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Agnew, A. M., D. H. Shull, and R. N. Buchsbaum. 2003. Growth of a salt marsh invertebrate on several species of marsh grass detritus. Biological Bulletin 205:238-239

Agrawal, A. 2001. Uncertainty analysis of land-use change modeling in GIS. MS Thesis. Clark University, Worcester.

Aldrich, S. 2002. Water quality as a function of land use. Honors, BS Thesis. Clark University, Worcester.

Alexander, R. B., J. F. Bohlke, E. W. Boyer, M. David, J. W. Harvey, P. J. Mulholland, S. P. Seitzinger, C. R. Tobias, C. Tonitto, and W. M. Wollheim. 2009. Dynamic modeling of nitrogen losses in river networks unravels the coupled effects of hydrological and biogeochemical processes. Biogeochemistry 93:91-116 DOI 10.1007/s10533-008-9274-8.

Allee, R. J., M. Dethier, D. Brown, L. Deegan, R. G. Ford, T. F. Hourigan, J. Maragos, C. Schoch, K. Sealey, R. Twilley, M. P. Weinstein, and M. Yoklavich. 2000. Marine and Estuarine Ecosystem and Habitat Classification. NOAA Technical Memorandum NMFS-FSPO-43, US Department of Commerce, National Oceanic and Atmospheric Administration, National marine Fisheries Service.

Bahr, M., B. C. Crump, V. Klepac-Ceraj, A. P. Teske, M. L. Sogin, and J. E. Hobbie. 2005. Molecular characterization of sulfate-reducing bacteria in a New England salt marsh. Environmental Microbiology 7:1175-1185 10.1111/j.1462-2920.2005.00796.x.

Battin, T. J., L. Kaplan, S. Findlay, C. Hopkinson, E. Marti, A. Packman, J. D. Newbold, and F. Sabater. 2008. Biophysical controls on organic carbon fluxes in fluvial networks. Nature Geoscience 1:95-100 doi: 10.1038/ngeo101.

Bernhard, A., T. M. Donn, A. E. Giblin, and D. A. Stahl. 2005. Loss of Diversity of Ammonia-Oxidizing Bacteria Correlates with Increasing Salinity in an Estuary System. Environmental Microbiology 7:1289-1297 10.1111/j.1462-2920.2005.00808.x.

Bernhard, A., Z. C. Landry, A. Blevins, J. R. de al Torre, A. E. Giblin, and D. A. Stahl. 2009 (accepted). Abundance of ammonia-oxidizing Archaea and Bacteria along an estuarine salinity gradient in relationship to potential nitrification rates. Applied and Environmental Microbiology

Bernhard, A. E., J. Tucker, A. E. Giblin, and D. A. Stahl. 2007. Functionally distinct communities of ammonia-oxidizing bacteria along an estuarine salinity gradient. Environmental Microbiology 9:1439-1447 10.1111/j.1462-2920.2007.01260.x.

Bernot, M. J., R. J. Bernot, and J. T. Morris. 2009. Nutrient cycling relative to d15N and d13C natural abundance in a coastal wetland with long-term nutrient additions. Aquatic Ecology doi:10.1007/s10452-008-9221-8.

Bouillon, S., and H. T. S. Boschker. 2006. Bacterial carbon sources in coastal sediments: a cross-system analysis based on stable isotope data of biomarkers. Biogeosciences 3:175-185

Bowen, J. L., B. C. Crump, L. A. Deegan, and J. E. Hobbie. 2009. Increased supply of ambient nitrogen has minimal effect on salt marsh bacterial production. Limnology and Oceanography 54:713 - 722

Bowen, J. L., B. C. Crump, L. A. Deegan, and J. E. Hobbie. 2009. Salt marsh sediment bacteria: their distribution and response to external nutrient inputs. The ISME Journal 3:924 - 934 doi:10.1038/ismej.2009.44.

Briggs, M. A., M. N. Gooseff, C. D. Arp, and M. A. Baker. 2009. A method for estimating surface transient storage parameters for streams with concurrent hyporheic storage. Water Resources Research 45 doi:10.1029/2008WR006959.

Briggs, M. A., M. N. Gooseff, B. J. Peterson, K. Morkeski, W. M. Wollheim, and C. S. Hopkinson. 2009 (in press). Surface and hyporheic transient storage dynamics throughout a coastal stream network. Water Resources Research

Broo, S. 2009. Sensitivity Analysis for Scenarios of Water Withdrawal in Massachusetts. MS Thesis. Clark University, Worcester, MA.

Buchsbaum, R. 2000. A Symposium Report: Marine Monitoring in Massachusetts - Water quality monitoring and related activities at Plum Island Sound. Massachusetts Office of Coastal Zone Managment, Boston, MA.

Buchsbaum, R. 2009. Striped bass: the coastal connection. Pages 9-11 in Sanctuary.

Buchsbaum, R., E. H. Catena, and M. J. James-Pirri. 2006. Changes in salt marsh vegetation, Phragmites australis, and nekton in response to increased tidal flushing in a New England salt marsh. Wetlands 26:544-557

Buchsbaum, R., A. Cooper, and J. LeBlanc. 1998. The Plum Island Sound/River ecosystem: Current status and future management. Plum Island Sound Minibay Project, Massachusetts Bays Program.

Buchsbaum, R., A. Cooper, and J. LeBlanc. 1999. Conserving the Plum Island Sound/Rivers Ecosystem - A research report and management plan. Produced for the Massachusetts Bays Program and the Towns of Ipswich, Rowley and Newbury by Massachusetts Audubon: North Shore Conservation Advocacy.

Buchsbaum, R., L. Deegan, and R. Garritt. 2002. Changes in the fish comunity of Plum Island Sound from 1965 through 1994. in R. Buchsbaum, T. Purinton, and B. Magnusson, editors. The marine resources of the Parker River-Plum Island Sound estuary: An update after 30 years. MCZM publications.

Buchsbaum, R., and J. C. Powell. 2008. Symposium Review: Long term shifts in faunal assemblages in North American estuaries: A review of a workshop held at the biennial meeting of the Coastal and Estuarine Research Federation (CERF), November 2007, Providence, Rhode Island. Reviews in Fisheries Biology and Fisheries 18:447-450 DOI 10.1007/s11160-008-9086-x.

Buchsbaum, R., T. Purinton, and B. Magnusson. 2002. The marine resources of the Parker River-Plum Island Sound estuary: An update after 30 years. Massachusetts Office of Coastal Zone Management, Massachusetts Executive Office of Environmental Affairs, Boston, MA.

Buchsbaum, R. N., L. A. Deegan, J. Horowitz, R. H. Garritt, J. P. Ludlam, and D. H. Shull. 2009. Effects of regular salt marsh haying on marsh plants, algae, invertebrates and birds at Plum Island Sound, Massachusetts. Wetlands Ecology and Management 17:469-487 DOI 10.1007/s11273-008-9125-3.

Buchsbaum, R. N., and C. A. Wigand. 2010 (in press). Chapter 14: Adaptive management and monitoring as fundamental tools to effective salt marsh restoration. in C. Roman and D. Burdick, editors. Restoring Tidal Flow to Salt Marshes: A Synthesis of Science and Management in New England (USA). Island Press.

Burdick, D., R. Buchsbaum, and E. Holt. 2001. Variation in soil salinity associated with the expansion of Phragmites australis in salt marshes. Environmental and Experimental Botany 46:247-261

Burgess, P. 1999. Conservation and development in conflict. MS Thesis. Clark University.

Canfield, S., L. Claessens, C. S. Hopkinson, E. Rastetter, and J. Vallino. 1999. Long-term effect of municipal water use on the water budget of the Ipswich River basin. Biological Bulletin 197:295-297

Cavatorta, J., M. Johnston, C. S. Hopkinson, and V. Valentine. 2003. Patterns of sedimentation in a salt marsh-dominated estuary. Biological Bulletin 205:239-241

Charles, H. 2007. Effects of Warming and Altered Precipitation on Plant and Nutrient Dynamics of a New England Salt Marsh. MS Thesis. University of Massachusetts, Boston, MA.

Claessens, L., C. Hopkinson, E. Rastetter, and J. Vallino. 2006. Effect of historical changes in land use and climate on the water budget of an urbanizing watershed. Water Resources Research 42 doi:10.1029/2005WR004131.

Clement, J., R. M. Holmes, B. J. Peterson, and G. Pinlay. 2004. Isotopic investigation of nitrogen retention in a riparian ecosystem. Journal of Applied Ecology 40:1035-1048

Crump, B. C., and J. E. Hobbie. 2005. Synchrony and seasonality in bacterioplankton communities of two temperate rivers. Limnology and Oceanography 50:1718-1729

Crump, B. C., C. S. Hopkinson, M. L. Sogin, and J. H. Hobbie. 2004. Microbial biogeography along an estuarine salinity gradient: the combined influences of bacterial growth and residence time. Applied and Environmental Microbiology 70:1494-1505 DOI: 10.1128/AEM.70.3.1494?1505.2004.

Day, J. W., R. R. Christian, D. M. Boesch, A. Yáñez-Arancibia, J. T. Morris, R. R. Twilley, L. Naylor, L. Schaffner, and C. Stevenson. 2008. Consequences of climate change on the ecogeomorphology of coastal wetlands. Estuaries and Coasts 31:477-491 DOI 10.1007/s12237-008-9047-6.

Deegan, L., L. A. Wright, J. Hughes, and E. Boynton. 1999. Establishing the Food Web Links between Estuaries and Nearshore Fisheries of New England. Final Report NA 76 FD 0106, NOAA.

Deegan, L. A. 2002. Lessons learned: the effects of nutrient enrichment on the support of nekton by seagrass and saltmarsh ecosystems. Estuaries 25:585-600

Deegan, L. A., J. L. Bowen, D. C. Drake, J. W. Fleeger, C. T. Friedrichs, K. A. Galvan, J. E. Hobbie, C. Hopkinson, D. S. Johnson, J. M. Johnson, L. E. LeMay, E. E. Miller, B. J. Peterson, C. Picard, S. Sheldon, M. Sutherland, J. Vallino, and R. S. Warren. 2007. Susceptibility of salt marshes to nutrient enrichment and predator removal. Ecological Applications 17:S-42-S63

Deegan, L. A., and R. Buchsbaum. 2005. The effect of habitat loss and degradation on fisheries. Pages 67-96 in R. Buchsbaum, J. Pederson, and W. E. Robinson, editors. The Decline of Fisheries Resources in New England: Evaluating the Impact of Overfishing, Contamination, and Habitat Degradation. University of Massachusetts Press.

Deegan, L. A., and C. o. E. E. o. Fishing. 2002. Effects of trawling and dredging on seafloor habitat. Pages 107 pp. in. National Academy Press, Washington, DC.

Deegan, L. A., J. E. Hughes, and R. A. Rountree. 2000. Salt marsh ecosystem support of marine transient species. Pages 333-365 in M. Weinstein and J. Kreeger, editors. Concepts and Controversies in Tidal Marsh Ecology. Kluwer Academic Publisher, The Netherlands.

Deegan, L. A., J. Kremer, T. Webler, and J. Brawley. 2001. The use of models in integrated resource management in the coastal zone. in B. V. Bodungen and R. K. Turner, editors. Science and Integrated Coastal Management. Dahlem University Press, Berlin.

Drake, D. C., B. J. Peterson, L. A. Deegan, L. A. Harris, E. E. Miller, and R. S. Warren. 2008. Plant nitrogen dynamics in fertilized and natural New England saltmarshes: a paired 15N tracer study. Marine Ecology Progress Series 354:35-46 doi: 10.3354/meps07170.

Drake, D. C., B. J. Peterson, K. A. Galván, L. A. Deegan, J. W. Fleeger, C. Hopkinson, J. M. Johnson, K. Koop-Jakobsen, L. E. Lemay, E. E. Miller, C. Picard, and R. S. Warren. 2009. Salt marsh ecosystem biogeochemical responses to nutrient enrichment: A paired 15N tracer study. Ecology 90:2535-2546

Driscoll, C., D. Whitall, J. Aber, E. Boyer, M. Castor, C. Cronan, C. Goodale, P. Groffman, K. Lambert, G. Lawrence, C. Hopkinson, and S. Ollinger. 2002. Nitrogen Pollution: From sources to the sea. Science Links - Hubbard Brook Research Foundation, Hanover, NH.

Driscoll, C., D. Whitall, J. Aber, E. Boyer, M. Castro, C. Cronan, C. Goodale, P. Groffman, C. Hopkinson, K. Lambert, G. Lawrence, and S. Ollinger. 2003. Nitrogen pollution in the northeastern United States: Sources, effects and managment options. BioSciences 53:357-374

Driscoll, C., D. Whitall, J. Aber, E. Boyer, M. Castro, C. Cronan, C. Goodale, P. Groffman, C. Hopkinson, K. Lambert, G. Lawrence, and S. Ollinger. 2003. Nitrogen pollution: Sources and consequences in the U.S. Northeast. Environment:8-22

El Fantroussi, S., H. Urakawa, A. E. Bernhard, J. J. Kelly, P. A. Noble, and D. A. Stahl. 2003. Direct profiling of environmental microbial populations by thermal dissociation analysis of native ribosomal RNAs hybridized to oligonucleotide microarrays. Applied Environmental Microbiology 69:2377-2382

Emeis, K. C., J. R. Benoit, L. Deegan, A. J. Gilbert, V. Lee, J. M. Glade, M. Meybeck, S. B. Olsen, and B. V. Bodungen. 2001. Group 4: Unifying concepts for integrated coastal management. in B. V. Bodungen and R. K. Turner, editors. Science and Integrated Coastal Management. Dahlem University Press, Berlin.

Fagherazzi, S., R. Torres, C. Hopkinson, and D. vanProosdij. 2004. The Salt Marsh Geomorphology: Physical and Ecological Effects on Landform. Pages 57-58 in AGU Chapman Conference. EOS, Halifax, Nova Scotia, Canada.

Farber, S., D. Costanza, D. Childers, J. Erikson, K. Gross, M. Grove, C. Hopkinson, J. Kahn, S. Pincetl, A. Troy, P. Warren, and M. Wilson. 2006. Linking ecology and economics for ecosystem management. BioScience 56:121-134

Fedorko, E. J., R. G. Pontius, Jr., S. P. Aldrich, L. Claessens, C. Hopkinson, and W. M. Wollheim. 2005. Spatial distribution of land type in regression models of pollutant loading. Journal of Spatial Hydrology 5:60-80

Fennel, K., D. Brady, D. DiToro, R. W. Fulweiler, W. S. Gardner, A. Giblin, M. J. McCarthy, A. Rao, S. Seitzinger, M. Thouvenot-Korppoo, and C. Tobias. 2009. Modeling denitrification in aquatic sediments. Biogeochemistry 93:159-178 DOI 10.1007/s10533-008-9270-z.

Ferry, K. 2003. Factors driving distribution of migratory striped bass across Massachusetts estuarties: predator-prey interactions and implications for multispecies managment. MS Thesis. University of Natural Resources.

Filoso, S., J. J. Vallino, C. Hopkinson, E. Rastetter, and L. Claessens. 2004. Modeling Nitrogen Transport in the Ipswich River Basin, Massachusetts, Using HSPF. Journal of the American Water Resources Association 40:1365-1384

Fisher, T. R., D. Correll, R. Costanza, J. Hollibaugh, C. Hopkinson, R. Howarth, N. Rabalais, J. Richey, C. Vorosmarty, and R. Wiegert. 2000. Synthesizing drainage basin inputs to coastal systems. Pages 81-105 in J. Hobbie, editor. Estuarine Science: A Synthetic Approach to Research and Practice. Island Press, Washington, DC.

Fleeger, J. W., D. S. Johnson, K. A. Galván, and L. A. Deegan. 2008. Top-down and bottom-up control of infauna varies across the saltmarsh landscape. Journal of Experimental Marine Biology and Ecology 357:20-34 doi:10.1016/j.jembe.2007.12.003.

Frank, H., M. E. Mather, R. M. Muth, S. M. Pautzke, J. M. Smith, J. T. Finn, and S. D. McCormick. 2009a. What is 'fallback': metrics needed to assess telemetry tag effects on anadromaous fish behaviour. Hydrobiologia 35:237 - 249

Frank, H. F., M. E. Mather, J. M. Smith, R. M. Muth, and J. T. Finn. 2009 (in review). Role of origin and release location in pre-spawning movements of anadromous alewives. Fisheries Management and Ecology

Frank, H. J. 2009. Improving Strategies for Coastal River Restoration: Tracking Anadromous River Herring in a Coastal Massachusetts Stream. MS Thesis. University of Massachusetts, Amherst, MA.

Frank, H. J., M. E. Mather, R. M. Muth, S. M. Pautzke, J. M. Smith, and J. T. Finn. 2009. The Adopt-a-Herring Program as a Fisheries Conservation Tool. Fisheries 34:496-507

Freeman, C. J., H. Haas, S. Warren, L. A. Deegan, and J. Logan. 2004. What makes mummichogs grow? The relationship between growth rates and gut contents of Fundulus heteroclitus held in enclosures along a salinity gradient in a New England salt marsh. in New England Estuarine Research Society (NEERS), Burlington, Vermont.

Fry, B., M. Cieri, J. Hughes, C. Tobias, L. A. Deegan, and B. Peterson. 2008. Stable isotope monitoring of benthic-pelagic coupling with salt marsh fish. Marine Ecology Progress Series 369:193-204 doi: 10.3354/meps07644.

Fry, B., C. Hopkinson, A. Nolin, and S. Wainright. 1998. 13C/12C composition of marine dissolved organic carbon. Chemical Geology 152:113 - 118

Galvan, K., J. W. Fleeger, and B. Fry. 2008. Stable isotope addition reveals dietary importance of phytoplankton and microphytobenthos to saltmarsh infauna. Marine Ecology Progress Series 359:37-49

Galvan, K., J. W. Fleeger, B. Peterson, D. Drake, L. A. Deegan, D. S. Johnson, M. Johnson, and C. Picard. 2009 (in review). Trophic plasticity and spatiotemporal variation revealed in a New England saltmarsh food web. Marine Ecology Progress Series

Galvan, K. A. 2008. Diet of saltmarsh invertebrates. Ph.D. Thesis. Louisiana State University, Baton Rouge, LA.

Gardner, L. R., and E. F. Faines. 2008. A method for estimating pore water drainage from marsh soils using rainfall and well records. Estuarine, Coastal and Shelf Science 79:51-58 doi:10.1016/j.ecss.2008.03.014.

Geyer, W. R., J. Morris, F. Prahl, and D. Jay. 2000. Interaction between physical processes and ecosystem structure: A comparative approach. Pages 177-206 in J. Hobbie, editor. Estuarine Science: A Synthetic Approach to Research and Practice. Island Press, Washington, DC.

Giblin, A. E., and J. Vallino. 2003. The Role of Models in Addressing Coastal Eutrophication Problems. Pages 327-343 in C. D. Canham, J. J. Cole, and W. K. Lauenroth, editors. The Role of Models in Ecosystems Science. Princeton University Press.

Giblin, A. E., N. B. Weston, G. T. Banta, J. Tucker, and C. S. Hopkinson. 2009 (accepted). The effects of salinity on nitrogen losses from an oligohaline estuarine sediment. Estuaries and Coasts

Green, M., W. M. Wollheim, N. Basu, G. M. Gettel, P. Rao, N. Morse, and R. Stewart. 2009. Effective denitrification scales predictably with water residence time across diverse systems. Nature Precedings hdl:10101/npre.2009.3520.1.

Green, P. A., C. J. Vorosmarty, M. Meybeck, J. N. Galloway, B. J. Peterson, and E. W. Boyer. 2003. Pre-industrial and contemporary fluxes of nitrogen through rivers: A global assessment based on typology. Biogeochemistry 68:1-35

Greenbaum, A., and A. Giblin. 2000. Differences in properties of salt marsh sediment between hayed and reference sites. Biological Bulletin 199:225-226

Greenbaum, A. H. 2001. Long-term fate of heavy metals in sediments of a Massachusetts salt marsh. Honors, BS Thesis. Wellesley College, Wellesley, MA.

Grimm, N., D. Foster, P. Groffman, M. Grove, C. Hopkinson, K. Nadelhoffer, D. Pataki, and D. Peters. 2008. Land change: Ecosystem responses to urbanization and pollution across climatic and societal gradients. Frontiers in Ecology and Environment 6:264-272 doi:10.1890/070147.

Haas, H. L., C. J. Freeman, J. M. Logan, L. Deegan, and E. F. Gaines. 2009. Examining mummichog growth and movement: Are some individuals making intra-season migrations to optimize growth? Journal of Experimental Marine Biology and Ecology 369:8-16 doi:10.1016/j.jembe.2008.09.027.

Haines, J. 2001. The feeding ecology of mummichog and Atlantic silversides in the Rowley River. BS Thesis. Conneticut College.

Harris, L. A. 2009 (submitted). A theoretical derivation of above- and below-ground biomass partitioning in clonal plants. Ecology Letters

Harris, L. A., and M. M. Bush. 2009 (submitted). Prediction of phytoplankton production: using the metabolic theory of ecology to move from empirical to mechanistic origins for numerical models. Limnology and Oceanography

Harris, L. A., C. M. Duarte, and S. W. Nixon. 2006. Allometric laws and prediction in estuarine and coastal ecology (Invited essay Perspectives section). Estuaries and Coasts 29:340-344

Harrison, J., R. Maranger, R. B. Alexander, J. Cornwell, A. Giblin, P. Jacinthe, E. Mayorga, S. Seitzinger, and W. M. Wollheim. 2009. The regional and global significance of reactive N removal in lakes and reservoirs. Biogeochemistry 93:147-158 DOI 10.1007/s10533-008-9272-x.

Head, J. 2002. Identifying impermeable surface from remotely sensed images. MS Thesis. Clark University, Worcester.

Hill, T., and C. Polsky. 2006. Adaptation to Drought in the Context of Suburban Sprawl and Abundant Rainfall. Geographical Bulletin 47:85-100

Hobbie, J. 2000. Estuarine Science: A Synthetic Approach to Research and Practice. Island Press, Washington, DC.

Hobbie, J., S. Carpenter, N. Grimm, J. Gosz, and T. Seastedt. 2003. The United States Long Term Ecological Research program. BioSciences 53:21-32

Hobbie, J. E. 2000. Estuarine Science: The key to progress in coastal ecological research. Pages 1-16 in J. Hobbie, editor. Estuarine Science: A Synthetic Approach to Research and Practice. Island Press, Washington, DC.

Hobbie, J. E. 2003. Scientific accomplishments of the Long Term Ecological Research program: an introduction. BioSciences 53:17-20

Holden, M., C. Lippitt, R. G. Pontius, and C. Williams. 2003. Building a database of historic land cover to detect landscape change. Biological Bulletin 205:257-258

Holmes, R. M., A. Aminot, R. Kerouel, B. A. Hooker, and B. J. Peterson. 1999. A simple and precise method for measuring ammonium in marine and freshwater ecosystems. Canadian Journal of Fisheries and Aquatic Science 56:1801-1808

Holmes, R. M., J. McClelland, D. M. Sigman, B. Fry, and B. J. Peterson. 1998. Measuring 15N-NH4 in marine, estuarine, and freshwaters: an adaptation of the ammonium diffusion method for samples with low ammonium concentrations. Marine Chemistry 60:235-243

Holmes, R. M., B. J. Peterson, L. Deegan, J. Hughes, and B. Fry. 2000. Nitrogen biogeochemistry in the oligohaline zone of a New England estuary. Ecology 81:416-432

Holt, E., and R. Buchsbaum. 2000. Bird use of Phragmites australis in coastal marshes of northern Massachusetts. Pages 232-240 in J. Pederson, editor. Proceedings of the 1st National Conference on Marine Bioinvasions. MIT Sea Grant, Cambridge, MA.

Hopkinson, C., and A. Giblin. 2008. Salt marsh N cycling. Pages 991-1036 in R. Capone, D. Bronk, M. Mulholland, and E. Carpenter, editors. Nitrogen in the Marine Environment, 2nd Edition. Elsevier Publishers.

Hopkinson, C., and E. Smith. 2004. Estuarine respiration. Pages 122-146 in P. d. a. P. J. l. Williams, editor. Respiration of Aquatic Ecosystems of the World. Academic Press, New York, NY.

Hopkinson, C. S., I. Buffam, J. Hobbie, J. Vallino, M. Perdue, B. Eversmeyer, F. Prahl, J. Covert, R. Hodson, M. A. Moran, E. Smith, J. Baross, B. Crump, S. Findlay, and K. Foreman. 1998. Terrestrial inputs of organic matter to coastal ecosystems: An intercomparison of chemical characteristics and bioavailability. Biogeochemistry 43:211-234

Hopkinson, C. S., A. E. Giblin, R. H. Garritt, J. Tucker, and M. A. J. Hullar. 1998. The influence of the benthic boundary layer on growth of pelagic bacteria. Aquatic Microbial Ecology 16:109-118

Hopkinson, C. S., A. E. Giblin, and J. Tucker. 2001. Benthic metabolism and nutrient regeneration on the continental shelf off eastern Massachusetts, USA. Marine Ecology Progress Series 224:1-19

Hopkinson, C. S., A. E. Giblin, J. Tucker, and R. H. Garritt. 1999. Benthic metabolism and nutrient cycling along an estuarine salinity gradient. Estuaries 22:825-843

Hopkinson, C. S., A. E. Lugo, M. Alber, A. Covich, and S. van Bloem. 2008. Understanding and forecasting the effects of sea level rise and intense windstorms on coastal and upland ecosystems: the need for a continental-scale netowrk of observatories. Frontiers in Ecology and Environment 6:255-263 doi:10.1890/070153.

Hopkinson, C. S., and J. Vallino. 2005. Efficient export of carbon to the deep ocean through dissolved organic matter. Nature 433:142-145

Hopkinson, C. S., J. Vallino, and A. Nolin. 2002. Decomposition of dissolved organic matter from the continental margin. Deep Sea Research II 49:4461-4478

Horowitz, J. 2001. Stable istopic analysis of food webs in hayed and reference salt marshes. Honors, BS Thesis. Hampshire College.

Howarth, R. W., D. Anderson, T. Church, H. Greening, C. Hopkinson, W. Huber, N. Marcus, R. Naiman, K. Segerson, A. Sharpley, and W. Wiseman. 2000. Clean Coastal Waters: Understanding and reducing the effects of nutrient pollution. National Academy of Sciences, Washington, DC.

Howarth, R. W., D. Anderson, J. Cloern, C. Elfring, C. Hopkinson, B. Lapointe, T. Malone, N. Marcus, K. McGlathery, A. Sharpley, and D. Walker. 2000. Nutrient pollution of coastal rivers, bays and seas. Issues in Ecology:1-15

Huang, X., and J. T. Morris. 2005. Distribution of phosphatase activity in marsh sediments along an estuarine salinity gradient. Marine Ecological Progress Series 292:75-83

Huffaker, D. 2003. The scale at which land change models are accurate. High Honors, BS Thesis. Clark University, Worcester.

Huffaker, D., and R. G. Pontius Jr. 2002. Reconstruction of Historical Land Cover in the Ipswich Watershed. Biological Bulletin 203:253-254

Hughes, J. E., L. A. Deegan, B. J. Peterson, R. M. Holmes, and B. Fry. 2000. Nitrogen flow through the food web in the oligohaline zone of a New England estuary. Ecology 81:433-452

Johnson, D. S. 2008. Trophic control of saltmarsh invertebrates. Ph.D. Thesis. Louisiana State University, Baton Rouge, LA.

Johnson, D. S., and J. W. Fleeger. 2009. Weak response of saltmarsh infauna to ecosystem-wide nutrient enrichment and fish predator reduction: A four-year study. Journal of Experimental Marine Biology and Ecology 373:35-44 doi:10.1016/j.jembe.2009.03.003.

Johnson, D. S., J. W. Fleeger, and L. A. Deegan. 2009. Large-scale manipulations reveal that top-down and bottom-up controls interact to alter habitat utilization by saltmarsh fauna. Marine Ecology Progress Series 377:33-41 doi: 10.3354/meps07849.

Johnson, D. S., J. W. Fleeger, K. A. Galvan, and E. B. Moser. 2007. Worm holes and their space-time continuum: Spatial and temporal variability of macroinfaunal annelids in a northern New England salt marsh. Estuaries and Coasts 30:226-237

Johnson, D. S., and B. J. Jessen. 2008. Do spur-throated grasshoppers, Melanoplus spp. (Orthoptera: Acrididae), exert top-down control on smooth cordgrass Spartina alterniflora in northern New England? Estuaries and Coasts 31:912-919 DOI 10.1007/s12237-008-9074-3.

Johnston, M. E., J. R. Cavatorta, C. S. Hopkinson, and V. Valentine. 2003. Importance of metabolism in the development of salt marsh ponds. Biological Bulletin 205:248-249

Kerry, J., D. Boorse, and R. Buchsbaum. 2004. The effect of nutrient enrichment and salinity on salt marsh invertebrates in the Plum Island Estuary. Biological Bulletin 207:174

Kiehn, W. M., and J. T. Morris. 2010 (in press). Variability in dimethylsulfoniopropionate (DMSP) in Spartina alterniflora and its effect on Littoraria irrorata. Marine Ecology Progress Series

Kirkby, R., L. Claessens, J. Hopkinson, C., E. Rastetter, and J. Vallino. 2000. Modeling the effects of land-use change on nitrogen biogeochemistry in the Ipswich watershed, Massachusetts. Biological Bulletin 199:218-219

Kirwan, M. L., G. R. Guntenspergen, and J. T. Morris. 2009. Latitudinal trends in Spartina alterniflora productivity and the response of coastal marshes to global change. Global Change Biology doi: 10.1111/j.1365-2486.2008.01834.x.

Klepac-Ceraj, V., M. Bahr, B. C. Crump, A. P. Teske, J. E. Hobbie, and M. F. Poltz. 2004. High overall diversity and dominance of microdiverse relationships in salt marsh sulfate-reducing bacteria. Environmental Microbiology 6:686-698

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