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Availability of Trace Elements in Sediments to Aquatic Organisms
Concentrations of potentially toxic elements in sediments are orders of magnitude higher than concentrations of these elements in water. The ability of the aquatic environment to assimilate many toxic wastes depends upon how available this concentrated sediment-bound pool of elements is to aquatic organisms. Development of realistic pollution regulations, in turn, depend upon predicting assimilation capacities. Assessment of biological indicator data for mineral exploration and pollution assessment also depend upon understanding factors affecting the biological availability of trace elements bound to sediments. It is established that the same biota in different environments may differ widely in their susceptibility or their response to trace elements, and that these differences may, at least partly, be related to the differences in the availability of metals in sediments; however, little is known about the geochemical and physiological factors which influence the transport of metals from sediments to organisms. Objectives of this project are to: (1) study the partitioning of trace metals among the components of sediments, and identify the processes which control partitioning; (2) study the influence of geochemical partitioning of trace metals in sediments upon metal uptake and metal effects in organisms which contact sediments directly; (3) Study physiological characteristics of aquatic organisms that affect metal uptake; (4) improve methodology that makes use of biota and sediments as indicators of geochemical conditions; (5) develop indices or models for predicting the bioavailability of metals, after their release to the aquatic environment; and (6) develop methods for assessing the presence of biological affects from toxic wastes in aquatic communities in nature. For additional information, see Ecology and Contaminants site.
REPORTS PUBLISHED 1999-2009
Carter, J L., and Fend, S.V., in press, Setting limits: the development and use of factor-ceiling distributions for an urban assessment using macroinvertebrates, in Brown, L.R., Hughes, R.M., Gray, R., and Meador, M.R., eds., Effects of urbanization on stream ecosystems: American Fisheries Society Symposium, Bethesda, Maryland.
Carter, J.L., Resh, V.H., Rosenberg, D.M., and Reynoldson, T.B., in press, Biomonitoring in North American rivers: a comparison of methods used for benthic macroinvertebrates in Canada and the United States, in Flaim, G., and Ziglio, G., eds., Biological Monitoring of Rivers: Applications and Perspectives: John Wiley and Sons, New York.
Fend, S.V., Carter, J.L., and Kearns, F.R., in press, Relationships of field habitat measurements, visual habitat indices and land cover to benthic macroinvertebrates in urbanized streams of the Santa Clara Valley, California, in Brown, L.R., Hughes, R.M., Gray, R., and Meador, M.R., eds., Effects of urbanization on stream ecosystems: American Fisheries Society Symposium, Bethesda, Maryland.
Thompson, J.K., Koseff, J.R., Monismith, S.G., and Lucas, L.V., in press, Shallow water processes govern system-wide phytoplankton bloom dynamics: A field study. Journal of Marine Systems, doi:10.1016/j.jmarsys.2007.12.006. (on-line abstract of preprint)
Lucas, L.V., Koseff, J.R., Monismith, S.G., and Thompson, J.K., 2009, Shallow water processes govern system-wide phytoplankton bloom dynamics - A modeling study: Journal of Marine Systems, v. 75, no. 1-2, p. 70-88. doi:10.1016/j.jmarsys.2008.07.011. (on-line abstract of journal article)
Lucas, L.V., Thompson, J.K., and Brown, L.R., 2009, Why are diverse relationships observed between phytoplankton biomass and transport time?: Limnology and Oceanography, v. 54, no. 1, 381-390. (on-line abstract or on-line article in pdf format, 694 KB, published by the Americal Society of Limnology and Oceanography with open acess)
Croteau, M.N., and Luoma, S.N., 2008, A biodynamic understanding of dietborne metal uptake by a freshwater invertebrate: Environmental Science and Technology, v. 42, p. 1,801-1,806. (on-line abstract or on-line journal article in pdf format, 232 KB, published by the American Chemical Society, not subject to US copyright)
Jones, N.L., Thompson, J.K., and Monismith, S.G., 2008, A note on the effect of wind waves on vertical mixing in Franks Tract Sacramento-San Joaquin Delta, California: San Francisco Estuary and Watershed Science, v. 6, no. 2, Article 4. (on-line abstract or on-line paper in pdf format, 2505 KB, open-access journal)
Luoma, S.N., Moore, J.N., Farag, A.M., Hillman, T.A., Cain, D.J., Hornberger, M., Axtmann, E., 2008, Mining impacts on fish in the Clark Fork River, Montana: a field ecotoxicological case study, in DiGuilio, R., and Hinton, D., eds: The Toxicology of Fishes, CRC Press, Boca Raton, p 779-805.
McLeod, P.B., Luoma, S.N., and Luthy, R.G., 2008, Biodynamic Modeling of PCB Uptake by Macoma balthica and Corbicula fluminea from Sediment Amended with Activated Carbon: Environmental Science and Technology, v. 42, p. 484 - 490. (on-line abstract of journal article)
Stewart, A.R., Saiki, M.K., Kuwabara, J.S., Alpers, C.N., Marvin DiPasquale, M., and Krabbenhoft, D.P., 2008, Influence of plankton mercury dynamics and trophic pathways on mercury concentrations of top predator fish of a mining-impacted reservoir: Canadian Journal of Fisheries and Aquatic Sciences, v. 65, no.11, p. 2351-2366(16). (on-line abstract of journal article).
Takesue, R.K., Bacon, C.R., and Thompson, J.K., 2008, Influences of organic matter and calcification rate on trace elements in aragonitic estuarine bivalve shells: Geochimica et Cosmochimica Acta, v. 72, no. 22, p. 5431-5445. (on-line abstract of journal article)
von Stackelberg, K., Luoma, S., McCormick, R., Skrabis, K., Dorward-King, E., and Polasky, S., 2007, Complexity in Ecological Systems in Valuation of Ecological Resources, in Stahl, Jr, R.G., Kapustka, L.A., Munns, Jr., W.R., and Bruins, R.J.F., eds., Integration of Ecological Risk Assessment and Socioeconomics in Environmental Decision Making: SETAC Press, Pensacola, Chapter 5, p. 98-128.
Xie, L., Lambert, D., Martin, C., Cain, D.J., Luoma, S.N., Buchwalter, D., 2008, Cadmium biodynamics in the oligochaete Lumbriculus variegatus and its implications for trophic transfer Aquatic Toxicology, v. 86, no. 2, p. 265-271. (on-line abstract of journal article)
Brown, L.R, Thompson, J.K., Higgins, K., and Lucas, L.V., 2007, Population density, biomass, and age-class structure of the invasive clam Corbicula fluminea in rivers of the lower San Joaquin River Watershed, California: Western North American Naturalist, v. 67, p. 572-586. (on-line abstract of journal article)
Buchwalter, D.B., Cain, D.J., Clements, W.H., and Luoma, S.N., 2007, Using biodynamic models to reconcile differences between laboratory toxicity tests and field biomonitoring with aquatic insects: Environmental Science and Technology, v. 41, p. 4,821-4,828. (on-line abstract of journal article)
Croteau, M.-N., and Luoma, S.N., 2007, Characterizing dissolved Cu and Cd uptake in terms of the biotic ligand and biodynamics using enriched stable isotopes: Environmental Science and Technology, v. 41, p. 3,140-3,145. (on-line abstract or on-line article in pdf format, 129KB, published by American Chemical Society; not subject to U.S. copyright)
Croteau, M-N., Luoma, S.N., and Pellet, B. 2007, Determining metal assimilation efficiency in aquatic invertebrates using enriched stable isotope tracers: Aquatic Toxicology, v. 83, p. 116-125. (on-line journal article)
Flegal, A.R., Brown, C.L., Squire, S., Ross, J.R.M., Scelfo, G.M., and Hibdon, S., 2007, Spatial and temporal variations in silver contamination and toxicity in San Francisco Bay: Environmental Research, v. 105, p. 34-52. (on-line abstract of journal article)
Kuwabara, J.S., Lynch, D.D., Topping, B.R., Murphy, F., Carter, J.L., Simon, N.S., Parchaso, F., Wood, T.M., Lindenberg, M.K., Wiese, K., and Avanzino, R., 2007, Quantifying the benthic source of nutrients to the water column of Upper Klamath Lake, Oregon: U.S. Geological Survey Open-File Report 2007-1276, 39 p. (on-line summary or on-line report in pdf format, 1.2 MB)
Kuwabara, J.S., Topping, B.R., Woods, P.F., and Carter, J.L., 2007, Free zinc ion and dissolved orthophosphate effects of phytoplankton from Coeur d-Alene Lake, Idaho: Environmental Science and Technology, v. 41, p. 2,811-2,817. (on-line abstract or on-line article in pdf format, 508KB, published by American Chemical Society; not subject to U.S. copyright)
Lorenzi, A.H., Cain, D. J., Parchaso, F. Thompson, J.K., Luoma, S.N., Hornberger, M.I., Dyke, J.L. Dyke, Cervantes, R., and Shouse, M.K., 2007, Near-Field Receiving Water Monitoring of Trace Metals and a Benthic Community Near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California, 2006: U.S. Geological Survey Open File Report 2007-1199, 128p. (on-line abstract or on-line report in pdf format, 1.3 MB)
Luoma, S.N., and Löfstedt, R.E., 2007, Contaminated salmon and the public's trust: Environmental Science & Technology, v. 41. no. 6, p. 1,811-1,814.
Martin, C.A., Luoma, S.N., Cain, D.J., Buchwalter, D.B, 2007, Cadmium Ecophysiology in Seven Stonefly (Plecoptera) Species: Delineating Sources and Estimating Susceptibility: Environmentat Science and Technology, v. 41, p. 7171-7177. (on-line abstract of journal article)
McLeod, P.B., Van den Heuvel-Greve, M.J., Luoma, S.N., Luthy, R.G., 2007, Biological uptake of polychlorinated biphenyls by Macoma balthica from sediment amended with activated carbon: Environmental Toxicolology and Chemistry, v. 26, no. 5, p. 980-987. (on-line abstract of journal article)
Thompson, B., Adelsbach, T., Brown, C., Hunt, J., Kuwabara, J., Neale, J., Ohlendorf, H., Schwarzbach, S., Spies, R., and Taberski, K., 2007, Biological effects of anthropogenic contaminants in the San Francisco estuary: Environmental Research, v.105, p. 156-174. (on-line abstract of journal article)
Cain, D.J., Buchwalter, D.B., and Luoma, S.N., 2006, Influence of metal exposure history on the bioaccumulation and subcellular distribution of aqueous cadmium in the insect Hydropsyche californica: Environmental Toxicology and Chemistry, v. 25, p. 1,042-1,049. (on-line abstract for journal article)
Cain, D.J., Parchaso, F., Thompson, J.K., Luoma, S.N., Lorenzi, A.H., Moon, E., Shouse, M.K., Hornberger, M.I., Dyke, J.L., and Cervantes, R., 2006, Near-field receiving water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in South San Francisco Bay, California -- 2005: U.S. Geological Survey Open-File Report 2006-1152, 120 p. (on-line abstract or on-line report in pdf format, 1.5MB)
Kuwabara, J.S., Topping, B.R., Woods, P.F., Carter, J.L., and Hager, S.W., 2006, Interactive effects of dissolved zinc and orthophosphate on phytoplankton from Coeur d'Alene Lake, Idaho: U.S. Geological Survey Scientific Investigations Report 2006-5091, 47 p. (on-line executive summary or on-line report in pdf format, 32.9MB)
Lopez, C.B., Cloern , J.E., Schraga, T.S., Little, A.J., Lucas, L.V., Thompson, J.K., and Burau, J.R., 2006, Ecological values of shallow-water habitats: Implications for the restoration of disturbed ecosystems: Ecosystems, v. 9, p. 422-440. (on-line abstract of journal article)
Presser, T.S. and Luoma, S.N. , 2006, Forecasting selenium discharges to the San Francisco Bay-Delta Estuary: Ecological effects of a proposed San Luis Drain extension: U.S. Geological Survey Professional Paper 1646, 196 p. (on-line abstract or on-line article in pdf format, 5.5MB)
Rainbow, P.S., Poirie, L., Smith, B.D., Brix, K.V. and Luoma, S.N., 2006, Trophic transfer of trace metals: Subcellular compartmentalization in a polychaete and assimilation by a decapod crustacean: Marine Ecology Progress Series, v. 308, p. 91-100. (on-line abstract of journal article)
Rainbow, P.S., Poirie, L., Smith, B.D., Brix, K.V. and Luoma, S.N., 2006, Trophic transfer of trace metals from the polychaete worm Nereis diversicolor to the polychaete N. virens and the decapod crustacean Palaemonetes varians: Marine Ecology Progress Series, v. 321, p. 167-181. (on-line abstract of journal article)
Buchwalter, D.B., and Luoma, S.N., 2005, Differences in dissolved cadmium and zinc uptake among stream insects: Mechanistic explanations: Environmental Science and Technology, v. 39, p. 498-504. (on-line abstract or on-line paper in pdf format, published by American Chemical Society; not subject to U.S. copyright)
Carter, J.L., and Resh, V.H., 2005, Pacific Coast Rivers of the coterminous United States, in Benke, A.C., and Cushing, C.E., eds., Rivers of North America: Amsterdam, Elsevier Academic Press, p. 541-589 .
Croteau, M.N., and Luoma, S.N., 2005, Delineating copper accumulation pathways for the freshwater bivalve Corbicula using stable copper isotopes: Environmental Toxicology and Chemistry, v. 24, no. 11, p. 2,871-2,878. (on-line abstract of journal article)
Croteau, M-N., Luoma, S.N, and Stewart, A.R., 2005, Trophic transfer of metals along freshwater food webs: Evidence of cadmium biomagnification in nature: Limnology & Oceanography v. 50, no 5, p. 1,511-1,519. (on-line abstract of journal article)
Kearns, F.R., Kelly, N.M., Carter, J.L., and Resh, V.H., 2005, A method for the use of landscape metrics in freshwater research and management: Landscape Ecology, v. 20, no. 1, p. 113-125. (on-line abstract of journal article)
Luoma, S.N., and Rainbow, P.S., 2005, Why is metal bioaccumulation so variable? -- Biodynamics as a unifying concept: Environmental Science and Technology, v. 39, no. 7, p. 1,921-1,931. (on-line abstract or on-line journal article in pdf format, 268 KB - published by American Chemical Society; not subject to U.S. copyright)
Thompson, J.K., 2005, One estuary, one invasion, two responses: Phytoplankton and benthic community dynamics determine the effect of an estuarine invasive suspension-feeder, in Dame, R.F., and Olenin, S., eds, The Comparative Roles of Suspension-Feeders in Ecosystems: The Netherlands, Springer Publishers, p. 291-316.
Kuwabara, J.S., Topping, B.R., Moon, G.E., Husby, P., Lincoff, A., Carter, J.L., and Croteau, M.N., 2005, Mercury accumulation by lower-trophic-level organisms in lentic systems within the Guadalupe River watershed, California: U.S. Geological Survey Scientific Investigations Report 2005-5037, 34 p. (on-line abstract or on-line report in pdf format, 8.6 MB)
Brown, C.L., Luoma, S.N., Parchaso, F., and Thompson, J.K, 2004, Lessons learned about metals in the Estuary: The importance of long-term clam accumulation data in The Pulse of the Estuary: Monitoring and Managing Water Quality in the San Francisco Estuary: San Francisco Estuary Institute Contribution 78, p. 38-45. (on-line publication in pdf format)
Cain, D.J., Luoma, S.N., and Wallace, W.G, 2004, Linking metal bioaccumulation of aquatic insects to their distributions in a mining-impacted river: Environmental Toxicology and Chemistry, v. 23, p. 1,463- 1,473. (on-line abstract)
Croteau, M.-N., Luoma, S.N., Topping, B.R., and Lopez, C.B., 2004, Stable metal isotopes reveal copper accumulation and loss dynamics in the freshwater bivalve Corbicula: Environmental Science and Technology, v. 38, p. 5,002-5,009. (on-line abstract or on-line pdf file, 114kb - published by the American Chemical Society; not subject to U.S. copyright.)
Dodge, K.A., Hornberger, M.I., Lavigne, I.R., 2004, Water-quality, bed-sediment and biological data (October 2002 through September 2003) and statistical summaries of data for streams in the upper Clark Fork Basin, Montana: U.S. Geological Survey Open-File Report 2004-1340, 107 p.
Lee, J-S., Lee, B-G., Luoma, S.N., Yoo, H., 2004, Importance of equilibration time in the partitioning and toxicity of zinc in spiked sediment bioassays: Environmental Toxicology and Chemistry, v. 23, no. 1; p. 65-71. (on-line abstract)
Luoma, S.N., and Cloern, J. E., 2004, Water 2025: The CALFED Bay-Delta Program: People, Land and Water, Department of Interior, v.2/04, p. 23.
McLeod, P.B., van den Heuvel-Greve, M.J., Allen-King, R.M., Luoma, S.N., Luthy, R.G., 2004, Effects of particulate carbonaceous matter on the bioavailability of benzo[a]pyrene and 2,2',5,5'-tetrachlorobiphenyl to the clam, Macoma balthica: Environmental Science and Technology, v. 38, no. 17; p. 4,549-45,56
Moon, E., Luoma, S.N., Cain, D.J., Hornberger M.I., and David, C.P.C., 2004, Near field receiving water monitoring of trace metals in clams (macoma balthic) and sediments near the Palo Alto water quality control plant in south San Francisco Bay, California, 2000: U.S. Geological Survey Open-File Report 2004-1213, 44 p. + appendices. (on-line abstract or on-line report, in pdf format - 828 KB)
Presser, T.S., and Luoma, S.N., 2004, Linking Selenium Sources to Ecosystems: San Francisco Bay-Delta Model: U.S. Geological Survey Fact Sheet 2004-3091. (on-line fact sheet and on-line fact sheet in pdf format, 1 MB)
Schlekat, C.E., Purkerson, D.G., and Luoma, S.N., 2004, Modeling selenium bioaccumulation through arthropod food webs in San Francisco Bay, California, USA. Environ Toxicol. Chem, v. 23, no. 12, p. 3003-3010. (on-line abstract)
Shouse, M.K., Parchaso, F., and Thompson, J.K., 2004, Near-field receiving water monitoring of a benthic community near the Palo Alto Water Quality Control Plant in South San Francisco Bay: February 1974 through December 2003: U.S. Geological Survey Open-File Report 2004-1210. (on-line abstract or on-line report in pdf format - 595 KB)
Stewart, A.R., Luoma, S.N., Schlekat, C.E., Doblin, M.A., and Hieb, K.A., 2004, Food web pathway determines how selenium affects aquatic ecosystems: A San Francisco Bay case study: Environmental Science and Technology, v. 38, no. 17, p. 4,519-4,526. .(on-line abstract)
Topping, B.R., Kuwabara, J.S., Marvin-DiPasquale, M.C., Agee, J.L., Kieu, L.H., Flanders, J.R., Parchaso, F., Hager, S.W., Lopez, C.B., and Krabbenhoft, D.P., 2004, Sediment remobilization of mercury in south San Francisco Bay, California: U.S. Geological Survey Scientific Investigations Report 2004-5196, 27 p. + appendices. (on-line executive summary or on-line report in pdf format, 6.9 MB)
Yoo, H., Lee, J.S., Lee, B.G., Lee, I.T., Schlekat, C.E., Koh, C.H., Luoma, S.N., 2004, Uptake pathway for Ag bioaccumulation in three benthic invertebrates exposed to contaminated sediments: Marine Ecology -Progress Series, v. 270, p. 141-152. (on-line abstract)
Brown, C.L., Parchaso, F., Thompson, J.K., and Luoma, S.N., 2003, Assessing toxicant effects in a complex estuary: A case study of effects of silver on reproduction in the bivalve, Potamocorbula amurensis, in San Francisco Bay: Human and Ecological Risk Assessment, v. 9, p. 95-119. (on-line abstract)
Chauvaud, L., Thompson, J.K., Cloern, J.E., and Thouzeau, G., 2003, Clams as CO2 generators: The Potamocorbula amurensis example in San Francisco Bay: Limnology and Oceanography, v. 48, p. 2,086-2,092. (on-line article, pdf format)
Davis, J.A., Yee, D., Collins, J.N., Schwarzbach, S.E., and Luoma, S.N., 2003, Potential for Increased Mercury Accumulation in the Estuary Food Web: San Francisco Estuary and Watershed Science: v. 1, no. 1, Article 4. (on-line abstract or on-line article in pdf format)
Dodge, K.A., Hornberger, M.I., Lavigne, I.R., 2003, Water-quality, bed-sediment, and biological data (October 2001 through September 2002) and statistical summaries of data for streams in the upper Clark Fork basin, Montana: U.S. Geological Survey Open-File Report 03-0356, 95 p.
Jacobs, K.L., Luoma, S.N., and Taylor, K.A., 2003, CALFED: An Experiment in Science and Decisionmaking: Environment, v. 45, no. 1, p. 30-34. (on-line article)
Kuwabara, J.S., Alpers, C.N., Marvin-Dipasquale, M., Topping, B.R., Carter, J.L.,. Stewart, A.R.,. Fend, S.V., Parchaso, F., Moon, G.E., and Krabbenhoft, D.P., 2003, Sediment-water interactions affecting dissolved-mercury distributions in Camp Far West Reservoir, California: U.S. Geological Survey Water-Resources Investigations Report 03-4140. (on-line abstract or on-line report in pdf format, 4.3MB)
Kuwabara, J.S., Woods, P.F., Berelson, W.M., and Balistrieri, L.S., Carter, J.L., Topping, B.R., and Fend, S.V., 2003, Importance of sediment-water interactions in Coeur d'Alene Lake, Idaho, USA: Management implications: Environmental Management, v. 32, p. 348-359. (on-line abstract or on-line report in pdf format, 975KB)
Maret, T. R., Cain, D. J., MacCoy, D. E., and Short, T. M., 2003, Response of benthic invertebrate assesmblages to metal exposure and bioaccumulation associated with hard-rock mining in northwestern streams, USA: Journal of the North American Benthological Society, v. 22, no. 4, p. 598-620. (on-line abstract)
Moon, E., David, C.C., Luoma, S.N., Cain, D.J., Hornberger, M.I., Lavigne, I.R., 2003, Near field receiving water monitoring of trace metals in clams (Macoma balthica) and sediments near the Palo Alto Water Quality Control Plant in South San Francisco Bay, California: 2002: U.S. Geological Survey Open-File Report 03-339, 12 p. (on-line abstract)
National Research Council, 2003, Bioavailability of contaminants in soils and sediments; processes, tools, and applications: National Academy Press, Washington, D.C., 420 p. (on-line book)
Purkerson, D.G., Dobin, M.A., Bollens, S.M., Luoma, S.N., and Cutter, G.A., 2003, Selenium in San Francisco Bay zooplankton: Potential effects of hydrodynamics and food web interactions: Estuaries, v. 26, no 4A, p. 956-969.
Shouse, M.K., Parchaso, F., and Thompson, J.K., 2003, Near-field receiving water monitoring of a benthic community near the Palo Alto Water Quality Control Plant in South San Francisco Bay, February 1974 through December 2002: U.S. Geological Survey Open-File Report 03-224, 36 p. and appendices. (on-line abstract or on-line report in pdf format - 0.52 MB)
Stewart, A.R., Stern, G.A., Lockhart, W.L., Kidd, K.A., Salki, A.G., Stainton, M.P., Koczanski, K., Rosenberg, G.B., Savoie, D.A., Billeck, B.N., Wilkinson, P., and Muir, D.C.G., 2003, Assessing trends in organochlorine concentrations in Lake Winnipeg fish following the 1997 Red River Flood: Journal of Great Lakes Research, v. 29, no. 2, p. 332-354. (on-line abstract)
Taylor, K.A., Jacobs, K.L., Luoma, S.N., 2003, CALFED: An experiment in science and decisionmaking: Environment, v. 45, no. 1, p. 30-41.
Wallace, W.G., and Luoma, S.N., 2003, Subcellular compartmentalization of Cd and Zn in two bivalves. II. Significance of trophically available metal (TAM): Marine Ecology - Progress Series, v. 257, p. 125-137. (on-line abstract)
Wallace, W.G., Lee, B.G., and Luoma, S.N., 2003, Subcellular compartmentalization of Cd and Zn in two bivalves. I. Significance of metal-sensitive fractions (MSF) and biologically detoxified metal (BDM): Marine Ecology - Progress Series, v. 249, p. 183-197. (on-line abstract)
Baines, S.B., Fisher, N.S., and Stewart, A.R., 2002, Assimilation and retention of selenium and other trace elements from crustacean food by juvenile striped bass (Morone saxatilis): Limnology and Oceanography, v. 47, no. 3, p. 646-655. (on-line abstract)
Crimaldi, J.P., Thompson, J.K., Rosman, J.H., Lowe, R.J., Koseff, J.R., 2002, Hydrodynamics of larval settlement: The influence of turbulent stress events at potential recruitment sites: Limnology and Oceanography, v. 47, p. 1137-1151. (on-line abstract or on-line pdf file)
David, C.P.C. Luoma, S.N., Brown, C.L., Cain, D.J., Hornberger, M.I., and Lavigne, I.R., 2002, Near field receiving water monitoring of trace metals in clams (macoma balthica) and sediments near the Palo Alto water quality control plant in South San Francisco Bay, California: 1999-2001: U.S. Geological Survey Open-File Report 02-453, 44 p. (on-line abstract or on-line report in pdf format, 1.6MB)
Dodge, K.A., Hornberger, M.I., and David, C.P., 2002, Water-quality, bed-sediment, and biological data (October 2000 through September 2001) and statistical summaries of data for streams in the Upper Clark Fork Basin, Montana: U.S. Geological Survey Open-File Report 02-358.
Griscom, S.B., Fisher, N.S., and Luoma, S.N., 2002, Kinetic modeling of Ag, Cd, and Co bioaccumulation in the clam Macoma balthica: quantifying dietary and dissolved sources: Marine Ecology Program Series, v. 240, p. 127-141. (on-line abstract)
Kuwabara, J.S., Marvin-Dipascuale. M., Praskins, W., Byron, E., Topping, B.R., Carter, J.L., Fend, S.V., Parchaso, F., Krabbenhoft, D.P., and Gustin, M.S., 2002, Flow of dissolved forms of mercury across the sediment-water interface in Lahontan Reservoir, Nevada: U.S. Geological Survey Water-Resources Investigations Report 02-4138, 48 p. (on-line abstract or on-line report in pdf format, 2.7MB)
Linville R.G., Luoma S.N., Cutter L., and Cutter G.A., 2002, Increased selenium threat as a result of invasion of the exotic bivalve Potamocorbula amurensis into the San Francisco Bay-Delta: Aquatic Toxicology, v. 57, p. 51-64. (on-line abstract)
Lucas, L.V., Cloern, J.E., Thompson, J.K., and Monsen, N.E., 2002, Functional variability of habitats in the Sacramento-San Joaquin Delta: restoration implications: Ecological Applications, v.12, no. 5, p. 1528-1547. (on-line abstract)
Luoma, S.N., 2002, Processes affecting trophic transfer and resultant effects of metals: Implications for monitoring metal pollution in the sea: CIESM, Metal and Radionuclides bioaccumulation in marine organisms, Monaco, CIESM Workshop Monographs no. 19, p. 75-78.
Luoma, S.N., Brown, S.S., Foster, W.G., Leckie, J.O., Teisi, M.F., Thomas, J.K., and Williams-Fleetwood, S.O., 2002, Interconnections between human health and ecological integrity - Characteristics and implications, in DiGiulio, R.T., and Benson, W.H., eds., Interconnections Between Human Health and Ecological Integrity, Chapter 4: Society of Environmental Toxicology and Chemistry (SETAC) Press, p. 65-100.
Luoma, S.N., Hogstrand, C., Bell, R.A., Bielmyyer, G.K., Galvez, G., LeBlanc, G.A., Lee, B.G., Purcell, T.W., Santore, R.C., Santschi, P.H., and Shaw, J.R., 2002, Biological Processes, Chapter 3, in Andren, A.W., and Bober, T.W., eds., Silver in the Environment: Transport, Fate and Effects: Society of Environmental Toxicology and Chemistry (SETAC), Pensacola, FL., p. 65-95.
Parchaso, F., and Thompson, J.K., 2002, Influence of hydrologic processes on reproduction of the introduced bivalve Potamocorbula Amurensis in Northern San Francisco Bay, California: Pacific Science, v. 56, no. 3, p. 329-345. (on-line abstract)
Peterson, H.A., 2002, Long-term benthic community change in a highly invaded estuary, M.A. Thesis, San Francisco State University, 108 p.
Schlekat, C.E., Lee, B-G., and Luoma, S.N., 2002, Dietary metals exposure and toxicity to aquatic organisms: Implications for ecological risk assessment in Newman, M.C., Roberts, M.H., Jr., and Hale, R.C., eds., Coastal and Esturaine Risk Assessment: Boca Raton, Lewis Publishers, Chapter 7.
Shouse, M.K., 2002, The effects of decreasing trace metal concentrations on benthic community structure, MA Thesis, San Francisco State University, 177 pp.
Thompson, J.K., 2002, The evolving benthic community: Science and Strategies for Restoration, San Francisco Estuary Project, p. 66-67.
Thompson, J.K., Parchaso, F., and Shouse, M.K., 2002, Near field receiving water monitoring of benthic community near the Palo Alto Water Quality control plant in South San Francisco Bay: February 1974 through December 2000: U.S. Geological Survey Open-File Report 02-394, 117 p. (on-line abstract and on-line report in pdf format, 0.79MG)
Carter, J.L., and Fend, S.V., 2001, Inter-annual changes in the benthic community structure of riffles and pools in reaches of contrasting gradient: Hydrobiologia, v. 459, no.1-3, p. 187-200. (on-line abstract)
Carter, J.L., and Resh, V.H., 2001, After site selection and before data analysis: sampling, sorting, and laboratory procedures used in stream benthic macroinvertebrate monitoring programs by USA state agencies: Journal of the North American Benthological Society, v. 20, no. 4., p. 658-682. (on-line abstract)
Clements, W., Luoma, S.N., Gerritsen, J., Hatch, A., Jepson, P., Reynoldson, T., and Thom, R., 2001, Stressor interactions in ecological systems in Baird, D.J., and Burton, G.A., eds., Ecological Variability: Separating Natural from Anthropogenic Causes of Ecosystem Impairment: Pensacola, SETAC Press, p. 215-233.
Dodge, K.A., Hornberger, M.I., and David, C.P.C., 2001, Water-quality, bed-sediment, and biological data (October 1999 through September 2000) and statistical summaries of data for streams in the upper Clark Fork basin, Montana: U.S. Geological Survey Open-File Report 01-280, 59 p.
Giddings, E.M., Hornberger, M.I., and Hadley, H. K., 2001, Trace-metal concentrations in sediment and water and health of aquatic macroinvertebrate communities of streams near Park City, Summit County, Utah: U.S. Geological Survey Water-Resources Investigations Report 01-4213, 22 p.
Lee, J.S., Lee, B.G., Yoo, H., Koh, C.H., Luoma, S.N., 2001, Influence of reactive sulfide (AVS) and supplementary food on Ag, Cd and Zn bioaccumulation in the marine polychaete Neanthes arenaceodentata: Marine Ecology-Progress Series, v. 216, p. 129-140. (on-line abstract)
Luoma, S.N., Clements, W., DeWitt, T., Gerritsen, J., Hatch, A., Jepson, P., Reynoldson, T., and Thom, R., 2001, Role of environmental variability in evaluating stressor effects in Baird D.J., and Burton, G.A., eds., Ecological Variability: Separating Natural from Anthropogenic Causes of Ecosystem Impairment: Pensacola, SETAC Press, p. 141-176
Luoma, S.N., Clements, W., DeWitt, T., Gerritsen, J., Hatch, A., Jepson, P., Reynoldson, T., and Thom, R., 2001, Separating stressor influences from environmental variability: Eight case studies from aquatic and terrestrial ecosystems in Baird, D.J., and Burton, G.A., eds., Ecological Variability: Separating Natural from Anthropogenic Causes of Ecosystem Impairment: Pensacola, SETAC Press, p. 179-214.
Alpers, C.N., Taylor, H.E., Roth, D.A., Cain, D.J., Ball, J.W., Unruh, D.M., and Deleanis, P.D., 2000, Study design: field and laboratory methods, in Alpers, C.N., Taylor, H.E., and Domagalski, J.J., eds., Metals transport in the Sacramento River, California, 1996-97: Volume 1. Methods and Data: U.S. Geological Survey Water-Resources Investigations Report 99-4286, p. 19-37
Cain, D.J., Carter, J.L., Fend, S.V., Luoma, S.N., Alpers, C.N., and Taylor, H.E., 2000, Metal exposure to a benthic macroinvertebrate, Hydropsyche californica, related to mine drainage in the Sacramento River: Canadian Journal of Fisheries, v. 57, p. 380-390. (on-line abstract)
Cain, D.J., Carter, J.L., Fend, S.V., Luoma, S.N., Alpers, C.N., and Taylor, H.E., 2000, Metal exposure to a benthic invertebrate, hyropsyche californica, in the Sacramento River downstream of Keswick Reservoir, California: U.S. Geological Survey Open-File Report No. 98-654, 26 p.
Carter, J.L., and Fend, S.V., 2000, The distribution and abundance of loctic macroinvertebrates during Spring 1997 in seven streams of the Santa Clara Valley area, California: U.S. Geological Survey Open-File Report 00-68. (on-line abstract)
Dodge, K A., Hornberger, M.I., and David, C.P., 2000, Water-quality, bed-sediment and biological Data (October 1998 through September 1999) and statistical summaries of data for streams in the Upper Clark Fork Basin, Montana: U.S. Geological Survey Open-File Report 00-370. (on-line report)
Emmett, R., Thom, R., Morgan, C., Copping, A., Llanso, R, Newton, Hornberger, M., Levings, C., Fishman, P., 2000, Geographic signatures of North American west coast estuaries: Estuaries, v. 23, p. 765-792.
Griscom, S.B., Fisher, N.S., and Luoma, S.N., 2000, Geochemical influences on assimilation of sediment-bound metals in clams and mussels: Environmental Science and Technology, v. 34, p. 91-99. (on-line abstract)
Hornberger, M.I., Luoma, S.N., Cain, D., Parchaso, F., Brown, C., Bouse, R., Wellise, C., and Thompson, J., 2000, Linkage of bioaccumulation and biological effects to changes in polutant loads in South San Francisco Bay: Environmental Science and Technology, v. 34, p. 2401-2409. (on-line abstract or on-line pdf file - published by the American Chemical Society; not subject to U.S. copyright.)
Lee, B.-G., Griscom, S.B., Lee, J.-S., Choi, H.J., Koh, C.-H., Luoma, S.N., and Fisher, N.S., 2000, Influence of dietary uptake and realctive sulfides on metal bioavailability from aquatic sediments: Science, v. 287, p. 282-284. (on-line abstract)
Lee, B.-G., Lee, J.-S., Luoma, S.N., Choi, H.J., and Koh, C.-H., 2000. Influence of acid volatile sulfides and metal concentrations on metal bioavailability to marine invertebrates in contaminated sediments: Environmental Science and Technology, v. 34, p. 4517-4523. (on-line abstract)
Lee, J.-S., Lee, B.-G., Luoma, S.N., Choi, H.J., Koh, C.-H., and Brown, C.L., 2000. Influence of acid volatile sulfides and metal concentrations on metal partitioning in contaminated sediments: Environmental Science and Technology, v. 34, p. 4511-4516. (on-line abstract)
Luoma, S.N., and Presser, T.S., 2000, Forecasting selenium discharges to the San Francisco Bay-Delta Estuary: Ecological dffects of a proposed San Luis Drain extension: U.S. Geological Survey Open-File Report 00-416, 359 p. (on-line abstract and to download pdf file)
Moulton, S.R., II, Carter, J.L., Grotheer, S.A., Cuffney, T.F., and Short, T.M., 2000, Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory -- Processing, taxonomy, and quality control of benthic macroinvertebrate samples: U.S. Geological Survey Open-File Report 00-212. (on-line abstract)
Schlekat, C.E., Dowdle, P.R., Lee, B.G., Luoma, S.N., and Oremland, R.S., 2000, Bioavailability of particle-associated Se to the bivalve Potamocorbula amurensis: Environmental Science and Technology, v. 34, p. 4504 - 4510. (on-line abstract or on-line pdf file - - published by the American Chemical Society; not subject to U.S. copyright.)
Schlekat, C.E., and Luoma, S.N., 2000, You are what you eat: Incorporating dietary metals uptake into environmental quality guidelines for aquatic ecosystems: SETAC Globe, v. 1(2), p. 38-39.
Brown, C., and Luoma, S., 1999, Metal trends and effects in Potamocorbula amurenis in North San Francisco Bay, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 2--Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 17-21. (on-line abstract)
Cain, D.J., and Luoma, S.N., 1999, Metal exposures to native popluations of the caddisfly Hydrosyche (Trichopter: Hydropsychidae) determined from cytosolic and whole body metal concentrations: Hydrobiologia, v. 386, p. 103-117. (on-line abstract)
Dodge, K.A., Hornberger, M.I., and Bouse, R.M., 1999, Water quality, bed sediment and biological data (October 1997 through September 1998) and statistical summaries of data for streams in the Upper Clark Fork Basin, Montana: U.S. Geological Survey Open File Report 99-251. (on-line abstract)
Fuller, C.C., VanGeen, A., Baskaran, M., and Anima, R., 1999, Sediment chronology in San Francisco Bay defined by 210Pb, 234Th, 137Cs, and 239,240Pu: Marine Chemistry, v. 64, p. 7-27. (on-line abstract)
Hornberger, M.I., Luoma, S.N., Cain, D.J., Parchaso, F. Brown, C.L., Bouse, R.M., Wellise, C. and Thompson, J. 1999. Bioaccumulation of metals by the bivalve Macoma balthica at a site in South San Francisco Bay between 1977 and 1997: Long-term trends and associated biological effects with changing pollutant loadings. U.S. Geological Survey, Open File Report 99-55. 42 pp. (on-line abstract)
Hornberger, M.I., Luoma, S.N., van Geen, A., Fuller, C.C., and Anima, R., 1999, Historical trends of trace metals in the sediments of San Francisco Bay, CA: Marine Chemistry, v. 64, p. 39-56. (on-line abstract)
Hostettler, F.D., Pereira, W.E., Kvenvolden, K.A., van Geen, A., Luoma, S.N., Fuller, C.C., Anima, R., 1999, A record of contaminant input to San Francisco Bay as traced by biomarker profiles in surface sediment and sediment cores: Marine Chemistry, v. 64, p. 115-127. (on-line abstract)
Hutchins, D.A., Stupakoff, I., Hook, S., Luoma, S.N., and Fisher, N.S., 1999, Effects of arctic temperatures on uptake and retention of nuclear waste radionuclides 241Am, 57Co and 137Cs by the bioindicator bivalve Macoma balthica: Mar. Envir. Research, v.75, p17-28.
Luoma, S.N., 1999, Emerging contaminant issues from an ecological perspective, in Morganwalp, D.W., and Buxton, H.T., eds., U.S. Geological Survey Toxic Substances Hydrology Program--Proceedings of the Technical Meeting, Charleston, South Carolina, March 8-12, 1999--Volume 2--Contamination of Hydrologic Systems and Related Ecosystems: U.S. Geological Survey Water-Resources Investigations Report 99-4018B, p. 3-8. (on-line abstract or to obtain pdf file)
Luoma, S.N., and DiGiulio, 1999, Biomarkers of Cellular Damage: Biomarkers, v. 4, p. 392-294.
Pereira, W.E., Hostettler, F.D., Luoma, S.N., van Geen, A., Fuller, C.C., and Anima, R.J., 1999, Sedimentary record of anthropogenic and biogenic polycyclic aromatic hydrocarbons in San Francisco Bay, California: Marine Chemistry, v. 64, p. 99-113. (on-line abstract)
Ringwood, A.H., Jameedi, M.J. Lee, R.F., Brouwer, M., Peters, E.C., Scott, G.I., Luoma, S.N., and DiGiulio, R.T., 1999, Bivalve biomarker workshop: overview and discussion group summaries:overview and discussion group summaries: Biomarkers, v. 4, no. 6, p. 391-399.
Ritson, P., Bouse, R.M., Luoma, S.N., and Flegal, A.R., 1999, Stable lead isotopic Identification of historical and contemporary lead contamination of San Francisco Bay estuary: Marine Chemistry, v. 64, p. 71-84. (on-line abstract)
Teh, S., Clark, S.L., Brown, C.L., Luoma, S.N., and Hinton, D.E.,1999, Enzymatic and histopathologic biomakers as indicators of contaminant exposure and effect in the asian clam, Potamocorbula amurenis: Biomarkers, v. 4, p. 497-509. (on-line abstract)
Van Geen, A., and Luoma, S.N., 1999, The impact of human activities on sediments of San Francisco Bay, California: an overview: Marine Chemistry, v. 64, p. 1-6. (on-line abstract)
Van Geen, A., and Luoma, S.N., 1999, A record of estuarine water contamination from the Cd content of foraminifera in San Francisco Bay, CA: Marine Chemistry, v. 64, p. 57-70. on-line abstract)
Van Geen, A., Valette-Silver, N.J., Luoma, S.N., Fuller, C.C., Baskaran, M., Tera, F., and Klein, J., 1999, Constraints on the sedimentation history of San Francisco Bay from isotopes of 14C to 10Be: Marine Chemistry, v. 64, p. 29-38. (on-line abstract)
Venkatesan, M.I., de Leon, R.P., van Geen, A., and Luoma, S.N., 1999, Chlorinated hydrocarbon pesticides and polychorinated biphenyls in sediment cores from San Francisco Bay: Marine Chemistry, v. 64, p. 85-98. (on-line abstract)
For bibliographic citations for Janet Thompson prior to 2001, see Environmental Influences on Estuarine Benthic Community Dynamics
FOR ADDITIONAL INFORMATION ON THIS PROJECT, CONTACT
Samuel N. Luoma
U.S. Geological Survey, 345 Middlefield Rd, MS 465, Menlo Park, CA 94025
Internet: snluoma@usgs.gov
Telephone: 650-329-4481
Cindy Brown
U.S. Geological Survey, 345 Middlefield Rd, MS 465, Menlo Park, CA 94025
Internet: clbrown@usgs.gov
Telephone: 650-329-4477
Daniel J Cain
U.S. Geological Survey, 345 Middlefield Rd, MS 465, Menlo Park, CA 94025
Internet: djcain@usgs.gov
Telephone: 650-329-4478
James L Carter
U.S. Geological Survey, 345 Middlefield Rd, MS 465, Menlo Park, CA 94025
Internet: jlcarter@usgs.gov
Telephone: 650-329-4439
Steven V Fend
U.S. Geological Survey, 345 Middlefield Rd, MS 465, Menlo Park, CA 94025
Internet: svfend@usgs.gov
Telephone: 650-329-4465
Michelle Hornberger
U.S. Geological Survey, 345 Middlefield Rd, MS 465, Menlo Park, CA 94025
Internet: mhornber@usgs.gov
Telephone: 650-329-4467
Janet K Thompson
U.S. Geological Survey, 345 Middlefield Rd, MS 472, Menlo Park, CA 94025
Internet: jthompso@usgs.gov
Telephone: 650-329-4364
For information on additional projects in the National Research Program, see Indexes to NRP projects and bibliographies
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