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Journal
Beller, E. E.; Spotswood, E.; Robinson, A.; Anderson, M. G.; Higgs, E. S.; Hobbs, R. J.; Suding, K. N.; Zavaleta, E. S.; Grenier, L.; Grossinger, R. M. 2018. Building Ecological Resilience in Highly Modified Landscapes.

Ecological resilience is a powerful heuristic for ecosystem management in the context of rapid environmental change. Significant efforts are underway to improve the resilience of biodiversity and ecological function to extreme events and directional change across all types of landscapes, from intact natural systems to highly modified landscapes such as cities and agricultural regions. However, identifying management strategies likely to promote ecological resilience remains a challenge. In this article, we present seven core dimensions to guide long-term and large-scale resilience planning in highly modified landscapes, with the objective of providing a structure and shared vocabulary for recognizing opportunities and actions likely to increase resilience across the whole landscape. We illustrate application of our approach to landscape-scale ecosystem management through case studies from two highly modified California landscapes, Silicon Valley and the Sacramento–San Joaquin Delta. We propose that resilience-based management is best implemented at large spatial scales and through collaborative, cross-sector partnerships.

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Journal Article (Peer-Reviewed)
Cohen, A. N.; Carlton, J. T. 1998. Accelerating invasion rate in a highly invaded estuary. Science 279, 555-558 . SFEI Contribution No. 226.
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Nordby, C. 2001. Adult song sparrows do not alter their song repertoires. Ethology . SFEI Contribution No. 482.
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Lowe, S.; Thompson, B. 2004. Assessment of macrobenthos resonse to sediment contamination in the San Francisco Estuary, USA. Environmental Toxicology and Chemistry 23 . SFEI Contribution No. 60.
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Greenfield, B. K.; Siemering, G.; Hayworth, J. D. 2008. Assessment of Potential Aquatic Herbicide Impacts to California Aquatic Ecosystems. Archives of Environmental Contamination and Toxicology . SFEI Contribution No. 539.
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Hoenicke, R.; Tsai, P.; Bamford, H. A.; Baker, J.; Yee, D. 2002. Atmospheric Concentrations and Fluxes of Organic Compounds in the Northern San Francisco Estuary. Environmental Science and Technology 36 (22), 4741-4747 . SFEI Contribution No. 474.
Flegal, A. R.; Rivera-Duarte, I. 1997. Benthic fluxes of silver in San Francisco Bay. Marine Chemistry 56, 15-26 . SFEI Contribution No. 214.
Flegal, A. R.; Rivera-Duarte, I. 1994. Benthic lead fluxes in San Francisco Bay, California, USA. Geochimica et Cosmochimica Acta 58, 3307-3313 . SFEI Contribution No. 180.
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Bruland, K. W.; Anderson, L. A. 1991. Biogeochemistry of arsenic in natural waters: The importance of methylated species. Environmental Science & Technology 25, 420-427 . SFEI Contribution No. 160.
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Sutton, R.; Chen, D.; Sun, J.; Greig, D. J.; Wu, Y. 2019. Characterization of brominated, chlorinated, and phosphate flame retardants in San Francisco Bay, an urban estuary. Science of the Total Environment 652, 212-223 . SFEI Contribution No. 859.

Flame retardant chemical additives are incorporated into consumer goods to meet flammability standards, and many have been detected in environmental matrices. A uniquely wide-ranging characterization of flame retardants was conducted, including polybrominated diphenyl ethers (PBDEs) and 52 additional brominated, chlorinated, or phosphate analytes, in water, sediment, bivalves, and harbor seal blubber of San Francisco Bay, a highly urbanized estuary once considered a hot spot for PBDE contamination. Among brominated flame retardants, PBDEs remained the dominant contaminants in all matrices, though declines have been observed over the last decade following their phase-out. Hexabromocyclododecane (HBCD) and other hydrophobic, brominated flame retardants were commonly detected at lower levels than PBDEs in sediment and tissue matrices. Dechlorane Plus (DP) and related chlorinated compounds were also detected at lower levels or not at all across all matrices. In contrast, phosphate flame retardants were widely detected in Bay water samples, with highest median concentrations in the order TCPP > TPhP > TBEP > TDCPP > TCEP. Concentrations in Bay water were often higher than in other estuarine and marine environments. Phosphate flame retardants were also widely detected in sediment, in the order TEHP > TCrP > TPhP > TDCPP > TBEP. Several were present in bivalves, with levels of TDCPP comparable to PBDEs. Only four phosphate flame retardants were detected in harbor seal blubber: TCPP, TDCPP, TCEP, and TPhP. Periodic, multi-matrix screening is recommended to track contaminant trends impacted by changes to flammability standards and manufacturing practices, with a particular focus on contaminants like TDCPP and TPhP that were found at levels comparable to thresholds for aquatic toxicity.

Jabusch, T. W.; Tjeerdema, R. S. 2007. Chemistry and Fate of Triazolopyrimidine Sulfonamide Herbicides. Reviews of Environmental Contamination & Toxicology.
Cohen, A. N. 1991. China Camp: A salt marsh guide. Pacific Discovery (Calif. Acad. Sci.) 44, 24-29.
Cohen, A. N. 1995. Chinese mitten crabs in North America. Aquatic Nuisance Species Digest 1, 20-21.
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McKee, L. J. .; Lewicki, M.; Schoellhamer, D. H.; Ganju, N. K. 2013. Comparison of sediment supply to San Francisco Bay from watersheds draining the Bay Area and the Central Valley of California. Marine Geology Special Issue: A multi-discipline approach for understanding sediment transport and geomorphic evolution in an estuarine-coastal system.
Gilbreath, A. N.; McKee, L. J. . 2015. Concentrations and loads of PCBs, dioxins, PAHs, PBDEs, OC pesticides and pyrethroids during storm and low flow conditions in a small urban semi-arid watershed. Science of the Total Environment 526, 251-261 . SFEI Contribution No. 650.

Urban runoff has been identified in water quality policy documents for San Francisco Bay as a large and potentially controllable source of pollutants. In response, concentrations of suspended sediments and a range of trace organic pollutants were intensively measured in dry weather and storm flow runoff from a 100% urban watershed. Flow in this highly urban watershed responded very quickly to rainfall and varied widely resulting in rapid changes of turbidity, suspended sediments and pollutant concentrations. Concentrations of each organic pollutant class were within similar ranges reported in other studies of urban runoff, however comparison was limited for several of the pollutants given information scarcity. Consistently among PCBs, PBDEs, and PAHs, the more hydrophobic congeners were transported in larger proportions during storm flows relative to low flows. Loads for Water Years 2007-2010 were estimated using regression with turbidity during the monitored months and a flow weighted mean concentration for unmonitored dry season months. More than 91% of the loads for every pollutant measured were transported during storm events, along with 87% of the total discharge. While this dataset fills an important local data gap for highly urban watersheds of San Francisco Bay, the methods, the uniqueness of the analyte list, and the resulting interpretations have applicability for managing pollutant loads in urban watersheds in other parts of the world.

Hoenicke, R. 1997. Creating data-quality objectives: A case study. Water Environment Laboratory Solutions 7-9 . SFEI Contribution No. 31.
Cohen, A. N. 1997. Damming the Bay. Switzer Fellowship Network 5, 1,4.
Cohen, A. N. 1996. Damming the Bay. Watershed 35, 6-8.
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Flegal, A. R.; Squire, S.; Scelfo, G. H.; Revenaugh, J. 2002. Decadal trends of silver and lead contamination in San Francisco Bay surface waters. Environmental Science and Techology 36, 2379-2386 . SFEI Contribution No. 276.
Cloern, J. E.; Cole, B. E.; Jassby, A. D. 1997. The design of sampling transects for characterizing water quality in estuaries. Estuarine, Coastal and Shelf Science 45, 285-302 . SFEI Contribution No. 23.
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Flegal, A. R.; Sanudo-Wilhelmy, S. A.; Rivera-Duarte, I. 1996. Distribution of Colloidal trace metals in the San Francisco Bay estuary. Geochimica et Cosmochimica Acta 60, 4933-4944 . SFEI Contribution No. 194.
Sommers, F.; Mudrock, E.; Labenia, J.; Baldwin, D. 2016. Effects of salinity on olfactory toxicity and behavioral responses of juvenile salmonids from copper. Aquatic Toxicology 175.

Dissolved copper is one of the more pervasive and toxic constituents of stormwater runoff and is commonly found in stream, estuary, and coastal marine habitats of juvenile salmon. While stormwater runoff does not usually carry copper concentrations high enough to result in acute lethality, they are of concern because sublethal concentrations of copper exposure have been shown to both impair olfactory function and alter behavior in various species in freshwater. To compare these results to other environments that salmon are likely to encounter, experiments were conducted to evaluate the effects of salinity on the impairment of olfactory function and avoidance of copper. Copper concentrations well within the range of those found in urban watersheds, have been shown to diminish or eliminate the olfactory response to the amino acid, l-serine in freshwater using electro-olfactogram (EOG) techniques. The olfactory responses of both freshwater-phase and seawater-phase coho and seawater-phase Chinook salmon, were tested in freshwater or seawater, depending on phase, and freshwater-phase coho at an intermediate salinity of 10‰. Both 10‰ salinity and full strength seawater protected against the effects of 50μg copper/L. In addition to impairing olfactory response, copper has also been shown to alter salmon behavior by causing an avoidance response. To determine whether copper will cause avoidance behavior at different salinities, experiments were conducted using a multi-chambered experimental tank. The circular tank was divided into six segments by water currents so that copper could be contained within one segment yet fish could move freely between them. The presence of individual fish in each of the segments was counted before and after introduction of dissolved copper (<20μg/L) to one of the segments in both freshwater and seawater. To address whether use of preferred habitat is altered by the presence of copper, experiments were also conducted with a submerged structural element. The presence of sub-lethal levels of dissolved copper altered the behavior of juvenile Chinook salmon by inducing an avoidance response in both freshwater and seawater. While increased salinity is protective against loss of olfactory function from dissolved copper, avoidance could potentially affect behaviors beneficial to growth, survival and reproductive success.

Oros, D. R. 2005. Emerging Contaminants: Endocrine Disrupting Chemicals (EDCs). RMP Regional Monitoring News, San Francisco Estuary Regional Monitoring Program for Trace Substances 10, p.1-11 . SFEI Contribution No. 502.
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Melwani, A. R.; Greenfield, B. K.; Byron, E. R. 2009. Empirical estimation of biota exposure range for calculation of bioaccumulation parameters. Integrated Environmental Assessment and Management 5 . SFEI Contribution No. 573.
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David, N.; Gluchowski, D. C.; Leatherbarrow, J. E.; Yee, D.; McKee, L. J. . 2015. Estimation of Contaminant Loads from the Sacramento-San Joaquin River Delta to San Francisco Bay. Water Environment Research 87 (4), 334-346.

Contaminant concentrations from the Sacramento-San Joaquin River watershed were determined in water samples mainly during flood flows in an ongoing effort to describe contaminant loads entering San Francisco Bay, CA, USA. Calculated PCB and total mercury loads during the 6-year observation period ranged between 3.9 and 19 kg/yr and 61 and 410 kg/yr, respectively. Long-term average PCB loads were estimated at 7.7 kg/yr and total mercury loads were estimated at 200 kg/yr. Also monitored were PAHs, PBDEs (two years of data), and dioxins/furans (one year of data) with average loads of 392, 11, and 0.15/0.014 (OCDD/OCDF) kg/yr, respectively. Organochlorine pesticide loads were estimated at 9.9 kg/yr (DDT), 1.6 kg/yr (chlordane), and 2.2 kg/yr (dieldrin). Selenium loads were estimated at 16 300 kg/yr. With the exception of selenium, all average contaminant loads described in the present study were close to or below regulatory load allocations established for North San Francisco Bay.

David, N.; Greenfield, B. K.; Siemering, G. S. 2006. Evaluating impacts of Lake Maid plant control. Journal of Aquatic Plant Management 44, 60-66.
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Greenfield, B. K.; Siemering, G.; David, N. 2005. Evaluating impacts of Lake Sweeper plant control. J. of Aquatic Plant Management . SFEI Contribution No. 461.
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Cohen, A. N. 2002. Exotic organisms in southern California Bays and Harbors. Marine Bioinvasions Conference . SFEI Contribution No. 481.
Schoellhamer, D. H. 1996. Factors affecting suspended-solids concentrations in South San Francisco Bay, California. Journal of Geophysical Research 101, 12,087-12,095 . SFEI Contribution No. 10.
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Connor, M. S.; Montagna, P. A.; Alber, M.; Doering, P. 2002. Freshwater inflow: Science, Policy, and Managment. Estuaries 25, 1243-1245 . SFEI Contribution No. 271.
Beller, E. E.; Downs, P. W.; Grossinger, R. M.; Orr, B. K.; Salomon, M. 2016. From past patterns to future potential: using historical ecology to inform river restoration on an intermittent California river. Landscape Ecology 31 (3), 20.

Context  Effective river restoration requires understanding a system’s potential to support desired functions. This can be challenging to discern in the modern landscape, where natural complexity and heterogeneity are often heavily suppressed or modified. Historical analysis is therefore a valuable tool to provide the long-term perspective on riverine patterns, processes, and ecosystem change needed to set appropriate environmental management goals and strategies.

Objective In this study, we reconstructed historical (early 1800s) riparian conditions, river corridor extent, and dry-season flow on the lower Santa Clara River in southern California, with the goal of using this enhanced understanding to inform restoration and management activities.

Method Hundreds of cartographic, textual, and visual accounts were integrated into a GIS database of historical river characteristics.

Results We found that the river was characterized by an extremely broad river corridor and a diverse mosaic of riparian communities that varied by reach, from extensive ([100 ha) willow-cottonwood forests to xeric scrublands. Reach-scale ecological heterogeneity was linked to local variations in dry-season water availability, which was in turn underpinned by regional geophysical controls on groundwater and surface flow.

Conclusions Although human actions have greatly impacted the river’s extent, baseflow hydrology, and riparian habitats, many ecological attributes persist in more limited form, in large part facilitated by these fundamental hydrogeological controls. By drawing on a heretofore untapped dataset of spatially explicit and long-term environmental data, these findings improve our understanding of the river’s historical and current conditions and allow the derivation of reach-differentiated restoration and management opportunities that take advantage of local potential.

Wu, Y.; Tan, H.; Sutton, R.; Chen, D. 2017. From Sediment to Top Predators: Broad Exposure of Polyhalogenated Carbazoles in San Francisco Bay (U.S.A.). Environmental Science and Technology 51, 2038-2046.

The present study provides the first comprehensive investigation of polyhalogenated carbazoles (PHCZ) contamination in an aquatic ecosystem. PHCZs have been found in soil and aquatic sediment from several different regions, but knowledge of their bioaccumulation and trophodynamics is extremely scarce. This work investigated a suite of 11 PHCZ congeners in San Francisco Bay (United States) sediment and organisms, including bivalves (n = 6 composites), sport fish (n = 12 composites), harbor seal blubber (n = 18), and bird eggs (n = 8 composites). The most detectable congeners included 3,6-dichlorocarbazole (36-CCZ), 3,6-dibromocarbazole (36-BCZ), 1,3,6-tribromocarbazole (136-BCZ), 1,3,6,8-tetrabromocarbazole (1368-BCZ), and 1,8-dibromo-3,6-dichlorocarbazole (18-B-36-CCZ). The median concentrations of ΣPHCZs were 9.3 ng/g dry weight in sediment and ranged from 33.7 to 164 ng/g lipid weight in various species. Biomagnification was observed from fish to harbor seal and was mainly driven by chlorinated carbazoles, particularly 36-CCZ. Congener compositions of PHCZs differed among species, suggesting that individual congeners may be subject to different bioaccumulation or metabolism in species occupying various trophic levels in the studied aquatic system. Toxic equivalent (TEQ) values of PHCZs were determined based on their relative effect potencies (REP) compared to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). The median TEQ was 1.2 pg TEQ/g dry weight in sediment and 4.8 – 19.5 pg TEQ/g lipid weight in biological tissues. Our study demonstrated the broad exposure of PHCZs in San Francisco Bay and their characteristics of bioaccumulation and biomagnification along with dioxin-like effects. These findings raise the need for additional research to better elucidate their sources, environmental behavior, and fate in global environments.

Yarnell, S. M.; Petts, G. E.; Schmidt, J. C.; Whipple, A. A.; Beller, E. E.; Dahm, C. N.; Goodwin, P.; Viers, J. H. 2015. Functional Flows in Modified Riverscapes: Hydrographs, Habitats and Opportunities. BioScience.

Building on previous environmental flow discussions and a growing recognition that hydrogeomorphic processes are inherent in the ecological functionality and biodiversity of riverscapes, we propose a functional-flows approach to managing heavily modified rivers. The approach focuses on retaining specific process-based components of the hydrograph, or functional flows, rather than attempting to mimic the full natural flow regime. Key functional components include wet-season initiation flows, peak magnitude flows, recession flows, dry-season low flows, and interannual variability. We illustrate the importance of each key functional flow using examples from western US rivers with seasonably predictable flow regimes. To maximize the functionality of these flows, connectivity to morphologically diverse overbank areas must be enhanced in both space and time, and consideration must be given to the sediment-transport regime. Finally, we provide guiding principles for developing functional flows or incorporating functional flows into existing environmental flow frameworks.

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Thompson, B.; Chapman, J. 1997. General guidelines for using the sediment quality triad. Mar. Poll. Bull 34, 368-372 . SFEI Contribution No. 198.
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Cohen, A. N. 1997. Have claw, will travel. Aquatic Nuisance Species Digest 2, 1, 16-17. . SFEI Contribution No. 200.
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Hatje, V.; Bruland, K. W.; A. Flegal, R. 2016. Increases in Anthropogenic Gadolinium Anomalies and Rare Earth Element Concentrations in San Francisco Bay over a 20 Year Record. Environ. Sci. Technol. 50 (8).

We evaluated both the spatial distribution of gadolinium (Gd) and other rare earth elements (REE) in surface waters collected in a transect of San Francisco Bay (SFB) and their temporal variations within the Bay over two decades. The REE were preconcentrated using the NOBIAS PA-1 resin prior to analysis by high-resolution inductively coupled plasma mass spectrometry. Measurements revealed a temporal increase in the Gd anomaly in SFB from the early 1990s to the present. The highest Gd anomalies were observed in the southern reach of SFB, which is surrounded by several hospitals and research centers that use Gd-based contrast agents for magnetic resonance imaging. Recent increases in that usage presumably contributed to the order of magnitude increase in anthropogenic Gd concentrations in SFB, from 8.27 to 112 pmol kg–1 over the past two decades, and reach the northeast Pacific coastal waters. These measurements (i) show that “exotic” trace elements used in new high-tech applications, such as Gd, are emerging contaminants in San Francisco Bay and that anthropogenic Gd concentrations increased substantially over a 20 year period; (ii) substantiate proposals that REE may be used as tracers of wastewater discharges and hydrological processes; and (iii) suggest that new public policies and the development of more effective treatment technologies may be necessary to control sources and minimize future contamination by REE that are critical for the development of new technologies, which now overwhelm natural REE anomalies.