James (Jim) Cloern is a senior scientist emeritus at the U.S. Geological Survey's Water Resources Mission Area in Menlo Park, California.
James (Jim) Cloern is a senior scientist emeritus at the U.S. Geological Survey in Menlo Park, California. His research over four decades addresses comparative ecology and biogeochemistry of estuaries to understand how they respond as ecosystems to climatic-hydrologic variability and human disturbance. His team investigation of San Francisco Bay included studies of primary production, nutrient cycling, algal and zooplankton community dynamics, ecosystem metabolism and food web dynamics, disturbance by introduced species, ecosystem restoration, and past and projected future responses to a changing climate. His career achievements have been recognized with selection as Fellows of the American Geophysical Union (AGU) and Association for the Sciences of Limnology and Oceanography (ASLO), and as recipient of the Woods Hole Oceanographic Institution B.H. Ketchum Award, Delta Science Program Brown-Nichols Achievement Award, ASLO Ruth Patrick Award, Coastal and Estuarine Research Federation Odum Lifetime Achievement Award, and Department of Interior's Distinguished Service Award. He is currently an Adjunct Senior Fellow at the Public Policy Institute of California, a member of the Delta Stewardship Council's Independent Science Board, and editor-in-chief of Limnology and Oceanography Letters.
Science and Products
Sampling Locations for the Water Quality of San Francisco Bay Project
Sampling Methods for the Water Quality of San Francisco Bay Project
Research Vessel David H. Peterson
Water Quality of San Francisco Bay Research and Monitoring Project
Stable isotope analysis of San Francisco Bay-Delta primary producers (1990-2000)
USGS Measurements of Water Quality in San Francisco Bay (CA), 2016-2021 (ver. 4.0, March 2023)
Phytoplankton Species Composition, Abundance and Cell Size in San Francisco Bay: Microscopic Analyses of USGS Samples Collected 1992-2014
USGS Measurements of Water Quality in San Francisco Bay (CA), 1969-2015 (ver. 4.0, March 2023)
On the human appropriation of wetland primary production
Nutrient status of San Francisco Bay and its management implications
Machine learning identifies a strong association between warming and reduced primary productivity in an oligotrophic ocean gyre
Prediction of unprecedented biological shifts in the global ocean
Blurred lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California
Why large cells dominate estuarine phytoplankton
The land-sea interface: A source of high-quality phytoplankton to support secondary production
Novel analyses of long-term data provide a scientific basis for chlorophyll-a thresholds in San Francisco Bay
Water quality measurements in San Francisco Bay by the U.S. Geological Survey, 1969–2015
Ecosystem variability along the estuarine salinity gradient: Examples from long-term study of San Francisco Bay
Estuary-ocean connectivity: Fast physics, slow biology
Primary production in the Delta: Then and now
Science and Products
- Science
Sampling Locations for the Water Quality of San Francisco Bay Project
Since 1969, the Water Quality of San Francisco Bay Research and Monitoring Project has conducted water-column sampling along the deep channel of the San Francisco Bay-Delta system. Learn more about when and where we collect data.Sampling Methods for the Water Quality of San Francisco Bay Project
The Water Quality of San Francisco Bay Research and Monitoring Project measures changes in water quality along the deep channel of the San Francisco Bay-Delta system using submersible sensors and discrete water samples. Learn more about how we collect and measure water-quality data.Research Vessel David H. Peterson
The Research Vessel David H. Peterson begain service with the U.S. Geological Survey in 2015. Named after a founder of the Water Quality of San Francisco Bay Research and Monitoring Project, this vessel is a high-tech scientific platform for estuarine research. Learn more about how the R/V David H. Peterson makes our research possible.Water Quality of San Francisco Bay Research and Monitoring Project
Since 1969, the U.S. Geological Survey has maintained a research project in the San Francisco Bay-Delta system to measure and understand how estuarine systems and tidal river deltas function and change in response to hydro-climatic variability and human activities. - Data
Stable isotope analysis of San Francisco Bay-Delta primary producers (1990-2000)
This dataset is a compilation of multiple studies over different periods and in many environments as described below. These data were collected to measure temporal fluctuations in plant isotopic composition associated with seasonal cycles of growth and environmental variability. In 1990, 1992, and 1998-2000, a total of 868 samples were collected and analyzed to determine carbon and nitrogen mass aUSGS Measurements of Water Quality in San Francisco Bay (CA), 2016-2021 (ver. 4.0, March 2023)
The U.S. Geological Survey maintains a program of water-quality studies in San Francisco Bay (CA) that began in 1969. This U.S.G.S. Data Release is a continuation of the previously published 1969-2015 dataset (Cloern and Schraga, 2016; Schraga and Cloern, 2017), it will archive and make available all measurements from 2016 and thereafter. Each year, a data file containing the previous years data wPhytoplankton Species Composition, Abundance and Cell Size in San Francisco Bay: Microscopic Analyses of USGS Samples Collected 1992-2014
This Data Release makes available measurements of phytoplankton species composition, abundance and cell size made on samples collected in San Francisco Bay (CA) from April 1992 through March 2014. Phytoplankton samples were collected at 31 stations along a 145-km transect where the variability of salinity, temperature, turbidity and nutrient concentrations reflected a broad range of environmentalUSGS Measurements of Water Quality in San Francisco Bay (CA), 1969-2015 (ver. 4.0, March 2023)
The U.S. Geological Survey maintains a program of water-quality studies in San Francisco Bay (CA) that began in 1969. We plan a USGS Data Release to archive and make available all measurements made from 1969 through 2015. Water-quality constituents include salinity, temperature, light attenuation coefficient, and concentrations of chlorophyll-a, dissolved oxygen, suspended particulate matter, nitr - Publications
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On the human appropriation of wetland primary production
Humans are changing the Earth's surface at an accelerating pace, with significant consequences for ecosystems and their biodiversity. Landscape transformation has far-reaching implications including reduced net primary production (NPP) available to support ecosystems, reduced energy supplies to consumers, and disruption of ecosystem services such as carbon storage. Anthropogenic activities have reAuthorsJames E. Cloern, Samuel M. Safran, Lydia Smith Vaughn, April Robinson, Alison Whipple, Katharyn E. Boyer, Judith Z. Drexler, Robert J. Naiman, James L. Pinckney, Emily R. Howe, Elizabeth A. Canuel, J. Letitia GrenierNutrient status of San Francisco Bay and its management implications
Nutrient enrichment has degraded many of the world’s estuaries by amplifying algal production, leading to hypoxia/anoxia, loss of vascular plants and fish/shellfish habitat, and expansion of harmful blooms (HABs). Policies to protect coastal waters from the effects of nutrient enrichment require information to determine if a water body is impaired by nutrients and if regulatory actions are requireAuthorsJames E. Cloern, Tara Schraga, Erica Nejad, Charles A. MartinMachine learning identifies a strong association between warming and reduced primary productivity in an oligotrophic ocean gyre
Phytoplankton play key roles in the oceans by regulating global biogeochemical cycles and production in marine food webs. Global warming is thought to affect phytoplankton production both directly, by impacting their photosynthetic metabolism, and indirectly by modifying the physical environment in which they grow. In this respect, the Bermuda Atlantic Time-series Study (BATS) in the Sargasso SeaAuthorsDomenico D’Alelio, Salvatore Rampone, Luigi Maria Cusano, Valerio Morfino, Luca Russo, Nadia Sanseverino, James E. Cloern, Michael W. LomasPrediction of unprecedented biological shifts in the global ocean
Impermanence is an ecological principle1 but there are times when changes occur nonlinearly as abrupt community shifts (ACSs) that transform the ecosystem state and the goods and services it provides2. Here, we present a model based on niche theory3 to explain and predict ACSs at the global scale. We test our model using 14 multi-decadal time series of marine metazoans from zooplankton to fish, spAuthorsG. Beaugrand, A. Conversi, A. Atkinson, James Cloern, S. Chiba, S. Fonda-Umani, R.R. Kirby, C.H. Greene, E. Goberville, S.A. Otto, P.C. Reid, L. Stemmann, M. EdwardsBlurred lines: Multiple freshwater and marine algal toxins at the land-sea interface of San Francisco Bay, California
San Francisco Bay (SFB) is a eutrophic estuary that harbors both freshwater and marine toxigenic organisms that are responsible for harmful algal blooms. While there are few commercial fishery harvests within SFB, recreational and subsistence harvesting for shellfish is common. Coastal shellfish are monitored for domoic acid and paralytic shellfish toxins (PSTs), but within SFB there is no routineAuthorsMelissa B. Peacock, Corinne M. Gibble, David B. Senn, James E. Cloern, Raphael M. KudelaWhy large cells dominate estuarine phytoplankton
Surveys across the world oceans have shown that phytoplankton biomass and production are dominated by small cells (picoplankton) where nutrient concentrations are low, but large cells (microplankton) dominate when nutrient-rich deep water is mixed to the surface. I analyzed phytoplankton size structure in samples collected over 25 yr in San Francisco Bay, a nutrient-rich estuary. Biomass was dominAuthorsJames E. CloernThe land-sea interface: A source of high-quality phytoplankton to support secondary production
Coastal-estuarine systems are among the most productive marine ecosystems and their special role in producing harvestable fish and shellfish has been attributed to high primary production fueled by nutrient runoff from land and efficient trophic transfer. Here we ask if phytoplankton species composition and their food quality based on the percentage of long-chain essential fatty acids (LCEFA) is aAuthorsMonika Winder, Jacob Carstensen, Aaron W.E. Galloway, Hans H. Jakobsen, James E. CloernNovel analyses of long-term data provide a scientific basis for chlorophyll-a thresholds in San Francisco Bay
San Francisco Bay (SFB), USA, is highly enriched in nitrogen and phosphorus, but has been resistant to the classic symptoms of eutrophication associated with over-production of phytoplankton. Observations in recent years suggest that this resistance may be weakening, shown by: significant increases of chlorophyll-a (chl-a) and decreases of dissolved oxygen (DO), common occurrences of phytoplanktonAuthorsMartha Sutula, Raphael Kudela, James D. Hagy, Lawrence W. Harding, David Senn, James E. Cloern, Suzanne B. Bricker, Gry Mine Berg, Marcus W. BeckWater quality measurements in San Francisco Bay by the U.S. Geological Survey, 1969–2015
The U.S. Geological Survey (USGS) maintains a place-based research program in San Francisco Bay (USA) that began in 1969 and continues, providing one of the longest records of water-quality measurements in a North American estuary. Constituents include salinity, temperature, light extinction coefficient, and concentrations of chlorophyll-a, dissolved oxygen, suspended particulate matter, nitrate,AuthorsTara Schraga, James E. CloernEcosystem variability along the estuarine salinity gradient: Examples from long-term study of San Francisco Bay
The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use variability along the salinity gradient of San Francisco Bay to illustrate some lessons about the diversity of spatial structures in estuaries and their variability over time. Spatial patterns of dissolved constituents (e.g., silAuthorsJames E. Cloern, Alan D. Jassby, Tara Schraga, Erica S. Kress, Charles A. MartinEstuary-ocean connectivity: Fast physics, slow biology
Estuaries are connected to both land and ocean so their physical, chemical, and biological dynamics are influenced by climate patterns over watersheds and ocean basins. We explored climate-driven oceanic variability as a source of estuarine variability by comparing monthly time series of temperature and chlorophyll-a inside San Francisco Bay with those in adjacent shelf waters of the California CuAuthorsMélanie Raimonet, James E. CloernPrimary production in the Delta: Then and now
To evaluate the role of restoration in the recovery of the Delta ecosystem, we need to have clear targets and performance measures that directly assess ecosystem function. Primary production is a crucial ecosystem process, which directly limits the quality and quantity of food available for secondary consumers such as invertebrates and fish. The Delta has a low rate of primary production, but it iAuthorsJames E. Cloern, April Robinson, Amy Richey, Letitia Grenier, Robin Grossinger, Katharyn E. Boyer, Jon Burau, Elizabeth A. Canuel, John F. DeGeorge, Judith Z. Drexler, Chris Enright, Emily R. Howe, Ronald Kneib, Anke Mueller-Solger, Robert J. Naiman, James L. Pinckney, Samuel M. Safran, David H. Schoellhamer, Charles A. Simenstad