Publications contributed to the program of the Institute of Ecosystem Studies

Books

Canham, C. D., J. J. Cole, and W. K. Lauenroth (eds.).   2003.   Models in Ecosystem Science.   Princeton University Press, Princeton, New Jersey.   456 pp.

Kemp, P. F., B. F. Sherr, E. B. Sherr, and J. J. Cole (eds.).   1993.   Handbook of Methods in Aquatic Microbial Ecology.   Lewis Publishers.   777 pp.

Cole, J., G. Lovett, and S. Findlay (eds.).   1991.   Comparative Analyses of Ecosystems: Patterns, Mechanisms and Theories.   Springer-Verlag New York, Inc.   375 pp.

Book Review

Cole, J. J.   1993.   [Microbial Production and Consumption of Greenhouse Gases: Methane, Nitrogen Oxides and Halomethanes. J. E. Rogers and W. B. Whitman (eds.). 1991. American Society of Microbiology, Washington, D. C. 198 pp.]   Ecology   74:637-638.

Published Papers

Aneja, V. P., J. Blunden, K. James, W. H. Schlesinger, R. Knighton, W. Gilliam, G. Jennings, D. Niyogi, and S. Cole.   2008.   Ammonia assessment from agriculture: US status and needs.   J. Environ. Qual.   37(2):515-520.

Bastviken, D., J.J. Cole, M.L. Pace, and M.C.V. de Bogert.   2008.   Fates of methane from different lake habitats: Connecting whole-lake budgets and CH4 emissions.   Journal of Geophysical Research-Biogeosciences   113 (G2): Art. No. G02024

Carpenter, S. R., W. A. Brock, J. J. Cole, J. F. Kitchell, and M. L. Pace.   2008.   Leading indicators of trophic cascades.   Ecol. Lett.   11:128-138.

Coloso, J.J., J.J. Cole, P.C. Hanson, and M.L. Pace.   2008.   Depth-integrated, continuous estimates of metabolism in a clear-water lake.   Canadian Journal of Fisheries and Aquatic Sciences   65 (4): 712-722

Downing, J. A., J. J. Cole, J. J. Middelburg, R. G. Striegl, C. M. Duarte, P. Kortelainen, Y. T. Prairie, and K. A. Laube.   2008.   Sediment organic carbon burial in agriculturally eutrophic impoundments over the last century.   Global Biogeochem. Cycles.   22(1):GB1018.

Solomon, C. T., S. R. Carpenter, J. J. Cole, and M. L. Pace   2008.   Support of benthic invertebrates by detrital resources and current autochthonous primary production: Results from a whole-lake C-13 addition.   Freshwat. Biol.   53(1):42-54.

Strayer, D. L., M. L. Pace, N. F. Caraco, J. J. Cole, and S.E.G. Findlay.   2008.   Hydrology and grazing jointly control a large-river food web. Ecology   89(1):12-18.

Bade, D. L., S. R. Carpenter, J. J. Cole, M. L. Pace, E. S. Kritzberg, M. C. Van de Bogert, R. M. Cory, and D. M. McKnight.   2007.   Sources and fates of dissolved organic carbon in lakes as determined by whole-lake carbon isotope additions.   Biogeochemistry   84:115-129.

Baines, S. B., N. S. Fisher, and J. J. Cole.   2007.   Dissolved organic matter and persistence of the invasive zebra mussel (Dreissena polymorpha) under low food conditions. Limnol. Oceanogr.   52:70-78.

Cole, J. J., Y. T. Prairie, N. F. Caraco, W. H. McDowell, L. J. Tranvik, R. G. Striegl, C. M. Duarte, P. Kortelainen, J. A. Downing, J. Middleburg, and J. Melack.   2007.   Plumbing the global carbon cycle: Integrating inland waters into the terrestrial carbon budget. Ecosystems   10:171-184.

Dodds, W. T., and J. J. Cole.   2007.   Expanding the concept of trophic state in aquatic ecosystems: It's not just the autotrophs. Aquat. Sci.   69:427-439.

Fernald, S. H., N. F. Caraco, and J. J. Cole.   2007.   Changes in cyanobacterial dominance following the invasion of the zebra mussel Dreissena polymorpha: Long-term results from the Hudson River estuary. Estuaries and Coasts   30(1):163-170.

Gould, G. G., C. G. Jones, P. Rifleman, A. Perez, and J. S. Coleman.   2007.   Variation in Eastern Cottonwood (Populus deltoides Bartr.) phloem sap content and toughness due to leaf development may affect feeding site selection behavior of the aphid, Chaitophorous populicola Thomas (Homoptera: Aphididae). Environ. Entomol.   36(5):1212-1225.

Pace, M. L., S. R. Carpenter, J. J. Cole, J. J. Coloso, J. F. Kitchell, J. R. Hodgson, J. J. Middelburg, N. D. Preston, C. T. Solomon, and B. Weidel.   2007.   Does terrestrial carbon subsidize plankton in a clear-water lake?   Limnol. Oceanogr.   52(5):2177-2189.

Sobek, S., L. J. Tranvik, Y. T. Prairie, P. Kortelainen, and J. J. Cole.   2007.   Patterns and regulation of dissolved organic carbon: An analysis of 7,500 widely distributed lakes. Limnol. Oceanogr.   52:1208-1219.

Van de Bogert, M. C., S. R. Carpenter, J. J. Cole, and M. L. Pace.   2007.   Assessing pelagic and benthic metabolism using free water measurements. Limnol. Oceanogr. Methods   5:145-155.

Weidel, B. C., T. Ushikubo, S. R. Carpenter, N. T. Kita, J. J. Cole, J. F. Kitchell, M. L. Pace, and J. W. Valley.   2007.   Diary of a bluegill (Lepomis macrochirus): Daily delta C-13 and delta O-18 records in otoliths by ion microprobe.   Can. J. Fish. Aquat. Sci.   64(12):1641-1645.

Bade, D. L., and J. J. Cole.   2006.   Impact of chemically enhanced diffusion on dissolved inorganic carbon stable isotopes in a fertilized lake. J. Geophys. Res.   111, C01014.

Bade, D. L., M. L. Pace, J. J. Cole, and S. R. Carpenter.   2006.   Can algal photosynthetic fractionation in lakes be predicted from existing models? Aquat. Sci.   68:142-153

Caraco, N. F., and J. J. Cole.   2006.   Hydrologic control of external carbon loads and primary production in the tidal freshwater Hudson. pp. 63-74. In: J. R. Waldman, K. E. Limburg, and D. L. Strayer (eds.). Hudson River Fishes and their Environment.   American Fisheries Society.  

Caraco, N. F., J. J. Cole, and D. L. Strayer.   2006.   Top down control from the bottom: Regulation of eutrophication in a large river by benthic grazing. Limnol. Oceanogr.   51:664-670.

Caraco, N. F., J. J. Cole, S. E. G. Findlay, and C. Wigand.   2006.   Vascular plants as engineers of oxygen in aquatic systems.   BioScience   56(3):219-225.

Chapin III, F. S., G. M. Woodwell, J. T. Randerson, E. B. Rastetter, G. M. Lovett, … J. J. Cole, M. L. Goulden, J. W. Harden, M. Heimann, R. W. Howarth, P. A. Matson, A. D. McGuire, J. M. Melillo, H. A. Mooney, J. C. Neff, … M. L. Pace, et al.   2006.   Reconciling carbon-cycle concepts, terminology, and methods.   Ecosystems   9:1041-1050.

Cole, J. J., and N. F. Caraco.   2006.   Primary production and its regulation in the tidal-freshwater Hudson River. pp. 107-120. In: J. S. Levinton and J. R. Waldman (eds.). The Hudson River Estuary.   Cambridge University Press, New York.  

Cole, J. J., S. R. Carpenter, M. L. Pace, M. C. Van De Bogert, J. F. Kitchell, and J. R. Hodgson.   2006.   Differential support of lake food webs by three types of terrestrial organic carbon. Ecol. Lett.   9:558-568.

Downing, J. A., Y. T. Prairie, J. J. Cole, C. M. Duarte, L. J. Tranvik, R. G. Striegl, W. H. McDowell, P. Kortelainen, N. F. Caraco, J. M. Melack, and J. Middelburg.   2006.   The global abundance and size distribution of lakes, ponds, and impoundments. Limnol. Oceanogr.   51(5):2388-2397.

Huszar, V. L. M., N. F. Caraco, F. Roland, and J. Cole.   2006.   Nutrient-chlorophyll relationships in tropical-subtropical lakes: Do temperate models fit?   Biogeochemistry   79(1-2):239- 250.

Kritzberg, E. S., J. J. Cole, M. L. Pace, and W. Granéli.   2006.   Bacterial growth on allochthonous carbon in humic and nutrient enriched lakes: Results from whole lake experiments.   Ecosystems   9:489-499.

Lovett, G. M., J. J. Cole, and M. L. Pace.   2006.   Is net ecosystem production equal to ecosystem carbon accumulation? Ecosystems   9:152-155.

Rubbo, M., J. J. Cole, and J. M. Kiesecker..   2006.   Terrestrial subsidies of organic carbon support net ecosystem production in temporary forest ponds: Evidence from an ecosystem experiment. Ecosystems   9:1170-1176.

Baines, S., N. Fisher, and J. J. Cole.   2005.   Uptake of dissolved organic matter (DOM) and its importance to metabolic requirements of the zebra mussel, Dreissena polymorpha. Limnol. Oceanogr.   50:36-47.

Carpenter, S. R. J. J. Cole, M. L. Pace, M. Van de Bogert, D. L. Bade, D. Bastviken, C. M. Gille, J. R. Hodgson, J. F. Kitchell, and E. S. Kritzberg.   2005.   Ecosystem subsidies: Terrestrial support of aquatic food webs from 13C addition to contrasting lakes. Ecology   86:2737-2750.

Cole J. J.   2005.   Communication between terrestrial and marine ecologists: Loud, sometimes abrasive, but healthy and occasionally useful.   Mar. Ecol. Progr. Ser.   304:272-274.

Fahey, T. J., T. G. Siccama, C. T. Driscoll, G. E. Likens, J. Campbell, C. E. Johnson, J. J. Battles, J. D. Aber, J. J. Cole, M. C. Fisk, P. M. Groffman, S. P. Hamburg, R. T. Holmes, P. A. Schwarz, and R. D. Yanai.   2005.   The biogeochemistry of carbon at Hubbard Brook.   Biogeochemistry   75(1):109-176.

Kritzberg, E. S., J. J. Cole, M. L. Pace, and W. Granéli.   2005.   Does autochthonous primary production drive variability in bacterial metabolism and growth efficiency in lakes dominated by terrestrial C inputs? Aquat. Microb. Ecol.   38:103-111.

Maranger, R. J., M. L. Pace, P. A. del Giorgio, N. F. Caraco, and J. J. Cole.   2005.   Longitudinal spatial patterns of bacterial production and respiration in a large river-estuary: Implications for ecosystem carbon consumption. Ecosystems   8(3):318-330.

Sobek, S., L. J. Tranvik , and J. J. Cole.   2005.   Temperature independence of carbon dioxide supersaturation in global lakes.   Global Biogeochem. Cycles   19(2): Art. No. GB2003.

Strayer, D. L., E. A. Blair, N. F. Caraco, J. J. Cole, S. Findlay, W. C. Nieder, and M. L. Pace.   2005.   Interactions between alien species and restoration of large-river ecosystems.   Arch. Hydrobiol. Suppl.   155(1-4):133-145.

Bade, D. L., S. R. Carpenter, J. J. Cole, P. C. Hanson, and R. H. Hesslein.   2004.   Controls of d13C-DIC in lakes: Geochemistry, lake metabolism, and morphometry. Limnol. Oceanogr.   49:1160-1172.

Bastviken, D., J. J. Cole, M. L. Pace, and L. Tranvik.   2004.   Methane emissions from lakes: Dependence of lake characteristics, two regional assessments, and a global estimate. Global Biogeochem. Cycles.   18(4). Art. No. GB 4009.

Caraco, N. F., and J. J. Cole.   2004.   When terrestrial organic matter is sent down the river: Importance of allochthonous C inputs to the metabolism in lakes and rivers. pp. 301-316. In: A. Polis, M. E. Power, and G. Huxell (eds.). Food Webs at the Landscape Level.   University of Chicago Press, Chicago, Illinois.  

Kritzberg, E. S., J. J. Cole, M. L. Pace, W. Granéli, and D. L. Bade.   2004.   Autochthonous and allochthonous carbon sources to bacteria: Results from whole lake 13C addition experiments. Limnol. Oceanogr.   49:588-596.

Pace, M. L., J. J. Cole, S. R. Carpenter, J. F. Kitchell, J. R. Hodgson, M. Van de Bogert, D. L. Bade, E. S. Kritzberg, and D. Bastviken.   2004.   Whole lake carbon-13 additions reveal terrestrial support of aquatic food webs. Nature   427:240-243.

Raymond, P. A., J. E. Bauer, N. F. Caraco, J. J. Cole, B. Longworth, and S. T. Petsch.   2004.   Controls on the variability of organic matter and dissolved inorganic carbon age in Northeast U.S. Rivers.   Mar. Chem.   92(1-4):353-366.

Canham, C. D., J. J. Cole, and W. K. Lauenroth.   2003.   The Role of Modeling in Ecosystem Science. pp 1-12. In: Canham, C. D., J. S. Cole, and W. K. Lauenroth (eds.). Models in Ecosystem Science. Princeton University Press, Princeton, New Jersey.  

Caraco, N. F., and J. J. Cole.   2003.   The importance of organic nitrogen production in aquatic systems: A landscape perspective. pp. 263-283. In: S. E. G. Findlay, and R. L. Sinsabaugh (eds.). Aquatic Ecosystems: Interactivity of Dissolved Organic Matter.   Academic Press/Elsevier Science, San Diego, California.  

Caraco, N. F., J. J. Cole, G. E. Likens, G. M. Lovett, and K. C. Weathers.   2003.   Variation in NO3 export from flowing waters of vastly different sizes: Does one model fit all? Ecosystems   6(4):344-352.

Harris, G. P., S. W. Bigelow, J. J. Cole, H. Cyr, L. L. Janus, A. P. Kinzig, J. F. Kitchell, G. E. Likens, K. H. Rechow, D. Scavia, D. Soto, L. M. Talbot, and P. H. Templer.   2003.   The role of models in ecosystem management. pp. 299-307. In: C. D. Canham, J. J. Cole, and W. K. Lauenroth (eds.). Models in Ecosystem Science.   Princeton University Press, Princeton, New Jersey.  

Houser, J. N., D. L. Bade, J. J. Cole, and M. L. Pace.   2003.   The dual influences of dissolved organic carbon on hypolimnetic metabolism: organic substrate and photosynthetic inhibition. Biogeochemistry   64:247-269.

Marino, R., R. W. Howarth, F. Chan, J. J. Cole, and G. E. Likens.   2003.   Sulfate inhibition of molybdenum-dependent nitrogen fixation by planktonic cyanobacteria under seawater conditions: A non-reversible effect.   Hydrobiologia   500:277-293.

Raymond, P. A., and J. J. Cole.   2003.   Increase in the export of alkalinity from North America's largest river. Science   301:88-91.

Raymond, P. A., and J. J. Cole.   2003.   Increased alkalinity in the Mississippi, a response to Jones et al.   Science   302:985-987.

Raymond, P. A., and J. J. Cole.   2003.   Alkalinity Export and Carbon Balance, a Response to Lackner.   Science   302:985.

Caraco, N. F., and J. J. Cole.   2002.   Contrasting impacts of a native and alien macrophyte on dissolved oxygen in a large river. Ecol. Appl.   12(5):1496-1509.

Cole, J. J., S. R. Carpenter, J. F. Kitchell, and M. L. Pace.   2002.   Pathways of organic carbon utilization in small lakes: Results from a whole-lake 13C addition and coupled model. Limnol. Oceanogr.   47:1664-1675.

Pace, M. L., and J. J. Cole.   2002.   Synchronous variation of dissolved organic carbon and color in lakes. Limnol. Oceanogr.   47:333-342.

Prairie, Y. T., D. F. Bird, and J. J. Cole.   2002.   The summer metabolic balance in the epilimnion of southeastern Quebec lakes. Limnol. Oceanogr.   47:316:321.

Wait, D. A., J. S. Coleman, and C. G. Jones.   2002.   Chrysomela scripta, Plagiodera versicolora (Coleoptera: Chrysomelidae), and Trichoplusia ni (Lepodoptera: Noctuidae) track specific leaf developmental stages. Environ. Entomol.   31(5):836-843.

Caraco, N. F., and J. J. Cole.   2001.   Human influence on nitrogen export: a comparison of mesic and xeric catchments.   Mar. Freshwat. Res.   52:119-125.

Carpenter, S. R., J. J. Cole, J. R. Hodgson, J. F. Kitchell, M. L. Pace, D. Bade, K. L. Cottingham, T. E. Essington, J. N. Houser, and D. E. Schindler.   2001.   Trophic cascades, nutrients and lake productivity: experimental enrichment of lakes with contrasting food webs. Ecol. Monogr.   71:163-186.

Cole J. J., and N. F. Caraco.   2001.   Carbon in catchments: connecting terrestrial carbon losses with aquatic metabolism. Mar. Freshwat. Res.   52:101-110.

Cole, J. J., and N. F. Caraco.   2001.   Emissions of nitrous oxide (N2O) from a tidal, freshwater river, the Hudson River, New York.   Environ. Sci. Technol.   35:991-996.

Lampman G. G., N. F. Caraco, and J. J. Cole.   2001.   A method for the measurement of particulate C and P on the same filtered sample. Mar. Ecol. Prog. Ser.   217:59-65.

Raymond, P. A., and J. J. Cole.   2001.   Gas exchange in rivers and estuaries: choosing a gas transfer velocity. Estuaries   24:312-317.

Roland, F., and J. J. Cole.   2001.   Prediction of bacterial growth efficiency in a large river ecosystem.   Verh. Int. Ver. Limnol.   27:2846-2847.

Caraco, N. F., J. J. Cole, S. E. G. Findlay, D. T. Fischer, G. G. Lampman, M. L. Pace, and D. L. Strayer.   2000.   Dissolved oxygen declines in the Hudson River associated with the invasion of the zebra mussel (Dreissena polymorpha). Environ. Sci. Technol.   34:1204-1210.

Cole, J. J.   2000.   Microbial carbon cycling in pelagic ecosystems: microbial methods for ecosystem scientists. In: O. E. Sala, R. B. Jackson, H. A. Mooney, and R. W. Howarth (eds.). Methods in Ecosystem Science.   Springer-Verlag New York, Inc.   pp. 138-150.

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. Limnol. Oceanogr.   45:1718-1730.

del Giorgio, P. A., and J. J. Cole.   2000.   Bacterial growth efficiency and energetics. In: D. L. Kirchman (ed.). Microbial Ecology of the Oceans.   Plenum Press.   pp. 289-325.

Houser, J. N., S. R. Carpenter, and J. J. Cole.   2000.   Food web structure and nutrient enrichment: effects on phosphorus retention in whole-lake experiments.   Can. J. Fish. Aquat. Sci.   57:1524-1533.

Lake, P. S., M. A. Palmer, P. Biro, J. Cole, A. Covich, C. Dahm, J. Gibert, W. Goedkoop, K. Martens, and J. Verhoeven.   2000.   Global change and biodiversity of freshwater ecosystems: impacts on linkages between above sediment and sediment biota.   BioScience   50:1099-1107.

Pace, M. L., and J. J. Cole.   2000.   Effects of whole lake manipulations of nutrient loading and food web structure on planktonic respiration.   Can. J. Fish. Aquat. Sci.   57:487-496.

Palmer, M. A., A. P. Covich, S. Lake, P. Biro, J. J. Brooks, J. Cole, C. Dahm, J. Gibert, W. Goedkoop, K. Martens, J. Verhoeven, and W. J. van de Bund.   2000.   Linkages between aquatic sediment biota and life above sediments as potential of biodiversity and ecological processes?   BioScience   50:1062-1075.

Raymond, P. A., J. E. Bauer, and J. J. Cole.   2000.   Atmospheric CO2 evasion, dissolved inorganic carbon production, and net heterotrophy in the York River Estuary.   Limnol. Oceanogr.   45:1707-1717.

Reche, I., M. L. Pace, and J. J. Cole.   2000.   Modeled effects of dissolved organic carbon and solar spectra on photobleaching in lake ecosystems.   Ecosystems   3:419-432.

Caraco, N. F., and J. J. Cole.   1999.   Regional-scale export of C, N, P and sediment: what river data tell us about key controlling variables. In: J. D. Tenhunen and P. Kabat (eds.). Integrating Hydrology, Ecosystem Dynamics and Biogeochemistry in Complex Landscapes.   J. Wiley and Sons, Inc., New York.   pp. 239-253.

Caraco, N. F., and J. J. Cole.   1999.   Human impact on nitrate export: an analysis using major world rivers. Ambio   28(2):167-170.

Carpenter, S. R., J. F. Kitchell, J. J. Cole, and M. L. Pace.   1999.   Predicting responses of chlorophyll and primary production to changes in phosphorus, grazing, and dissolved organic carbon (Reply to comment by Nürnberg).   Limnol. Oceanogr.   44:1179-1182.

Cole J. J.   1999.   Aquatic microbiology for ecosystem scientists: new and recycled paradigms in ecological microbiology. Ecosystems   2(3):215-225.

del Giorgio, P. A., J. J. Cole, N. F. Caraco, and R. H. Peters.   1999.   Linking planktonic biomass structure to plankton metabolism and net gas flux in northern temperate lakes.   Ecology   80(4):1422-1431.

Duarte, C., S. Agusti, P. A. del Giorgio, and J. J. Cole.   1999.   Regional carbon imbalances in the oceans: is the open ocean heterotrophic? [Response : Technical comments] Science   284:1735.

Lampman, G., N. F. Caraco, and J. J. Cole.   1999.   Spatial and temporal patterns of nutrient concentration and export in the tidal Hudson River.   Estuaries   22:285-296.

Pace, M. L., J. J. Cole, S. R. Carpenter, and J. F. Kitchell.   1999.   Trophic cascades revealed in diverse ecosystems. Trends Ecol. Evol.   14:483-488.

Reche, I., M. L. Pace, and J. J. Cole.   1999.   Relationship of trophic and chemical conditions to photobleaching of dissolved organic matter in lake ecosystems. Biogeochemistry   44:259-280.

Roland, F., and J. J. Cole.   1999.   Regulation of bacterial growth efficiency in a large turbid estuary.   Aquat. Microb. Ecol.   20:31-38.

Roland, F., N. F. Caraco, J. J. Cole, and P. A. del Giorgio.   1999.   Rapid and precise determination of dissolved oxygen by spectrophotometry: evaluation of interference from color and turbidity.   Limnol. Oceanogr.   44 (4):1148-1154.

Strayer, D. L., N. F. Caraco, J. J. Cole, S. Findlay, and M. L Pace.   1999.   Transformation of freshwater ecosystems by bivalves: a case study of zebra mussels in the Hudson River. BioScience   49:19-27.

Bastviken, D. T. E., N. F. Caraco, and J. J. Cole.   1998.   Experimental measurements of zebra mussel (Dreissena polymorpha) impacts on phytoplankton community composition. Freshwat. Biol.   39(2):375-386.

Caraco, N. F., G. Lampman, J. J. Cole, K. E. Limburg, M. L. Pace, and D. Fischer.   1998.   Microbial assimilation of DIN in a nitrogen rich estuary: implications for food quality and isotope studies.   Mar. Ecol. Prog. Ser.   167:59-71.

Carpenter, S. R., J. J. Cole, J. F. Kitchell, and M. L. Pace.   1998.   Impact of dissolved organic carbon, phosphorus and grazing on phytoplankton biomass and production in experimental lakes. Limnol. Oceanogr.   43:73-80.

Carpenter, S. R., J. J. Cole, T. E. Essington, J. R. Hodgson, J. N. Houser, J. F. Kitchell, and M. L. Pace.   1998.   Evaluating alternative explanations in ecosystem experiments.   Ecosystems   1(4):335-344.

Cole, J. J., and M. L. Pace.   1998.   Hydrologic variability of small, northern Michigan lakes measured by the addition of tracers.   Ecosystems   1(3):310-320.

Cole, J. J., and N. F. Caraco.   1998.   Atmospheric exchange of carbon dioxide in a low-wind oligotrophic lake measured by the addition of SF6. Limnol. Oceanogr.   43(4):647-656.

del Giorgio, P. A., and J. J. Cole.   1998.   Bacterial growth efficiency in natural aquatic systems.   Ann. Rev. Ecol. Syst.   29:503-541.

Pace, M. L., J. J. Cole, and S. R. Carpenter.   1998.   Trophic cascades and compensation: differential responses of microzooplankton in whole lake experiments.   Ecology   79(1):138-152.

Reche, I., M. L. Pace, and J. J. Cole.   1998.   Interactions of photobleaching and inorganic nutrients in determining bacterial growth on colored dissolved organic carbon.   Microb. Ecol.   36:270-280.

Smith, T. E., R. J. Stevenson, N. F. Caraco, and J. J. Cole.   1998.   Changes in phytoplankton community structure during the zebra mussel (Dreissena polymorpha) invasion of the Hudson River (New York).   J. Plank. Res.   20:1567-1579.

Wait, D. A., C. G. Jones, and J. S. Coleman.   1998.   Effects of nitrogen fertilization on leaf chemistry and beetle feeding are mediated by leaf development.   Oikos   82:502-514.

Caraco, N. F., J. J. Cole, P. A. Raymond, D. L. Strayer, M. L. Pace, S. E. G. Findlay, and D. T. Fischer.   1997.   Zebra mussel invasion in a large, turbid river: phytoplankton response to increased grazing. Ecology   78:588-602.

Cottingham, K. L., S. E. Knight, S. R. Carpenter, J. J. Cole, M. L. Pace, and A. E. Wagner.   1997.   Response of phytoplankton and bacteria to nutrients and zooplankton: a mesocosm experiment.   J. Plank. Res.   19:995-1010.

del Giorgio, P. A., and J. J. Cole.   1997.   Photosynthesis or planktonic respiration [reply to comments of R. J. Geider, 388:132.]   Nature   388:132-133.

del Giorgio, P. A., J. J. Cole, and A. Cimberlis.   1997.   Respiration rates in bacteria exceed phytoplankton production in unproductive aquatic systems. Nature   385:148-151.

Raymond, P. A., N. F. Caraco, and J. J. Cole.   1997.   CO2 concentration and atmospheric flux in the Hudson River. Estuaries   20:381-390.

Schindler, D. E., S. R. Carpenter, J. J. Cole, J. F. Kitchell, and M. L. Pace.   1997.   Influence of food web structure on carbon exchange between lakes and the atmosphere. Science   277:248-251.

Christensen, D. L., S. R. Carpenter, K. L. Cottingham, S. E. Knight, J. P. LeBouton, D. E. Schindler, N. Voichick, J. J. Cole, and M. L. Pace.   1996.   Pelagic responses to changes in dissolved organic carbon following division of a seepage lake.   Limnol. Oceanogr.   41(3):553-559.

Felip, M., M. L. Pace, and J. J. Cole.   1996.   Regulation of planktonic bacterial growth rates: the effects of temperature and resources.   Microb. Ecol.   31:15-28.

Pace, M. L., and J. J. Cole.   1996.   Regulation of bacteria by resources and predation tested in whole-lake experiments.   Limnol. Oceanogr.   41:1448-1460.

Roditi, H. A., N. F. Caraco, J. J. Cole, and D. L. Strayer.   1996.   Filtration of Hudson River water by the zebra mussel (Dreissena polymorpha). Estuaries   19:824-832.

Carpenter, S. R., D. L. Christensen, J. J. Cole, K. L. Cottingham, X. He, J. R. Hodgson, J. F. Kitchell, S. E. Knight, M. L. Pace, D. M. Post, D. E. Schindler, and N. Voichick.   1995.   Biological control of eutrophication in lakes.   Environ. Sci. Technol.   29:784-786.

Cole, J. J., and M. L. Pace.   1995.   Bacterial secondary production in oxic and anoxic freshwaters. Limnol. Oceanogr.   40(6):1019-1027.

Cole, J. J., and M. L. Pace.   1995.   Why measure bacterial production? [reply to comment by Jahnke and Craven]. Limnol. Oceanogr.   40:441-444.

Hartvigsen, G., D. A. Wait, and J. S. Coleman.   1995.   Tri-trophic interactions influenced by resource availability: predator effects on plant performance depend on plant resources.   Oikos   74(3):463-468.

Ochs. C. A., J. J. Cole, and G. E. Likens.   1995.   Population dynamics of bacterioplankton in an oligotrophic lake.   J. Plank. Res.   17(2):365-391.

Oviatt, C., P. Doering, B. Nowicki, L. Reed, J. J. Cole, and J. Frithsen.   1995.   An ecosystem level experiment on nutrient limitation in temperate coastal marine environments.   Mar. Ecol. Prog. Ser.   116:171-179.

Ashizawa, D., and J. J. Cole.   1994.   Long-term temperature trends of the Hudson River: a study of the historical data.   Estuaries   17(18):166-171.

Cole, J. J., N. F. Caraco, G. W. Kling, and T. W. Kratz.   1994.   Carbon dioxide supersaturation in the surface waters of lakes. Science   265:1568-1570.

Jones, C. G., J. S. Coleman, and S. Findlay.   1994.   Effects of ozone on interactions among plants, consumers and decomposers. In: R. G. Alscher, and A. R. Wellburn (eds.). Plant Responses to the Gaseous Environment.   Chapman & Hall, Inc., London.   pp. 339-363.

Pace, M. L., and J. J. Cole.   1994.   Comparative and experimental approaches to top-down and bottom-up regulation of bacteria.   Microb. Ecol.   28:181-193.

Pace, M. L., and J. J. Cole.   1994.   Primary and bacterial production in lakes: are they coupled over depth?   J. Plank. Res.   16:661-672.

Caraco, N. F., J. J. Cole, and G. E. Likens.   1993.   Sulfate control of phosphorus availability in lakes: a test and re-evaluation of Hasler and Einsele's Model.   Hydrobiologia   253:275-280.

Cole, J. J., and N. F. Caraco.   1993.   The microbial food-web of oligotrophic lakes. Chapter 5, In: T. Ford (ed.). Aquatic Microbiology.   Blackwell Scientific Press.   pp. 101-112.

Cole, J. J., B. L. Peierls, N. F. Caraco, and M. L. Pace.   1993.   Nitrogen loading of rivers as a human-driven process. In: M. J. McDonnell and S. T. A. Pickett (eds.). Humans as Components of Ecosystems: The Ecology of Subtle Human Effects and Populated Areas.   Springer-Verlag New York, Inc.   pp. 141-157.

Cole, J. J., J. M. Lane, R. Marino, and R. W. Howarth.   1993.   Molybdenum assimilation by cyanobacteria and phytoplankton in freshwater and salt water. Limnol. Oceanogr.   38(1):25-35.

Cole, J. J., M. L. Pace, N. F. Caraco, and G. S. Steinhart.   1993.   Bacterial biomass and cell size distributions in lakes: more and larger cells in anoxic waters. Limnol. Oceanogr.   38:1627-1632.

Johnson, D. W., S. E. Lindberg, H. Van Miegroet, G. M. Lovett, D. W. Cole, M. J. Mitchell, and D. Binkley.   1993.   Atmospheric deposition, forest nutrient status, and forest decline: implications of the Integrated Forest Study. In: R. F. Huettl and D. Mueller-Dombois (eds.). Forest Decline in the Atlantic and Pacific Regions.   Springer-Verlag, Berlin.   pp. 66-81.

Jones, C. G., R. F. Hopper, J. S. Coleman, and V. A. Krischik.   1993.   Control of systemically induced herbivore resistance by plant vascular architecture.   Oecologia   93:452-456.

Caraco, N. F., J. J. Cole, and G. E. Likens.   1992.   New and recycled primary production in an oligotrophic lake: insights for summer phosphorus dynamics. Limnol. Oceanogr.   37(3):590-602.

Cole, J. J., N. F. Caraco, and B. Peierls.   1992.   Can phytoplankton achieve a positive carbon balance in a turbid river, the Hudson River, New York? Limnol. Oceanogr.   37:1608-1617.

Coleman, J. S., C. G. Jones, and V. A. Krischik.   1992.   Phytocentric and exploiter perspectives of phytopathology.   Adv. Plant Pathol.   8:149-195.

Caraco, N. F., J. J. Cole, and G. E. Likens.   1991.   Phosphorus release from anoxic sediments: lakes that break the rules.   Verh. Int. Ver. Limnol.   24(5):2985-2988.

Caraco, N., J. J. Cole, and G. E. Likens.   1991.   A cross-system study of phosphorus release from lake sediments. In: J. Cole, G. Lovett, and S. Findlay (eds.). Comparative Analyses of Ecosystems: Patterns, Mechanisms and Theories.   Springer-Verlag New York, Inc.   pp. 241-258.

Cole, J. J., N. F. Caraco, and B. Peierls.   1991.   Phytoplankton primary production in the tidal, freshwater Hudson River, New York (USA).   Verh. Int. Ver. Limnol.   24(3):1715-1719.

Coleman, J. S., and C. G. Jones.   1991.   A phytocentric perspective of phytochemical induction by herbivores. In: D. W. Tallamy and M. J. Raupp (eds.). Phytochemical Induction by Herbivores.   J. Wiley and Sons, Inc., New York.   pp. 3-45.

Findlay, S., M. L. Pace, D. Lints, J. J. Cole, N. F. Caraco, and B. Peierls.   1991.   Weak coupling of bacterial and algal production in a heterotrophic ecosystem, the Hudson Estuary. Limnol. Oceanogr.   36:268-278.

Jones, C. G., and J. S. Coleman.   1991.   Plant stress and insect herbivory: toward an integrated perspective. In: H. A. Mooney, W. E. Winner, and E. J. Pell (eds.). Response of Plants to Multiple Stresses.   Academic Press, Inc., San Diego, California.   pp. 249-280.

Peierls, B. L., N. F. Caraco, M. L. Pace, and J. J. Cole.   1991.   Human influence on river nitrogen.   Nature   350:386-387.

Caraco, N. F., J. J. Cole, and G. E. Likens.   1990.   A comparison of phosphorus immobilization in sediments of freshwater and coastal marine systems.   Biogeochemistry   9:277-290.

Caraco, N. F., J. J. Cole, G. E. Likens, and S. S. Nolan.   1990.   Atmospheric inputs of phosphorus to an oligotrophic lake. In: I. G. Poppoff, C. R. Goldman, S. L. Loeb, and L. B. Leopold (eds.).   Proceedings International Mountain Watershed Symposium Subalpine Processes and Water Quality, South Lake Tahoe, California, June 1988.   pp. 361-369.

Cole, J. J., N. F. Caraco, and G. E. Likens.   1990.   Short-range atmospheric transport: a significant source of phosphorus to an oligotrophic lake. Limnol. Oceanogr.   35(6):1230-1237.

Caraco, N. F., J. J. Cole, and G. E. Likens.   1989.   Evidence for sulphate-controlled phosphorus release from sediments of aquatic systems.   Nature   341(6240):316-318.

Caron, D. A., L. P. Madin, and J. J. Cole.   1989.   Composition and degradation of salp fecal pellets: implications for vertical flux in oceanic environments.   J. Mar. Res   47:829-850.

Cole, J. J., N. F. Caraco, D. L. Strayer, C. Ochs, and S. S. Nolan.   1989.   A detailed carbon budget as an ecosystem-level calibration of bacterial respiration in an oligotrophic lake during mid-summer.   Limnol. Oceanogr.   34:286-296.

Jones, C. G., and J. S. Coleman.   1989.   Biochemical indicators of air pollution effects in trees: unambiguous signals based on secondary metabolites and nitrogen in fast-growing species? In: Biologic Markers of Air Pollution Stress and Damage in Forests.   Nat. Res. Counc., National Academy Press, Washington, D. C.   pp. 261-273.

Pace, M. L., and J. J. Cole.   1989.   What questions, systems, or phenomena warrant long-term ecological study? In: G. E. Likens (ed.). Long-Term Studies in Ecology: Approaches and Alternatives.   Springer-Verlag New York, Inc.   pp. 183-185.

Caraco, N. F., J. J. Cole, G. E. Likens, M. D. Mattson, and S. Nolan.   1988.   A very imbalanced nutrient budget for Mirror Lake, New Hampshire, U.S.A.   Verh. Int. Ver. Limnol.   23(1):170-175.

Cole, J. J., S. Findlay, and M. L. Pace.   1988.   Bacterial production in fresh and saltwater ecosystems: a cross-system overview.   Mar. Ecol. Prog. Ser.   43:1-10.

Coleman, J. S., and C. G. Jones.   1988.   Plant stress and insect performance: cottonwood, ozone and a leaf beetle.   Oecologia   76:57-61.

Coleman, J. S., and C. G. Jones.   1988.   Acute ozone stress on eastern cottonwood (Populus deltoides Bartr.) and the pest potential of the aphid, Chaitophorus populicola Thomas (Homoptera: Aphidae).   Environ. Entomol.   17:207-212.

Coleman, J. S., C. G. Jones, and W. H. Smith.   1988.   Interactions between an acute ozone dose, eastern cottonwood, and Marssonina leaf spot: implications for pathogen community dynamics.   Can. J. Bot.   66:863-868.

Howarth, R. W., R. Marino, and J. J. Cole.   1988.   Nitrogen fixation in freshwater, estuarine and marine ecosystems. 2. biogeochemical controls.   Limnol. Oceanogr.   33:688-701.

Howarth, R. W., R. Marino, J. Lane, and J. J. Cole.   1988.   Nitrogen fixation in freshwater, estuarine, and marine ecosystems. 1. Rates and importance.   Limnol. Oceanogr.   33:669-687.

Jones, C. G., and J. S. Coleman.   1988.   Leaf disc size and insect feeding preference: implications for assays and studies on induction of plant defense.   Entomol. Exp. Appl.   47:167-172.

Jones, C. G., and J. S. Coleman.   1988.   Plant stress and insect behavior: cottonwood, ozone and the feeding and oviposition preference of a beetle.   Oecologia   76:51-56.

Cole, J. J., S. Honjo, and J. Erez.   1987.   Particulate flux and benthic decomposition of organic matter at a deep-water site in the Panama Basin.   Nature   327:703-704.

Coleman, J. S., C. G. Jones, and W. H. Smith.   1987.   The effect of ozone on cottonwood-leaf rust interactions: independence of abiotic stress, genotype and leaf ontogeny.   Can. J. Bot.   65:949-953.

Johnson, D. W., S. E. Lindberg, E. A. Bondietti, D. W. Cole, G. M. Lovett, M. J. Mitchell, L. H. Ragsdale, and L. F. Pitelka.   1987.   The integrated forest study on effects of atmospheric deposition: a status report.   Air Pollution Control Association Conference Proceedings, APCA, Pittsburgh, Pennsylvania.   Paper 87-34.

McDowell, W. H., J. J. Cole, and C. T. Driscoll.   1987.   Simplified version of the ampoule-persulfate method for the determination of dissolved organic carbon.   Can. J. Fish. Aquat. Sci.   44(1):214-218.

Alldredge, A., J. J. Cole, and D. A. Caron.   1986.   Production of heterotrophic bacteria on amorphous macroaggregates (marine snow) in neritic and open ocean waters.   Limnol. Oceanogr.   31:68-76.

Cole, J. J., and C. Lee.   1986.   Rapid microbial metabolism of betaalanine, a non-protein amino acid, in brackish and oceanic waters.   Biogeochemistry   2:299-312.

Cole, J. J., R. W. Howarth, S. S. Nolan, and R. Marino.   1986.   Sulfate inhibition of molybdate assimilation by planktonic algae and bacteria: implications for the aquatic nitrogen cycle.   Biogeochemistry   2:179-196.

Coleman, J. S.   1986.   Leaf development and leaf stress: increased susceptibility associated with sink-source transition.   Tree Physiol.   2:289-299.

Cole, J. J.   1985.   Decomposition. In: G. E. Likens (ed.). An Ecosystem Approach to Aquatic Ecology: Mirror Lake and Its Environment.   Springer-Verlag New York, Inc.   pp. 302-310.

Cole, J. J., S. Honjo, and N. Caraco.   1985.   Seasonal variation in the flux of algal pigments to a deep-water site in the Panama Basin.   Hydrobiologia   122:193-197.

Coleman, J. S., C. W. Murdoch, R. J. Campana, and W. H. Smith.   1985.   Investigations on the decay resistance of elm wetwood.   Can. J. Plant Pathol.   7:151-154.

Howarth, R. W., and J. J. Cole.   1985.   Molybdenum availability, nitrogen limitation and phytoplankton growth in natural waters.   Science   229:653-655.

Likens, G. E., B. J. Peterson, and J. J. Cole.   1985.   Species composition, distribution, population, biomass and behavior: periphyton. In: G. E. Likens (ed.). An Ecosystem Approach to Aquatic Ecology: Mirror Lake and Its Environment.   Springer-Verlag New York, Inc.   pp. 175-177.

Walter, R. A., R. E. Moeller, D. L. Strayer, and J. J. Cole.   1985.   The profundal region. In: G. E. Likens (ed.). An Ecosystem Approach to Aquatic Ecology: Mirror Lake and Its Environment.   Springer-Verlag New York, Inc.   pp. 317-322.

Cole, J. J., G. E. Likens, and J. E. Hobbie.   1984.   Decomposition of planktonic algae in an oligotrophic lake.   Oikos   42:257-266.

Cole, J. J., W. H. McDowell, and G. E. Likens.   1984.   Sources and molecular weight of "dissolved" organic carbon in an oligotrophic lake.   Oikos   42:1-9.

Hobbie, J. E., and J. J. Cole.   1984.   Response of a detrital foodweb to eutrophication.   Bull. Mar. Sci.   35:357-363.

Hobbie, J. E., J. J. Cole, J. Dungan, R. A. Houghton, and B. Peterson.   1984.   Role of biota in global CO2 balance: the controversy.   BioScience   34:492-498.

Miscellaneous Publications

Quillen, L. M and J. J. Cole.   2004.   November 28. Life depends on freshwater.   Poughkeepsie Journal   Sect. B:7-8.

Wurtsbaugh, W., J. Cole, D. McKnight, P. Bresonik, S. MacIntyre, and K. Potter (eds.).   2003.   Emerging Research Questions for Limnology – The Study of Inland Waters.   American Society of Limnology and Oceanography.   48 pp.

Cole, J. J., and N. F. Caraco.   1993.   Nitrogen pollution of coastal waters: the role of anthropogenically derived atmospheric deposition.   Report to the New York State Electric Power Pool [IES, Millbrook, New York].   40 pp.

Likens, G. E., J. J. Cole, J. Kolasa, J. B. McAninch, M. J. McDonnell, G. G. Parker, and D. L. Strayer.   1987.   Status and future of ecosystem science.   Occasional Publication of the Institute of Ecosystem Studies, Number 3, Millbrook, New York.   23 pp.