Pelagic Organism Decline
The Interagency Ecological Program (IEP), a consortium of nine state and federal agencies, has been monitoring aquatic organisms and water quality in the San Francisco estuary for decades. Since late 2004, scientific and public attention has focused on the unexpected decline of several pelagic (open-water) fishes (delta smelt, longfin smelt, juvenile striped bass, and threadfin shad) in the freshwater portion of the estuary known as the Delta. This decline has collectively become known as the Pelagic Organism Decline (POD). In 2005, the IEP formed a multi-agency POD Management Team tasked with designing and managing a comprehensive study to evaluate the causes of the decline and to synthesize and report the results. The causes under investigation include stock-recruitment effects, a decline in habitat quality; increased mortality rates; and reduced food availability due to invasive species.
IEP POD Publications
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2010
- Baxa, D. V., T. Kurobe, K. A. Ger, P. W. Lehman and S. J. Teh. 2010. Estimating the abundance of toxic Microcystis in the San Francisco Estuary using quantitative real-time PCR. Harmful Algae 9: 342349.
Abstract access: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B73D7-4Y3TXBF-1&_user=10&_coverDate=03%2F31%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_ sort=d&_docanchor=&view=c&_searchStrId=1568230288&_rerunOrigin=google&_acct=C000050221&_version=1&_ urlVersion=0&_userid=10&md5=5313009b77318456513311f8e18abd0d&searchtype=a
Corresponding author e-mail: dvbaxa@ucdavis.edu - Beggel S., Werner I., Connon R.E., Geist J. 2010. Sublethal toxicity of commercial insecticide formulations and their active ingredients to larval fathead minnow (Pimephales promelas). Science of the Total Environment 408: 3169–3175.
Abstract access: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V78-4YYWRKT-3&_user=10&_coverDate=07%2F15%2F2010&_rdoc=1&_fmt=high&_orig=search&_origin=search&_ sort=d&_docanchor=&view=c&_searchStrId=1568229955&_rerunOrigin=google&_acct=C000050221&_version=1&_ urlVersion=0&_userid=10&md5=6a2eb5ee6b4ff52831fb30879704eff3&searchtype=a
Corresponding author e-mail: reconnon@ucdavis.edu - Connon R.E., Beggel S., D’Abronzo L.S., Geist J., Loguinov A.S., Vulpe C.D., Werner I. 2010. Linking molecular biomarkers with higher level condition indicators to identify effects of copper exposures on the endangered delta smelt (Hypomesus transpacificus). Environmental Toxicology and Chemistry. In press.
Abstract access: http://onlinelibrary.wiley.com/doi/10.1002/etc.400/abstract
Corresponding author e-mail: reconnon@ucdavis.edu - D. Deng, K. Zheng, F. Teh, P. W. Lehman, S. J. Teh. 2010. Toxic Threshold of Dietary Microcystin (-LR) for Quart Medaka. Toxicon 55: 787794.
Full article access: http://www.water.ca.gov/ssr/docs/toxic_threshold_of_mc.pdf - Feyrer, F., M. Nobriga, T. Sommer, and K. Newman. 2010. Modeling the effects of future freshwater flow on the abiotic habitat of an imperiled estuarine fish. Estuaries and Coasts. Published online 28 September 2010, DOI 10.1007/s12237-010-9343-9
Full article access: http://www.springerlink.com/content/d22u618x244n7j46/
Corresponding author e-mail: FFeyrer@usbr.gov - Ger, Kemal A. Swee J. Teh, Dolores V. Baxa, Sarah Lesmeister, and Charles R. Goldman. 2010. The effects of dietary Microcystis aeruginosa and microcystin on the copepods of the upper San Francisco Estuary. Freshwater Biology - Published Online: 4 Feb 2010.
Abstract access: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2427.2009.02367.x/abstract
Corresponding author e-mail: aligerger@gmail.com - Ger, Kemal Ali, Patty Arneson, Charles R. Goldman, Swee J. Teh. 2010. Species specific differences in the ingestion of Microcystis cells by the calanoid copepods Eurytemora affinis and Pseudodiaptomus forbesi. Journal of Plankton Research Advance Access published on June 18, 2010.
Abstract access: http://plankt.oxfordjournals.org/content/early/2010/06/17/plankt.fbq071.abstract
Corresponding author e-mail: aligerger@gmail.com - Gould, A.L. and W.J. Kimmerer. 2010. Development, growth, and reproduction of the cyclopoid copepod Limnoithona tetraspina in the upper San Francisco Estuary. Marine Ecology Progress Series 412: 163-177.
Abstract access: http://www.int-res.com/abstracts/meps/v412/p163-177/
Corresponding author e-mail: kimmerer@sfsu.edu - Hobbs, J.A., L. L Lewis, N. Ikemiyagi, T. Sommer and R. Baxter. 2010. Identifying critical nursery habitat for an estuarine fish with otolith strontium isotopes. Environmental Biology of Fishes. 89:557-569. DOI 10.1007/s10641-010-9762-3.
Full article access: http://www.springerlink.com/content/vn8q01l315kp2669/fulltext.pdf
Corresponding author e-mail: jahobbs@ucdavis.edu - Israel, J.A., B. May. 2010. Characterization and evaluation of polymorphic microsatellite markers in the anadromous fish Spirinchus thaleichthys. Conservation Genetics Resources 2: 227-230.
Full article access: http://www.springerlink.com/content/px67r50j24wx7130/fulltext.pdf
Corresponding author e-mail: JAIsrael@usbr.gov - Kimmerer, W.J. and A.L. Gould. 2010. A Bayesian approach to estimating copepod development times from stage frequency data. Limnology and Oceanography Methods 8:118-126.
Abstract access: http://www.aslo.org/lomethods/free/2010/0118.html
Corresponding author e-mail: kimmerer@sfsu.edu - Lehman, P. W., S. Mayr, L. Mecum and C. Enright. 2010. The freshwater tidal wetland Liberty Island, CA was both a source and sink of inorganic and organic material to the San Francisco Estuary. Aquatic Ecology 44:359–372.
Full article access: http://www.springerlink.com/content/n4617315633702x0/fulltext.pdf
Corresponding author e-mail: plehman@water.ca.gov - Lehman, P. W., S. Teh, G. L. Boyer, M. Nobriga, E. Bass and C. Hogle. 2010. Initial impacts of Microcystis on the aquatic food web in the San Francisco Estuary. Hydrobiologia 637: 229-248. Full article access: http://www.springerlink.com/content/00j9382742167k36/fulltext.pdf
Corresponding author e-mail: plehman@water.ca.gov
- Mac Nally, Ralph, James R. Thomson, Wim J. Kimmerer, Frederick Feyrer, Ken B. Newman, Andy Sih, William A. Bennett, Larry Brown, Erica Fleishman, Steven D. Culberson, and Gonzalo Castillo. 2010. An analysis of pelagic species decline in the upper San Francisco Estuary using Multivariate Autoregressive modeling (MAR). Ecological Applications, 20: 167-180. NCEAS POD working group publication
Abstract access: http://www.esajournals.org/doi/abs/10.1890/09-1724.1
Corresponding author e-mail: Ralph.McNally@sci.monash.edu.au - Peterson, Heather A, and Marc Vayssieres. 2010. Benthic Assemblage Variability in the Upper San Francisco Estuary: A 27-Year Retrospective. San Francisco Estuary and Watershed Science, 8(1).
Full article access: http://escholarship.org/uc/item/4d0616c6 - Stoms, David M. 2010. Change in Urban Land Use and Associated Attributes in the Upper San Francisco Estuary, 1990-2006. San Francisco Estuary and Watershed Science, 8(3). NCEAS POD working group publication
Full article access: http://escholarship.org/uc/item/5db1g3pq
Corresponding author e-mail: stoms@bren.ucsb.edu - Thomson, J.R., W. J. Kimmerer, L. R. Brown, K. B. Newman, R. Mac Nally, W. A. Bennett, F. Feyrer, E. Fleishman. 2010. Bayesian change-point analysis of abundance trends for pelagic fishes in the upper San Francisco Estuary. Ecological Applications, 20: 181-198. NCEAS POD working group publication
Abstract access: http://www.esajournals.org/doi/abs/10.1890/09-0998.1?journalCode=ecap
Corresponding author e-mail: jim.thomson@monash.edu - Werner, I., L.A. Deanovic, D. Markiewicz, J. Khamphanh, C.K. Reece, M. Stillway, C. Reece. 2010. Monitoring acute and chronic water column toxicity in the northern Sacramento-San Joaquin Estuary, California, USA, using the euryhaline amphipod, Hyalella azteca: 2006-2007. Environmental Toxicology and Chemistry 29(10): 2190–2199.
Abstract access: http://onlinelibrary.wiley.com/doi/10.1002/etc.281/abstract
Corresponding author e-mail: iwerner@ucdavis.edu - Weston D. P. and M. J. Lydy. 2010. Urban and Agricultural Sources of Pyrethroid Insecticides to the Sacramento-San Joaquin Delta of California. Environ. Sci. Technol. 44 (5): 1833–1840. Full article access:
http://www.waterboards.ca.gov/waterrights/water_issues/programs/bay_delta/deltaflow/docs/exhibits/sfwc/spprt_docs/sfwc_exh3_weston_urban_and_ag.pdf
Corresponding author e-mail: dweston@berkely.edu - Winder, Monika, and Alan D. Jassby. 2010. Zooplankton dynamics in the upper San Francisco Estuary: Long-term trends and food web implications. Estuaries and Coasts DOI: 10.1007/s12237-010-9342-x.
Abstract access: http://www.springerlink.com/content/b30544u2xx0l235u/
Corresponding author e-mail: mwinder@ucdavis.edu
2009
- Brander Susanne M., Werner I., White J.W., Deanovic L.A. 2009. Toxicity of a dissolved pyrethroid mixture to Hyalella azteca at environmentally relevant concentrations. Environmental Toxicology and Chemistry: Vol. 28, No. 7 pp. 1493–1499.
Full article access: http://magister.ucdavis.edu/~jwwhite/pdfs/Brander_etal_2009_ETC.pdf
Abstract access: http://www.setacjournals.org/perlserv/?request=get-abstract&doi=10.1897%2F08-374.1
Corresponding author e-mail: smbrander@ucdavis.edu - Brown, Larry R. and Marissa L. Bauer. 2009. Effects of hydrologic infrastructure on flow regimes of California's Central Valley rivers: Implications for fish populations. River Research and Applications, online edition.
Abstract access: http://www3.interscience.wiley.com/journal/122508164/abstract?CRETRY=1&SRETRY=0
Corresponding author e-mail: lrbrown@usgs.gov - Feyrer, Frederick, Ted Sommer, and Steven B. Slater. Old school vs. new school: status of threadfin shad (Dorosoma petenense) five decades after its introduction to the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science. Vol. 7, Issue 1, Article 3.
Full article access: http://escholarship.org/uc/item/4dt6p4bv - Fisch, Kathleen M., Jessica L. Petersen, Melinda R. Baerwald, John K. Pedroia And Bernie May. 2009. Characterization of 24 microsatellite loci in delta smelt, Hypomesus transpacificus, and their cross-species amplification in two other smelt species of the Osmeridae family. Molecular Ecology Resources, Volume 9 Issue 1, Pages 405 – 408.
Abstract access: http://www3.interscience.wiley.com/journal/121655125/abstract
Corresponding author e-mail: kmfisch@ucdavis.edu - Ger, Kemal A., Swee J. Teh and Charles R. Goldman. 2009. Microcystin-LR toxicity on dominant copepods Eurytemora affinis and Pseudodiaptomus forbesi of the upper San Francisco Estuary. Science of the Total Environment, Volume 407, Issue 17, Pages 4852-4857
Abstract access: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V78-4WJ91BK-2&_user=10&_coverDate=08%2F15%2F2009&_rdoc=1&_fmt=high&_orig=browse&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10 &md5=bcb402a441cc129b4f51ee0c906567ec
Corresponding author e-mail: aligerger@gmail.com - Grimaldo, L.F., A.R. Stewart, W. Kimmerer. 2009. Dietary segregation of pelagic and littoral fish assemblages in a highly modified tidal freshwater estuary. Marine Coastal Fisheries: Dynamics, Management & Ecosystems Sciences. 1: 200–217.
Full article access: http://www.bioone.org/doi/pdf/10.1577/C08-013.1
Corresponding author e-mail: lgrimaldo@usbr.gov - Grimaldo, L.F., T.S. Sommer, N. Van Ark, G. Jones, E. Holland, P.B. Moyle, B. Herbold, P.Smith.2009. Factors affecting fish entrainment into massive water diversions in a tidal freshwater estuary: Can fish losses be managed? North American Journal of Fisheries Management 29: 1253-1270
Abstract access: http://afsjournals.org/doi/abs/10.1577/M08-062.1?cookieSet=1&journalCode=fima
Corresponding author e-mail: lgrimaldo@usbr.gov - Kimmerer, W.J., E.S. Gross, and M.L. MacWilliams. 2009. Is the Response of Estuarine Nekton to Freshwater Flow in the San Francisco Estuary Explained by Variation in Habitat Volume? Estuaries and Coasts 32:375-389.
Full article access: http://online.sfsu.edu/~kimmerer/Files/KimmererEtAl2009EstuariesCoasts.pdf
Abstract access: http://www.springerlink.com/content/26pr3h5574605083/
Corresponding author e-mail: kimmerer@sfsu.edu - Lehman, P. W., S. Mayr, L. Mecum and C. Enright. 2009. The freshwater tidal wetland Liberty Island, CA was both a source and sink of inorganic and organic material to the San Francisco Estuary. Aquatic Ecology – online 04 November 2009
Abstract access: http://www.springerlink.com/content/n4617315633702x0/?p=acbe2c9403e549ebaf7fa83542cc9f1c&pi=0
Corresponding author e-mail: plehman@water.ca.gov - Moisander, P. H., P. W.Lehman, M. Ochiai and S. Corum. 2009. Diversity of the toxic cyanobacterium Microcystis aeruginosa in the Klamath River and San Francisco Bay delta, California. Aquatic Microbial Ecology 57: 19–31.
Abstract access: http://www.int-res.com/abstracts/ame/v57/n1/p19-31/
Corresponding author e-mail: pmoisander@pmc.ucsc.edu - Nobriga, M. L. 2009. Bioenergetic modeling evidence for a context-dependent role of food limitation in California’s Sacramento-San Joaquin Delta. In press, California Fish and Game.
2008
- Jassby, Alan. 2008. Phytoplankton in the Upper San Francisco Estuary: Recent Biomass Trends, Their Causes and Their Trophic Significance. San Francisco Estuary and Watershed Science. Vol. 6, Issue 1 (February), Article 2.
Full article access: http://repositories.cdlib.org/jmie/sfews/vol6/iss1/art2 - Kimmerer, Wim J.. 2008. Losses of Sacramento River Chinook Salmon and Delta Smelt to Entrainment in Water Diversions in the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science. Vol. 6, Issue 2 (June), Article 2.
Full article access: http://repositories.cdlib.org/jmie/sfews/vol6/iss2/art2 - Kimmerer, Wim J. and Matthew L. Nobriga. 2008. Investigating Particle Transport and Fate in the Sacramento-San Joaquin Delta Using a Particle Tracking Model. San Francisco Estuary and Watershed Science. Vol. 6, Issue 1 (February), Article 4.
Full article access: http://repositories.cdlib.org/jmie/sfews/vol6/iss1/art4 - Hestir, Erin L., Shruti Khanna, Margaret E. Andrew, Maria J. Santos, Joshua H. Viers, Jonathan A. Greenberg, Sepalika S. Rajapakse, Susan L. Ustin Identification of invasive vegetation using hyperspectral remote sensing in the California Delta ecosystem Remote Sensing of Environment, Volume 112, Issue 11, 15 November 2008, Pages 4034-4047
Abstract access: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V6V-4T4WM1M-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=7364247ee9da4d23fd8d13c7599bce6f
Corresponding author e-mail: elhestir@ucdavis.edu - Lehman P. W., Boyer G., Satchwell M., and S. Waller. 2008. The influence of environmental conditions on the seasonal variation of Microcystis cell density and microcystins concentration in San Francisco Estuary Hydrobiologia. 2008 600(1). p.187
Full article access: http://www.springerlink.com/content/2386p327252j6327/ - Newman, Ken B.. 2008. Sample design-based methodology for estimating delta smelt abundance. San Francisco Estuary and Watershed Science. Vol. 6, Issue 3 (October), Article 3.
Full article access: http://repositories.cdlib.org/jmie/sfews/vol6/iss3/art3 - Nobriga, Matthew L.; Ted R. Sommer; Frederick Feyrer; and Kevin Fleming. 2008. Long-Term Trends in Summertime Habitat Suitability for Delta Smelt (Hypomesus transpacificus). San Francisco Estuary and Watershed Science. Vol. 6, Issue 1 (February), Article 1.
Full article access: http://repositories.cdlib.org/jmie/sfews/vol6/iss1/art1 - Nobriga, M., and F. Feyrer. 2008. Diet composition in San Francisco Estuary striped bass: does trophic adaptability have its limits? Environmental Biology of Fishes 83 (4): 495-503.
Abstract access: http://www.springerlink.com/content/83270g72633j3118/?p=3e07cb212a004a4bb343bba53680e0a1&pi=15
Corresponding author e-mail: Matthew Nobriga MNOBRIGA@dfg.ca.gov - Ostrach, David J., Janine M. Low-Marchelli, Kai J. Eder, Shaleah J. Whiteman, and Joe G. Zinkl. 2008. transfer of xenobiotics and effects on larval striped bass in the San Francisco Estuary. PNAS 2008 105:19354-19359
Abstract access: http://www.pnas.org/content/early/2008/11/24/0802616105.abstract
Corresponding author e-mail: djostrach@ucdavis.edu
2007
- Feyrer, F., M. Nobriga, and T. Sommer. 2007. Multi-decadal trends for three declining fish species: habitat patterns and mechanisms in the San Francisco Estuary, California, U.S.A. Canadian Journal of Fisheries and Aquatic Sciences 64:723-734
Abstract access: http://rparticle.web-p.cisti.nrc.ca/rparticle/AbstractTemplateServlet?calyLang=eng&journal=cjfas&volume=64&year=0&issue=4&msno=f07-048
Corresponding author e-mail: FFEYRER@mp.usbr.gov - Geist, Juergen, Inge Werner, Kai J. Eder, and Christian M. Leutenegger. 2007. Comparisons of tissue-specific transcription of stress response genes with whole animal endpoints of adverse effect in striped bass (Morone saxatilis) following treatment with copper and esfenvalerate. Aquatic Toxicology 85 (2007) 28–39
Abstract access: http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T4G-4P961WD-2&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=a0e37c1499eb02e3b956c8bf35a2d7fb
Corresponding author e-mail: iwerner@ucdavis.edu - Lehman, P.W. 2007. The influence of phytoplankton community composition on primary productivity along the riverine to freshwater tidal continuum in the San Joaquin River, California. Estuaries and Coasts 30 (1): 82-93.
Full article access: http://www.springerlink.com/content/l37687720454850x/ - Sommer, T., C. Armor, R. Baxter, R. Breuer, L. Brown, M. Chotkowski, S. Culberson, F. Feyrer, M. Gingras, B. Herbold, W. Kimmerer, A. Mueller-Solger, M. Nobriga, and K. Souza. 2007. The collapse of pelagic fishes in the upper San Francisco Estuary. Fisheries 32:270-277.
Full article access: http://www.fisheries.org/afs/docs/fisheries/fisheries_3206.pdf
2006
- Manly, FJ Bryan, Chotkowski, M. 2008. Two new methods for Regime Change Analyses Archiv für Hydrobiologie, Vol. 167, No. 1-4. (September 2006), pp. 593-607.
Abstract access: http://www.ingentaconnect.com/content/schweiz/afh/2006/00000167/ F0040001/art00035
Corresponding author e-mail: MCHOTKOWSKI@mp.usbr.gov
