General Bibliography

General bibliography of works on the Plum Island Sound area

Abele, R. W. 1977. Analysis of short term variations in veach morphology for summer and winter periods, 1971-72, Plum Island, Massachusetts. Miscellaneous Report #77-5, US Army Corps of Engineers, Coastal Engineering Research Center, Fort Belvoir, VA.

Acinas, S. G., K. Klepac-Ceraj, D. E. Hunt, C. Pharino, C. Ceraj, D. L. Distel, and M. F. Polz. 2004. Fine-scale phylogenetic architecture of a complex bacterial community. Nature 430:551-554

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.

Alderman, D., B. Balsis, I. D. Buffam, R. H. Garritt, C. S. Hopkinson, and J. J. Vallino. 1995. Pelagic metabolism in the Parker River/Plum Island Sound Estuarine System. Biological Bulletin 189:250-251

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.

Anan, F. S., J. C. Boothroyd, J. M. DaBoll, S. C. Farrell, V. Goldsmith, S. A. Greer, A. D. Harrtwell, M. O. Hayes, C. L. McCormick, and B. S. Timson. 1969. Coastal environments to Northeastern Massachusetts and New Hampshire. Field Trip Guidebook. Geology Dept., Univ. of Massachusetts, Amherst, MA.

Armstrong, D. S., T. A. Richards, and G. W. Parker. 2001. Assessment of habitat, fish communities and stramflow requirements for habitat protection, Ipswich River, Massachusetts, 1998-99. Water-Resources Investigations Report 01-4161, U.S. Geological Survey.

Ayotte, J. D., M. G. Nielsen, G. R. Robinson, and R. B. Moore. 1999. Relationship of arsenic, iron and manganese in ground water to aquifer type, bedrock lithogeochemistry and land use in the New England coastal basins. Water-Resources Investigations Report 99-4162, U.S. Geological Survey.

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.

Balsis, B., D. Alderman, I. D. Buffam, R. H. Garritt, C. S. Hopkinson, and J. J. Vallino. 1995. Total system metabolism in the Plum Island Sound estuary. Biological Bulletin 189:252-254

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 ?15N and ?13C natural abundance in a coastal wetland with long-term nutrient additions. Aquatic Ecology doi:10.1007/s10452-008-9221-8.

Berry, J. C. 1936-1990. Newburyport Christmas bird count. in. National Audubon Society.

Bertness, M. D. 1991. Zonation of Spartina Patens And Spartina Altenaflora In A New England Salt Marsh. Ecology 72:138-148

Bircher, L., and E. Ruber. 1988. The effects of altosid on various life cycle stages of the salt marsh copepod Apocyclops spartinus with a correlation to dosage effectiveness against Aedes mosquitoes. Journal of the American Mosquito Control Association 4:520-523

Bochman, A. 1991. The effect of buffer zones on water quality in the Parker River/Essex Bay ACEC: A correlational study. MS Thesis. Harvard University Extension School, Cambridge, MA.

Boothroyd, J. C. 1985. Tidal inlets and deltas. Pages 444-525 in R. A. Davis, editor. Coastal Sedimentary Environments. Springer-Verlag, New York, NY.

Boothroyd, J. C., and D. M. Fitzgerald. 1988. Coastal environments of the Merrimack embayment, northeastern Massachusetts-southeastern New Hampshire. Society of Economic Paleontologists and Mineralogist, Northeastern Section Field Trip.

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

Boumans, R. M. J., and J. J. W. Day. 1993. High precision measurements of sediment elevation in shallow coastal areas using a sediment-erosion table. Estuaries 16:375-380

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.

Bowling, A., and J. Morrison. 2002. 2001 Annual Results Report. Ipswich River Watershed Association, Ipswich, MA.

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

Bronk, D. A., M. W. Lomas, P. M. Glibert, K. J. Schukert, and M. P. Sanderson. 2000. Total dissolved nitrogen analysis: comparisons between the persulfate, UV and high temperature oxidation methods. Marine Chemistry 69:163-178

Bronstein, A. 1981. The origin, transport, and decomposition of plant macro-litter on a northern Massachusetts salt marsh. MS Thesis. Northeastern University, Boston, MA.

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

Brush, T., R. A. Lent, T. Hruby, R. M. Marshall, and W. G. Montgomery. 1986. Habitat use by salt marsh birds and responses to open marsh water management. Colonial Waterbirds 9:189-195

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. 1996. Resource protection in the Plum Island Sound/Rivers Ecosystem. Final Project Report of the Plum Island Sound Minibay Project of the Massachusetts Bay Program.

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.

Callaway, D. W., I. Valiela, K. Foreman, and L. A. Soucy. 1995. Effects of Nitrogen Loading and Salt Marsh Habitat on Gross Primary Production and Chlorophyll a in Esutaries of Waquoit Bay. Biological Bulletin 189:254-255

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

Carini, S. S., N. B. Weston, J. C. Hopkinson, J. Tucker, A. E. Giblin, and J. J. Vallino. 1996. Gas exchange rates in the Parker River estuary, Massachusetts. Biological Bulletin 191:333-334

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

Chalmers, A. 2002. Trace elements and organic compounds in streambed sediment and fish tissue of coastal New England Streams, 1998-99. Water-Resources Investigations Report 02-4179, USGS.

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.

Chesmore, A. P., D. Brown, and R. D. Anderson. 1973. A study of the marine resources of Essex Bay. Monograph Series No. 13, Publication No. 2500-4-73-074986, Massachusetts Division of Marine Fisheries.

Chiaravalle, K., J. Hughes., R. Javonillo, and L. Deegan. 1997. Tidal river riffle habitats support high diversity and abundance of Gammaridean amphipods. Biological Bulletin 192:283-285

Chute, N. E., and R. L. Nichols. 1941. The geology of the coast of northeastern Massachusetts. Bulletin No. 7, Massachusetts Dept. of Public Works.

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.

Clarke, J. A., B. A. Harrington, T. Hruby, and F. Wasserman. The effect of ditching for mosquito control on salt marsh use by birds in Rowley, Massachusetts. Journal of Field Ornithology 55:160-180

Clayton, G. 1976. Reproduction, first year growth, and distribution of anadromous rainbow smelt, Osmerus mordax (Mitchill), in the Park River-Plum Island Sound EstuaryThesis. University of Massachusetts, Amherst, MA.

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

Coffin, R. B., B. Fry, B. J. Peterson, and R. T. Wright. 1989. Carbon isotopic compositions of estuarine bacteria. Limnology and Oceanography 34:1305-1310

Coles, J. F., T. F. Cuffney, G. McMahon, and K. M. Beaulieu. 2004. The effects of urbanization on the biological, physical and chemical characterizations of coastal New England streams. Professional Paper 1695, U.S. Geological Survey.

Colosi, P. 1979. Life history and population characteristics of a common mummichog, Fundulus Heteroclitus, in a salt marsh pond system of Plum Island, Massachusetts. MS Thesis. Northeastern University, Boston, MA.

Cook, A. 2001. The Voice Of The River. The Ipswich Watershed Association.

Cornell, S. E., and T. D. Jickells. 1999. Water-soluble organic nitrogen in atmospheric aerosol: a comparison of UV and persulfate oxidation methods. Atmospheric Environment 33:833-840

Cronon, W. 1983. Changes in the land. Hill and Wang, New York, NY.

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.

Cummings, E., and E. Ruber. 1987. Copepod colonization of natural and artificial substrates in a salt marsh pool. Estuarine and Coastal Shelf Science 25:637-645

DaBoll, J. M. 1969. Holocene sediments of the Parker River estuary, Massachusetts. MS Thesis. University of Massachusetts, Amherst, MA.

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.

Deblinger, R. D., and J. R. E. Jenkins. In press. Preserving coastal biodiversity: the private, non-profit approach. Journal of Coastal Management

Deblinger, R. D., and D. W. Rimmer. In press. Piping plover nest and habitat protection in Massachusetts. Transactions of the Northeast Section of the Wildlife Society

Deblinger, R. D., and D. W. Rimmer. In press. Solving suburban deer overpopulation problems: The Crane Beach, Ipswich, Massachusetts story. The Trustees of Reservations, Beverly, MA.

Deblinger, R. D., J. J. Vaske, and M. P. Donnelly. 1989. Integrating ecological and social impacts into barrier beach management. Transactions of the Northeast Recreation Research Conference. NE-132, Northeast Forest Experiment Station, Saratoga, NY.

Deegan, L. 1976. Analysis of the ecology of the mummichog, Fundulus Heteroclitus, in a New England salt marsh: Growth, population size, distribution, consumption, and net production. Senior honors thesis Thesis. Northeastern University, Boston, MA.

Deegan, L. 1993. Nutrient and energy transport between estuaries and coastal marine ecosystems by fish migration. Canadian J. Fish Aquatic Sci. 50:74-79

Deegan, L., J. Finn, C. S. Hopkinson, B. J. Peterson, A. E. Giblin, B. Fry, and J. Hobbie. 1995. Flow model analysis of the effects of organic matter-nutrient interactions on estuarine trophic dynamics. Pages 273-281 in K. Dyer and R. Orth, editors. International Symposium Series, Changes in Fluxes in Estuaries: Implications from Science to Management. Olsen and Olsen, Pub., Fredensborg, DK.

Deegan, L., J. T. Finn, S. G. Ayvasian, C. A. Ryder, and J. Buonaccorsi. 1997. Development and validation of an estuarine biotic integrity index. Estuaries 20:601-617

Deegan, L., and R. H. Garritt. 1997. Evidence for spatial variability in estuarine food webs. Marine Ecology Progress Series 147:31-47

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

Duerring, C. 1989. North coastal water quality surveys, 1987-1988. Publication No. 15965-140-25-5-89-C.R., Massachusetts Division of Water Pollution Control, Technical Services Branch, Westboro, MA.

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.

Fagherazzi, S., R. Torres, C. Hopkinson, and D. vanProosdij. 2005. Salt marsh geomorphology: physical and ecological effects on landform. EOS 86:57-58

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.

Ferland, D. 2002. Assesing Gradients in Vegetation and Soil Along the Parker River. Merrimack College.

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.

Fitzgerald, D. M. 1982. Sediment bypassing at mixed energy tidal inlets. Pages 1094-1112 in 18th Coastal Engineering Conference, American Society of Civil Engineers, Cape Town, South Africe.

Fitzgerald, D. M. In press. Origin and stability of tidal inlets in Massachusetts. in D. Aubrey and G. Geise, editors. Tidal Inlets of New England.

Fitzgerald, D. M., I. V. Buynevich, R. A. Davis, and M. S. Fenster. 2002. New England tidal inlets with special reference to riverine -associated inlet systems. Geomorpology 48:179-208 10.1016/S0169-555X(02)00181-2.

Flanagan, S. M., D. L. Montgomery, and J. D. Ayotte. 2001. Shallow Ground-Water Quality in the Boston, Massachusetts Metropolitan Area. Water-Resources Investigations Report 01-4042, U.S. Geological Survey.

Flanagan, S. M., M. G. Nielsen, K. W. Robinson, and J. F. Coles. 1999. Water-quality assessment of the New England Coastal Basins in Maine, Massachusetts, New Hampshire, and Rhode Island: environmental settings and implications for water quality and aquatic biota. Water-Resources Investigations Report 98-4249, USGS.

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.

Fog, K. 1988. The Effect of Added Nitrogen on the Rate of Decomposition of Organic Matter. Biol. Rev. 63:433-462

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

Fry, B., C. S. Hopkinson, A. L. Nolin, B. Norrman, and U. Zweifel. 1996. Long term decomposition of DOC from experimental diatom blooms. Limnology and Oceanography 41:1344-1347

Fry, B., E. Peltzer, C. S. Hopkinson, A. L. Nolin, and L. Rdmond. 1996. Analysis of marine DOC using a reference dry combustion method. Marine Chemistry 54:191-201

Fry, B., S. Saupe, M. A. J. Hullar, and B. J. Peterson. 1993. Platinum-catalyzed combustion of DOC in sealed tubes for stable isotopic analysis. Marine Chemistry 41:187-193

Gallagher, J. L. 1975. Effect of an ammomium nitrate pulse on the growth and elemental composition of natural stands of Spartina alterniflora and Juncus roemerianus. American Journal of Botany 62:644-648

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., K. H. Foreman, and G. T. Banta. 1994. Biogeochemical processes and marine benthic community structure: A comparative approach. Pages 37-44 in C. G. Jones and J. H. Lawton, editors. Linking Species and Ecosystems. Chapman and Hall, New York, NY.

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

Gilbert, A. T., and E. Ruber. 1986. A water column sampler for invertebrates of salt marsh tidal pools. Estuaries 9:380-381

Gillis, G. 1977. Energy flow in a harpacticoid community of a salt pool. Ph.D. Thesis. Northeastern University, Boston, MA.

Goodbred, S. L., and T. M. Montello. 1989. A study of the morphological characteristics of Plum Island, Crane, Coffins, and Wingaersheek Beaches, MA. Boston University, Geology Dept., Boston, MA.

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.

Hansson, S., J. E. Hobbie, R. Elmgren, U. Larsson, B. Fry, and S. Johansson. 1997. The stable nitrogen isotope ratio as a marker of food-web interactions and fish migration. Ecology 78:2249-2257

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

Harris, S. K. 1975. A Flora of Essex County, Massachusetts. Peabody Museum, Salem, MA.

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.

Head, J. 2002. Identifying impermiable 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. 1994. The state of microbes: A summary of a symposium honoring Lawrence Pomeroy. Microbial Ecology 28:113-116

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

Hobbie, J. E., and R. T. Wright. 1979. An assessment of quantitative measurements of aquatic microbes. Archives Hydrobiol. Beih. 13:85-95

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. 1992. A comparison of ecosystem dynamics in freshwater wetlands. Estuaries 15:549-562

Hopkinson, C. S., D. Allen, R. Buchsbaum, L. Deegan, M. Dionne, A. Giblin, J. Hobbie, J. Morris, B. Peterson, J. Vallino, and C. Vorosmarty. 1997. Long-Term Ecological Research (LTER) in Land/Ocean Margin Ecosystems. NSF Award: OCE-9726921, National Science Foundation.

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., L. Cifuentes, D. Burdige, S. Fitzwater, D. Hansell, S. Henrichs, P. Kahler, I. Koike, T. Walsh, and B. Bergamaschi. 1993. The DON Controversy - A report. Marine Chemistry 41:23-36

Hopkinson, C. S., B. Fry, and A. L. Nolin. 1997. Stoichiometry of dissolved organic matter dynamics on the continental shelf of the Northeastern U.S.A. Continental Shelf Research 17:473-489

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

Hopkinson, C. S., and J. J. Vallino. 1994. Towards the development of generally-applicable models of the microbial loop in aquatic ecosystems. Microbial Ecology 28:321-326

Hopkinson, C. S., and J. J. Vallino. 1995. The relationship among man's activities in watersheds and estuaries: A model of runoff effects on estuarine community metabolism. Estuaries 18:598-621

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

Hruby, T., W. G. Montgomery, R. A. Lent, and N. Dobson. 1985. Open marsh water management in Massachusetts: Adapting the techniques to local conditions and its impact on mosquito larvae during the first season. Journal of the American Mosquito Control Association 1:85-88

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

Hullar, M. A. J., B. Fry, B. J. Peterson, and R. T. Wright. 1996. Microbial utilization of estuarine dissolved organic carbon: a stable isotope tracer approach tested by mass balance. Applied and Environmental Microbiology 62:2489-2493

Ingram, K., C. S. Hopkinson, K. Bowman, R. H. Garritt, and J. J. Vallino. 1994. From watershed to estuary: Assessment of nutrient loading, retention and export from the Ipswich River Basin. Biological Bulletin 193:288-289

Ip, J. T. C., D. R. Lynch, and C. T. Friedrichs. 1998. Simulation of Estuarine Flooding and Dewatering with Application to Great Bay, New Hampshire. Estuarine, Coastal & Shelf Science 47:119-141

Javonillo, R., L. Deegan, K. Chiarvalle, and J. Hughes. 1997. The importance of access to salt-marsh surface to short-term growth of Fundulus heteroclitus in a New England salt marsh. Biological Bulletin 193:288-289

Jay, D. A., R. J. Uncles, J. Largier, W. R. Geyer, J. J. Vallino, and W. R. Boynton. 1997. A review of recent developments in estuarine scalar flux estimation. Estuaries 20:262-280

Jerome, W. C., A. P. Chesmore, and C. O. Anderson. 1968. A study of the marine resources of the Park River-Plum Island Sound estuary. Monograph Series No. 6, Publication No. 2M-6-947687, Massachusetts Division of Marine Fisheries.

Jewitt, A. E. 1949. The Tidal Marshes of Rowley and Vicinity with an Account of the Old-Time Methods of "Marshing". The Essex Institute Historical Collections, Rowley Massachusetts.

Johnson, A. S. 1986. A water quality and deepwater habitat assessment of the Parker River basin. MA # 14579-40-50-9-86-CR, Massachusetts Department of Environmental Quality Engineering, Division of Water Pollution Control, Technical Services Branch, Westborough, MA.

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

Jones, J. R. 1977. An alternative hypothesis for barrier island migration. Ph.D. Thesis. Boston University, Boston, MA.

Jones, J. R., and B. Cameron. 1976. Sedimentary and geomorphic origin and development of Plum Island, Massachusetts: An example of a barrier island system. Pages 188-204 in B. Cameron, editor. Geology of Southern New England: A Guidebook for Field Trips to the Boston Area and Vicinity. Science Press.

Kennedy, L. E., S. Kiras, and R. McVoy. 2001. Merrimack River Basin: 1999 Water Quality Assessment Report. 84-AC-1, Department of Environmental Protection: Division of Watershed Managment, Worcester, MA.

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

Komarow, S., T. Young, L. Deegan, and R. Garritt. 1999. Influence of marsh flooding on the abundance and growth of Fundulus heteroclitus in salt marsh creeks. Biological Bulletin 197:299-300

Koop-Jakobsen, K. 2003. Ammonium dynamics in tidal salt marshes - an experimental study of ammonium adsorption, tidal flushing and ammonium volatilization. MS Thesis. Roskilde University.

Koop-Jakobsen, K. 2008. The impact of increased Nitrogen Loading on Gaseous Loss of Nitrogen from Salt Marsh Seciments. Ph.D. Thesis. Boston University, Boston, MA.

Koop-Jakobsen, K., and A. E. Giblin. 2002. Tidal flushing of ammonium from intertidal salt marsh sediments - the relative importance of adsorbed ammonium. Biological Bulletin 203:258-259

Koop-Jakobsen, K., and A. E. Giblin. 2009. Anammox in tidal marsh sediments: The role of salinity, nitrogen loading, and marsh vegetation. Estuaries and Coasts 32:238-245 DOI 10.1007/s12237-008-9131-y.

Koop-Jakobsen, K., and A. E. Giblin. 2009. A new approach for measuring denitrification in the rhizosphere of vegetated marsh sediments. Limnology and Oceanography, Methods 7:626 - 637

Koop-Jakobsen, K., and A. E. Giblin. 2009 (in press). The effect of increased nitrate loading on nitrate reduction via denitrification and DNRA in salt marsh sediments. Limnology and Oceanography

Kratz, T. K., L. A. Deegan, M. E. Harmon, and W. K. Lauenroth. 2003. Understanding Ecological Variability in Space and Time from Long-Term Observations. BioSciences 53:57-67

Kremer, J., W. Kemp, A. Giblin, I. Valiela, S. Seitzinger, and E. Hoffman. 2000. Linking biogeochemical processes to higher trophic levels. Pages 299-246 in J. Hobbie, editor. Estuarine Science, A Synthetic Approach to Research and Practice. Island Press, Washington, DC.

Krest, J. M., W. S. Moore, L. R. Gardner, and J. T. Morris. 2000. Marsh nutrient export supplied by ground water discharge: Evidence from radium measurements. Global Biogeochemical Cycles 14:167-176

LaFrance, K., and E. Ruber. 1985. The life cycle and productivity of the amphipod Gammarus mucronatus on a northern Massachusetts salt marsh. Limnology and Oceanography 30:1067-1077

LaMontange, M. G., A. E. Giblin, and I. Valiela. 2002. Denitrification and the stoichiometery of nutrient regeneration in Waquoit Bay, MA. Estuaries 25:272-281

Lastavica, C. C., A. Spielman, V. P. Berardi, M. L. Wilson, and R. D. Deblinger. 1989. Rapid emergence of a focal epidemic of Lyme disease in coastal Massachusetts. New England Journal of Medicine 320:133-137

Leahy, K., and R. Buchsbaum. 1998. Nonpoint source comprehensive implementation program for the Mill River sub-watersheds. Prep. for Mass DEP and US EPA.

Lee, W. M. 2004. Factors affecting sedimentation patterns of a tidal marsh in Plum Island Sound Estuary, Massachusetts. B.S. Thesis. College of William and Mary.

Lemay, L. E. 2007. The impact of drainage ditches on salt marsh flow patterns, sedimentation and morphology: Rowley River, Massachusetts. M.S. Thesis. Virginia Institute of Marine Science, Gloucester Point, VA.

Levine, U. Y., and B. C. Crump. 2002. Bacteroplankton Community Composition in Flowing Waters of the Ipswich River Watershed. Biological Bulletin 203:251-252

Lim, E. L., D. Caron, and E. DeLong. 1996. Development and field application of a quantitative method for examining natural assemblages of protists with oligonucleotide probes. Applied and Environmental Microbiology 62:1416-1423

Link, J. S., and J. K. T. Brodziak. 2002. Status of the Northeast U.S. Continental Shelf Ecosystem. 02-11, North East Fisheries Science Center: Ecosystem Status Working Group, Woods Hole, MA.

Loder, T. C., and P. M. Glibert. 1977. Blank and Salinity Corrections for Automated Nutrient Analysis of Estuarine and Sea Waters. Pages 48-56 in 7th Technicon International Congress.

Logan, J., H. Hass, L. A. Deegan, and E. Gaines. 2006. Turnover rates of nitrogen stable isotopes in the salt marsh mummichog, Fundulus heteroclitus, following a laboratory diet switch. Oecologia 147:391-395

Luciano, K. E. 2007. Investigation into the relationship between morphology and

Tidal flux in ditched and non-ditched salt marsh creek systems, Rowley, Massachuset. B.S. Thesis. Virginia Institute of Marine Science, Gloucester Point, VA.

Ludlam, J. P., D. H. Shull, and R. Buchsbaum. 2002. Effects of haying on salt marsh surface invertebrates. Biological Bulletin 203:250-251

Lunsford, T. L. 2002. Comparison of the fate of dissolved organic matter in two coastal systems: Hog Island Bay, VA (USA) and Plum Island Sound, MA (USA). MS Thesis. The College of William and Mary, Williamsburg, VA.

MacConnell, W. P. Land use and vegetative cover mapping, 1951-1972. Massachusetts Agricultural Experiment Station, University of Massachusetts, Amherst, MA.

MacDougall, J. S. 1988. Field list of the Birds of Essex County. Essex County Ornithological Club, Peabody Museum of Salem, Salem, MA.

Machas, R. 1999. Analise isotopica da cadeia alimentar da Ria Formosa: Conribuicao relitiva dos produtores primaries. MS Thesis. University of Coimbra, Coimbra, Portugal.

Machas, R., and R. Santos. 1999. Sources of organic matter in Ria Formosa revealed by stable isotope analysis. Acta Oecologica 20:463-469

Machas, R., R. Santos, and B. Peterson. 2003. Tracing the flow of organic matter from primary producers to filter feeders in Ria Formosa Lagoon, Southern Portugal. Estuaries 26:846-856

Maly, M. 1980. A study of the effects of pesticides on single and mixed species cultures of salt marsh algae. Ph.D. Thesis. Northeastern University, Boston, MA.

Maly, M., and E. Ruber. 1983. The effects of pesticides on pure and mixed species cultures of salt marsh pool algae. Bulletin of Environmental Contamination and Toxicology 30:464-472

Mandracchia, M., and E. Ruber. 1990. Production and life cycle of the gastropod Hydrobia truncata with notes on Spurwinkia in Massachusetts salt marsh pools. Estuaries 13:479-485

Mather, M. E., J. T. Finn, K. H. Ferry, L. A. Deegan, and G. A. Nelson. 2009. Use of non-natal estuaries by migratory striped bass (Morone saxatilis) in summer. Fishery Bulletin 107:329 - 337

Mather, M. E., J. T. Finn, S. M. Pautzke, D. Fox, T. Savoy, H. M. Brundage III, L. A. Deegan, and R. M. Muth. 2009 (in review). Destinations, routes, and timing of adult striped bass on their southward fall migration: implications for coastal movements. Journal of Fish Biology

Mayo, R. K. 1974. Population structure, movement, and fecundity of the anadeomous alewife, Alosa pseudoharengus (Wilson), in the Parker RIver, Massachusetts, 1971-72. MS Thesis. University of Massachusetts, Amherst, MA.

McCormack, C. L. 1968. Holocene stratigraphy of the marshes at Plum Island, Massachusetts. Ph.D. Thesis. University of Massachusetts, Amherst, MA.

McDonnell, M. J. 1979. The flora of Plum Island, Essex County, Massachusetts. Station Bulletin 513, New Hampshire Agricultural Experiment Station, University of New Hampshire, Durham, NH.

McDonnell, M. J. 1979. The vascular flora of Plum Island, Essex County, Massachusetts with an analysis of the impact of human trampling on the coastal dune vegetationThesis. University of New Hampshire, Durham, NH.

McIntire, W., and J. Morgan. 1964. Recent geomorphic history of Plum Island, Massachusetts and adjacent coasts. Louisiana State University.

Menard, S. 1999. Land-use change and regional growth in the Ipswich watershed basin. BS Thesis. Clark University, Worcester.

Mendelssohn, I. A., and J. T. Morris. 2000. Ecophysiological controls on the growth of Spartina alterniflora. Pages 59-80 in M. P. Weinstein and D. A. Kreeger, editors. Concepts and Controversies in Tidal Marsh Ecology. Kluwer Academic Publishers, Dordredt, the Netherlands.

Meybeck, M., and C. J. Vorosmarty. 2005. Fluvial filtering of land to ocean fluxes: from Holocene variations to Anthrocene. Compte Rendus 337:107-123

Miller, E. E. 2006. Experimental nutrient enrichment of a New England salt marsh: plant productivity and community composition responses. M.S. Thesis. Connecticut College, New London, CT.

Millette, T. L., B. Argow, E. Marcano, C. Hayward, C. Hopkinson, and V. Valentine. 2009 (in review). Salt marsh geomorphological analyses via integration of multi-temporal multispectral remote sensing with LIDAR and GIS. Journal of Coastal Research

Monaghan, E., and A. E. Giblin. 1995. The effects of coupling between the oxic and anoxic layers of sediment on nutrient release to overlying water. Biological Bulletin 187:288-289

Mondrup, T. 1999. Salinity effects on nitrogen dynamics in estuarine sediment investigated by a plug-flux method. Biological Bulletin 197:287-288

Mondrup, T. 2000. Salinity effects on tolerance and adaptation of estuarine nitrifying bacteria investigated by a plug-flux method. MS Thesis. Roskilde University (Denmark).

Montagna, P. A. 1975. Rates of decomposition of Spartina alterniflora and the occurrence of associated organisms in a Massachusetts salt marsh. MS Thesis. Northeastern University, Boston, MA.

Montagna, P. A., and E. Ruber. 1981. Decomposition of Spartina alterniflora in different seasons and habitats of a northern Massachusetts salt marsh and a comparison with other Atlantic regions. Estuaries 3:61-64

Montgomery, D. L., G. R. Robinson, J. D. Ayotte, S. M. Flanagan, and K. W. Robinson. 2002. Fact Sheet FS-003-02, U.S. Geological Survey.

Moore, N. 2002. A leakage detection model for determining the value of conservation. MS Thesis. Clark University, Worcester.

Morlock, S., D. Taylor, A. Giblin, C. Hopkinson, and J. Tucker. 1997. Effect of salinity on the fate of inorganic nitrogen in sediments of the Parker River estuary, Massachusetts. Biological Bulletin 193:290-292

Morris, J., P. V. Sundareshwar, C. T. Nietch, B. Kjerfve, and D. R. Cahoon. 2002. Responses of coastal wetlands to rising sea level. Ecology 83:2869-2877

Morris, J. T. 2000. Effects of sea level anomalies on estuarine processes. Pages 107-127 in J. Hobbie, editor. Estuarine Science: A Synthetic Approach to Research and Practice. Island Press, Washington, DC.

Morris, J. T. 2005. Effects of changes in sea level and productivity on the stability of intertidal marshes. Pages 121-127 in P. Lasserre, P. Viaroli, and C. P., editors. UNESCO Proceeding Series on Lagoons and Coastal Wetlands in the Global Change Context: Impact and Management Issues, Venice.

Morris, J. T. 2006. Competition among marsh macrophytes by means of geomorphological displacement in the intertidal zone. Estuarine and Coastal Shelf Science 69:395-402

Morris, J. T. 2007. Ecological engineering in intertidal saltmarshes. Hydrobiologia 577:161-168

Morris, J. T. 2007. Estimating net primary production of salt marsh macrophytes. Pages 106-119 in T. J. Fahey and A. K. Knapp, editors. Principles and Standards for Measuring Primary Production. Oxford University Press.

Morris, J. T., R. R. Christian, and R. E. Ulanowicz. 2005. Analysis of size and complexity of randomly constructed food webs by information theoretic metrics. Pages 73-85 in A. Belgrano, U. M. Scharler, J. Dunne, and R. E. Ulanowicz, editors. Aquatic Food Webs: an Ecosystem Approach. Oxford University Press.

Morris, J. T., D. Porter, M. Neet, P. A. Noble, L. Schmidt, L. A. Lapine, and J. Jensen. 2005. Integrating LIDAR, multispectral imagery and neural network modeling techniques for marsh classification. International Journal of Remote Sensing 26:5221-5234 DOI: 10.1080/01431160500219018.

Mosher, T. D. 1976. Comparison of landlocked and estuarine populations of the white perch (Morone americana, Gmelin) in the Parker River, Massachusetts. MS Thesis. University of Massachusetts, Amherst, MA.

Mudd, S. M., S. Fagherazzi, J. T. Morris, and D. J. Furbish. 2004. Flow, sedimentation, and biomass production on a vegetated salt marsh in South Carolina: toward a predictive model of marsh morphologic and ecologic evolution. Pages 165-187 in S. Fagherazzi, A. Marani, and L. K. Blum, editors. The Ecogeomorphology of Tidal Marshes. American Geophysical Union, Washington, D.C.

Mudd, S. M., S. Howell, and J. T. Morris. 2009. Impact of the dynamic feedback between sedimentation, sea level rise, and biomass production on near surface marsh stratigraphy and carbon accumulation. Estuarine, Coastal and Shelf Science 82:377-389 doi:10.1016/j.ecss.2009.01.028.

Mulholland, P. J., A. M. Helton, G. C. Poole, J. Hall, R.O., S. K. Hamilton, B. J. Peterson, J. L. Tank, L. R. Ashkenas, L. W. Cooper, C. N. Dahm, W. K. Dodds, S. E. G. Findlay, S. V. Gregory, N. B. Grimm, S. L. Johnson, W. H. McDowell, J. L. Meyer, H. M. Valett, J. R. Webster, C. P. Arango, J. J. Beaulieu, M. J. Bernot, A. J. Burgin, C. L. Crenshaw, L. T. Johnson, B. R. Niederlehner, J. M. O?Brien, J. D. Potter, R. W. Sheibley, D. J. Sobota, and S. M. Thomas. 2008. Stream denitrification across biomes and its response to anthropogenic nitrate loading. Nature 452:202-206 doi:10.1038/nature06686.

Murawski, S. A., G. R. Clayton, R. R. Reed, and C. F. Cole. 1980. Movements of spawning rainbow smelt, Osmerus mordax, in a Massachusetts estuary. Estuaries 3:308-314

Murawski, S. A., and C. F. Cole. 1978. Population dynamics of anadromous rainbow smelt, Osmerus mordax, in a Massachusetts river system. Transactions of the American Fisheries Society 107:535-542

Murray, R. 1978. Detrital standing crop and flux in a New England salt marsh. MS Thesis. Northeastern University, Boston, MA.

Neckles, H., M. Dionne, D. Burdick, R. Buchsbaum, T. Diers, E. Hutchins, and C. Roman. 2002. A monitoring protocol to assess tidal restoration of salt marshes on local and regional scales. Restoration Ecology 10:556-563

Nelson, A. 2001. Quantifying the effectivness of conservation projects. MS Thesis. Clark University, Worcester.

Nielsen, J. L., A. Schramm, A. E. Bernhard, v. d. EnghG.J., and D. A. Stahl. 2004. Flow Cytometry-Assisted Cloning of Specific Sequence Motifs from Complex 16S rRNA Gene Libraries. Applied and Environmental Microbiology 70:7550-7554

Niering, W. A., and R. S. Warren. 1980. Vegetation Patterns and Processes in New England Salt Marshes. BioScience 30:301-307

Norrman, B., U. Zweifel, C. S. Hopkinson, and B. Fry. 1995. Production and utilization of dissolved organic carbon during an experimental bloom. Limnology and Oceanography 40:898-907

Nove, J. C. 1936-1990. Cape Ann Christmas bird count. in. National Audubon Society.

Oczkowski, A. J., B. A. Pellerin, C. W. Hunt, W. M. Wollheim, C. J. Vorosmarty, and T. C. Loder. 2006. The role of snowmelt and spring rainfall in inorganic nutrient fluxes from a large temperate watershed, the Androscoggin River basin (Maine and New Hampshire). Biogeochemistry 80:217-234

Oldale, R. N., L. E. Wommack, and A. B. Whitney. 1983. Evidence for a postglacial low relative sea level stand in the drowned delta of the Merrimack River, Western Gulf of Maine. Pages 325-336 in.

Parker, D. 2002. A method to produce hydrologically corrected DEMs. MS Thesis. Clark University, Worcester.

Parmentier, B., and R. G. Pontius, Jr. 2007. Improvements in the use of the ROC statistic for landscape ecology. Pages 2 in Conference proceedings of the World Congress of the International Association for Landscape Ecology, Wageningen, The Netherlands.

Pate, W. M., and J. T. Morris. 2009 (in press). Relationships between smooth cord-grass Spartina alterniflora (Loisel.) and the periwinkle snail Littorina irrorata (Say) in a South Carolina salt marsh. Wetlands

Pautzke, S. M. 2008. Distribution Patterns of Migratory Striped Bass in Plum Island Estuary, Massachusetts. M.S. Thesis. University of Massachusetts, Amherst, MA.

Pautzke, S. M., M. E. Mather, J. T. Finn, L. A. Deegan, and R. M. Muth. 2010. Seasonal use of a New England estuary by foraging contingents of migratory striped bass. Transactions of the American Fisheries Society 139:257 - 269 DOI: 10.1577/T08-222.1.

Pease, K. M., L. Claessens, C. Hopkinson, E. Rastetter, J. Vallino, and N. Kilham. 1999. Ipswich River nutrient dynamics: Preliminary assessment of a simple nitrogen-processing model. Biological Bulletin 197:289-290

Pellerin, B. A. 2004. The influence of urbanization on runoff generation and stream chemistry in Massachusetts watersheds. PhD. Thesis. University of New Hampshire, Durham, NH.

Pellerin, B. A., W. Wollheim, C. Hopkinson, W. McDowell, M. Williams, C. Vorosmarty, and M. Daley. 2004. Role of wetlands and developed land use on dissolved organic nitrogen concentrations and DON / TDN in northeastern U.S. rivers and streams. Limnology and Oceanography 49:910-918

Pellerin, B. A., W. M. Wollheim, X. Feng, and C. J. Vorosmarty. 2007. The application of electrical conductivity as a tracer for hydrograph separation in urban catchments. Hydrological Processes doi: 10.1002/hyp.6786.

Perring, A., M. Williams, C. Hopkinson Jr., E. Rastetter, and J. Vallino. 2000. Solute dynamics in storm flow of the Ipswich River Basin: Effects of land use. Biological Bulletin 199:219-221

Peterson, B., R. Howarth, and R. Garritt. 1986. Sulfur and Carbon Isotopes as Tracers of Salt-Marsh Organic Matter Flow. Ecology 67:865-874

Peterson, B. J. 1999. Stable isotopes as tracers of organic matter input and transfer in benthic food webs: A review. Acta Oecologia 20:479-487

Peterson, B. J., B. Fry, M. A. J. Hullar, S. Saupe, and J. R. T. Wright. 1994. The distribution and stable isotopic composition of dissolved organic carbon in estuaries. Estuaries 17:111-121

Pieri, N. 2001. Quantifying the effectivness of conservation projects. MS Thesis. Clark University, Worcester.

Poltz, M. F., S. Bertilsson, S. G. Acinas, and D. Hunt. 2003. A (r)Ray of hope in analysis of function and diversity of microbial communities. Biological Bulletin 204:196-199

Pontius Jr., R. G. 2000. Quantification error versus location error in comparison of categorical maps. Photogrammetric Engineering & Remote Sensing 66:1011-1016

Pontius Jr., R. G., A. Agrawal, and D. Huffaker. 2002. Uncertainty Analysis in Land Change Modeling: Constucting a Gridded Map from Tabular Data. Pages 141-142 in Conference Proceedings, The Second International Conference on Geographic Information Science, Boulder, CO.

Pontius Jr., R. G., A. Agrawal, and D. Huffaker. 2003. Estimating the uncertainty of land-cover extrapolations while constructing a raster map from tabular data. Journal of Gegraphical Systems 5:253-273

Pontius Jr., R. G., L. Claessens, C. Hopkinson, A. Marzouk, E. B. Rastetter, L. C. Schneider, and J. Vallino. 2000. Scenarios of land-use change and nitrogen release in the Ipswich watershed, Massachusetts, USA. in B. O. Parks, K. M. Clarke, and M. P. Crane, editors. Proceedings of the 4th International Conference on Integrating Geographic Information Systems and Environmental Modeling: Problems, prospects, and Needs for Research. Cooperative Institute for Research in Environmental Science, Boulder, CO.

Pontius Jr., R. G., and E. Fedorko. 2005. Spatial distribution of land type in regression models of pollutant loading. Pages 5 in Conference Proceedings of the meeting of the American Society for Photogrammetry and Remote Sensing, Baltimore MD.

Pontius Jr., R. G., D. Huffaker, and K. Denman. 2004. Useful techniques of validation for spatially explicit land-change models. Ecological Modeling 179:445-461

Pontius Jr., R. G., and L. Schneider. 2001. Land-use change model validation by a ROC method for the Ipswich watershed, Massachusetts, USA. Agriculture, Ecosystems & Environment 85:239-248

Pontius Jr., R. G., A. J. Versluis, and N. R. Malizia. 2006. Visualizing certainty of extrapolations from models of land change. Landscape Ecology 21:1151-1166

Pontius, R. G., Jr., and J. Connors. 2006. Expanding the conceptual, mathematical, and practical methods for map comparison. Pages 16 in Conference proceedings of the meeting of Spatial Accuracy 2006, Lisbon, Portugal.

Pontius, R. G., Jr., and J. Connors. 2009. Range of categorical associations for comparison of maps with mixed pixels. Photogrammetric Engineering & Remote Sensing 75:963-969

Pontius, R. G., Jr., and X. Li. 2008. Estimating the land transition matrix based on erroneous maps. Pages 8 in Conference proceedings of Studying, Modeling and Sense Making of Planet Earth, Mytilene, Greece.

Pontius, R. G., Jr., and X. Li. 2009. Land transition estimates from erroneous maps. Journal of Land Use Science doi:10.1080/17474230903222473.

Pontius, R. G., Jr., and N. Neeti. 2009 (in press). Uncertainty in the difference between maps of future land change scenarios. Sustainability Science

Pontius, R. G., Jr., A. J. Versluis, and N. R. Malizia. 2005. Visualizing the certainty for extrapolations from models of landscape change. Pages 6 in Conference proceedings of the meeting of Geocomputation, Ann Arbor, MI. USA.

Portnoy, J. W., and A. E. Giblin. 1997. Biogeochemical effects of seawater restoration to diked salt marshes. Ecological Applications 7:1054-1063

Portnoy, J. W., and A. E. Giblin. 1997. Effects of historic tidal restrictions on salt marsh sediment chemistry. Biogeochemistry 36:275-303

Primack, P. 2001. Going Under. Pages 173, 237-238 in Boston Magazine.

Randall, J. 2005. The effects of nutrient enrichment and predator removal on algal communities in a New England Marsh. B.S. Thesis. Middlebury College, Middlebury, VT.

Raymond, P. A., and J. E. Bauer. 2000. Bacterial utilization and transport of DOC in a temperate estuary: Implications for export to the coastal ocean. Aquatic Microbial Ecology 22:1-12

Raymond, P. A., and J. E. Bauer. 2001. DOC cycling in a temperate estuary: A mass balance approach using natural 14C and 13C isotopes. Limnology and Oceanography 46:655-667

Raymond, P. A., and J. E. Bauer. 2001. Riverine export of aged terrestrial organic matter to the North Atlantic Ocean. Nature 409:497-500

Raymond, P. A., and J. E. Bauer. 2001. Use of 14C and 13C natural abundances for evaluating riverine, estuarine, and coastal DOC and POC sources and cycling: Review and Synthesis. Organic Geochemistry 32:469-485

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. Marine Chemistry 92:353-366

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. Limnology and Oceanography 45:1707-1717

Raymond, P. A., and J. J. Cole. 2001. Gas exchange in rivers and estuaries: Choosing a gas transfer velocity. Estuaries 24:312-217

Raymond, P. A., and C. S. Hopkinson. 2003. Ecosystem modulation of dissolved carbon age in a temperate marsh dominated estuary. Ecosystems 6:694-705

Reed, D. J. 1989. Patterns of Sediment Deposition in Subsiding Coastal Salt Marshes, Terrebonne Bay, Louisianna: The Role of Winter Storms. Estuaries 12:222-227

Rhodes, E. G. 1973. Pleistocene-Holocene sediments interpreted by seismic refraction and wash bore sampling, Plum Island-Castle Neck, MA. Technical Memo No. 40, US Army Corps of Engineers, Coastal Engineering Research Center, Vicksburg, MS.

Rimmer, D. W., and R. D. Deblinger. 1990. Use of a predator exclosure to protect piping plover nests. Journal of Field Ornithology 61:217-223

Riskin, M. L., J. R. Deacon, M. L. Liebman, and K. W. Robinson. 2003. Nutrient and chlorophyll relations in selected streams of the New England Coastal Basins in Massachusetts and New Hampshire, June-September 2001. Water Resources Investigation Report 03-4191, USGS.

Robinson, K. W., J. P. Campbell, and N. A. Jaworski. 2003. Water-quality trends in New England Rivers during the 20th century. Water-Resources Investigation Report 03-4012, USGS.

Robinson, K. W., S. M. Flanagan, J. D. Ayotte, K. W. Campo, A. Chalmers, J. F. Coles, and T. F. Cuffney. 2004. Water Quality in the New England Coastal Basins, Maine, New Hampshire, Massachusetts, and Rhode Island, 1999-2001. Circular 1226, USGS.

Ruber, E., G. Gillis, and P. A. Montagna. 1981. Production of dominant emergent vegetation and of pool algae on a northern Massachusetts salt marsh. Bulletin of the Torrey Botanical Club 108:152-165

Ruber, E., and K. LeFrance. 1983. The effects of temephos (abate) on the respiratory rate of the salt marsh amphipod, Gammarus mucronatus. Bulletin of Environmental Contamination and Toxicology 31:148-151

Ruber, E., and R. E. Murray. 1978. Some ideas about coastal management from production and export studies on a Massachusetts salt marsh. Proceedings of the New Jersey Mosquito Control Association 65:51-58

Salgado, J., M.-J. Costa, H. Cabral, and L. Deegan. 2004. Comparison of fish assemblages in tidal salt marsh creeks and in adjoining mudflat areas in the Tejo estuary. Cahiers de Biologie Marine 45:213-224

Salgado, J., M.-J. Costa, H. Cabral, and L. Deegan. 2004. Nekton use of salt marsh creeks in the upper Tejo Estuary. Estuaries 27:818-825

San Gil, I., K. Baker, J. Campbell, E. G. Denny, K. Vanderbilt, B. Riordan, R. Koskela, J. Downing, S. Grabner, E. Melendez, J. M. Walsh, M. Kortz, J. Conners, L. Yarmey, N. Kaplan, E. R. Boose, L. Powell, C. Gries, R. Schroeder, T. Ackerman, K. Ramsey, B. Benson, J. Chipman, J. Laundre, H. Garritt, D. Henshaw, B. Collins, C. Gardner, S. Bohm, M. O'Brien, J. Gao, W. Sheldon, S. Lyon, D. Bahauddin, M. Servilla, D. Costa, and J. Brunt. 2009. The Long-Term Ecological Research community metadata standardisation project: a progress report. International Journal of Metadata, Semantics and Ontologies 4:141-153

San Gil, I., W. Sheldon, T. Schmidt, M. Servilaa, R. Aguilar, C. Gries, T. Gray, D. Field, J. Cole, J. Yun Pan, G. Palanisamy, D. Henshaw, M. O'Brien, L. Kinkel, K. McMahon, R. Kottman, L. Amaral-Zettler, J. Hobbie, P. Goldstein, R. P. Guralnick, J. Brunt, and W. K. Michener. 2008. Defining Linkages between the GSC and NSF?s LTER Program: How the Ecological Metadata Language (EML) Relates to GCDML and Other Outcomes. Omics 12:151-156 DOI: 10.1089/omi.2008.0015.

Schmitt, C., N. B. Weston, and C. Hopkinson. 1998. A preliminary evaluation of sedimentation rates and species distribution in Plum Island estuary, Massachusetts. Biological Bulletin 195:232-233

Schneider, L., and R. G. Pontius Jr. 2001. Modeling land-use change in the Ipswich watershed, Massachusetts, USA. Agriculture, Ecosystems & Environment 85:83-94

Sears, J. H. 1905. The physical geography, geology, mineralogy, and paleontology of Essex County. Essex Institute, Salem, MA.

Seitzinger, S. P., and A. E. Giblin. 1996. Estimating denitrification in North Atlantic continental shelf sediments. Biogeochemistry 35:235-260

Sheldon, S. P., S. Twichell, and L. A. Deegan. 2004. The effects of long term nutrient addition on a salt marsh community. in New England Estuarine Research Society (NEERS), March 7-9, 2004, Burlington, Vermont.

Simenstad, C., S. Brandt, A. Chalmers, R. Dame, L. Deegan, R. Hodson, and E. Houde. 2000. Habitat-biotic interactions. Pages 427-460 in J. Hobbie, editor. Estuarine Science: A Synthetic Approach to Research and Practice. Island Press, Washington, DC.

Simurda, S. J. 2001. Mass. Destruction. Pages 170, 172, 229-231, 233-234, 236 in Boston Magazine.

Smith, J. B. 1991 (unpublished). Morphodynamics and stratigraphy of the Essex River ebb-tidal delta, Essex, Massachusetts. MS Thesis. Boston University, Boston, MA.

Smith, J. S., M. E. Mather, H. J. Frank, R. M. Muth, J. T. Finn, and S. D. McCormick. 2009. Evaluation of a gastric radio tag insertion technique for anadromous river herring. North American Journal of Fisheries Management 29:367-377 DOI: 10.1577/M08-111.1.

Solorzano, L. 1969. Determination of Ammonia in Natural Waters by the Phenolhypochlorite Method.799-801

Som, M. R. 1990 (unpublished). Stratigraphy and the evolution of a backbarrier region along a glaciated coast of New England: Castle Nec-Essex Bay, MA. MS Thesis. Boston University, Boston, MA.

Sorrensen, C., C. Polsky, and R. Neff. 2006. The Human-Environment Regional Observatory (HERO) Project: Undergraduate Research Findings from Four Study Sites. Geographical Bulletin 47:65-72

Stewart, R. 2009. Separation of river network scale nitrogen removal between surface and hyporheic transient storage compartments. M.S. Thesis. University of New Hampshire, Durham, NH.

Sundareshwar, P. V., J. T. Morris, E. K. Koepfler, and B. Fornwalt. 2003. Phosphorus Limitation of Coastal Ecosystem Processes. Science 299

Sundareshwar, P. V., J. T. Morris, P. J. Pellechia, H. J. Cohen, D. E. Porter, and B. C. Jones. 2001. Occurrence and Ecological Implications of Pyrophosphate in Estuaries. Limnology and Oceanography 46:1570-1577

Sweeney, J., L. Deegan, and R. Garritt. 1998. Population size and site fidelity of Fundulus heteroclitus in a macrotidal saltmarsh creek. Biological Bulletin 195:238-239

Tada, T. 2001. Land use and nitrate loading in small stream catchments. MS Thesis. Clark University, Worcester.

Tessler, S., J. F. Coles, and K. M. Beaulieu. 1999. Inventory of Selected Freshwater-Ecology Studies from the New England Coastal Basins (Maine, New Hampshire, Massachusetts, Rhode Island), 1937-97. Open-File Report 99-467, U.S. Geological Survey.

Thompson, J. R., S. Pacocha, C. Pharino, V. Klepac-Ceraj, D. E. Hunt, J. Benoit, R. Sarma-Rupavtarm, D. L. Distel, and M. F. Polz. 2005. Genotypic diversity within a natural coastal bacterioplankton population. Science 307:1311-1313

Thouin, J. 2008. The biogeochemical influences of nitrate, dissolved oxygen, and dissolved organic carbon on stream nitrate uptake. M.S. Thesis. University of New Hampshire, Durham, NH.

Thouin, J. A., W. M. Wollheim, C. J. Vorosmarty, J. Jacobs, and W. H. McDowell. 2009. The biogeochemical influences of nitrate, dissolved oxygen, and dissolved organic carbon on stream nitrate uptake. Journal of the North American Benthological Society 28:894-907 doi:10.1899/08-183.1.

Tobias, C., A. E. Giblin, J. McClelland, J. Tucker, and B. Peterson. 2003. Sediment DIN fluxes and preferential recycling of benthic microalgal nitrogen in shallow macrotidal estuary. Marine Ecological Progress Series 257:25-36

Tobias, C. R., M. Cieri, B. J. Peterson, L. A. Deegan, J. Vallino, and J. Hughes. 2003. Processing watershed-derived nitrogen in a well-flushed New England estuary. Limnology and Oceanography 48:1766-1778

Tobias, C. R., S. A. Macko, I. C. Anderson, E. A. Canuel, and J. W. Harvey. 2001. Tracking the fate of a high concentration groundwater nitrate plume through a fringing marsh: A combined groundwater tracer and in situ isotope enrichment study. Limnology and Oceanography 46:1977-1989

Tomczyk, R. 2002. Parker River Watershed: Year 3 Watershed Assessment Report. Massachusetts Watershed Initiative, Wilmington, MA.

Torres, R., S. Fagherazzi, D. van Proosdij, and C. Hopkinson. 2006. Salt marsh geomorphology: Physical and ecological effects on landform. Estuarine, Coastal and Shelf Science 69:309-310

Townsend, C. W. 1905. Birds of Essex County. Nuttall Ornithological Club, Cambridge, MA.

Townsend, C. W. 1913. Sand dunes and salt marshes. Dana Estes and Co., Boston, MA.

Townsend, C. W. 1920. Supplement to Birds of Essex County. Nuttall Ornithological Club, Cambridge, MA.

Townsend, C. W. 1923. Beach grass. Marshall Jones Co., Boston, MA.

Twitchell, S. 2003. The effects of long term nutrient addition on a salt marsh community. Honors, BS Thesis. Middleburry College, Middlebury, VT.

Uhlenhopp, A. G., J. E. Hobbie, and J. J. Vallino. 1995. Effects of land use on the degradability of dissolved organic matter in three watersheds of the Plum Island Sound estuary. Biological Bulletin 189:256-257

Vallino, J. 2000. Improving marine ecosystem models: Use of data assimilation and mesocosm experiments. Journal of Marine Research 58:117-164

Vallino, J., C. S. Hopkinson, R. Garritt, and J. Tucker. 1999. A non-linear inverse technique to estimate estuarine ecosystem metabolism from whole system oxygen measurements. in Proceedings of the 3rd International Symposium on Ecohydraulics, Salt Lake City, UT.

Vallino, J., C. S. Hopkinson, and R. H. Garritt. 2005. Estimating estuarine gross production, community respiration and net ecosystem production: A nonlinear inverse technique. Ecological Modeling 187:281-296

Vallino, J. J. 2003. Modeling microbial consortiums as distributed metabolic networks. Biological Bulletin 204:174-179

Vallino, J. J. 2009 (in press). Ecosystem biogeochemistry considered as a distributed metabolic network ordered by maximum entropy production. Philosophical Transactions of The Royal Society B

Vallino, J. J., and C. S. Hopkinson. 1998. Estimation of dispersion and characteristic mixing times in Plum Island Sound Estuary. Estuarine, Coastal and Shelf Science 46:333-350

Vallino, J. J., C. S. Hopkinson, and J. E. Hobbie. 1996. Modeling bacterial utilization of dissolved organic matter: Optimization replaces Monod growth kinetics. Limnology and Oceanography 41:1591-1609

Vallino, J. J., and G. Stephanopoulos. 1993. Metabolic flux distributions in Corynebacterium glutamicum during growth and lysine production. Biotechnology and Bioengineering 41:633-646

Versluis, A. J., R. G. Pontius Jr., and N. R. Malizia. 2004. Visualizing the rate at which the accuracy of a land change prediction decays. Pages 29 in Conference proceedings of the meeting of the University Consortium for Geographic Information Science, Silver Spring, MD.

Vorosmarty, C., and B. Peterson. 2000. Macro-scale models of water and nutrient flux to the coastal zone. Pages 43-80 in J. Hobbie, editor. Estuarine Science: A Synthetic Approach to Research and Practice. Island Press, Washington, DC.

Vorosmarty, C. J., C. Li, J. Sun, and Z. Dai. 1998. Emerging impacts of anthropogenic change on global river systems: The Chinese example. Pages 210-244 in J. Galloway and J. Melillo, editors. Asian Change in the Context of Global CHange: Impacts of Natural and Anthropogenic Changes in Asia on Global Biogeochemical Cycles. Cambridge University Press, Cambridge.

Wainright, S. C., and C. S. Hopkinson. 1997. Effects of sediment resuspension on organic matter processing in coastal environments: A simulation model. Journal of Marine Systems 11:353-368

Walsh, T. W. 1989. Total Dissolved Nitrogen in Seawater: a New High-temperature Combustion Method and a Comparison with Photo-Oxidation. Marine Chemistry 26:295-311

Walter, J. F., A. S. Overton, K. H. Ferry, and M. E. Mather. 2003. Atlantic coast feeding habits of striped bass: a synthesis of data supporting a comprehensive coast-wide understanding of the trophic biology. Fisheries Management and Ecology 10:349 - 360

Wan, Z., and J. Vallino. 2005. An inverse ecosystem model of year-to-year variations with first order appoximation to the annual mean fluxes. Ecological Modeling 187:369-388

Wang, W., J. T. Morris, A. Prokopenko, and S. Neubauer. 2009 (in review). Stable isotope signatures of CO2 evolution and carbon dynamics in east coast salt marsh soils, USA.

Weinstein, M. J., and S. G. Connors. 2001. Parker River Watershed: Water Quality Assesment Report. 91-AC-1, Department of Environmental Protection: Division of Watershed Managment, Worcester, MA.

Weston, N. B., S. S. Carini, A. E. Giblin, G. T. Banta, C. S. Hopkinson, and J. Tucker. 1996. Estimating denitrification in sediments of the Parker River estuary, Massachusetts. Biological Bulletin 191:334-335

Weston, N. B., A. E. Giblin, G. Banta, C. S. Hopkinson, and J. Tucker. 2009 (accepted). The effects of varying salinity on ammonium exchange in estuarine sediments of the Parker River, Massachusetts. Estuaries and Coasts

Weston, S., B. McAneney, M. Fregeau, and J. Buttner. 2003. Moving towards commercialization of softshell clam culture on Massachusetts' Northshore. J. Shellfish Res. 22:302

Wilkner, J., J. J. Vallino, G. Steward, D. C. Smith, and F. Azam. 1993. Nucleic acids from the host bacterium as a major source of nucleotides for three marine bacteriophages. FEMS Microbiology Ecology 12:237-248

Williams, L., G. C. Noblitt IV, and R. Buchsbaum. 2001. The effects of salt marsh haying on benthic algal biomass. Biological Bulletin 201:287-288

Williams, M., C. Hopkinson, E. Rastetter, and J. Vallino. 2004. N budgets and aquatic uptake in the Ipswich River basin, northeastern Massachusetts. Water Resources Research 40:1-12

Williams, M., C. Hopkinson, E. Rastetter, J. Vallino, and L. Claussens. 2005. Relationships of land use and streamwater solute concentrations in the Ipswich River basin, northeastern Massachusetts. Water, Air, and Soil Pollution 161

Williams, M., C. S. Hopkinson, and R. H. Garritt. 2010 (in review). Effects of urbanization on the water quality of the Ipswich River basin, Massachusetts. Journal of Environmental Quality

Williams, M. R., S. Filoso, and P. Lefebvre. 2004. Effect of land-use change on solute inputs to floodplain lakes of the central Amazon. Biogeochemistry 68:259-275

Wollheim, W., B. Pellerin, C. Vorosmarty, and C. Hopkinson. 2005. N retention in urbanizing headwater catchments. Ecosystems 8:871-884 DOI: 10.1007/s10021-005-0178-3.

Wollheim, W. M. 2005. The controls of watershed nutrient export. Ph.D. Thesis. University of New Hampshire, Durham, NH.

Wollheim, W. M., B. J. Peterson, C. Vorosmarty, C. Hopkinson, and S. A. Thomas. 2008. Dynamics of N removal over annual time scales in a suburban river network. Journal of Geophysical Research-Biogeosciences 113 doi:10.1029/2007JG000660.

Wollheim, W. M., C. J. Vorosmarty, A. F. Bouwman, P. A. Green, J. Harrison, E. Linder, B. J. Peterson, P. A. Green, S. Seitzinger, and J. P. M. Syvitski. 2008. Global N removal by freshwater aquatic systems A spatially distributed, within-basin approach. Global Biogeochemical Cycles 22 doi:10.1029/2007GB002963.

Wollheim, W. M., C. J. Vorosmarty, B. J. Peterson, S. P. Seitzinger, and C. S. Hopkinson. 2006. Relationship between river size and nutrient removal. Geophysical Research Letters 33 doi:10.1029/2006GL025845 2006.

Wright, R. T. 1984. Dynamics of pools of dissolved organic carbon. in J. E. Hobbie and P. L. Williams, editors. Heterotrophic Activity in the Sea. Plenum Publishing Co.

Wright, R. T. 1988. Methods for evaluating the interaction of substrate and grazing as factors controlling planktonic bacteria. Archives Hydrobiol. Beih. 31:229-242

Wright, R. T. 1988. A model for short-term control of the bacterioplankton by substrate and grazing. Hydrobiologia 159:111-117

Wright, R. T., and R. B. Coffin. 1983. Planktonic bacteria in estuaries and coastal waters of northern Massachusetts: Spatial and temporal distribution. Marine Ecology Progress Series 11:205-216

Wright, R. T., and R. B. Coffin. 1984. Factors affecting bacterioplankton density and productivity in microbial ecology. in M. J. Klug and C. A. Reddy, editors. Current Perspectives in Microbial Ecology.

Wright, R. T., and R. B. Coffin. 1984. Measurements of bacterial production and microzooplankton in an estuarine-coastal water system of northern Massachusetts. Microbial Ecology 10:137-149

Wright, R. T., and R. B. Coffin. 1987. Dynamics of planktonic bacteria and heterotrophic microflagellates in the Parker Estuary, Northern Mass. Continental Shelf Research 7:1383-1397

Wright, R. T., R. B. Coffin, C. P. Ersing, and D. Pearson. 1982. Field and laboratory measurements of bivalve filtration of natural marine bacterioplankton. Limnology and Oceanography 27:91-98

Young, T., S. Komarow, L. Deegan, and R. Garritt. 1999. Population size and summer home range of the green crab, Carcinus maenus, in salt marsh tidal creeks. Biological Bulletin 197:292-299

Yuval, B. 1990. Mating behavior of male deer ticks, Ixodes dammini, (Acari: Ixodidae). Journal of Insect Bechavior 3:765-772

Zappa, C. J., W. R. McGillis, P. A. Raymond, J. B. Edson, E. J. Hintsa, H. J. Zemmelink, J. W. H. Dacey, and D. T. Ho. 2007. Environmental turbulent mixing controls on air-water gas exchange in marine and aquatic systems. Geophysical Research Letters 34 doi:10.1029/2006GL028790.

Zappa, C. J., P. A. Raymond, E. A. Terray, and W. R. McGillis. 2003. Variation in surface turbulence and the gas transfer velocity in estuaries over a tidal cycle in a macrotidal estuary. Estuaries 26:1401-1415

Zarriello, P. J. 2002. Simulation of resevoir storage and firm yields of three surface-water supplies, Ipswich River basin, Massachusetts. Water-Resources Investigation Report 02-4278, U.S. Geological Survey.

Zarriello, P. J., and K. G. Ries III. 2000. A precipitation-runoff model for analysis of the effects of water withdrawals on streamflow, Ipswich River basin, Massachusetts. Water-Resources Investigation Report 00-4029, U.S. Geological Survey.

Zarriello, P. J., and K. G. Ries III. 2001. Effects of water withdrawals on streamflow in the Ipswich River basin, Massachusetts. Fact Sheet FS-00-160, U.S.Geological Survey.

Zwart, G., B. C. Crump, M. P. Kamst-van Agterveld, F. Hagen, and S. K. Han. 2002. Typical freshwater bacteria: an analysis of available 16S rRNA gene sequences from plankton of freshwater lakes and rivers. Aquatic Microbial Ecology 28:141-155

Zwart, G., E. J. van Hannen, M. P. Kamst-van Agerveld, K. van der Gucht, E. S. Lindstrom, J. Van Wichelen, T. Lauridsen, B. C. Crump, S. K. Han, and S. Declerck. 2003. Rapid screening for freshwater bacterial groups using reverse line blot hybridization. Applied Environmental Microbiology 69:5875-5883