National Research Program


Mechanisms of biological and ecological response in disturbed aquatic ecosystems

Human activities from climate change to waste discharges to water management are modifying ecosystems across the earth, often in ways that are not well understood. This project addresses the problem of better understanding changes in aquatic ecosystems as driven by human disturbances interacting with natural processes. More specifically, the project studies a) the mechanisms of biological and ecological response to stressors such as metal contamination, nutrient enrichment, physical habitat alteration, climate change, and introduced species; and b) the influence of species, communities, and ecosystem processes on the distribution, transport, and fate of chemical contaminants (e.g., metals, nutrients). Most studies on the project ultimately consider physical, chemical and biological processes that interact in ecosystem change, as well as mechanisms of stressor-specific responses in species, populations, and communities, with an emphasis on invertebrate organisms/communities. Both intensive laboratory and field experimentation as well as long term field observation are typical of project work. An important goal is development of models to improve understanding of biological and ecological responses to stressors. For example, biodynamic models are an important focus of metal contamination studies (and studies of the implications of developing nanotechnologies) because they provide a mechanistic explanation of many biological and ecological responses to metals. These models are based upon laboratory-based experimental studies of contaminant uptake, loss and detoxification in different species linked to field observations of contaminant concentrations. Understanding differences in contaminant biodynamics, when linked with carefully designed studies of benthic communities, for example, can lead to process-based predictions of ecological change. Ongoing or past project includes studies in streams, rivers, lakes and estuaries. Historically, the project has introduced many new methodologies. Continued refinement of those and the development of novel new methods is another important ongoing and future goal of this project. Perpetuation of long-term (multi-decadal) ecological, metal and geochemical data sets, in collaboration with non-USGS partners, is also an ongoing goal in ecosystems from South San Francisco Bay, North San Francisco Bay, Santa Clara Valley streams, and the Clark Fork River Montana. The unique capacity to integrate laboratory and field studies across levels of biological organization in diverse aquatic ecosystems establishes our ability to identify, tackle, and inform managers and scientists of newly emerging issues which is a critical need of the USGS and an important part of our work into the future. For additional information, see Ecology and Contaminants site.

REPORTS PUBLISHED 2003-2012

Franco J.N., Ceia F.R., Patrício, J., Modesto, V., Thompson, J, Marques, J.C., and Neto, J.M.., in press (web publication 7/27/11) Population dynamics of Corbicula fluminea (Müller,1774) in mesohaline and oligohaline habitats: invasion success in a Southern Europe estuary: Estuarine, Coastal, and Shelf Science. (on-line abstract of preprint)

Thompson, J.K., in press, Corbula amurensis.  Invasive Species Compendium (produced by CABI).

Fend, S.V., and Lenat, D.R., 2012, New Eclipidrilus species (Annelida, Clitellata, Lumbriculidae) from southeastern North America: Zootaxa, Issue 3194, p. 51-67. (on-line abstract of journal article)

Kuwabara, J.S., Topping, B.R., Carter, J.L., Wood, T.M., Parchaso, F., Cameron, J.M., Asbill, J.R., Carlson, R.A., and Fend, S.V., 2012, Time scales of change in chemical and biological parameters after engineered levee breaches adjacent to Upper Klamath and Agency Lakes, Oregon: U.S. Geological Survey Open-File Report 2012-1057, 26 p. (on-line abstract or on-line report in pdf format, 2.4 MB)

Selck, H., Drouillard, K., Eisenreich, K.,. Koelmans, A.A., Palmqvist, A., Ruus, A., Salvito, D., Schultz, I.,. Stewart, A.R.,Weisbrod, A., van den Brink, N.W., and van den Heuvel-Greve, M., 2012 (web publication 8/11/11), Explaining differences between bioaccumulation measurements in laboratory and field data through use of a probabilistic modeling approach: Integrated Environmental Assessment and Management, v. 8, no. 1, p. 42–63. doi: 10.1002/ieam.217. (on-line abstract of journal article)

Cain, D., Croteau, M.-N., and Luoma, S.N., 2011, Bioaccumulation dynamics and exposure routes of Cd and Cu among species of aquatic mayflies: Environmental Toxicology and Chemistry, v. 30, no. 11, p. 2532-2541. (on-line abstract of journal article)

Croteau, M.-N., Dybowska, A.D., Luoma, S.N., and Valsami-Jones, E., 2011, A novel approach reveals that ZnO nanoparticles are bioavailable and toxic after dietary exposure: Nanotoxicology, v. 5, no. 1, p. 79-90. (on-line abstract of journal article)

Croteau, M.-N., Misra, S.K., Luoma, S.N., and Valsami-Jones, E. , 2011, Silver bioaccumulation dynamics in a freshwater invertebrate after aqueous and dietary exposures to nanosized and ionic Ag: Environmental Science & Techology, v. 45, no. 5, p. 6600-6607. (on-line abstract of journal article)

Dyke, J.L., Parchaso, F., Thompson, J.K., Cain, D.J., Luoma, S.N., and Hornberger, M.I., 2011, 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 - 2010: U.S. Geological Survey Open-File Report 2011-1163, 114 p. (on-line abstract or on-line report in pdf format, 2.7 MB)

Dybowska, A.D., Croteau, M.-N., Misra, S.K., Berhanu, D., Luoma, S.N., Christian, P., O'Brien, P., and Valsami-Jones, E., 2011, Synthesis of isotopically modified ZnO nanoparticles and their potential as nanotoxicity tracers: Environmental Pollution, v. 159, no. 1, p. 266-273. (on-line abstract of journal article)

Greene, V.E., Sullivan, L.J., Thompson, J.K., Kimmerer, W.J., 2011, Grazing impact of the invasive clam Corbula amurensison the microplankton assemblage of the northern San Francisco Estuary: Marine Ecology Progress Series, v. 431, p. 183-193. (on-line abstract or on-line journal article in pdf format, 512 KB, published by Inter-Research with open access)

Janssen, E.M., Oen, A.M., Luoma, S.N., and Luthy, R.G., 2011, Assessment of field-related influences on polychlorinated biphenyl exposures and sorbent amendment using polychaete bioassays and passive sampler measurements: Environmental Toxicology and Chemistry, v. 30, no. 1, p. 173-180. (on-line abstract of journal article)

Janssen, E.M.-L., Thompson, J.K., Luoma, S.N., and Luthy, R.G., 2011, PCB-induced changes of a benthic community and expected ecosystem recovery following in situ sorbent amendment: Environmental Toxicology and Chemistry, v. 30, no. 8, p. 1819-1826. (on-line abstract of journal article)

Bouse, R.M., Fuller, C.C., Luoma, S.N., Hornberger, M.I., Jaffe, B.E., and Smith, R.E., 2010, Mercury-Contaminated Hydraulic Mining Debris in San Francisco Bay: San Francisco Estuary and Watershed Science, v. 8, no. 1, 28 p. (on-line article in pdf format, 786 KB, San Francisco Estuary and Watershed Science is an open access journal)

Chapman, P.M., Adams, W.J., Brooks, M., Delos, C.G., Luoma, S.N., Maher, W.M., Ohlendorf, H.M., Presser, T.S., and Shaw, P., eds., 2010, Ecological Assessment of Selenium in the Aquatic Environment: CRC Press, 368 p. (on-line book information)

Dodge, K.A., Hornberger, M.I., and Dyke, J.L., 2010, Water-quality, bed-sediment, and biological data (October 2008 through September 2009) and statistical summaries of long-term data for streams in the Clark Fork basin, Montana: U.S. Geological Survey Open-File Report 2010–1267, 137 p. (on-line abstract or on-line report in pdf format, 2.3 MB)

Dyke, J.L., Parchaso, J.K., Thompson, J.K., Cain, D.J., Luoma, S,N., and Hornberger, M.I., 2010, 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: U.S. Geological Survey Open-File Report 2010-1188, 46 p. (on-line abstract or on-line report in pdf format, 17.1 MB)

Fend, S.V., and Brinkhurst, R.O., 2010, Contributions towards a review of the genus Rhynchelmis Hoffmeister (Clitellata: Lumbriculidae):Zootaxa, v. 2407, p. 1-27. (on-line abstract of journal article, pdf format)

Fend, S.V., and Lenat, D.R., 2010, New southeastern Nearctic Rhynchelmis (Rhynchelmoides) species and the description of Pararhynchelmis n. gen. (Annelida: Clitellata: Lumbriculidae): Zootaxa, v. 2554, p. 1-22, (on-line abstract of journal article, pdf format)

Janssen, E.M.-L., Croteau, M.-N., Luoma, S.N., and Luthy, R.G., 2010, Measurement and modeling of polychlorinated biphenyl bioaccumulation from sediment for the marine polychaete neanthes arenaceodentata and response to sorbent amendment: Environmental Science & Technology, v. 44, no. 8, 15 p. 2857-2863. (on-line abstract of journal article)

Kleckner, A.E., Stewart, A.R., Elrick, K., and Luoma, S.N., 2010, Selenium and stable isotopes of carbon and nitrogen in the benthic clam Corbula amurensis from Northern San Francisco Bay, California: May 1995 - February 2010: U.S. Geological Survey Open-File Report 2010-1252, 34 p. (on-line abstract or on-line report in pdf format, 1.22 KB)

Kuwabara, J.S., Topping, B.R., Carter, J.L., Parchaso, F., Asbill, J.R., Cameron, J.M., Asbill, J.R., Fend, S.V., Duff, J.H., and Engelstad, A.C., 2010, The transition of benthic nutrient sources after planned levee breaches adjacent to Upper Klamath and Agency Lakes, Oregon: U.S. Geological Survey Open-File Report 2010-1062, 21 p. (on-line abstract or on-line report in pdf format, 7.1 MB)

Luoma, S.N., Cain, D. J. and Rainbow, P.S., 2010, Calibrating biomonitors: A new technique for deciphering metal effects in natural waters: Integrated Environmental Assessment and Management, v. 6, no. 2, p. 199-209. (on-line abstract of journal article)

Pfrender, M.E., Hawkins, C.P., Bagley, M., Courtney, G.W., Creutzburg, B.R., Epler, J.H., Fend, S., Ferrington Jr., L.C., Hartzell, P.L., Jackson, S., Larsen, D.P., Lévesque, C.A., Morse, J.C., Petersen, M.J., and Whiting, M., 2010, Assessing macroinvertebrate biodiversity in freshwater ecosystems: Advances and challenges in dna-based approaches: Quarterly Review of Biology, v. 85, no.3, p. 319-340. (on-line abstract of journal article)

Presser, T.S., and Luoma, S.N., 2010, A Methodology for Ecosystem-Scale Modeling of Selenium: Integrated Environmental Assessment and Management, v. 6, no. 4, p. 685-710. (on-line abstract of journal article)

Silalom, S. , Carter, J.L. , and Chantaramongkol, P., 2010, Calculation of weighted averages approach for the estimation of Ping tolerance values: Chiang Mai Journal of Science, v. 37, no. 1, p. 151-159.

Stewart, R., Grosell, M., Buchwalter, D., Fisher, N., Luoma, S., Mathews, T., Orr, P., and Wang, W.-X., Bioaccumulation and Trophic Transfer of Selenium, 2010, in Chapman, P.M., Adams, W.J., Brooks, M.L., Delos, C.G., Luoma, S.N., Maher, W.A., Ohlendorf, H.M., Presser, T.S., Shaw, D.P., eds., Ecological Assessment of Selenium in the Aquatic Environment: CRC Press, chapter 5, p. 93-140.Ecological Assessment of Selenium in the Aquatic Environment, SETAC Workshop on Ecological Assessment of Selenium in the Aquatic Environment Pensacola, Florida, USA, Coordinating Editor of SETAC Books: Joseph W. Gorsuch, Copper Development Association, Inc., New York, NY, USA

Zhou, H., Fend, S.V., Gustafson, D.L., De Wit, P., and Erséus, C., 2010, Molecular phylogeny of Nearctic species of Rhynchelmis (Annelida): Zoologica Scripta, v. 39, no. 4, p. 378-393. (on-line abstract of journal article)

Berhanu, D., Dybowska, A., Misra, S.K., Stanley, C.J., Ruenraroengsak, P., Boccaccini, A.R., Tetley, T.D., Luoma, S.N., Plant, J.A., and Valsami-Jones, E., 2009, Characterisation of carbon nanotubes in the context of toxicity studies: Environmental Health, v. 8(Suppl 1):S3, doi:10.1186/1476-069X-8-S1-S3. (on-line abstract or on-line article in pdf format, 560 KB, open-access journal)

Cain, D. J., Thompson, J. K., Dyke, J. L., Parchaso, F., Luoma, S. N., and Hornberger, M. I., 2009, 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, 2008: US Geological Survey Open-file Report 2009-1193. (on-line abstract or on-line report in pdf format, 2.3 MB)

Carter, J.L., Purcell, A.H., Fend, S.V., and Resh, V.H., 2009, Development of a local-scale urban stream assessment method using benthic macroinvertebrates: and example from the Santa Clara Basin, California: Journal of the North American Benthological Society, v. 28, no. 4, p. 1007-1021. (on-line abstract of journal article)

Casado-Martinez, M. C., Smith, B.D., Luoma, S.N., and Rainbow, P.S., 2009, Biodynamic modelling and the prediction of accumulated trace metal concentrations in the polychaete Arenicola marina: Environmental Pollution, v. 157, no. 10, p. 2743-2750. (on-line abtract of journal article)

Chapman, P.M., Adams, W.J., Brooks, M.L., Delos, C.G., Luoma, S.N., Maher, W.A., Ohlendorf, H.M., Presser, T.S., and Shaw, D.P., 2009, Ecological assessment of selenium in the aquatic environment: Summary of a SETAC Pellston Workshop. Pensacola FL (USA): Society of,Environmental Toxicology and Chemistry (SETAC), 35 p. (on-line report in pdf format, 2423 KB, copyright by the Society of Environmental Toxicology and Chemistry (SETAC) with photoduplication encouraged)

Chasar, L.C., Scudder, B.C., Stewart, A.R., Bell, A.H., and Aiken, G.R., 2009, Mercury cycling in stream ecosystems. 3. Trophic dynamics and methylmercury bioaccumulation: Environmental Science and Technology, v. 43, no. 8, p. 2733–2739. (on-line abstract or on-line article in pdf format, 124 KB, published by the American Chemical Society, not subject to U.S. copyright)

Croteau, M-N., and Luoma, S.N.,. 2009, Predicting dietborne metal toxicity from metal influxes: Environmental Science and Technology, v. 43, no. 13, p. 4915-4921. (on-line abstract or on-line article in pdf format, 418 KB, published by the American Chemical Society, not subject to U.S. copyright)

Fend, S.V., 2009, An evaluation of the genus Kincaidiana Altman, 1936, with the designation of Altmanella n. gen. (Annelida, Clitellata, Lumbriculidae): Zootaxa, v. 2077), p. 1-30. (on-line abstract of journal article, pdf format, 20 KB)

Grimaldo, L.F., Stewart, A.R., and Kimmerer, W., 2009, Dietary segregation of pelagic and littoral fish assemblages in a highly modified tidal freshwater estuary: Marine Coastal Fisheries: Dynamics, Management and Ecosystems Sciences, v. 1, no. 1, p. 200-217. (on-line abstract or on-line article in pdf format, 401 KB, published in an open-access journal by the American Fisheries Society)

Hornberger, M.I., Luoma, S.N., Johnson, M.L., and Holyoa, M., 2009, Influence of remediation in a mine-impacted river: metal trends over large spatial and temporal scales: Ecological Applications, v. 19, no. 6, p.1522–1535. (on-line abstract of journal article)

Jones, N.L., Thompson, J.K., Arrigo, K.R., Monismith, S.G. 2009. Hydrodynamic control of phytoplankton loss to the benthos in an estuarine environment. Limnology and Oceanography, v. 54, no. 3, p. 952-969. (on-line abstract of journal article)

Kuwabara, J.S., Topping, B.R., Lynch, D.D., Carter, J.L., and Essaid, H.I., 2009, Benthic nutrient sources to hypereutrophic Upper Klamath Lake, Oregon: Environmental Toxicology and Chemistry, v. 28, p. 516-524. (on-line abstract of journal article)

Kuwabara, J.S., Topping, B.R., Parchaso, F., Engelstad, A.C., and Greene, V.D., 2009, Benthic Flux of nutrients and trace metals in the northern component of San Francisco Bay, California: U.S. Geological survey Open File Report 2009-1286. (on-line abstract or on-line report in pdf format, 921 MB)/

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)

Luoma, S.N., 2009, Ingredients in sustainably managing water in semi-arid environments: Environmental Science & Policy, v. 12, no. 6, p. 737-740. (on-line abstract of journal article)

Luoma, S.N. and Presser, T.S., 2009, Emerging opportunities in management of selenium contamination: Environmental Science and Technology, v. 43, no. 22, p.8483-8487. (on-line abstract or on-line article in pdf format, 2767 KB, published by the American Chemical Society, not subject to U.S. Copyright.).

Presser, T.S., and Luoma, S.N., 2009, Modeling of selenium for the San Diego Creek watershed and Newport Bay, California: U.S. Geological Survey Open-File Report 2009-1114, 48 p. (on-line abstract or on-line report in pdf format, 5.4 MB)

Purcell, A.H., Bressler, D.W., Paul, M.J., Barbour, M.T., Rankin, E.T., Carter, J.L., and Resh, V.H., 2009, Assessment tools for urban catchments: Developing biological indicators based on benthic macroinvertebrates: Journal of the American Water Resources Association, v. 45, no. 2, p. 306-319. (on-line abstract of journal article)

Stewart, A.R., Grosell, M., Buchwalter, D.B., Fisher, N., Luoma, S.N., Mathews, T., Orr, P.L. and Wang, W.X., 2009, Bioaccumulation and trophic transfer of selenium, in Chapman, P.M., Adams, W.J., Brooks, M.L., Delos, C.G., Luoma, S.N., Maher, W.A., Ohlendorf, H.M., Presser, T.S., and Shaw, D.P., 2009, Ecological assessment of selenium in the aquatic environment: Summary of a SETAC Pellston Workshop. Pensacola FL (USA): Society of,Environmental Toxicology and Chemistry (SETAC), p. 19 - 21.

Alpers, C.N., Stewart, A.R., Saiki, M.K., Marvin-DiPasquale, M.C., Topping, B.R., Rider, K.M., Gallanthine, S.K., Kester, C.A., Rye, R.O., Antweiler, R.C., and De Wild, J.F., 2008, Environmental factors affecting mercury in Camp Far West Reservoir, California, 2001–03: U.S. Geological Survey Scientific Investigations Report 2006-5008, 358 p. (on-line abstract or on-line report in pdf format, 3.16 MB)

Buchwalter, D.B., Martin, C.A., Xie, L., Luoma, S.N., and Garland, T. Jr., 2008, Aquatic insect ecophysiological traits reveal phylogenetically based differences in dissolved cadmium susceptibility: Proceedings of the National Academy of Sciences, v. 105, no. 24, p. 8321-8326. (on-line abstract of journal article)

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)

Lorenzi, A.H., Cain, D. J., Parchaso, F. Thompson, J.K., Luoma, S.N., Hornberger, M.I., and Dyke, J.L., 2008, 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, 2007: U.S. Geological Survey Open File Report 2008-1180, 120p. (on-line abstract or on-line report in pdf format, 2.2 MB)

Luoma, S.N., 2008, Silver Nanotechnologies and the Environment: Old Problems or New Challenges: Project on Emerging Nanotechnologies Publication 15. Woodrow Wilson International Center for Scholars and PEW Charitable Trusts, Washington D. C. 67p.

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.

Luoma, S.N. and Rainbow, P.S. 2008. Metal Contamination in Aquatic Environments: science and lateral management.  Cambridge University Press, Cambridge,  588 p. (on-line book information)

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)

Thompson, J.K., Koseff, J.R., Monismith, S.G., and Lucas, L.V., 2008, Shallow water processes govern system-wide phytoplankton bloom dynamics: A field study. Journal of Marine Systems, v. 74, no. 1-2, p.153-166, doi:10.1016/j.jmarsys.2007.12.006. (on-line abstract of journal article)

Valsami-Jones, E, Berhanu, D., Dybowska, A., Misra, S., Boccaccini, A.R., Tetley, T.D., Luoma, S.N., Plant, J.A., 2008, Nanomaterial synthesis and characterisation for toxicological studies: TiO2 case study: Mineralogical Magazine, v. 72, no. 1, p. 515-519. (on-line abstract of journal article)

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)

Cloern, J.E., Jassby, A.D., Thompson, J.K., and Hieb, K.A., 2007, A cold phase of the East Pacific triggers new phytoplankton blooms in San Francisco Bay: Proceedings of the National Academy of Sciences USA, v. 104, p.18,561-18,565, doi:10.1073/pnas.0706151104, (on-line abstract or on-line article in pdf format, 1664 KB, published with Open Access)

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)

Fend, S.V. and Lenat, D.R., 2007, Two new genera of Lumbriculidae (Annelida, Clitellata) from North Carolina, USA: Zootaxa, v. 1666, p. 1-22. (on-line abstract and introduction in pdf format)

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., 2007, Case Study 6: The CALFED Bay-Delta Program: A Case Study in Intertwined Ecological and Environmental Resource Issues, in Stahl, R.G., Jr., Kapustka, L.A., Munns W.R., Jr., Bruins, R.J.F., eds., Valuation of Ecological Resources: Integration of Ecological Risk Assessment and Socioeconomics in Environmental Decision Making: SETAC Press, Pensacola, p. 209-218.

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)

Marvin-DiPasquale, M., Stewart, A.R., Fisher, N.S., Pickhardt, P., Mason, R.P., Heyes, A., and Winham-Myers, L., 2007, Evaluation Of Mercury Transformations and Trophic Transfer in the San Francisco Bay/Delta: Identifying Critical Processes for the Ecosystem Restoration Program: Annual Report for Project # ERP-02-P40 to the California Bay Delta Authority (CBDA), 39 p. (on-line report in pdf format)

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)

Thompson JK, Hieb K, McGourty K, Cosentio-Manning N, Wainwright-De La Cruz S, Elliot M, Allen S, 2007. Habitat type and associated biological assemblages: soft bottom substrate, in Schaeffer K, McGourty K, Cosentio-Manning N, eds. Report on the Subtidal Habitats and Associated Biological Taxa in San Francisco Bay. Santa Rosa, CA: US. National Oceanic and Atmospheric Administration, 18-23 (Table 3a), 37-46. (to download entire report)

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.

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)

Carter, J.L., Resh, V.H, Hannaford, M.J., and Myers, M.J., 2006, Macroinvertebrates of biotic indicators of environmental quality, in Hauer, F.R., and Lamberti, G.A., eds., Methods in stream ecology (Second Edition): Academic Press, San Diego, California, p. 805-833.

Carter, J.L., Resh, V.H., Rosenberg, D.M., and Reynoldson, T.B., 2006, Biomonitoring in North American rivers: a comparison of methods used for benthic macroinvertebrates in Canada and the United States, in Ziglio, G., Flaim, G., and Siligardi, M., eds., Biological Monitoring of Rivers: Applications and Perspectives: John Wiley and Sons, New York, p. 203-228.

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)

Lee, B-G., Lee, J-S, and Luoma, S.N. 2006. Comparison of selenium bioaccumulation in the clams Corbicula Fluminea and Potamocorbula amurensis: A bioenergetic modeling approach: Environmental Toxicology and Chemistry, v. 25, no. 7, p. 1933-1940. (on-line abstract of journal article)

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 Fend, S.V., 2005, Setting limits: the development and use of factor-ceiling distributions for an urban assessment using macroinvertebrates, in Brown, L.R., Gray, R., Hughes, R.M., and Meador, M.R., eds., Effects of urbanization on stream ecosystems: American Fisheries Society Symposium 47, Bethesda, Maryland, p.179-191.

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)

Fend, S.V., 2005, Rhynchelmis aleutensis n. sp. (Clitellata: Lumbriculidae) from Adak Island, Alaska: Zootaxa v. 1093, p. 45-53. (on-line abstract and introduction, in pdf format)

Fend, S.V., Carter, J.L., and Kearns, F.R., 2005, 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., Gray, R., Hughes, R.M., and Meador, M.R., eds., Effects of urbanization on stream ecosystems: American Fisheries Society Symposium 47, Bethesda, Maryland, p. 193-212.

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.

Fend, S.V. and Rodriguez, P., 2003, Eremidrilus n. gen. (Annelida, Clitellata, Lumbriculidae) and new species from California, USA: Canadian Journal of Zoology, v. 81, no. 3, p. 515-542. (on-line abstract of journal article)

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)


FOR ADDITIONAL INFORMATION ON THIS PROJECT, CONTACT
Janet K Thompson
U.S. Geological Survey, 345 Middlefield Rd, MS 496, Menlo Park, CA 94025
Internet: jthompso@usgs.gov
Telephone: 650-329-4364

Samuel N. Luoma
U.S. Geological Survey, 345 Middlefield Rd, MS 496, Menlo Park, CA 94025
Internet: snluoma@usgs.gov
Telephone: 650-329-4481

Daniel J Cain
U.S. Geological Survey, 345 Middlefield Rd, MS 496, Menlo Park, CA 94025
Internet: djcain@usgs.gov
Telephone: 650-329-4478

James L Carter
U.S. Geological Survey, 345 Middlefield Rd, MS 496, Menlo Park, CA 94025
Internet: jlcarter@usgs.gov
Telephone: 650-329-4439

Steven V Fend
U.S. Geological Survey, 345 Middlefield Rd, MS 496, Menlo Park, CA 94025
Internet: svfend@usgs.gov
Telephone: 650-329-4465

Michelle Hornberger
U.S. Geological Survey, 345 Middlefield Rd, MS 496, Menlo Park, CA 94025
Internet: mhornber@usgs.gov
Telephone: 650-329-4467

Robin Stewart
U.S. Geological Survey, 345 Middlefield Rd, MS 496, Menlo Park, CA 94025
Internet: rastewar@usgs.gov
Telephone: 650-329-4550

For information on additional projects in the National Research Program, see Indexes to NRP projects and bibliographies.

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