & Ives, A. R. (2001). Compensatory dynamics in zooplankton community responses to acidification: measurement and mechanisms. Ecological Applications11(4), 1060-1072.
  • Frost, T. M., Fischer, J. M., Klug, J. L., Arnott, S. E., & Montz, P. K. (2006). Trajectories of zooplankton recovery in the little rock lake whole‐lake acidification experiment. Ecological Applications, 16(1), 353-367.
  • Frost, T. M., Montz, P. K., Kratz, T. K., Badillo, T., Brezonik, P. L., Gonzalez, M. J., … & Morris, D. P. (1999). Multiple stresses from a single agent: diverse responses to the experimental acidification of Little Rock Lake, Wisconsin. Limnology and oceanography44, 784-794.
  • Frost, T. M., & Montz, P. K. (1988). Early zooplankton response to experimental acidification in Little Rock Lake, Wisconsin, USA. Internationale Vereinigung für theoretische und angewandte Limnologie: Verhandlungen23(4), 2279-2285.
  • Frost, T. M., Montz, P. K., & Kratz, T. K. (1998). Zooplankton community responses during recovery from acidification in Little Rock Lake, Wisconsin. Restoration Ecology6(4), 336-342.
  • Hrabik, T. R., & Watras, C. J. (2002). Recent declines in mercury concentration in a freshwater fishery: isolating the effects of de-acidification and decreased atmospheric mercury deposition in Little Rock Lake. Science of the Total Environment297(1-3), 229-237.
  • Gonzalez, M., Frost, T. M., & Montz, P. (1990). Effects of experimental acidification on rotifer population dynamics in Little Rock Lake, Wisconsin, USA. Internationale Vereinigung für theoretische und angewandte Limnologie: Verhandlungen, 24(1), 449-456.
  • King, S. O., Mach, C. E., & Brezonik, P. L. (1992). Changes in trace metal concentrations in lake water and biota during experimental acidification of Little Rock Lake, Wisconsin, USA. Environmental pollution78(1-3), 9-18.
  • Sampson, C. J., Brezonk, P. L., Frost, T. M., Webster, K. E., & Simonson, T. D. (1995). Experimental acidification of Little Rock Lake, Wisconsin: The first four years of chemical and biological recovery. Water, Air, and Soil Pollution85, 1713-1719.
  • Watras, C. J., Morrison, K. A., Regnell, O., & Kratz, T. K. (2006). The methylmercury cycle in Little Rock Lake during experimental acidification and recovery. Limnology and Oceanography51(1), 257-270.
  • Watras, C. J., & Frost, T. M. (1989). Little Rock Lake (Wisconsin): perspectives on an experimental ecosystem approach to seepage lake acidification. Archives of Environmental Contamination and Toxicology18, 157-165.
  • Webster, K. E., Newell, A. D., Baker, L. A., & Brezonik, P. L. (1990). Climatically induced rapid acidification of a softwater seepage lake. Nature347(6291), 374-376.
  • Webster, K. E., Frost, T. M., Watras, C. J., Swenson, W. A., Gonzalez, M., & Garrison, P. J. (1992). Complex biological responses to the experimental acidification of Little Rock Lake, Wisconsin, USA. Environmental pollution78(1-3), 73-78.


External EDI link


NSF DEB 9020195: LTREB: Ecological Recovery Following Six Years of Experimental Acidification of Little Rock Lake, Wisconsin

NSF DEB 9527669: LTREB: Continuing Assessment of Ecological Recovery Following Experimental Acidification of Little Rock Lake, Wisconsin

NSF IOS 9815519: LTREB: Continuing Assessment of Ecological Recovery Following Experimental Acidification of Little Rock Lake, Wisconsin


USGS WEBB program (1991-2019)

USGS initiated the Water, Energy, and Biogeochemical Budgets (WEBB) program to understand the processes controlling water, energy, and biogeochemical fluxes over a range of temporal and spatial scales, and the effects of atmospheric and climatic variables. Trout Lake is one of five small, geographically and ecologically diverse watersheds representing a range of hydrologic and climatic conditions.

Publications and Datasets:

Managing Macrophytes to Improve Fish Growth: A Multilake Experiment (1993-1996)

Since the 1960s many lakes in southern Wisconsin supported dense beds of Eurasian watermilfoil. The dense vegetation excluded fish and interfered with food web processes in the littoral zone. Technology existed to clear lanes through the vegetation and potentially improve habitat for fishes. NTL and WDNR researchers collaborated on a set of whole-lake manipulations to test the effects of habitat management on fish response. Research was funded by WDNR through the Sport Fish Restoration fund.  Subject lakes included all of the NTL ‘southern’ lakes:  Fish Lake and lakes Mendota, Monona, and Wingra.

Preliminary modeling studies showed that statistical power could be an issue because of the high variability of food web dynamics and fish population responses (Carpenter et al. 1995; Nibbelink and Carpenter 1998; Trebitz et al. 1997; Trebitz et al. 1993).  Therefore we conducted a multi-lake experiment in which 4 lakes were manipulated and 9 lakes served as undisturbed reference ecosystems (Carpenter et al. 1997).  In August 1994 we cut channels through the milfoil beds in 4 lakes, removing about 20% of the macrophyte biomass from each lake. We observed striking increases in growth rates of 4, 5 and 6 year-old bluegill and 2, 5 and 6 year old largemouth bass in the manipulated lakes (Olson et al. 1998).  By 1996 about 75% of the channels were filled by regrowing plants, but nonetheless growth responses persisted. Variation in fish responses was large, as expected, but growth responses were also large and discernible due to large sample size in this replicated ecosystem experiment (Carpenter 1998; Olson et al. 1998).  Results showed that habitat manipulation was a viable method for improving fish growth and fisheries in lakes infested with Eurasian watermilfoil.

Select Publications:

  • Carpenter, S. R. 1998. The need for large-scale experiments to assess and predict the response of ecosystems to perturbation, p. 287-312. In M. L. Pace and P. M. Groffman [eds.], Successes, Limitations and Frontiers in Ecosystem Science. Springer.
  • Carpenter, S. R. and others 1995. Responses of Bluegill to Habitat Manipulations: Power to Detect Effects. North American Journal of Fisheries Management 15: 519-527.;2
  • Carpenter, S. R. and others 1997. Macrophyte structure and growth of bluegill (Lepomis macrochirus):  design of a multi-lake experiment, p. 217-226. In E. Jeppesen, M. Sondergaard, M. Sondergaard and K. Christoffersen [eds.], The Structuring Role of Submerged Macrophytes in Lakes. Springer.
  • Nibbelink, N. P., and S. R. Carpenter. 1998. Interlake variation in growth and size structure of bluegill (Lepomis macrochirus): inverse analysis of an individual-based model. Canadian Journal of Fisheries and Aquatic Sciences 55: 387-396.
  • Olson, M. H. and others 1998. Managing Macrophytes to Improve Fish Growth: A Multi-lake Experiment. Fisheries 23: 6-12.10.1577/1548-8446(1998)023<0006:MMTIFG>2.0.CO;2
  • Trebitz, A. and others 1997. A model of bluegill-largemouth bass interactions in relation to aquatic vegetation and its management. Ecological Modelling 94: 139-156.
  • Trebitz, A. S., S. A. Nichols, S. R. Carpenter, and R. C. Lathrop. 1993. Patterns of vegetation change in Lake Wingra following a Myriophyllum spicatum decline. Aquatic Botany 46: 325-340.

Lake Mendota Priority Watershed Project (1993-2008)

The Lake Mendota Priority Watershed Project (LMPWP) was intended to reduce nutrient runoff and improve water quality of Lake Mendota.  The project was approved for state funding by the Wisconsin Dept. Natural Resources (DNR) Nonpoint Source Water Pollution Abatement Program in 1993.  The Dane County Land Conservation Department was responsible for implementing/installing most of the watershed practices.  The project’s inventory phase of pollution sources was conducted in 1994-1997; the project’s implementation phase for installing practices was in 1998-2008.

Limnologists at the UW-Madison Center for Limnology and the DNR working on the North Temperature Lakes (NTL) Long-Term Ecological Research Project were responsible for establishing Lake Mendota’s water quality goals and the watershed’s phosphorus (P) loading reductions needed to achieve those goals.  First, the highly variable annual phosphorus (P) loadings to Lake Mendota from long-term tributary P loading data and from other sources were calculated from available data.  In-lake modeling utilizing Mendota’s long-term limnological data was then conducted to estimate the lake responses to future P loading reductions realized by the priority watershed project.  The goals were to reduce P loading to decrease the predicted frequency of summer days with cyanobacteria blooms >2 mg/L.

Thus, NTL viewed the LMPWP as a long-term experiment in evaluating a lake’s response to reductions in agricultural and urban nonpoint pollution, a seemingly intractable problem causing lake eutrophication.  By the end of the project in 2008 there was little progress in reducing P loads to Lake Mendota because most of the agricultural land management practices were voluntary with too few farmer sign-ups, and the huge problems of animal manure management and high soil P were not adequately addressed.  The LMPWP segued within a couple of years to the Yahara CLEAN project with similar support from NTL.

Select Publications:

  • Stow, C.A., S.R. Carpenter, and R.C. Lathrop. 1997. A Bayesian observation error model to predict cyanobacterial biovolume from spring total phosphorus in Lake Mendota, Wisconsin. Can. J. of Fish. Aquat. Sci. 54:464-473.
  • Lathrop, R.C., S.R. Carpenter, C.A. Stow, P.A. Soranno, and J.C. Panuska. 1998. Phosphorus loading reductions needed to control blue-green algal blooms in Lake Mendota. Can. J. Fish. Aquat. Sci. 55:1169-1178.
  • Carpenter, S.R. and R.C. Lathrop.  1999.  Lake restoration: capabilities and needs.  Hydrobiologia 395/396:19-28.
  • Ventelä, A.-M. and R.C. Lathrop. 2005. Comprehensive approaches for managing and restoring two large lakes and their catchments: Pyhäjärvi (Finland) and Lake Mendota (USA). Verh. Internat. Verein. Limnol. 29:830-836.
  • Carpenter, S.R., R.C. Lathrop, P. Nowak, E.M.Bennett, T. Reed, and P.A. Soranno. 2006. The ongoing experiment: restoration of Lake Mendota and its watershed, p. 236-256. In: J.J. Magnuson, T.K. Kratz, and B.J. Benson [eds.], Long-term dynamics of lakes in the landscape. Oxford University Press, New York.

Biocomplexity: Divergent Dynamics: Complex Interactions of Riparian Land, People and Lakes (2001-2011)

Our proposal to the NSF Biocomplexity program was prompted by NTL P.I.s’ interests in the land-water interface, stability, thresholds, and regime shifts. Major components of the project included a cross-lakes comparative study of riparian and littoral ecosystem structure and processes, whole-lake experimental studies of the effects of coarse woody habitat on fish communities and production, and a whole-lake manipulation of Sparkling Lake to investigate tools for suppression of invasive rusty crayfish and rainbow smelt. Ecosystem comparisons and experiments were supplemented by modeling and theoretical studies in all cases.

Littoral-Riparian Interactions on a Landscape Gradient

Earlier work by CFL scientists showed that residential development along lakeshores was associated with massive reductions in coarse woody habitat (fallen trees) that supports fish communities and their prey (Christensen et al. 1996).  Loss of coarse woody habitat was associated with steep declines in growth rates of bluegill and largemouth bass (Schindler et al. 2000).  These correlations were provocative but lacked a mechanism for aquatic regime shifts due to losses of coarse woody habitat and direct experimental demonstrations of habitat effects.  The Biocomplexity project addressed these shortcomings.

Comparative and Modeling Studies

The best predictor of coarse woody habitat in lakes was the density of woody habitat on adjacent riparian land (Marburg et al. 2006).  Within a lake, pattern of coarse woody habitat was best predicted by exposure (fetch) and density of built structures (Marburg et al. 2006).

Across a gradient of lakeshore residential development in 16 Vilas County lakes, Gaeta et al. (2011) showed that juvenile largemouth bass size-specific growth rates were positively correlated with lakeshore development.  Adult largemouth bass growth rates were negatively correlated with lakeshore residential development. At the fish community level, a recent study using Biocomplexity cross-lakes fish data revealed distinct species-specific response to lakeshore residential development. Moreover, fish communities were affected by lakeshore residential development independently of effects on habitat alone (Perales and Vander Zanden)

An ecosystem model showed the benefits of coarse woody habitat for fish production interacted sharply with the rate at which fish were harvested (Roth et al. 2007a).  At the landscape scale,  production and  resilience of lake fisheries in the Northern Highland lake district of Wisconsin depended on habitat complexity around lakes and within them, and the capacity of management to sustain this complexity (Carpenter 2004).  In workshops, we met with local people and Wisconsin Department of Natural Resources managers to discuss ways to “expect the unexpected” and cope with surprising shifts in lake ecosystems (Carpenter and Gunderson 2001) and developed scenarios of possible abrupt shifts of regional ecosystem services (Peterson et al. 2003).  A decision-theory analysis of the Northern Highland lake district showed that there are no panaceas; each problem that emerges is likely to require new data and new ways of thinking (Brock and Carpenter 2007).  Modeling studies showed why variance (or its inverse) can be a misleading measure of ecosystem stability whereas multivariate analyses of covariation can provide powerful indicators of stability or resilience of complex ecological systems (Ives and Carpenter 2007).

Whole-Lake Experiments on Woody Habitat

Researchers removed 75% of the woody habitat from one basin of Little Rock Lake while the other basin of this divided lake served as a reference ecosystem (Sass et al. 2006).  After habitat removal largemouth bass ate less fish, more terrestrial prey and grew more slowly. Yellow perch populations declined steeply due to predation and loss of critical habitat.  In contrast yellow perch in the reference basin were replenished by successful year classes.  Helmus and Sass (2008) confirmed the rapid depletion of yellow perch in the treatment basin following CWH removal and found no change in the macroinvertebrate community between lake basins.  Sass et al. (2006b) showed that abundant littoral structural habitat provided critical refuge habitat for forage fishes, with high predation risk of forage fish immediately adjacent to the littoral refuge.

While humans directly remove coarse woody habitat from lakes, drought can cause declining lake levels and produce a similar effect by leaving coarse woody habitat high and dry. Perales et al. (2020) identified which lakes in the region are most vulnerable to drought-induced lake-level declines.In Little Rock Lake, drought reduced lake level and decreased woody habitat in both basins.  Results corroborated the earlier experiment:  growth rates of largemouth bass declined and yellow perch nearly disappeared from the lake (Gaeta et al. 2014).  These studies showed that precipitation trends interact with riparian management to change woody habitat and fish production.

To complement the woody habitat removal from Little Rock Lake, researchers added woody habitat to the treatment basin of Camp Lake while the other basin served as an untreated reference ecosystem (Sass et al. 2012). Largemouth bass consumed more fishes and grew faster after woody habitat addition. However differences between basins in fish population trends were not discernible in this relatively brief (4-year) experiment.

The CWH removal and addition experiments were leveraged for additional studies on fish behavior, spawning, catch-and-release influences on fish, and a comparison with eutrophic, small reservoirs (Sass et al. 2023).  Largemouth bass home ranges were negatively correlated with CWH abundance (Ahrenstorff et al. 2009).  Coarse woody habitat availability was positively, yet not significantly, correlated with largemouth bass nest density suggesting that CWH may not be a limiting factor in largemouth bass spawning (Weis and Sass 2011).  Angling of largemouth bass during the Little Rock Lake experiment showed no negative population consequences of the practice (Sass et al. 2018).  More recently, Sass et al. (2022) showed that fish population size structure and productivity responses to coarse woody habitat additions may differ between small, eutrophic reservoirs and small, oligotrophic natural lakes.

These experiments showed that removal of woody habitat had sharp adverse effects on fish growth and populations.  These adverse effects were not reversible by adding woody habitat. Thus it is crucial to maintain woody habitat for sustaining desirable fish and fisheries of lakes. Losses of woody habitat cause complex long-lasting changes in lake ecosystems.

Can Invasive Crayfish and Smelt Be Controlled by Intensive Harvest?

Predation and harvest are powerful forces in lake ecosystems and it is reasonable to expect that invasive species may be controlled by targeted harvest. Sparkling Lake, a core NTL lake, had changed extensively after invasion by rusty crayfish and rainbow smelt.  Biocomplexity researchers attempted massive removals of each invader.

Rusty Crayfish

Preliminary studies suggested that lakes may occupy low-crayfish states or high-crayfish states depending on initial conditions, habitat structure and capacity of fishes to consume crayfish  (Roth et al. 2007b).  Experimental removal of invasive rusty crayfish caused extensive changes in littoral zone ecology, including habitat structure, composition and biomass of benthic invertebrates, density of bluegill, declines of invasive crayfish, and recovery of native crayfish (Hein et al. 2006; Hein et al. 2007) (Hansen et al. 2013b). These ecosystem-wide changes have persisted for >10 years following the cessation of invasive crayfish removal (Perales et al. 2021) . Evidence for alternate stable states was ambiguous (Hansen et al. 2013a).  A model of linear population dynamics with a discontinuous threshold separating low-invader from high-invader states fit the data better than a nonlinear model with an unstable critical transition.  However, as noted by the title of Hansen et al. (2013) the implications for management are the same:  intensive harvest can force the crayfish population into a low-density state, provided that other environmental factors are unchanged.

Rainbow Smelt

Biocomplexity, NTL-LTER, and WDNR researchers removed more than 4170 kg of rainbow smelt by netting during the spring spawning event from 2002-2009 (Gaeta et al. 2015). In addition Walleye populations were enhanced by stocking, restrictions on angling harvest, and GLIFWCs agreement to forego Tribal harvest. Up to 93% of the smelt population was removed each year, and smelt stocks fell to low populations. However smelt populations (measured by NTL-LTER annual surveys) began to increase immediately after cessation of removal.  In a few years smelt recovered to their former densities (Gaeta et al. 2015).  The experiment showed that invasive rainbow smelt are extremely resilient to intensive harvest.

Select Publications:

  • Ahrenstorff, T.D., G.G. Sass, and M.R. Helmus.  2009.  The influence of littoral zone coarse woody habitat on home range size, spatial distribution, and feeding ecology of largemouth bass (Micropterus salmoides).  Hydrobiologia  623:223-233.
  • Brock, W. A., and S. R. Carpenter. 2007. Panaceas and diversification of environmental policy. Proceedings of the National Academy of Sciences 104: 15206-15211.10.1073/pnas.0702096104
  • Carpenter, S. R., Brock, W.A. 2004. Spatial complexity, resilience and policy diversity: Fishing on lake-rich landscapes. Ecology and Society 9.
  • Carpenter, S. R., and L. H. Gunderson. 2001. Coping with Collapse: Ecological and Social Dynamics in Ecosystem Management: Like flight simulators that train would-be aviators, simple models can be used to evoke people’s adaptive, forward-thinking behavior, aimed in this instance at sustainability of human–natural systems. BioScience 51: 451-457. 10.1641/0006-3568(2001)051[0451:Cwceas]2.0.Co;2
  • Christensen, D. L., B. R. Herwig, D. E. Schindler, and S. R. Carpenter. 1996. Impacts of Lakeshore Residential Development on Coarse Woody Debris in North Temperate Lakes. Ecological Applications 6: 1143-1149.10.2307/2269598
  • Gaeta, J. W., T. R. Hrabik, G. G. Sass, B. M. Roth, S. J. Gilbert, and M. J. Vander Zanden. 2015. A whole-lake experiment to control invasive rainbow smelt (Actinoperygii, Osmeridae) via overharvest and a food web manipulation. Hydrobiologia 746: 433-444.10.1007/s10750-014-1916-3
  • Gaeta, J. W., G. G. Sass, and S. R. Carpenter. 2014. Drought-driven lake level decline: effects on coarse woody habitat and fishes. Canadian Journal of Fisheries and Aquatic Sciences 71: 315-325.10.1139/cjfas-2013-0451
  • Hansen, G. J., A. R. Ives, M. J. Vander Zanden, and S. R. Carpenter. 2013a. Are rapid transitions between invasive and native species caused by alternative stable states, and does it matter? Ecology 94: 2207-2219.10.1890/13-0093.1
  • Hansen, G. J. A. and others 2013b. Food web consequences of long-term invasive crayfish control. Canadian Journal of Fisheries and Aquatic Sciences 70: 1109-1122.10.1139/cjfas-2012-0460
  • Hein, C. L., B. M. Roth, A. R. Ives, and M. J. V. Zanden. 2006. Fish predation and trapping for rusty crayfish (Orconectes rusticus) control: a whole-lake experiment. Canadian Journal of Fisheries and Aquatic Sciences 63: 383-393.10.1139/f05-229
  • Hein, C. L., M. J. Vander Zanden, and J. J. Magnuson. 2007. Intensive trapping and increased fish predation cause massive population decline of an invasive crayfish. Freshwater Biology 52: 1134-1146.
  • Ives, A. R., and S. R. Carpenter. 2007. Stability and Diversity of Ecosystems. Science 317: 58-62.10.1126/science.1133258
  • Marburg, A. E., M. G. Turner, and T. K. Kratz. 2006. Natural and anthropogenic variation in coarse wood among and within lakes. Journal of Ecology 94: 558-568.
  • Perales, K. M. and others 2021. Spatial and temporal patterns in native and invasive crayfishes during a 19-year whole-lake invasive crayfish removal experiment. Freshwater Biology 66: 2105-2117.
  • Perales, K. M., C. L. Hein, N. R. Lottig, and M. J. V. Zanden. 2020. Lake water level response to drought in a lake-rich region explained by lake and landscape characteristics. Canadian Journal of Fisheries and Aquatic Sciences 77: 1836-1845.10.1139/cjfas-2019-0270
  • Perales, K. M., and M. J. Vander Zanden. Lakeshore residential development as a driver of aquatic habitat and littoral fish communities: A cross-system study. Ecological Applications e2896.
  • Peterson, G. D. and others 2003. Assessing Future Ecosystem Services: a Case Study of the Northern Highlands Lake District, Wisconsin. Conservation Ecology 7.
  • Roth, B. M. and others 2007a. Linking terrestrial and aquatic ecosystems: The role of woody habitat in lake food webs. Ecological Modelling 203: 439-452.
  • Roth, B. M., J. C. Tetzlaff, M. L. Alexander, and J. F. Kitchell. 2007b. Reciprocal Relationships Between Exotic Rusty Crayfish, Macrophytes, and Lepomis Species in Northern Wisconsin Lakes. Ecosystems 10: 74-85.
  • Sass, G. G., S. R. Carpenter, J. W. Gaeta, J. F. Kitchell, and T. D. Ahrenstorff. 2012. Whole-lake addition of coarse woody habitat: response of fish populations. Aquatic Sciences 74: 255-266.10.1007/s00027-011-0219-2
  • Sass, G. G., J. F. Kitchell, S. R. Carpenter, T. R. Hrabik, A. E. Marburg, and M. G. Turner. 2006. Fish Community and Food Web Responses to a Whole-lake Removal of Coarse Woody Habitat. Fisheries 31: 321-330.10.1577/1548-8446(2006)31[321:FCAFWR]2.0.CO;2
  • Sass, G. G., S. L. Shaw, C. C. Fenstermacher, A. P. Porreca, and J. J. Parkos III. 2023. Structural Habitat in Lakes and Reservoirs: Physical and Biological Considerations for Implementation. North American Journal of Fisheries Management 43: 290-303.
  • Schindler, D. E., S. I. Geib, and M. R. Williams. 2000. Patterns of Fish Growth along a Residential Development Gradient in North Temperate Lakes. Ecosystems 3: 229-237.10.1007/s100210000022
  • Weis, J. J., and G. G. Sass. 2011. Largemouth Bass Nest Site Selection in Small, North Temperate Lakes Varying in Littoral Coarse Woody Habitat Abundances. North American Journal of Fisheries Management 31: 943-951.10.1080/02755947.2011.633688


External EDI link


All of the field research conducted under the NSF Biocomplexity grant depended on the historical data and concurrent collaboration of NTL-LTER researchers.  All studies of fish and fisheries, and manipulations to remove invasive species from Sparkling Lake were conducted in collaboration with Wisconsin Department of Natural Resources and the Great Lakes Indian Fish and Wildlife Commission.  Research on nonlinear ecological-economic-social dynamics of lake fisheries in relation to habitat complexity and connections of lakes on the landscape were partially funded by grants from J.S. McDonnell Foundation to the Resilience Alliance and Packard Foundation to the International Council of Science.

NSF DEB 0083545: Biocomplexity: Divergent Dynamics: Complex Interactions of Riparian Land, People and Lakes

Hydrologic and Biogeochemical Fluxes in Land-Water Mosaics (2004-2010)

We studied hydrologic and biogeochemical fluxes between the terrestrial landscape and lakes in the Northern Highlands Lake District (NHLD) of northern Wisconsin and and the Upper Peninsula of Michigan, with a focus on carbon cycling. At the beginning of this project, we set an ambitious set of goals for understanding the integrated lakes, uplands, and wetlands of lake-rich districts like the NHLD. We have achieved many of these goals, with projects ranging in scale from spatially dense measurements in individual lakes to regional integration at the scale of thousands of square kilometers; and using a range of approaches with a primary emphasis on process-based modeling.  Data needed for the integrative modeling research relied on databases of NTL-LTER, USGS, and WDNR.

We summarize some key findings below and describe major results from the research areas contributing to this project.

Key Findings:

  • Climatic variations typically had a strong effect on the regional surface water balance in the short term (season or year-to-year variations), but land cover change had influence on water balance over the long-term (6 years and beyond) (Vano et al. 2008)
  • Small lakes are abundant in the region and have different chemical characteristics than larger lakes, demonstrating that lake size is important to account for in C cycling models (Hanson et al. 2004, 2007)
  • By measuring metabolism in several locations within a lake researchers can provide a good estimate of whole-lake metabolism despite spatial heterogeneity (Van de Bogert, 2012)
  • Growing forests make up the largest regional flux of carbon into the NHLD, but organic matter in peat wetlands and in lake sediments make up the largest regional C pool (Buffam et al. 2010a,b)
  • Wetland vegetation growth, lake sedimentation, lake CO2 evasion, wetland methane emission, and riverine export are all of consequence for the regional C budget (Buffam et al. 2010a,b)
  • Relatively simple lake models may adequately represent lake metabolism and water column C cycling, based on a comparison of models of varying complexity (Hanson et al. 2008)
  • Models intended to predict long-term carbon dynamics need to include processes that act slowly, and in many cases subtly, on transport between terrestrial and aquatic ecosystems (Hanson et al. 2015)
  • Due largely to wide variation in carbon loading from watersheds, modeled C cycling responses to climate perturbation vary substantially among lakes (Cardille et al. 2007, Cardille et al. 2009)
  • Using an integrated regional model, landscape-scale CO2 emissions from lakes are predicted to increase under a wet climate scenario, and decrease under a dry climate scenario (Cardille et al. 2009)
  • Applications of landscape carbon models to agricultural watersheds of southern Wisconsin NTL-LTER lakes quantified the tradeoffs between carbon storage and agricultural production (West et al. 2010, 2011).

Select Publications:

  • Buffam, I., S.R. Carpenter, W. Yeck, P.C. Hanson and M.G. Turner. 2010a. Filling holes in regional carbon budgets: Predicting peat depth in a north temperate lake district. Journal of Geophysical Research 115. G01005, doi:10.1029/2009JG001034
  • Buffam, I., Turner, M.G., Desai, A.R., Hanson, P., Rusak, J., Lottig, N.R., Stanley, E.H., and Carpenter, S.R., 2010b. Integrating aquatic and terrestrial components to construct a complete carbon budget for a north temperate lake district. Global Change Biology 17: 1193-1211, doi:10.1111/j.1365-2486.2010.02313.x.
  • Cardille, J. A., S. R. Carpenter, M. T. Coe, J. A. Foley, P. C.   Hanson, M. G. Turner, and J. A. Vano. 2007. Carbon and water cycling in lake-rich landscapes: Landscape connections, lake hydrology, and  biogeochemistry, J. Geophys. Res., 112, G02031, doi: 10.1029/2006JG000200.
  • Cardille, J.A., S.R. Carpenter, J.A. Foley, P.C. Hanson, M.G. Turner, and J.A. Vano. 2009. Climate perturbations and lakes: estimating sensitivities of water and carbon budgets. Journal of Geophysical Research 114: G0311: 1-11. doi:10.1029/2008JG000891
  • Hanson, P.C., A.I. Pollard, D.L. Bade, K. Predick, S.R. Carpenter and J.A. Foley.  2004.  A model of carbon evasion and sedimentation in temperate lakes.  Global Change Biology 10:  1285-1298.
  • Hanson, P.C., S.R. Carpenter, J.A. Cardille, M.T. Coe and L.A. Winslow.  2007.  Small lakes dominate a random sample of regional lake characteristics.  Freshwater Biology 52: 814-822.
  • Hanson, P.C., S.R. Carpenter, N. Kimura, C.-H. Wu, S. Cornelius, T.K. Kratz. 2008. Evaluation of metabolism models for free-water dissolved oxygen methods in lakes. Limnology and Oceanography Methods 6: 454-465.
  • Hanson, P.C., M.L. Pace, S.R. Carpenter, J.J. Cole, E.H. Stanley.  2015.  Integrating landscape carbon cycling: research needs for resolving organic carbon budgets in lakes.  Ecosystems: 18: 363-375.  DOI: 10.1007/s10021-014-9826-9
  • Van de Bogert, M.C., D.L. Bade, S.R. Carpenter, J.J. Cole, M.L. Pace, P.C. Hanson and O.C. Langman. 2012. Spatial heterogeneity strongly affects estimates of ecosystem metabolism in two north temperate lakes. Limnology and Oceanography 57: 1689-1700.
  • Vano, J. A., J. A. Foley, C. J. Kucharik, and M. T. Coe. 2008. Controls of climatic variability and land cover on land surface hydrology of northern Wisconsin, USA. Journal of Geophysical Research: Biogeosciences 113.
  • West, P.C., H.K. Gibbs, C. Monfreda, J. Wagner, C.C. Barford, S.R. Carpenter and J.A. Foley. 2010. Trading carbon for food: Global comparison of carbon stocks vs. crop yields on agricultural land. Proceedings of the National Academy of Sciences 107: 19645-19648.
  • West, P.C., H.K. Gibbs, C. Monfreda, J. Wagner, C. Barford, S.R. Carpenter and J. Foley. 2011. Reply to Vermeulen and Wollenberg: Distinguishing food security and crop yields. Proceedings of the National Academy of Sciences 108. 10.1073/pnas.1019348108.


Awards from the Andrew W. Mellon Foundation to S.R. Carpenter, J.A. Foley, and M.G. Turner

Crystal Lake Mixing (2010-2013)

Researchers conducted a whole-lake mixing experiment on Crystal Lake (Vilas County, WI) to eradicate an invasive fish from the lake. Rainbow smelt invaded Crystal Lake in the early 1980s, and a sharp decline in native yellow perch populations followed shortly thereafter. To specifically target this invasive for removal from the lake, researchers took advantage of the smelt’s need for cold water habitat in a lake with no other cold water fishes. Scientists experimentally mixed the lake to remove this cold water habitat, stressing the rainbow smelt beyond the limits of survival.

NTL has been studying the lake for many years, but have recently intensified this effort by introducing new sampling to more effectively monitor fish, aquatic plants, algae, water clarity and other properties of the lake during 2010 and 2011. This broad sampling regime allows the researchers to monitor effects of the mixing experiment on the entire ecosystem and see if the lake can return to pre-invasion conditions after the smelt are removed. The mixing experiment began in June 2011, with continued mixing and monitoring until 2012.

Select Publications:


Crystal Lake data is contained within the core NTL-LTER datasets

South Sparkling Bog Snow Removal (2019-2021)

Winter is a period of significant biological activity in the annual cycle of north-temperate lakes. Research suggests a future of reduced ice cover duration and altered snow conditions could significantly change the functioning of aquatic ecosystems. This study sought to explore the possible repercussions of changing ice and snow dynamics on aquatic biological communities, particularly at lower trophic levels. To explore plankton community responses to changing under-ice light conditions, researchers performed a whole-lake manipulation by removing all of the snow from the surface of a north temperate bog lake in northern Wisconsin. Over three winters, samples were collected under ice in the study lake, South Sparkling Bog. The first winter, 2018–2019, served as a reference year during which snow was not removed from the lake and was followed by two subsequent winters of snow removal during 2019–2020 and 2020–2021. Data collected included phytoplankton and zooplankton abundances and taxa, chlorophyll a, dissolved organic carbon, light, Secchi depth, and ice and snow thickness. In the snow removal years, increased light availability in the water column shifted the phytoplankton community from low-biomass, mixed community of potential mixotrophs, unicellular cyanobacteria and Chlorophytes to dominance by photoautotrophs, and rotifer zooplankton densities increased. Ice condition, specifically the thickness of white ice vs. black ice, was a major driver in the magnitude of change between years. This research improved our understanding of how plankton communities might respond to climate-change driven shifts in winter dynamics for north temperate systems.

Select Publications:


Lake snow removal experiment snow, ice, and Secchi depth, 2019-2021

Lake snow removal experiment phytoplankton community data, under ice, 2019-2021

Lake snow removal experiment zooplankton community data, under ice, 2019-2021

Lake snow removal experiment buoy, light, and chlorophyll data, 2019-2021


NSF DEB 185622: SG: The ecosystem ecology of lake ice loss in north-temperate lakes