Takekawa, J.Y., Ackerman, J.T., Brand, L.A., Graham, T.R., Eagles-Smith, C.A., Herzog, M.P., Topping, B.R., Shellenbarger, G.G., Kuwabara, J.S., Mruz, E., Piotter, S.L., Athearn. N.D., 2015, Unintended consequences of management actions in salt pond restoration: cascading effects in trophic interactions: Plos One: 10: e0119345. doi:10.1371/journal.pone.0119345
James S Kuwabara, Ph.D.
Serves as Scientist emeritus within the USGS Water Mission Area's National Research Program. Access project Web site at: http://wwwrcamnl.wr.usgs.gov/solutetransport/index.htm
Biography
Studies quantitatively describe processes that regulate the transport of trace inorganic contaminants in surface-water systems. For example, in many aquatic systems facing a long (decadal to century) history of anthropogenic inputs, solute accumulation in bottom sediments and biologically mediated chemical gradients at the sediment-water interface can generate a benthic source that may rival or even dramatically exceed regulated point sources. Therefore, the importance of this benthic flux relative to regulated or monitored sources is a focus of the project. To aid in the evaluation of remediation and load-allocation strategies, factors contributing to the temporal and spatial variability of the benthic flux of contaminants are also being examined.
EDUCATION
California Institute of Technology: Ph.D. Environmental Engineering Science, June 1980
Ph.D. minor – Economics; M.S. Environmental Engineering Science, June 1976
University of Hawaii at Manoa: B.S. with academic honors in Civil Engineering, June 1975
Honors and Special Appointments (since 2000):
Editorial Board Member, Estuaries Newsletter, San Francisco Estuary Institute (1997 to present)
Coordinator, Benthic-flux study of contaminants into the water column of Lake Coeur d'Alene, ID, USEPA-funded (1998 to 2001)
CALFED Technical Review Panel, Contaminants Proposals (August 2000)
Special Session Chairman, American Society of Limnology and Oceanography, Albuquerque, NM (February 2001)
Associate Editor, Water Resources Research (2000 to 2002)
Excellence in Review Award, American Chemical Society, Environmental Science and Technology (November 2003)
Deputy Editor , Water Resources Research (January, 2002 to 2004)
Associate Editor, Water Resources Research (2004 to 2006)
Assistant Research Advisor, NRP Ecology Discipline, USGS (2006-2009)
Research Advisor, NRP Ecology Discipline, USGS (2009-present)
EMPLOYMENT (since 2000)
U. S. Geological Survey, Water Resources Division, National Research Program, Hydrologist (1982 – present)
City College of San Francisco, Adjunct faculty in Earth Sciences Department (2005 – present)
Cañada College, Adjunct faculty in Division of Science and Technology (2003-2006)
LECTURES AND INSTRUCTION
24 technical presentations and 11 invited lectures (since 2000).
Training (since 2000)
City College of San Francisco, Earth Sciences Department, Oceanography (January 2005 – present)
Cañada College, Department of Science and Technology, Oceanography (August 2003- May 2006)
National Water Quality Assessment Program, U.S. Geological Survey, Importance of sediment-water interactions on contaminant transport in mine-drainage systems, September, 2002.
Instructional Outreach (since 2000)
Project Web site: http://wwwrcamnl.wr.usgs.gov/solute_transport/index.html
Presentations at USGS Western Region Open Houses
MENTORING EXPERIENCE
Thesis committees for 4 graduate students and advisor for 2 post-doctoral fellows (1992-2008)
Publications:
Kuwabara, J.S., 1975, An optimization scheme for the controlled culture of Macrobrachium rosenbergii (giant prawn) larvae: University of Hawaii, Honolulu, HI, undergraduate thesis, 57 p.
Wang, J.K. and Kuwabara, J.S., 1976, Engineering analysis of prawn larvae culture: Transactions of the American Society of Agricultural Engineering, v. 19, p. 1197‑1200 .
Kuwabara, J.S., 1980, Micronutrient requirements for Macrocystis pyrifera (L.) (giant kelp) gametophytes determined by means of a chemically defined medium, Aquil: California Institute of Technology, Pasadena, CA, doctoral thesis, 170 p.
Kuwabara, J.S. and North, W.J., 1980, Culturing microscopic stages of Macrocystis pyrifera (Phaeophyta) in Aquil: a chemically defined medium: Journal of Phycology, v. 16, p. 546‑549.
North, W.J., V. Gerard and Kuwabara, J.S., 1980, Recent research on biomass production by freshwater and marine macrophytes: In Klass, D.L., ed., Biomass as a Non‑Fossil a Fuel Source, Chap. 4: ACS Symp. Ser., No. 144, American Chemical Society, Washington, D.C. p. 77‑98.
Kuwabara, J.S., 1981, Gametophytic growth by Macrocystis pyrifera in response to various iron and zinc concentrations: Journal of Phycology, v. 17, p. 417‑419.
North, W.J., Gerard, V. and Kuwabara, J.S., 1981, Farming Macrocystis at coastal and oceanic sites, In Srivastava, L.M., ed., Synthetic and degradative processes in marine macrophytes: Water de Gruyter, N.Y. p. 247‑264.
Kuwabara, J.S., 1982, Micronutrients and kelp cultures, evidence for cobalt and manganese deficiency in Southern California deep seawater: Science, v. 216, p. 1219‑1221.
North, W.J., Gerard, V., Manley, S.L. and Kuwabara, J.S., 1982, Environmental considerations involved in farmingMacrocystis: In Proceedings Second International Gas Research Conference, Newport Beach, CA.
Anderson, L.M., Kuwabara, J.S. and North, W.J., 1983, Effects of Cu, Zn, Fe and Mn on growth of Macrocystisgametophytes and sporophytes, In Soule, D.F. and Walsh, D., eds., Waste Disposal in the Oceans: Minimizing Impact Maximizing Benefits: Westview, CO, p. 140‑151.
Kuwabara, J.S., 1983, Effects of trace metals and natural organic materials on coastal communities, In Bascom, W., ed., Effects of Waste Disposal on Coastal Communities: Southern California Coastal Water Research Project, CA, p. 136‑146.
Kuwabara, J.S., Leland, H.V. and Bencala, K.E., 1984, Copper transport along a Sierra Nevada stream: Journal of Environmental Engineering, v. 110, p. 646‑655.
Kuwabara, J.S., Davis, J.A. and Chang, C.C.Y., 1985, Culturing Selenastrum capricornutum (Chlorophyta) in a synthetic algal nutrient medium with defined mineral particulates: Hydrobiologia, v. 124, p. 23‑27.
Kuwabara, J.S., 1985, Phosphorus‑zinc interactive effects on growth by Selenastrum capricornutum (Chlorophyceae): Environmental Science and Technology, v. 19, p. 417‑421.
Leland, H.V. and Kuwabara, J.S., 1985, Heavy metal toxicity to aquatic organisms, In Rand, G.M. and Petrocelli, S.R., eds., Fundamentals of Aquatic Toxicoloty Methods and Applications: Hemisphere Publications, N.Y., p. 374‑415.
Kuwabara, J.S., 1986, Physico‑chemical processes affecting copper, tin and zinc toxicity to algae, In Evans, L.V. and Hoagland, K.D., eds., Algal Biofouling, Chapter 9: Elsevier Science Publishers, Amsterdam, Netherlands, p. 129‑144.
Kuwabara, J.S. and Leland, H.V., 1986, Adaptation by Selenastrum capricornutum (Chlorophyceae) to copper: Environmental Toxicology and Chemistry, v. 5, p. 197‑203.
Kuwabara, J.S., Davis, J.A. and Chang, C.C.Y., 1986, Algal growth response to particle‑bound orthophosphate and zinc: Limnology and Oceanography, v. 31, p. 503‑511.
Chang, C.C.Y., Davis, J.A., and Kuwabara, J.S., 1987, A study of metal ion adsorption at low suspended-solid concentrations: Estuarine, Coastal and Shelf Science, v. 24, p. 419-424.
Kuwabara, J.S. and Helliker, P. 1988, Trace contaminants in streams, In Cheremisinoff, P.N., Cheremisinoff, N.P. and Cheng, S.L., eds., Encyclopedia of Civil Engineering Practice, Chapter 26: Technomic Press, v. 5, p. 739‑766.
Kuwabara, J.S., Chang, C.C.Y. and Pasilis, S.P., 1988, Effects of algal growth on arsenic transport in Whitewood Creek, South Dakota: Preliminary Results, In Mallard, G.E., ed., U.S. Geological Survey Toxic Substance Hydrology Program ‑ Surface‑Water Contamination: Proceedings of the Technical Meeting, Denver, Colorado, February 2‑4, 1987: U.S. Geological Survey Open File Report 87‑764, p. 33‑37.
Kuwabara, J.S. and Robinson, J.R., 1988, Development of a hollow fiber tangential flow filtration system for concentration of suspended sediment samples from natural waters, In G.E. Mallard, ed., U.S. Geological Survey Toxic Substance Hydrology Program ‑ Surface‑Water Contamination: Proceedings of the Technical Meeting, Denver, Colorado, February 2‑4, 1987: U.S. Geological Survey Open File Report 87‑764, p. 157‑160.
Kuwabara, J.S., Cain, D.J., Carter, J.L. and Fend, S.V., 1988, Biological investigations ‑ Surface‑Water Toxics Program, Whitewood Creek and the Belle Fourche and Cheyenne Rivers, South Dakota, In Goddard, K.E., ed., U.S. Geological Survey Applied Research Studies of the Cheyenne River System, South Dakota: Description and Collation of Data, Water Years 1985‑86: U.S. Geological Survey Open File Report 88‑484, p. 148‑158.
Kuwabara, J.S., Chang, C.C.Y., Cloern, J.E., Fries, T.L., Davis, J.A. and Luoma, S.N., 1989, Trace metal associations in the water column of South San Francisco Bay, California: Estuarine Coastal and Shelf Science, v. 26, p. 307‑325.
Kuwabara, J.S., Chang, C.C.Y. and Pasilis, S.P., 1989, Periphyton effects on arsenic transport in Whitewood Creek, South Dakota, In Mallard, G.E. and Ragone, S.E., eds., U.S. Geological Survey Toxic Substances Hydrology Program ‑ Proceedings of the Technical Meeting, Phoenix, Arizona, September 26‑30, 1988: U.S. Geological Survey Water Resources Investigations Report 88‑4220, p. 247‑256.
Kuwabara, J.S., Chang, C.C.Y. and Pasilis, S.P., 1990, Effects of benthic flora on arsenic transport: Journal of Environmental Engineering, v. 116, p. 394‑409.
Kuwabara, J.S. and Harvey, R.W., 1990, Application of a hollow‑fiber tangential‑flow device for sampling suspended bacteria and particles from natural waters: Journal of Environmental Quality, v. 19, p. 625‑629.
Stream Solute Workshop, 1990, Concepts and methods for assessing solute dynamics in stream ecosystems: Journal of the North American Benthological Society, v. 9, p. 95‑119.
Chang, C.C.Y., Kuwabara, J.S. and Pasilis, S.P., 1990, Trace‑metal concentrations in three streams during spring runoff in the Tahoe Basin, California/Nevada, In Poppoff, I.G., Goldman, C.R., Loeb, S.L. and Leopold, L.B., eds., Proceedings of the International Watershed Symposium, Lake Tahoe, June 8‑10, 1988: Tahoe Research Conservation District, p. 103‑115.
Kuwabara, J.S., 1992, Associations between benthic flora and diel changes in dissolved arsenic, phosphorus, and related physio‑chemical parameters: Journal of the North American Benthological Society, v. 11, p. 218‑228.
Chang, C.C.Y., Kuwabara, J.S. and Pasilis, S.P., 1992, Phosphate and iron limitation of phytoplankton biomass in Lake Tahoe: Canadian Journal of Fisheries and Aquatic Sciences, v. 49, p. 1206‑1215.
Kuwabara, J.S. and Baker, J.E., 1993, Trace contaminants and nutrients in estuaries: The importance of process interdependence (Introduction for the Dedicated Issue): Estuaries, v. 16, p. 383-384.
Kuwabara, J.S. and Luther, G.W., III, 1993, Dissolved sulfides in the oxic water column of San Francisco Bay, California: Estuaries, v. 16, p. 567-573.
Hunter, Y.R. and Kuwabara, J.S., 1994, Ionic strength and DOC determinations from various freshwater sources to the San Francisco Bay: Bulletin of Environmental Contamination and Toxicology, v. 52, p. 311-318.
Wood, T.M., Baptista, A.M., Kuwabara, J.S. and Flegal, A.R., 1995, Diagnostic modeling of trace metal partitioning in south San Francisco Bay: Limnology and Oceanography, v. 40, p. 345-358.
Kuwabara, J.S., Hunter, Y.R. and Chang, C.C.Y., 1996a, Distributions and benthic flux of dissolved sulfides in the oxic water column of San Francisco Bay, California, In Morganwalp, D.W., and Aronson, D.A., eds., U.S. Geological Survey Toxic Substances Hydrology Program ‑- Proceedings of the Technical Meeting, Colorado Springs, Colorado, September 20-24, 1993: U.S. Geological Survey Water-Resources Investigations Report 94-4015, p. 747-751.
Kuwabara, J.S., Chang, C.C.Y., Khechfe, A.I. and Hunter, Y.R., 1996b, Implications of dissolved sulfides and organic substances for the chemical speciation of trace contaminants in the water column of San Francisco Bay, California, in Hollibaugh, J.T., ed., San Francisco Bay: the Ecosystem: Amercian Association for the Advancement of Science, Pacific Division, San Francisco, p. 157-172.
Caffrey, J., Hammond, D., Kuwabara, J., Miller, L. and Twilley, R., 1996, Benthic processes in San Francisco Bay: the role of organic inputs and bioturbation, in Hollibaugh, J.T., ed., San Francisco Bay: the Ecosystem: Amercian Association for the Advancement of Science, Pacific Division, San Francisco, p. 425-442.
Kuwabara, J.S., van Geen, A., McCorkle, D.C., and Bernhard, J.M., 1999a, Dissolved sulfide distributions in the water column and sediment pore waters of the Santa Barbara Basin: Geochimica et Cosmochimica Acta, v. 63, No. 15, pp. 2199-2209.
Kuwabara, J.S., Topping, B.R. Coale, K.H. and Berelson, W.M., 1999b, Processes affecting the benthic flux of trace metals into the water column of 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. 115-119.
Kuwabara, J.S., Nichols, F.H., Kuivila, K.M., and DiLeo, J.S., 1999c, Understanding the human influence on the San Francisco Bay‑Delta estuary ecosystem ‑ The Toxic Substances Hydrology (Toxics) Program and Integrated Natural Resource Science (INATURES) Program provide complimentary approaches and results, 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. 109-113.
Kuwabara, J.S., van Geen, A., McCorkle, D.C., Bernhard, J.M., Zheng, Y., and Topping, B.R., 1999d, Redox gradients in the vicinity of the Santa Barbara Basin: Application of techniques developed within the San Francisco Bay Toxics Study, 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. 121-130.
Topping, B.R. and Kuwabara, J.S., 1999, Flow-injection-ICP-MS method applied to benthic flux studies of 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. 131-134.
Kuwabara, J.S., Berelson, W.M., Balistrieri, L.S., Woods, P.F., Topping, B.R., Steding, D. J., and Krabbenhoft, D.P., 2000, Benthic flux of metals and nutrients into the water column of lake Coeur d'Alene, Idaho: Report of an August, 1999 Pilot Study: USGS Water-Resources Investigations Report 00-4132, 74 p.
(Internet access at: http://water.usgs.gov/pubs/wri/wri004132/).
Zheng, Y., Anderson, R.F., van Geen, A., Kuwabara, J., 2000, Authigenic molybdenum formation in marine sediments: a link to pore-water sulfide in the Santa Barbara Basin: Geochimica et Cosmochimica Acta, v. 64, No. 24, p. 4165-4178. (Advised Doctoral candidate and prepared and revised sections of the manuscript dealing with sulfide interactions).
Topping, B.R., Kuwabara, J.S., Parchaso, F, Hager, S.W., Arnsberg, A.J., and Murphy, F., 2001, Benthic flux of dissolved nickel into the water column of South San Francisco Bay: U.S. Geological Survey Open-file Report 01-89, 50 p. (Internet access at: http://pubs.water.usgs.gov/ofr01089/).
Kuwabara, J.S., Marvin-Dipasquale, M., Praskins, W., Byron, E., Topping, B.R., Carter, J.L., Fend, S.V., Parchaso, F. and Krabbenhoft, D.P., 2002, Flux 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. (Internet access at: http://water.usgs.gov/pubs/wri/wri024138/).
Kuwabara, J.S., Alpers, C.N., Marvin-Dipasquale, 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 Investigation Report 03-4140, 61 p. (Internet access at: http://water.usgs.gov/pubs/wri/wri034140/).
Topping, B.R. and Kuwabara, J.S., 2003, Dissolved nickel and benthic flux in south San Francisco Bay: A potential for natural sources to dominate: Bulletin of Environmental Toxicology and Chemistry, v. 71, p. 46-51. (Supervised project member and edited manuscript).
Kuwabara, J.S., Woods, P.F., Berelson, W.M., Balistrieri, L.S., Carter, J.L., Topping, B.R., Fend, S.V., 2003, Importance of sediment-water interactions in Coeur d’Alene Lake, Idaho: Management Implications: Environmental Management, v. 32, No. 3, p. 348-359.
Kuwabara, J.S., Chang, C.C.Y., and Pasilis, S.P., 2003, Effects of benthic fauna on arsenic transport in Whitewood Creek, South Dakota in Kuwabara, J.S., and Fuller, C.C., eds., Toxic substances in surface waters and sediments -- A study to assess the effects of arsenic-contaminated alluvial sediment in Whitewood Creek, South Dakota: U.S. Geological Survey Professional Paper 1681, p. 1-26 (Internet access at:http://pubs.water.usgs.gov/pp1681/ ).
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, 60p. (Internet access at:http://pubs.water.usgs.gov/sir2004-5196).
Kuwabara, J.S., Topping, B.R., Moon, G.E., Husby, P., Lincoff, A., Carter, J.L., 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, 52 p. (Internet access at:http://pubs.water.usgs.gov/sir2005-5037).
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 2006-1034, 47 p. (Internet access at: http://pubs.usgs.gov/sir/2006/5091).
Kuwabara, J.S., Arai, Yuji, Topping, B.R., Pickering, I. J., and George, G.N., 2007a, Mercury speciation in piscivorous fish from mining-impacted reservoirs: Environment Science and Technology, v. 41, No. 8, p. 2745-2749.
Kuwabara, J.S., Topping, B.R., Woods, P.F., and Carter, J.L., 2007b, Free zinc ion and dissolved orthophosphate effects on phytoplankton from Coeur d'Alene Lake, Idaho: Environment Science and Technology, v. 41, No. 8, p. 2811-2817.
Kuwabara, J.S., Lynch, D.D., Topping, B.R., Murphy, Fred, Carter, J.L., Simon, N.S., Parchaso, Francis, Wood, T.M., Lindenberg, M.K., Wiese, Katryn, and Avanzino, R.J., 2007, Quantifying the Benthic Source of Dissolved Nutrients to the Water Column of Upper Klamath Lake, Oregon: U.S. Geological Survey Open-file Report 2007-1276, 40 p. (Internet access at: http://pubs.usgs.gov/of/2007/1276/).
Gandhi, N., Bhavsar, S.P., Diamond, M.L., Kuwabara, J.S., Mark Marvin-DiPasquale, M., and Krabbenhoft, D.P., 2007,Development of a mercury speciation, fate and biotic uptake (BIOTRANSPEC) model: Application to Lahontan Reservoir (Nevada, USA): Environmental Toxicology & Chemistry, v. 26, p. 2,260-2,273.
Thompson, Bruce, Adelsbach, Terry, Brown, C.L., Hunt, Jennifer, Kuwabara, J.S., Neale, J.C.C., Ohlendorf, H.M., Schwarzbach, S.E., Spies, R.B., and Taberski, K.M., 2007, Biological Effects of Anthropogenic Contaminants in the San Francisco Estuary: Environmental Research, v. 105, p. 156-174.
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, p. 2,351-2,366.
Kuwabara, J.S., Topping, B.R., Lynch, D.D., Carter, J.L., Essaid, H.I., 2009, Benthic nutrient sources to hypereutrophic Upper Klamath Lake, Oregon: Environmental Toxicology & Chemistry, v. 28, p. 516-524.
Topping, B.R. Kuwabara, J.S., Athearn, N.D., Takekawa, J.Y., Parchaso, F., Henderson, K.D. and Piotter, S., 2009, Benthic Oxygen Demand in Three Former Salt Ponds Adjacent to South San Francisco Bay, California: U.S. Geological Survey Open-file Report 2009-1180, 25 p. (Internet access at: http://pubs.usgs.gov/of/2009/1180/).
Kuwabara, J.S., Topping, B.R., Parchaso, F., Engelstad, A.C., and Greene, V.A., 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, 30 p. (Internet access at: http://pubs.usgs.gov/of/2009/1286/).
Kuwabara, J.S., Topping, B.R., Carter, J.L., Parchaso, F., Asbill, J.R., Cameron, J.M., 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. (Internet access at: http://pubs.usgs.gov/of/2010/1062/).
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, 42 p. (Internet access at: http://pubs.usgs.gov/of/2012/1057). [Link
Topping, B.R. Kuwabara, J.S., Garrett, K.K., Takekawa, J.Y., Parchaso, F., Piotter, S., Clearwater, I., and Shellenbarger, G.G., 2013, Internal Nutrient Sources and Dissolved Nutrient Distributions in Alviso Salt Pond A3W, California: U.S. Geological Survey Open-file Report 2013-1128, 31 p. [Link]
Kuwabara, J.S., Topping, B.R., Carter, J.L., Wood, T.M., Cameron, J.M., Asbill-Case, J.R., and Carlson, R.A., 2012, Changes in benthic nutrient sources within a wetland after hydrologic reconnection: Environmental Toxicology & Chemistry, v. 31, 1995-2013.
Takekawa, J.Y., Ackerman, J.T., Brand, L.A., Graham, T.R., Eagles-Smith, C.A., Herzog, M.P., Topping, B.R., Shellenbarger, G.G., Kuwabara, J.S., Mruz, E., Piotter, S.L., Athearn. N.D., 2015, Unintended consequences of management actions in salt pond restoration: cascading effects in trophic interactions: Plos One: 10: e0119345. doi:10.1371/journal.pone.0119345.
Topping, B.R., Kuwabara, J.S., Carter, J.L., Garrett, K.K., Mruz, E., Piotter, S., Takekawa, J.Y., 2016, Effects of salt pond restoration on benthic flux: sediment as a source of nutrients to the water column: Journal of Environmental Protection, v. 7, p. 1064-1071, DOI: 10.4236/jep.2016.77095, https://pubs.er.usgs.gov/publication/70174041.
Science and Products
Year Published: 2016
Benthic processes affecting contaminant transport in Upper Klamath Lake, Oregon
Executive SummaryMultiple sampling trips during calendar years 2013 through 2015 were coordinated to provide measurements of interdependent benthic processes that potentially affect contaminant transport in Upper Klamath Lake (UKL), Oregon. The measurements were motivated by recognition that such internal processes (for example, solute benthic...
Kuwabara, James S.; Topping, Brent R.; Carter, James L.; Carlson, Rick A; Parchaso, Francis; Fend, Steven V.; Stauffer-Olsen, Natalie; Manning, Andrew J.; Land, Jennie M.Attribution: Water Resources,
View Citation
Kuwabara, J.S., Topping, B.R., Carter, J.L., Carlson, R.A., Parchaso, F., Fend, S.V., Stauffer-Olsen, N., Manning, A.J., Land, J.M., 2016, Benthic processes affecting contaminant transport in Upper Klamath Lake, Oregon (ver. 1.1, October 2016): U.S. Geological Survey Open-File Report 2016–1175, 103 p., http://dx.doi.org/10.3133/ofr20161175.
Year Published: 2016
Effects of salt pond restoration on benthic flux: Sediment as a source of nutrients to the water column
Understanding nutrient flux between the benthos and the overlying water (benthic flux) is critical to restoration of water quality and biological resources because it can represent a major source of nutrients to the water column. Extensive water management commenced in the San Francisco Bay, Beginning around 1850, San Francisco Bay wetlands were...
Topping, Brent R.; Kuwabara, James S.; Carter, James L.; Garrettt, Krista K.; Mruz, Eric; Piotter, Sarah; Takekawa, John Y.View Citation
Topping, B., Kuwabara, J.,, Carter, J., Garrett, K., Mruz, E., Piotter, S., and Takekawa, J., 2016, Effects of Salt Pond Restoration on Benthic Flux: Sediment as a Source of Nutrients to the Water Column: Journal of Environmental Protection, 7, 1064-1071. http://dx.doi.org/10.4236/jep.2016.77095
Year Published: 2015
Unintended consequences of management actions in salt pond restoration: cascading effects in trophic interactions
Salt evaporation ponds have played an important role as habitat for migratory waterbirds across the world, however, efforts to restore and manage these habitats to maximize their conservation value has proven to be challenging. For example, salinity reduction has been a goal for restoring and managing former salt evaporation ponds to support...
Takekawa, John Y.; Ackerman, Joshua T.; Brand, Arriana; Graham, Tanya R.; Eagles-Smith, Collin A.; Herzog, Mark P.; Topping, Brent R.; Shellenbarger, Gregory; Kuwabara, James S.; Mruz, Eric; Piotter, Sara L.; Athearn, Nicole D.Attribution: Forest and Rangeland Ecosystem Science Center (FRESC), Western Ecological Research Center, Ecosystems, Environmental Health, , Contaminant Biology Program, United States of America
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Takekawa JY, JT Ackerman, LA Brand, TR Graham, CA Eagles-Smith, MP Herzog, BR Topping, GG Shellenbarger, JS Kuwabara, E Mruz, SL Piotter, ND Athearn. 2015. Unintended consequences of management actions in salt pond restoration: cascading effects in trophic interactions. PLoS ONE 10(6): e0119345. doi:10.1371/journal.pone.0119345
Year Published: 2013
Technical evaluation of a total maximum daily load model for Upper Klamath and Agency Lakes, Oregon
We reviewed a mass balance model developed in 2001 that guided establishment of the phosphorus total maximum daily load (TMDL) for Upper Klamath and Agency Lakes, Oregon. The purpose of the review was to evaluate the strengths and weaknesses of the model and to determine whether improvements could be made using information derived from studies...
Wood, Tamara M.; Wherry, Susan A.; Carter, James L.; Kuwabara, James S.; Simon, Nancy S.; Rounds, Stewart A.Attribution: Oregon Water Science Center, Water Resources
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Technical evaluation of a total maximum daily load model for Upper Klamath and Agency Lakes, Oregon; 2013; OFR; 2013-1262; Wood, Tamara M.; Wherry, Susan A.; Carter, James L.; Kuwabara, James S.; Simon, Nancy S.; Rounds, Stewart A.
Year Published: 2013
Internal nutrient sources and nutrient distributions in Alviso Pond A3W, California
Within the Alviso Salt Pond complex, California, currently undergoing avian-habitat restoration, pore-water profilers (U.S. Patent 8,051,727 B1) were deployed in triplicate at two contrasting sites in Pond A3W (“Inlet”, near the inflow, and “Deep”, near the middle of the pond; figs. 1 and 2; table 1, note that tables in this report are provided...
Topping, Brent R.; Kuwabara, James S.; Garrett, Krista K.; Takekawa, John Y.; Parcheso, Francis; Piotter, Sara; Clearwater, Iris; Shellenbarger, GregoryAttribution: Water Resources,
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Internal nutrient sources and nutrient distributions in Alviso Pond A3W, California; 2013; OFR; 2013-1128; Topping, Brent R.; Kuwabara, James S.; Garrett, Krista K.; Takekawa, John Y.; Parchaso, Francis; Piotter, Sara; Clearwater, Iris; Shellenbarger, Gregory G.
Year Published: 2012
Time scales of change in chemical and biological parameters after engineered levee breaches adjacent to Upper Klamath and Agency Lakes, Oregon
Eight sampling trips were coordinated after engineered levee breaches hydrologically reconnected both Upper Klamath Lake and Agency Lake, Oregon, to adjacent wetlands. The reconnection, by a series of explosive blasts, was coordinated by The Nature Conservancy to reclaim wetlands that had for approximately seven decades been leveed for crop...
Kuwabara, James S.; Topping, Brent R.; Carter, James L.; Wood, Tamara M.; Parcheso, Francis; Cameron, Jason M.; Asbill, Jessica R.; Carlson, Rick A.; Fend, Steven V.View Citation
Time scales of change in chemical and biological parameters after engineered levee breaches adjacent to Upper Klamath and Agency Lakes, Oregon; 2012; OFR; 2012-1057; Kuwabara, James S.; Topping, Brent R.; Carter, James L.; Wood, Tamara M.; Parchaso, Francis; Cameron, Jason M.; Asbill, Jessica R.; Carlson, Rick A.; Fend, Steven V.
Year Published: 2010
The transition of benthic nutrient sources after planned levee breaches adjacent to upper Klamath and Agency Lakes, Oregon
Four sampling trips were coordinated after planned levee breaches that hydrologically reconnected both Upper Klamath Lake and Agency Lake, Oregon, to adjacent wetlands. Sets of nonmetallic pore-water profilers were deployed during these trips in November 2007, June 2008, May 2009, and July 2009. Deployments temporally spanned the annual cyanophyte...
Kuwabara, James S.; Topping, Brent R.; Carter, James L.; Parchaso, Francis; Cameron, Jason M.; Asbill, Jessica R.; Fend, Steven V.; Duff, John H.; Engelstad, Anita C.Attribution: Environmental Health, Toxic Substances Hydrology Program
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The Transition of Benthic Nutrient Sources after Planned Levee Breaches Adjacent to Upper Klamath and Agency Lakes, Oregon; 2010; OFR; 2010-1062; Kuwabara, James S.; Topping, Brent R.; Carter, James L.; Parchaso, Francis; Cameron, Jason M.; Asbill, Jessica R.; Fend, Steven V.; Duff, John H.; Engelstad, Anita C.
Year Published: 2009
Benthic flux of nutrients and trace metals in the northern component of San Francisco Bay, California
Two sets of sampling trips were coordinated in late summer 2008 (weeks of July 8 and August 6) to sample the interstitial and overlying bottom waters at 10 shallow locations (9 sites <3 meters in depth) within the northern component of the San Francisco Bay/Delta (herein referred to as North Bay). The work was performed to better understand...
Kuwabara, James S.; Topping, Brent R.; Parcheso, Francis; Engelstad, Anita C.; Greene, Valerie E.Attribution: Environmental Health, Toxic Substances Hydrology Program, San Francisco Bay and Sacramento-San Joaquin Delta Estuary
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Benthic flux of nutrients and trace metals in the northern component of San Francisco Bay, California; 2009; OFR; 2009-1286; Kuwabara, James S. ; Topping, Brent R. ; Parchaso, Francis ; Engelstad, Anita C. ; Greene, Valerie E.
Year Published: 2009
Benthic oxygen demand in three former salt ponds adjacent to south San Francisco Bay, California
Sampling trips were coordinated in the second half of 2008 to examine the interstitial water in the sediment and the overlying bottom waters of three shallow (average depth <1 meter) ponds adjacent to the southern reach of San Francisco Bay (herein referred to as South Bay), which were previously used in commercial salt production. In recent...
Topping, Brent R.; Kuwabara, James S.; Athearn, Nicole D.; Takekawa, John Y.; Parcheso, Francis; Henderson, Kathleen D.; Piotter, SaraAttribution: , California Water Science Center, Water Resources, Environmental Health, Toxic Substances Hydrology Program, San Francisco Bay and Sacramento-San Joaquin Delta Estuary
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Benthic Oxygen Demand in Three Former Salt Ponds Adjacent to South San Francisco Bay, California; 2009; OFR; 2009-1180; Topping, Brent R.; Kuwabara, James S.; Athearn, Nicole D.; Takekawa, John Y.; Parchaso, Francis; Henderson, Kathleen D.; Piotter, Sara
Year Published: 2007
Quantifying the benthic source of nutrients to the water column of Upper Klamath Lake, Oregon
Executive Summary Five sampling trips were coordinated in April, May and August 2006, and May and July 2007 to sample the water column and benthos of Upper Klamath Lake, OR (Fig. 1; Table 1), before, during and after the annual cyanophyte bloom of Aphanizomenon flos-aquae (AFA). A pore-water profiler was designed and fabricated to obtain the...
Kuwabara, James S.; Lynch, Dennis D.; Topping, Brent R.; Murphy, Fred; Carter, James L.; Simon, Nancy S.; Parcheso, Francis; Wood, Tamara M.; Lindenberg, Mary K.; Wiese, Katryn; Avanzino, Ronald J.Attribution: Environmental Health, Toxic Substances Hydrology Program
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Quantifying the Benthic Source of Nutrients to the Water Column of Upper Klamath Lake, Oregon; 2007; OFR; 2007-1276; Kuwabara, James S.; Lynch, Dennis D.; Topping, Brent R.; Murphy, Fred; Carter, James L.; Simon, Nancy S.; Parchaso, Francis; Wood, Tamara M.; Lindenberg, Mary K.; Wiese, Katryn; Avanzino, Ronald J.
Year Published: 2007
Biological effects of anthropogenic contaminants in the San Francisco Estuary
Concentrations of many anthropogenic contaminants in the San Francisco Estuary exist at levels that have been associated with biological effects elsewhere, so there is a potential for them to cause biological effects in the Estuary. The purpose of this paper is to summarize information about biological effects on the Estuary's plankton, benthos,...
Thompson, B.; Adelsbach, T.; Brown, Cynthia L.; Hunt, J.; Kuwabara, James S.; Neale, J.; Ohlendorf, H.; Schwarzbach, Steven E.; Spies, R.; Taberski, K.Attribution: Environmental Health, Toxic Substances Hydrology Program
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Biological effects of anthropogenic contaminants in the San Francisco Estuary; 2007; Article; Journal; Environmental Research; Thompson, B.; Adelsbach, T.; Brown, C.; Hunt, J.; Kuwabara, J.; Neale, J.; Ohlendorf, H.; Schwarzbach, S.; Spies, R.; Taberski, K.
Year Published: 2007
Development of a mercury speciation, fate, and biotic uptake (BIOTRANSPEC) model: Application to Lahontan Reservoir (Nevada, USA)
A mathematically linked mercury transport, speciation, kinetic, and simple biotic uptake (BIOTRANSPEC) model has been developed. An extension of the metal transport and speciation (TRANSPEC) model, BIOTRANSPEC estimates the fate and biotic uptake of inorganic (Hg(II)), elemental (Hg(0)) and organic (MeHg) forms of mercury and their species in the...
Gandhi, N.; Bhavsar, S.P.; Diamond, M.L.; Kuwabara, James S.; Marvin-DePasquale, Mark C.; Krabbenhoft, David P.Attribution: Environmental Health, Toxic Substances Hydrology Program
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Development of a mercury speciation, fate, and biotic uptake (BIOTRANSPEC) model: Application to Lahontan Reservoir (Nevada, USA); 2007; Article; Journal; Environmental Toxicology and Chemistry; Gandhi, N.; Bhavsar, S. P.; Diamond, M. L.; Kuwabara, J. S.; Marvin-DiPasquale, M.; Krabbenhoft, D. P.
Pre-USGS Publications
Topping, B.R., Kuwabara, J.S., Carter, J.L., Garrett, K.K., Mruz, E., Piotter, S., Takekawa, J.Y., 2016, Effects of salt pond restoration on benthic flux: sediment as a source of nutrients to the water column: Journal of Environmental Protection, v. 7, p. 1064-1071, DOI: 10.4236/jep.2016.77095, https://pubs.er.usgs.gov/publication/70174041.