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Baumgarten, S.; Clark, E.; Dusterhoff, S.; Grossinger, R. M.; Askevold, R. A. 2018. Petaluma Valley Historical Hydrology and Ecology Study. SFEI Contribution No. 861. San Francisco Estuary Institute: Richmond, CA.

This study reconstructs the historical landscape of the Petaluma River watershed and documents the major landscape changes that have taken place within the watershed over the past two centuries. Prior to Spanish and American settlement of the region, the Petaluma River watershed supported a dynamic and interconnected network of streams, riparian forests, freshwater wetlands, and tidal marshes. These habitats were utilized by a wide range of plant and animal species, including a number of species that are today listed as threatened or endangered such as Ridgway’s Rail, Black Rail, salt marsh harvest mouse, California red-legged frog, Central California Coast steelhead, and soft bird’s beak (CNDDB 2012, SRCD 2015). Agricultural and urban development beginning in the mid-1800s has significantly altered the landscape, degrading habitat for fish and wildlife and contributing to contemporary management challenges such as flooding, pollutant loading, erosion, and sedimentation. While many natural areas and remnant wetlands still exist throughout the watershed—most notably the Petaluma Marsh—their ecological function is in many cases seriously impaired and their long-term fate jeopardized by climate change and other stressors. Multi-benefit wetland restoration strategies, guided by a thorough understanding of landscape history, can simultaneously address a range of chronic management issues while improving the ecological health of the watershed, making it a better place to live for both people and wildlife.

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Barnard, P. L.; Schoellhamer, D. H.; Jaffe, B. E.; McKee, L. J. . 2013. Sediment transport in the San Francisco Bay Coastal System: An overview. Marine Geology Special Issue: A multi-discipline approach for understanding sediment transport and geomorphic evolution in an estuarine-coastal system.
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Associates, H. T. Harvey and; San Francisco Estuary Institute (SFEI). 2017. Annotated Bibliography for Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project.

One component of the Sycamore Alluvial Woodland Habitat Mapping and Regeneration Studies Project is this annotated bibliography of existing scientific literature pertaining to California sycamore ecology. This annotated bibliography is a product of an extensive review into documents, mapping efforts, and personal communications, and presents sources that have been determined to be relevant to understanding the factors that influence California sycamore health and regeneration in central California. The annotated bibliography is divided into the following sections by topic: General Ecology; Historical and Present Distribution; Restoration Ecology and Management; Wildlife Ecology; Geomorphology; Hydrology and Soils; and Health and Regeneration. Each item is briefly summarized and its relevance to the project is described. References that fall under multiple categories are cross-referenced within the document. Similarly, key words are indicated or each reference to highlight various subtopics affecting California sycamore ecology.

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Askevold, R. A.; Whipple, A.; Grossinger, R. M.; Stanford, B.; Salomon, M. N. 2011. East Contra Costa Historical Ecology Study GIS data, GIS data produced for the East Contra Costa County Historical Ecology Study.
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Anderson, B.; Phillips, B.; Voorhees, J. 2015. The Effects of Kaolin Clay on the Amphipod Eohaustorius estuarius. SFEI Contribution No. 755. Department of Environmental Toxicology, University of California, Davis: Davis, CA.

Several lines of evidence from the Regional Monitoring Program and other studies have suggested that sediment grain size characteristics influence amphipod (Eohaustorius estuarius) survival in 10 day toxicity tests.  Two workshops were convened to address the influence of non-contaminant factors on amphipod toxicity tests, and the current project was prioritized based on the recommendations of experts participating in these workshops.  The study was designed to investigate the effects of kaolin clay on amphipod survival since this is the dominant clay type in Francisco Estuary sediments.  In these experiments reference sand was spiked with increasing concentrations of kaolin to determine whether there was a dose-based relationship between amphipod mortality and increasing concentrations of this type of clay. Wild-caught E. estuarius were collected from Beaver Creek Beach (Oregon) and supplied by Northwest Aquatic Sciences. The initial experiment did not demonstrate a dose-response relationship: E. estuarius survival in all concentrations from 10% to 100% kaolin was lower than in the sand control, and survival in the clay spiked sand was also highly variable.  This experiment exposed a mixture of amphipod size classes representative of those typically provided by the amphipod supplier.  Reasoning that variable response to clay was related to variable tolerances by the different amphipod size classes, a follow-up experiment was conducted to investigate this relationship.  Amphipods were separated into small, medium and large size classes and these were exposed to 100% kaolin.  These results showed survival in 100% clay was 86%, 82% and 66% by small, medium and large amphipods, respectively.  To further investigate size-related responses to clay, small, medium and large amphipods were exposed to concentrations of sand spiked with clay from 0 to 100%.  The results of this experiment showed that smaller amphipods tolerated high clay concentrations better than larger animals, but there was not a strict monotonic dose-response relationship.  Conclusions based on this experiment were constrained by an inability to sort amphipods into three distinct size classes, because there were not enough of the largest animals present at the Oregon collection site.  In addition, grain size analysis of the sand spiked clay suggested that the clay tended to flocculate in the treatments above 70% kaolin.  This experiment was repeated when three distinct size classes were present in December 2014.  The results of this experiment also showed that smaller amphipods tolerated high kaolin better than larger amphipods.  As in the previous experiment, there was not a monotonic response to clay, especially at the higher kaolin concentrations, and the grain size analysis also showed flocculation occurred in the highest clay treatments.  Despite these inconsistencies, the results of this experiment suggest that tolerance of E. estuarius to clay varies with amphipod size.  Average survival was 81%, 79%, and 65% for small, medium and large amphipods, respectively in concentrations > 50% clay.  Possible mechanisms for size specific clay effects on this amphipod species include lower survival related to reduced energy reserves in larger animals, inhibition of gill function, and inhibition of feeding and locomotion through clogging of amphipod setae.  The results suggest that use of smaller amphipods in routine monitoring of high clay sediments will reduce the influence of this factor on test results.  Additional experiments with high clay reference site sediments from San Francisco Bay are recommended to confirm the size related response with field sediments.

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Anderson, B.; Phillips, B. M.; Hunt, J.; Taberski, K.; Thompson, B. 1997. Relationship Between Sediment Toxicity and Contamination in San Francisco Bay. SFEI Contribution No. 27. San Francisco Estuary Institute: Oakland, CA. pp 285-309.
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Ackerman, J.; Hartman, A.; Herzog, M. P.; Toney, M. 2016. San Francisco Bay Triennial Bird Egg Monitoring Program for Contaminants - 2016 Data Summary. U.S. Geological Survey: Dixon, CA. p 19 pp.

As part of the Regional Monitoring Program (RMP) and the USGS’s long-term Wildlife Contaminants Program, the USGS samples double-crested cormorant (Phalacrocorax auritus) and Forster’s tern (Sterna forsteri) eggs throughout the San Francisco Bay Estuary approximately every three years to assess temporal trends in contaminant concentrations. This sampling has been carried out in 2006, 2009, and 2012. Although RMP sampling was scheduled to take place in 2015, it was delayed until 2016. This document summarizes egg collections for 2016, as well as mercury concentrations in Forster’s tern eggs on an individual egg basis.

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Abu-Saba, K. E. 1998. Spatial and Temporal Variability in the Aquatic Cycling of Chromium. SFEI Contribution No. 220. University of California: Santa Cruz, CA.