Aquatic Ecology Across Scales

In press

Solomon CT, Dassow C, Iwicki C, Jensen O, Jones SE, Sass GG, Trudeau A, van Poorten B, Whittaker D. Frontiers in modeling social-ecological dynamics of recreational fisheries: a review and synthesis. Fish and Fisheries.

In print


Olsen CR, Jones SE. 2022. Chlorophyll-total phosphorus relationships emerge from multistate interactions from algae to catchments. Limnology and Oceanography Letters, 7: 483-491.

Mosley CL, Dassow CJ, Caffarelli J, Ross AJ, Sass GG, Shaw SL, Solomon CT, Jones SE. 2022. Species differences, but not habitat, influence catch rate hyperstability across a recreational fishery landscape. Fisheries Research, 255: 106438.

Hararuk O, Jones SE, Solomon CT. 2022. Hydrologic export of soil organic carbon: continental variation and implications. Global Biogeochemical Cycles, 36: e2021GB007161.

Bertolet BL, Louden SI, Jones SE. 2022. Microbial community composition, and not pH, influences lake sediment function. 2022. Ecosphere, 13: e4091.

Bishop CE, Gahm K, Hendry AP, Jones SE, Stange M, Solomon CT. 2022. Benthic-limnetic morphological variation in fishes: Dissolved organic carbon concentration produces unexpected patterns. Ecosphere, 13: e3965.

Vizza C, Jones SE, Hart JA, West WE, Lamberti GA. 2022. Pond methane dynamics, from microbial communities to ecosystem budget, during summer in Alaska. Limnology and Oceanography, 67: 450-467.

Tablot CJ, Bolster D, Medvigy D, Jones SE. 2022. A terrestrial-aquatic model reveals cross-scale interactions regulate lateral dissolvedf organic carbon transport from terrestrial ecosystems. Journal of Geophysical Research: Biogeosciences: e2021JG006604.

Bertolet BL, Koepfli C, Jones SE. 2022. Lake sediment methane responses to organic matter are related to microbial community composition in experimental microcosms. Frontiers in Environmental Science: 312.


Talbot C, Bolster D, Medvigy D, Jones SE. Cross-scale interactions regulate lateral carbon transport from terrestrial ecosystems and its fate across the terrestrial-aquatic continuum. AGU Fall Meeting Abstracts, 2021: EP12B-05.

Olesky IA, Jones SE, Solomon CT. 2021. Hydrologic setting dictates the sensitivity of ecosystem metabolism to climate variability in lakes. Ecosystems: 1-18.

Shoemaker WR, Jones SE, Muscarella ME, Behringer MG, Lehmkuhl BK, Lennon JT. 2021. Microbial population dynamics and evolutionary outcomes under extreme energy limitation. Proceedings of the National Academy of Sciences, 118: e2101691118.

Hanson Z, Zwart JA, Jones SE, Hamlet AF, Bolster D. 2021. Projected regional lake hydrologic characteristics in response to 21st century climate change. Inland Waters, 11: 335-350.

Lahne M, Brecker M, Jones SE, Hyde DR. 2021. The regenerating adult zebrafish retina recapitulates developmental fate specification programs. Frontiers in cell and developmental biology, 8: 617923.

Olesky IA, Olson CR, Jones SE, Solomon CT. 2021. Hydrologic setting affects ecosystem processes. 2021.

Ziegler JP, Jardine SL, Jones SE, van Poorten BT, Janssen MA, Solomon CT. 2021. Investing in the commons: transient welfare creates incentives despite open access. Ecology and Society, 26.

Trudeau A, Dassow CJ, Iwicki CM, Jones SE, Sass GG. 2021. Estimating fishing effort accross the landscape: A spatially extensive approach using models to integrate multiple data sources. Fisheries Research, 233: 105768.


Talbot CJ, Bolster D, Medvigy D, Jones SE. 2020. Interactions between climate and vegetation regulate lateral carbon export from terrestrial ecosystems. AGU Fall Meeting Abstracts, 2020: B053-03.

Armitage DW and Jones SE. 2020. Coexistence barriers confine the poleward reange of a globally distributed plant. Ecology Letters, 23: 1838-1848.

Olson CR, Solomon CT, Jones SE. 2020. Shifting limitation of primary production: experimental support for a new model in lake ecosystems. Ecology Letters, 23: 1800-1808.

Berlot BL, Olsen CR, Szydlowski, Solomon CT, Jones SE. 2020. Methane and primary productivity in lakes: Divergence of temporal and spatial relationships. Journal of Geophysical Research: Biogeosciences, 125: e2020JG005864.

Trentman MT, Tank JL, Jones SE, McMillian SK, Royer TV. 2020. Seasonal evaluation of biotic and abiotic factors suggests phosphorus retention in constructed floodplains in three agricultural streams. Science of the Total Environment, 729: 138744.

Locey  KJ, Muscarella ME, Larsen ML, Bray SR, Jones SE, Lennon JT. 2020. Dormancy dampens the microbial distance-decay relationship. Philosophical Transactions of the Royal Society B, 375: 20190243.

Hararuk O, Jones SE, Solomon CT. 2020. EGU General Assembly Conference Abstracts: 5514.

Dassow C, Ross A, Jensen OP, Sass GG, van Poorten BT, Solomon CT, Jones SE. 2020. Experimental demonstration of catch hyperstability from habitat aggregation, not effort sorting, in a recreational fishery. Candian Journal of Fisheries and Aquatic Sciences, 77: 762-769.


Armitage DW and Jones SE. 2019. How sample heterogeneity can obscure the signal of microbial interactions. The ISME Journal, 13: 2639-2646.

Ziegler JP, Jones SE, Solomon CT. 2019. Local stakeholders understand recreational fisheries as social-ecological systems but do not view governance systems as influential for system dynamics. International Journal of the Commons, 13: 1035-1048.

Bertolet BL, West WE, Armitage DW, Jones SE. 2019. Environmental drivers of methanogen community composition in north temperate lake sediments. Limnology and Oceanography Letters, 4: 164-172.

Zwart JA, Hanson ZJ, Read JS, Fienen MN, Hamlet AF, Bolster D, Jones SE. 2019. Cross-scale interactions dictate regional lake carbon flux and productivity response to future climate. Geophysical Research Letters, 46: 8840-8851.

Armitage DW and Jones SE. 2019. Negative frequency-dependent growth underlies the stable coexistence of two cosmopolitan aquatic plants. Ecology, 100: e02657. PDF

Zwart JA, Hararuk O, Prairie YT, Jones SE, Solomon CT. 2019. Improving estimates of lake carbon pools and fluxes using data assimilation. Limnology and Oceanography Methods, 17: 97-111. PDF

Hart JA, Vizza C, West WE, Jones SE, Lamberti GA. 2019. Methane cycling contributes to distinct patterns in carbon stable isotopes of wetland detritus. Wetlands, 39: 361-370. PDF

Ziegler J, Dassow C, Jones SE, Ross A, Solomon CT. 2019. Coarse woody habitat does not predict largemouth bass young of year mortality during the open water season. Canadian Journal of Fisheries and Aquatic Sciences, 76: 998-1005. PDF


Koizumi S, Craig N, Zwart JA, Kelly PT, Ziegler JP, Weidel BC, Jones SE, Solomon CT. 2018. Experimental whole-lake dissolved organic carbon increase alters fish diet and density but not growth or productivity. Canadian Journal of Fisheries and Aquatic Sciences, 75: 1859-1867. PDF

Hanson Z, Zwart JA, Vanderwall J, Solomon C, Jones SE, Hamlet A, Bolster D. 2018. Integrated, regional-scale hydrologic modeling of inland lakes. JAWRA, 54: 1302-1324. PDF

Kelly PT, Zwart JA, Solomon CT, Jones SE. 2018. A framework for understanding variation in pelagic gross primary production of lake ecosystems. Ecosystems, 21: 1364-1376. PDF

Zwart JA, Hanson ZJ, Vanderwall J, Bolster D, Hamlet A, Jones SE. 2018. Spatially-explicit, regional-scale simulation of lake carbon fluxes. Global Biogeochemical Cycles, 32: 1276-1293. PDF

Hall EK, Bernhardt ES, Bier RL, Bradford MA, Boot CM, Cotner JB, del Giorgio PA, Evans SE, Graham EB, Jones SE, Lennon JT, Locey KJ, Nemergut D, Osborne BB, Rocca JD, Schimel JP, Waldrop MP. Wallenstein MD. 2018. Understanding how microbiomes influence the systems they inhabit. Nature Microbiology, 3: 977-982. PDF

Jones SE, Zwart JA, Kelly PT, Solomon CT. 2018. Hydrologic context constrains lake heterotrophy and terrestrial carbon fate. Limnology and Oceanography Letters, 3: 256-264. PDF

Vizza C, Pechal JL, Benbow ME, Lang JM, Chaloner DT, Jones SE, Lambert GA. 2018. Nitrate amendment reduces biofilm biomass and shifts microbial communities in remote, oligotrophic ponds. Freshwater Science, 37: 251-263. PDF

Hararuk S, Zwart JA, Jones SE, Praire YT, Solomon, CT. 2018. Importance of physical and climated controls on lake carbon cycling revealed through data-model fusion. JGR - Biogeosciences, 123: 1130-1142. PDF

Maranger R, Jones SE, Cotner JB. 2018. Stoichiometry of major biogeochemcial cycles through the freshwater pipe. Limnology and Oceanography Letters, 3: 89-101. PDF

Ryan SF, Deines JM, Scriber JM, Pfrender ME, Jones SE, Emrich SJ, Hellman JJ. 2018. Climate-mediated hybrid zone movement revealed with genomics, museum collection, and simulation modeling. PNAS, 115: E2284-E2291. PDF


Vizza C, Zwart JA, Tiegs S, Jones SE, Lamberti G. 2017. Landscape patterns shape wetland pond ecosystem function from glacial headwaters to ocean. Limnology and Oceanography, 62, S207-S221. PDF

Kelly PT, Weidel BC, Paufve MR, O'Malley BP, Watkins JM, Rudstam LG, and Jones SE. 2017. Concentration and biochemical gradients of seston in Lake Ontario. Journal of Great Lakes Research, 43: 795-803. PDF

Craig N, Jones SE, Weidel BC, Solomon CT. 2017. Life history constraints explain negative relationship between fish productivity and dissolved organic carbon in lakes. Ecology and Evolution, 7: 6201-6209. PDF

Zwart JA, Sebestyen S, Solomon CT, Jones SE. 2017. The influence of hydrologic residence time on lake carbon cycling dynamics following extreme precipitation events. Ecosystems, 20: 1000-1014. PDF

Barberan A, Caceres Velazquez H, Jones SE, Fierer N. 2017. Hiding in plain sight: Mining bacterial species records for phenotypic trait information. mSphere, 2: e00237-17. PDF

Crawford JT, Loken LC, West WE, Crary B, Spawn SA, Gubbins N, Jones SE, Striegl RG, Stanley EH. 2017. Spatial heterogeneity of within-stream methane concentrations. JGR-Biogeosciences, 122: 1036-1048.  PDF

Weidel BC, Baglini K, Jones SE, Kelly PT, Solomon CT, Zwart JA. Light climate and dissolved organic carbon concentration influence species-specific changes in fish zooplanktivory. Inland Waters, 7: 210-217.  PDF

Jones SE. 2017. The University of Notre Dame Environmental Research Center (UNDERC): Sixty-five years of whole-ecosystem manipulations and counting. ASLO Bulletin, 26: 38-40. PDF

Tanentzap AJ, Kielstra BW, Wilkinson GM, Berggren M, Craig N, Grey J, Gunn JM, Jones SE, Karlsson J, Solomon CT, del Giorgio PA, Ziegler SE, Pace ML. 2017. Terrestrial support of lake food webs: synthesis reveals controls over cross-ecosystem resource use. Science Advances, 3: 31601765. PDF

Vizza C, West WE, Jones SE, Hart J, Lamberti G. 2017. Regulators of coastal wetland methane production and responses to simulated global change. Biogeosciences, 14: 431-446. PDF

Ziegler JP, Golebie EJ, Jones SE, Weidel BC, Solomon CT. 2017. Lakeshore development determines stocking and economic outcomes in inland recreational fisheries. Ecological Applications, 27: 56-65. PDF


West WE, Creamer KP, Jones SE. 2016. Productivity and depth regulate lake contributions to atmospheric methane. Limnology and Oceanography, 61: S51-S61. PDF

Muscarella ME, Jones SE, Lennon JT. 2016. Species sorting along  a subsidy gradient alters community stability. Ecology, 97: 2034-2043. PDF

Kelly PT, Craig N, Solomon CT, Weidel BC, Zwart JA, Jones SE. 2016. Experimental whole-lake increase of dissolved organic carbon concentration produces unexpected increase in zooplankton biomass and production. Global Change Biology, 22: 2766-2775. PDF

Zwart JA, Craig N, Kelly PT, Solomon CT, Weidel BC, Jones SE. 2016. Metabolic and physiochemical responses to a whole-lake experimental increase in dissolved organic carbon in a north-temperate lake. Limnology and Oceanography, 61: 723-734. PDF

Yoo B, Jing B, Jones SE, Lamberti GA, Zhu Y, Shah JK, Maginn EJ. 2016. Molecular mechanisms of ionic liquid cytotoxicity probed by an integrated experimental and computational approach. Scientific Reports, 6: 19889. PDF


Martiny JBH, Jones SE, Lennon JT, Martiny AC. 2015. Microbiomes in light of traits: a phylogenetic perspective. Science, 350: aac9323. PDF

Craig N, Jones SE, Weidel BC, Solomon CT. 2015. Habitat, not resource availability, limits consumer production in lake ecosystems. Limnology and Oceanography, 60: 2079-2089. PDF

West WE, McCarthy SM, Jones SE. 2015. Phytoplankton lipid content influences freshwater lake methanogenesis. Freshwater Biology, 60: 2261-2269. PDF

Livermore JA and Jones SE. 2015. Local-global overlap in diversity informs mechanisms of bacterial biogeography. ISME Journal, 9: 2413-2422. PDF

Leff JW, Jones SE, Prober SM, Barberan A, Borer ET, Firn JL, Harpole WS, Hobbie SE, Hofmockel KS, Knops JMH, McCulley RL, La Pierre K, Risch AC, Seabloom EW, Schuetz MC, Steenbock C, Stevens CJ, Fierer N. 2015. Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. PNAS, 112: 10967-10972. PDF

Zwart JA, Solomon CT, Jones SE. 2015. Phytoplankton traits predict ecosystem function in a global set of lakes. Ecology, 96: 2257-2264. PDF

Jones SE and Lennon JT. 2015. A test of the subsidy-stability hypothesis: the effects of terrestrial carobn in aquatic ecosystems. Ecology, 96: 1550-1560. PDF

Docherty KM, Aiello SW, Buehler BK, Jones SE, Szymczyna BR, Walker KA. 2015. Ionic liquid biodegradability depends on specific wastewater microbial consortia. Chemosphere, 136: 160-166. PDF

Solomon CT, Jones SE, Weidel BC, Buffam I, Fork ML, Karlsson J, Larsen S, Lennon JT, Read JS, Sadro S, Saros JE. 2015. Ecosystem consequences of changing inputs of terrestrial dissolved organic matter to lakes: current knowledge and future challenges. Ecosystems, 18: 376-389. PDF

Aanderud ZT, Jones SE, Fierer N, Lennon JT. 2015. Resuscitation of the rare biosphere contributes to pulses of ecosystem activity. Frontiers in Microbiology, 6: 24. PDF


Godwin SC, Jones SE, Weidel BC, Solomon CT. 2014. Dissolved organic carbon concentration controls benthic primary production: Results from in situ chambers in north-temperate lakes. Limnology and Oceanography, 59: 2112-2120. PDF

Kelly PT, Solomon CT, Weidel BC, Jones SE. 2014. Terrestrial carbon is a resource, but not a subsidy, for lake zooplankton. Ecology, 95: 1236-1242. PDF

Shade A, Jones SE, Caporaso JG, Handelsman J, Knight R, Fierer N, Gilbert JA. 2014. Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity. mBio, 5: e01371-14. PDF

Turner CR, Barnes MA, Xu CCY, Jones SE, Jerde CL, Lodge DM. 2014. Particle size distribution and optimal capture of aqueous macrobial eDNA. Methods in Ecology and Evolution, 5: 676-684. PDF

Zhang W, Zeng E, Liu D, Jones SE, Emrich SJ. 2014. Mapping genomic features to functional traits through microbial whole genome sequences. International Journal of Bioinformatics Research and Applications, 10: 461-478. PDF

Livermore JA, Emrich SE, Tan J, Jones SE. 2014. Freshwater bacterial lifestyles inferred from comparative genomics. Environmental Microbiology, 16: 746-758. PDF


Lennon JT, Hamilton SK, Muscarella ME, Grandy AS, Wickings K, Jones SE. 2013. A source of terrestrial organic carbon to investigate the browning of aquatic ecosystems.  PLoS ONE, 8: e75771. PDF

Aanderud ZA, Jones SE, Schoolmaster DR, Fierer N, Lennon JT. 2013. Sensitivity of soil respiration and microbial communities to altered snowfall.  Soil Biology & Biochemistry, 57: 217-227. PDF


Jones SE, Cadkin TA, Newton RJ, McMahon KD. 2012. Scales of variability in aquatic bacterial communities: a tale of two lakes. Frontiers in Aquatic Microbiology, 3: 318. PDF

Burgin AJ, Hamilton, SK, Jones SE, Lennon JT. 2012. Denitrification by sulfur-oxidizing bacteria in a eutrophic lake.  Aquatic Microbial Ecology, 66: 283-293. PDF

Jones SE, Solomon CT, Weidel BC. 2012. Subsidy or subtraction: How do terrestrial inputs influence consumer production in lakes? Freshwater Reviews, 5: 37-49. PDF

West WE, Coloso JJ, Jones SE. 2012. Effects of algal and terrestrial carbon on methane production rates and methanogen community structure in a temperate lake sediment. Freshwater Biology, 57: 949-955. PDF

Jennings E, Jones SE, Arvola L, Staehr PA, Gaiser E, Jones ID, Weathers KC, Weyhenmeyer GA, Chiu CY. 2012. Effects of weather-related episodic events in lakes: an analysis based on high-frequency data. Freshwater Biology, 57: 589-601. PDF


Newton RJ, Jones SE, Eiler A, McMahon KD, Bertilsson. 2011. A guide to the natural history of freshwater lake bacteria. Microbiology and Molecular Biology Reviews, 75: 14-49. PDF

Lennon JT and Jones SE. 2011. Microbial seed banks: the ecological and evolutionary implications of dormancy. Nature Reviews Microbiology, 9: 119-130.  PDF


Ball BA, Kominoski JS, Adams HE, Jones SE, Kane ES, Loecke TD, Mahaney WM, Martina JP, Prather CM, Robinson TMP, Solomon CT. 2010. Direct and terrestrial vegetation-mediated effects of  environmental change on aquatic ecosystem processes. BioScience, 60: 590-601.  PDF

Jones SE and Lennon JT. 2010. Dormancy contributes to the maintenance of microbial diversity. PNAS, 107: 5881-5886. PDF


Jones SE and Lennon JT. 2009. Evidence for limited microbial transfer of methane in planktonic food webs.  Aquatic Microbial Ecology, 58: 45-53.  PDF

Jones SE, Newton RJ, McMahon KD. 2009. Evidence for structuring of bacterial community composition by organic carbon source in temperate lakes. Environmental Microbiology, 11: 2463-2472.  PDF

Rusak JA, Jones SE, Kent AD, Shade A, McMahon KD. 2009. Spatial synchrony in microbial community dynamics: testing among-year and lake patterns. Verhandlungen Internationale Vereinigung fur Theoretische und Angewandte Limnologie, 30: 936-940.  PDF

Jones SE and McMahon KD. 2009. Species-sorting may explain an apparent minimal effect of immigration on freshwater bacterial communities. Environmental Microbiology, 11: 905-913.  PDF

Jones SE, Kratz TK, Chiu CY, McMahon KD. 2009. Typhoon disturbance patterns drive annual carbon dioxide flux from a sub-tropical, humic lake. Global Change Biology, 15: 243-254.  PDF


Shade A, Jones SE, McMahon KD. 2008. Habitat heterogeneity as a driver of aquatic bacterial communities. Environmental Microbiology, 10: 1057-1067.  PDF

Jones SE, Newton RJ, McMahon KD. 2008. Potential for atmospheric deposition of bacteria to influence bacterioplankton communities. FEMS Microbiology Ecology, 64: 388-394.  PDF

Jones SE*, Chiu CY*, Kratz TK, Wu JT, Shade A, McMahon KD. 2008. Typhoons cause predictable change in freshwater bacterial communities. Limnology and Oceanography, 53: 1319-1326.  PDF


Newton RJ, Jones SE, Helmus MR, McMahon KD. 2007. The phylogenetic ecology of the freshwater acI lineage. Applied and Environmental Microbiology, 73: 7169-7176.  PDF

Shade A, Kent AD, Jones SE, Newton RJ, Triplett EW, McMahon KD. 2007. Interannual dynamics and phenology of bacterial communities in a eutrophic lake. Limnology and Oceanography, 52: 487-494. PDF

Jones SE, Shade A, McMahon KD, Kent AD. 2007. Comparison of primer sets for use in automated ribosomal intergenic spacer analysis (ARISA) of aquatic bacterial communities: an ecological perspective. Applied and Environmental Microbiology, 73: 659-662.  PDF


Balser TC, McMahon KD, Bart D, Bronson D, Coyle DR, Craig N, Flores-Mangual ML, Forshay K, Jones SE, Kent AD, Shade A. 2006. Bridging the gap between micro- and macro-scale perspectives on the role of microbial communities in global change ecology. Plant and Soil, 289: 59-70.  PDF


Kent AD, Jones SE, Lauster GH, Graham JM, Newton RJ, McMahon KD. 2005. Experimental manipulations of microbial food web interactions in a humic lake: shifting biological drivers of bacterial community structure. Environmental Microbiology, 8: 1448-1459.  PDF


Kent AD, Jones SE, Yannarell AC, Graham JM, Lauster GH, Kratz TK, Triplett EW. 2004. Annual patterns in bacterioplankton variability in a humic lake. Microbial Ecology, 48: 550-560.  PDF