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2013 Annual Report
Table of Contents

Director's Message - Ocean Acidification


An adaptive, comprehensive monitoring strategy for chemicals of emerging concern (CECs) in California’s aquatic ecosystems     ABSTRACT     SUPPLEMENTAL INFORMATION
Keith A. Maruya, Daniel Schlenk, Paul D. Anderson, Nancy D. Denslow, Jörg E. Drewes, Adam W. Olivieri, Geoffrey I. Scott and Shane A. Snyder

The occurrence and fate of chemicals of emerging concern (CECs) in coastal urban rivers receiving discharge of treated municipal wastewater effluent     ABSTRACT     SUPPLEMENTAL INFORMATION
Ashmita Sengupta, J. Michael Lyons, Deborah J. Smith, Jörg E. Drewes, Shane A. Snyder, Ann Heil and Keith A. Maruya

Refocusing Mussel Watch on contaminants of emerging concern (CECs): The California Pilot Study (2009-10)     ABSTRACT     SUPPLEMENTAL INFORMATION
Keith A. Maruya, Nathan G. Dodder, Rebecca A. Schaffner, Stephen B. Weisberg, Dominic Gregorio, Susan Klosterhaus, David A. Alvarez, Edward T. Furlong, Kimani L. Kimbrough, Gunnar G. Lauenstein and John D. Christensen

Occurrence of contaminants of emerging concern in mussels (Mytilus spp.) along the California coast and the influence of land use, stormwater discharge, and treated wastewater effluent     ABSTRACT     SUPPLEMENTAL INFORMATION
Nathan G. Dodder, Keith A. Maruya, P. Lee Ferguson, Richard Grace, Susan Klosterhaus, Mark J. La Guardia, Gunnar G. Lauenstein and Juan Ramirez

Occurrence of contaminants of emerging concern along the California coast (2009-10) using passive sampling devices     ABSTRACT     SUPPLEMENTAL INFORMATION
David Alvarez, Keith A. Maruya, Nathan G. Dodder, Wenjian Lao, Edward Furlong and Kelly Smalling

The Mussel Watch California Pilot Study on contaminants of emerging concern (CECs): Synthesis and next steps     ABSTRACT     SUPPLEMENTAL INFORMATION
Keith A. Maruya, Nathan G. Dodder, Stephen B. Weisberg, Dominic Gregorio, Jonathan S. Bishop, Susan Klosterhaus, David A. Alvarez, Edward T. Furlong, Suzanne Bricker, Kimani L. Kimbrough and Gunnar G. Lauenstein

Passive sampling methods for contaminated sediments: State of the science for organic contaminants     ABSTRACT     SUPPLEMENTAL INFORMATION
Michael J. Lydy, Peter F. Landrum, Amy M.P. Oen, Mayumi Allinson, Foppe Smedes, Amanda D. Harwood, Heng Li, Keith A. Maruya and James Liu

Passive sampling methods for contaminated sediments: Practical guidance for selection, calibration and implementation     ABSTRACT     SUPPLEMENTAL INFORMATION
Upal Ghosh, Susan Kane Driscoll, Robert M. Burgess, Michiel T. O. Jonker, Danny Reible, Frank Gobas, Yongju Choi, Sabine E. Apitz, Keith A. Maruya, William R. Gala, Munro Mortimer and Chris Beegan



Genomics in marine monitoring: New opportunities for assessing marine health status     ABSTRACT
Sarah J. Bourlat, Angel Borja, Jack Gilbert, Martin I. Taylor, Neil Davies, Stephen B. Weisberg, John Griffith, Teresa Lettieri, Dawn Field, John Benzie, Frank Oliver Glöckner, Naiara Rodríguez- Ezpeleta, Daniel P Faith, Tim P. Bean and Matthias Obst

Gene expression of fathead minnows (Pimephales promelas) exposed to two types of treated municipal wastewater effluents     ABSTRACT     SUPPLEMENTAL INFORMATION
Doris E. Vidal-Dorsch, R. Cristina Colli-Dula, Steven M. Bay, Darrin J. Greenstein, Lan Wiborg, Dawn Petschauer and Nancy D. Denslow

Genomic and phenotypic response of hornyhead turbot exposed to municipal wastewater effluents     ABSTRACT     SUPPLEMENTAL INFORMATION
Doris E. Vidal-Dorsch, Steven M. Bay, Cataldo Ribecco, L. James Sprague, Mila Angert, Colleen Ludka, Oliana Carnevali, Darrin J. Greenstein, Daniel Schlenk, Kevin M. Kelley, Jesus A. Reyes, Shane Snyder, Brett Vanderford, Lan C. Wiborg, Dawn Petschauer, Roman Šášik, Michael Baker and Gary Hardiman

The use of sediment toxicity identification evaluation methods to evaluate clean-up targets in an urban estuary     ABSTRACT     SUPPLEMENTAL INFORMATION
Darrin Greenstein, Steven Bay, Diana Young, Stanford Asato, Keith Maruya and Wenjian Lao



Development and comparison of stream indices of biotic integrity using diatoms vs. non-diatom algae vs. a combination     ABSTRACT     SUPPLEMENTAL INFORMATION
A. Elizabeth Fetscher, Rosalina Stancheva, J. Patrick Kociolek, Robert G. Sheath, Eric D. Stein, Raphael D. Mazor, Peter R. Ode and Lilian B. Busse

Nitrogen-fixing cyanobacteria (free living and diatom endosymbionts): Their use in southern California stream bioassessment     ABSTRACT     SUPPLEMENTAL INFORMATION
Rosalina Stancheva, Robert G. Sheath, Betsy A. Read, Kimberly D. McArthur, Chrystal Schroepfer, J. Patrick Kociolek and A. Elizabeth Fetscher

A regional survey of the extent and magnitude of eutrophication in Mediterranean estuaries of southern California, USA     ABSTRACT
Karen McLaughlin, Martha Sutula, Lilian Busse, Sean Anderson, Jeffrey Crooks, Rosi Dagit, Doug Gibson, Karina Johnston and Lisa Stratton

Terrestrial nutrient loads and fluxes to the Southern California Bight, USA     ABSTRACT     SUPPLEMENTAL INFORMATION
Ashmita Sengupta, Martha A. Sutula, Karen McLaughlin, Meredith Howard, Leisl Tiefenthaler and Theodore Von Bitner

Coastal upwelling linked to toxic Pseudo-nitzschia australis blooms in Los Angeles coastal waters, 2005-2007     ABSTRACT
Astrid Schnetzer, Burton H. Jones, Rebecca A. Schaffner, Ivona Cetinic, Elizabeth Fitzpatrick, Peter E. Miller, Erica L. Seubert and David A. Caron

Seasonal and annual dynamics of harmful algae and algal toxins revealed through weekly monitoring at two coastal ocean sites off southern California, USA     ABSTRACT
Erica L. Seubert, Alyssa G. Gellene, Meredith D.A. Howard, Paige Connell, Matthew Ragan, Burton H. Jones, Jennifer Runyan and David A. Caron

Development, comparison and validation using ELISAs for the analysis of domoic acid in California sea lion body fluids     ABSTRACT
Erica L. Seubert, Meredith D.A. Howard, Raphael M. Kudela, Thomas N. Stewart, R. Wayne Litaker, Richard Evans and David A. Caron



Does DNA barcoding improve performance of traditional stream bioassessment metrics?     ABSTRACT
Eric D. Stein, Bryan P. White, Raphael D. Mazor, John K. Jackson, Juliann M. Battle, Peter E. Miller, Erik M. Pilgrim and Bernard W. Sweeney

Comparison of four species-delimitation methods applied to a DNA barcode data set of insect larvae for use in routine bioassessment     ABSTRACT
Bryan P. White, Erik M. Pilgrim, Laura M. Boykin, Eric D. Stein and Raphael D. Mazor

Evaluating the adequacy of a reference-site pool for the ecological assessment of streams in environmentally complex regions     ABSTRACT
Peter Ode, Andrew Rehn, Raphael Mazor, Kenneth Schiff, Eric Stein, Jason May, Larry Brown, David Herbst, David Gillett, Kevin Lunde and Charles P. Hawkins

Integrating intermittent streams into watershed assessments: Applicability of an index of biotic integrity     ABSTRACT     SUPPLEMENTAL INFORMATION
Raphael D. Mazor, Eric D. Stein, Peter R. Ode and Ken Schiff

Evaluation of design-based sampling options for monitoring stream and wetland extent and distribution in California     ABSTRACT
Leila G. Lackey and Eric D. Stein

A framework for evaluating regional hydrologic sensitivity to climate change using archetypal watershed modeling     ABSTRACT
Sonya R. Lopez, Terri S. Hogue and Eric D. Stein



Performance of forty-three microbial source tracking methods: A twenty-seven laboratory evaluation study     ABSTRACT     SUPPLEMENTAL INFORMATION
Alexandria B. Boehm, Laurie C. Van De Werfhorst, John F. Griffith, Patricia A. Holden, Jenny A. Jay, Orin C. Shanks, Dan Wang and Stephen B. Weisberg

Evaluation of the repeatability and reproducibility of a suite of qPCR-based microbial source tracking methods     ABSTRACT     SUPPLEMENTAL INFORMATION
Darcy L. Ebentier, Kaitlyn T. Hanley, Yiping Cao, Brian D. Badgley, Alexandria B. Boehm, Jared S. Ervin, Kelly D. Goodwin, Michèle Gourmelon, John F. Griffith, Patricia A. Holden, Catherine A. Kelty, Solen Lozach, Charles McGee, Lindsay A. Peed, Meredith Raith, Hodon Ryu, Michael J. Sadowsky, Elizabeth A. Scott, Jorge Santo Domingo, Alexander Schriewer, Christopher D. Sinigalliano, Orin C. Shanks, Laurie C. Van De Werfhorst, Dan Wang, Stefan Wuertz and Jennifer A. Jay

Performance of human fecal anaerobe-associated PCR-based assays in a multi-laboratory method evaluation study     ABSTRACT     SUPPLEMENTAL INFORMATION
Blythe A. Layton, Yiping Cao, Darcy L. Ebentier, Kaitlyn Hanley, Elisenda Ballesté,João Brandão, Muruleedhara Byappanahalli, Reagan Converse, Andreas H. Farnleitner, Jennifer Gentry- Shields, Maribeth L. Gidley, Michèle Gourmelon, Chang Soo Lee, Jiyoung Lee, Solen Lozach, Tania Madi, Wim G. Meijer, Rachel Noble, Lindsay Peed, Georg H. Reischer, Raquel Rodrigues, Joan B. Rose, Alexander Schriewer, Chris Sinigalliano, Sangeetha Srinivasan, Jill Stewart, Laurie C. Van De Werfhorst, Dan Wang, Richard Whitman, Stefan Wuertz, Jenny Jay, Patricia A. Holden, Alexandria B. Boehm, Orin Shanks and John F. Griffith

Evaluation of molecular community analysis methods for discerning fecal sources and human waste     ABSTRACT     SUPPLEMENTAL INFORMATION
Yiping Cao, Laurie C. Van De Werfhorst, Eric A. Dubinsky, Brian D. Badgley, Michael J. Sadowsky, Gary L. Andersen, John F. Griffith and Patricia A. Holden

Bacteroidales terminal restriction fragment length polymorphism (TRFLP) for fecal source differentiation in comparison to and in combination with universal bacteria TRFLP     ABSTRACT     SUPPLEMENTAL INFORMATION
Yiping Cao, Laurie C. Van De Werfhorst, Elizabeth A. Scott, Meredith R. Raith, Patricia A. Holden and John F. Griffith

Comparison of PCR and quantitative real-time PCR methods for the characterization of ruminant and cattle fecal pollution sources     ABSTRACT
Meredith R. Raith, Catherine A. Kelty, John F. Griffith, Alexander Schriewer, Stefan Wuertz, Sophie Mieszkin, Michele Gourmelon, Georg H. Reischer, Andreas H. Farnleitner, Jared S. Ervin, Patricia A. Holden, Darcy.L. Ebentier, Jennifer A. Jay, Dan Wang, Alexandria B. Boehm, Tiong Gim Aw, Joan B. Rose, E. Balleste, W.G. Meijer, Mano Sivaganesan and Orin C. Shanks

Performance of viruses and bacteriophages for fecal source determination in a multi-laboratory, comparative study     ABSTRACT
Valerie J. Harwood, Alexandria B. Boehm, Lauren M. Sassoubre, Kannappan Vijayavel, Jill R. Stewart, Theng-Theng Fong, Marie-Paule Caprais, Reagan R. Converse, David Diston, James Ebdon, Jed A. Fuhrman, Michele Gourmelon, Jennifer Gentry-Shields, John F. Griffith, Donna R. Kashian, Rachel T. Noble, Huw Taylor and Melanie Wicki

Multi-laboratory evaluations of the performance of Catellicoccus marimammalium PCR assays developed to target gull fecal sources     ABSTRACT     SUPPLEMENTAL INFORMATION
Christopher D. Sinigalliano, Jared Ervin, Laurie C. Van De Werfhorst, Brian Badgley, Elisenda Ballesté, Jakob Bartkowiak, Alexandria B. Boehm, Muruleedhara Byappanahalli, Kelly D. Goodwin, Michèle Gourmelon, John Griffith, Patricia A. Holden, Jenny Jay, Blythe Layton, Cheonghoon Lee, Jiyoung Lee, Wim G. Meijer, Rachel Noble, Meredith Raith, Hodon Ryu, Michael J. Sadowsky, Alexander Schriewer, Dan Wang, David Wanless, Richard Whitman, Stefan Wuertz and Jorge W. Santo Domingo

Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study     ABSTRACT     SUPPLEMENTAL INFORMATION
Alexander Schriewer, Kelly D. Goodwin, Christopher D. Sinigalliano, Annie M. Cox, David Wanless, Jakob Bartkowiak, Darcy L. Ebentier, Kaitlyn T. Hanley, Jared Ervin, Louise A. Deering, Orin C. Shanks, Lindsay A. Peed, Wim G. Meijer, John F. Griffith, Jorge SantoDomingo, Jennifer A. Jay, Patricia A. Holden and Stefan Wuertz

Characterization of fecal concentrations in human and other animal sources by physical, culture-based, and quantitative real-time PCR methods     ABSTRACT     SUPPLEMENTAL INFORMATION
Jared S. Ervin, Todd L. Russell, Blythe A. Layton, Kevan M. Yamahara, Dan Wang, Lauren M. Sassoubre, Yiping Cao, Catherine A. Kelty, Mano Sivaganesan, Alexandria B. Boehm, Patricia A. Holden, Stephen B. Weisberg and Orin C. Shanks

Towards establishing a human fecal contamination index for microbial source tracking     ABSTRACT
Yiping Cao, Charles Hagedorn, Orin C. Shanks, Dan Wang, Jared Ervin, John F. Griffith, Blythe A. Layton, Charles D. McGee, Timothy E. Riedel and Stephen B. Weisberg

Recommendations following a multi-laboratory comparison of microbial source tracking methods     ABSTRACT
Jill R. Stewart, Alexandria B. Boehm, Eric A. Dubinsky, Theng-Theng Fong, Kelly D. Goodwin, John F. Griffith, Rachel T. Noble, Orin C. Shanks, Kannappan Vijayavel and Stephen B. Weisberg

Human viruses and viral indicators in marine water at two beaches in southern California, USA     ABSTRACT
David C. Love, Roberto A. Rodriguez, Christopher D. Gibbons, John F. Griffith, Qilu Yu, Jill Stewart and Mark D. Sobsey

Swimmer illness associated with marine water exposure and water quality indicators: Impact of widely used assumptions     ABSTRACT     SUPPLEMENTAL INFORMATION
Benjamin F. Arnold, Kenneth C. Schiff, John F. Griffith, Joshua S. Gruber, Vincent Yau, Catherine C. Wright, Timothy J. Wade, Susan Burns, Jacqueline M. Hayes, Charles McGee, Mark Gold, Yiping Cao, Stephen B. Weisberg and John M. Colford, Jr



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