SFEWS Vol. 20, Issue 2 | June 2022
Climate Change Impacts on San Francisco Estuary Aquatic Ecosystems: A Review
Climate change is intensifying the effects of multiple interacting stressors on aquatic ecosystems, particularly in estuaries. In the San Francisco Estuary, signals of climate change are apparent in the long-term monitoring record. Here we synthesize current and potential future climate change effects on three main ecosystems (floodplain, tidal marsh, and open water) in the upper estuary and two representative native fishes that commonly occur in these ecosystems (anadromous Chinook Salmon, Oncorhynchus tshawytscha and estuarine resident Sacramento Splittail, Pogonichthys macrolepidotus).
Considerations for the Development of a Juvenile Production Estimate for Central Valley Spring-Run Chinook Salmon
Effective species management depends on accurate estimates of population size. There are, however, no estimates of annual juvenile production for Central Valley spring-run Chinook Salmon (“spring run”), a highly imperiled species in California, making it difficult to evaluate population status and effectively manage key issues such as entrainment of this species at water diversions. In recognition of this critical information gap, we initiated an effort to develop a juvenile production estimate (JPE) for spring run, defined here as an annual forecast of the number of juvenile Central Valley spring-run Chinook Salmon that enter the Sacramento–San Joaquin Delta (“Delta”) from the Sacramento Valley.
Machine Learning Forecasts to Reduce Risk of Entrainment Loss of Endangered Salmonids at Large-Scale Water Diversions in the Sacramento–San Joaquin Delta, California
Incidental entrainment of fishes at large-scale state and federal water diversion facilities in the Sacramento-San Joaquin Delta, California, can trigger protective management actions when limits imposed by environmental regulations are approached or exceeded. These actions can result in substantial economic costs, and likewise they can affect the status of vulnerable species. Here, we examine data relevant to water management actions during January–June; the period when juvenile salmonids are present in the Delta.
Gill Net Selectivity for Fifteen Fish Species of the Upper San Francisco Estuary
Gill-net size selectivity for 15 fish species occurring in the upper San Francisco Estuary was estimated from a data set compiled from multiple studies which together contained 7,096 individual fish observations from 882 gill net sets. The gill nets considered in this study closely resembled the American Fisheries Society’s recommended standardized experimental gill nets for sampling inland waters. Relationships between gill-net mesh sizes and the sizes for each fish species retained in them were estimated indirectly using generalized linear modeling and maximum likelihood.
Nutrient and Trace Element Contributions from Drained Islands in the Sacramento–San Joaquin Delta, California
Inventorying nutrient and trace element sources in the Sacramento-San Joaquin Delta (the Delta) is critical to understanding how changes—including alterations to point source inputs such as upgrades to the Sacramento Regional Wastewater Treatment Plant (SRWTP) and landscape-scale changes related to wetland restoration—may alter the Delta’s water quality. While island drains are a ubiquitous feature of the Delta, limited data exist to evaluate island drainage mass fluxes in this system. To better constrain inputs from island drains, we measured monthly discharge along with nutrient and trace element concentrations in island drainage on three Delta islands and surrounding rivers from June 2017 to September 2018.
Volume 12, Issue 3, 2014
Diet, Prey Selection, and Body Condition of Age-0 Delta Smelt, Hypomesus transpacificus, in the Upper San Francisco Estuary
The Delta Smelt, an endangered fish, has suffered a long-term decline in abundance, believed to result from, in part, to changes in the pelagic food web of the upper San Francisco Estuary. To investigate the current role of food as a factor in Delta Smelt well-being, we developed reference criteria for gut fullness and body condition based on allometric growth. We then examined monthly diet, prey selectivity, and gut fullness of larvae and juvenile Delta Smelt collected April through September in 2005 and 2006 for evidence of feeding difficulties leading to reduced body condition. Calanoid copepods Eurytemora affinis and Pseudodiaptomus forbesi remained major food items during spring and from early summer through fall, respectively. Other much larger copepods and macroinvertebrates contributed in lesser numbers to the diet of older juvenile fish from mid-summer through fall. In fall, juvenile Delta Smelt periodically relied heavily on very small prey and prey potentially associated with demersal habitat, suggesting typical pelagic food items were in short supply. We found a strong positive selection for E. affinis and P. forbesi, neutral to negative selection for evasive calanoid Sinocalanus doerrii, and neutral to negative selection for the small cyclopoid copepod Limnoithona tetraspina and copepod nauplii, which were consumed only when extremely numerous in the environment. Feeding incidence was significantly higher in 2006, but among successfully feeding fish we found no between year difference in gut fullness. However, we did detect differences in fullness across months in both years. We found no difference in body condition of Delta Smelt between years yet our sample sizes were low in September when Delta Smelt reverted to feeding on very small organisms and fullness declined, so the longer-term effect remains unknown. Our findings suggest that: Delta Smelt had difficulty obtaining prey in spring 2005 or obtaining proper-sized prey in fall of both years. We detected these difficulties in some regional feeding incidence and fullness indices, but not in body condition indices.
- 2 supplemental PDFs
Alameda Song Sparrow Abundance Related to Salt Marsh Vegetation Patch Size and Shape Metrics Quantified from Remote Sensing Imagery
Understanding the characteristics of high-quality avian habitat is critical for guiding salt marsh management and restoration. Existing insights into salt marsh avian habitat are often based on the composition of marsh vegetation, e.g., individual plant species cover. This study investigated whether the spatial configuration of marsh surface cover (e.g., patch number, density, size, shape complexity and compactness, degree of dissection of the landscape, variation and repetition of cover type, and the variance within these metrics) is a useful, additional indicator of avian habitat quality for the Alameda Song Sparrow (Melospiza melodia pusillula), a non-migratory California Species of Special Concern endemic to southern San Francisco Bay. M. m. pusillula density during the breeding seasons of 2002 through 2005 was estimated at 82 observation points in 10 marsh sites within the bird’s geographic range. The mean bird density index (overall mean: 5.61 birds detected per hectare of marsh) was not significantly different among marshes of different ages. We mapped the vegetation zones, open water, and upland areas within each marsh site using high resolution aerial photographs and automated classification analysis. We quantified the configuration of surface cover around each bird observation point by 31 metrics. Bird density index was best modeled by a multiple linear regression containing positive relationships with the metrics Mean Core Area Index and Patch Core Area Coefficient of Variation (R 2= 0.210, p < 0.0001). Qualitatively, this model suggested that M. m. pusillula abundance during the breeding season was greatest in marsh areas with compact patches that spanned a variety of patch sizes from moderate-to-large, uninterrupted by other cover. We conclude that configuration-based vegetation pattern analysis could usefully complement more customary composition-based habitat assessments to aid wetland habitat research, management, and restoration.
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Climate change is expected to progressively shift the freshwater environments of the San Francisco Bay Area (SFBA) to states that favor alien fishes over native species. Native species likely will have more limited distributions and some may be extirpated. Stream-dependent species may decline as portions of streams dry or become warmer due to lower flows and increased air temperatures. However, factors other than climate change may pose a more immediate threat to native fishes. Comparison of regional vs. statewide vulnerability (baseline and climate change) scores suggests that a higher proportion (56% vs. 50%) of SFBA native species, as compared to the state’s entire fish fauna, are vulnerable to existing anthropogenic threats that result in habitat degradation. In comparison, a smaller proportion of SFBA native species are vulnerable to predicted climate change effects (67% vs. 82%). In the SFBA, adverse effects from climate change likely come second to estuarine alteration, agriculture, and dams. However, the relative effect of climate change on species likely will grow in an increasingly warmer and drier California. Maintaining representative assemblages of native fishes may require providing flow regimes downstream from dams that reflect more natural hydrographs, extensive riparian, stream, and estuarine habitat restoration, and other management actions, such as modification of hatchery operations.