Adapting an ambient monitoring program to the challenge of managing emerging pollutants in the San Francisco Estuary

Abstract Fish monitoring programs often rely on the collection, species identification, and counting of individual fish over time to inform natural resource management decisions. Thus, the utility of the data used to inform these decisions can be negatively affected by species misidentification. Fish species misidentification bias can be minimized by confirming identification using genetic techniques, training observers, or adjusting monitoring data using estimates of incomplete detection and false-positive misidentification. Despite the existence of well-established fish identification training and quality control programs, there is considerable uncertainty about fish species false-positive misidentification rates and the effectiveness of fish identification training programs within the San Francisco Estuary. We evaluated the misidentification of fish species among Delta Juvenile Fish Monitoring Program observers by conducting five fish identification exams under controlled conditions at the Lodi Fish and Wildlife Office in Lodi, California, between 2012 and 2014. To assess the variability in false-positive misidentification, we fitted data to species and observer characteristics using hierarchical logistic regression. We found that fish species misidentification was fairly common, averaging 17% among 155 test specimens and 32 observers. False-positive misidentification varied considerably among species and was negatively related to fish size, the abundance of the species within monitoring samples, and observer experience. In addition, observers who were not formally trained or used as full-time observers were, on average, 6.0 times more likely to falsely identify a species. However, false-positive misidentification rates among observers and specimens still varied considerably after controlling for observer experience and training, and species and size, respectively. Our results could be used to improve fish identification training and testing, increase the accuracy of fish occupancy or abundance estimation, and justify the allocation of resources to continually use and formally train full-time observers within long-term monitoring programs operating in the system.

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Early Life History of Fishes in the San Francisco Estuary and Watershed

Early Life History of Fishes in the San Francisco Estuary and Watershed ◽

10.47886/9781888569599.ch15 ◽

2004 ◽

Keyword(s):

San Francisco ◽

Water Samples ◽

Early Life ◽

Solid Phase ◽

Life Stage ◽

Monitoring Program ◽

Complex Mixture ◽

Central Valley ◽

San Francisco Estuary ◽

Delta Smelt

<em>Abstract.</em>—The San Francisco Estuary is critical habitat for delta smelt <em>Hypomesus transpacificus</em>, a fish whose abundance has declined greatly since 1983 and is now listed as threatened. In addition, the estuary receives drainage from the Central Valley, an urban and agricultural region with intense and diverse pesticide usage. One possible factor of the delta smelt population decline is pesticide toxicity during vulnerable larval and juvenile stages, but pesticide concentrations are not well characterized in delta smelt spawning and nursery habitat. The objective of this study was to estimate the potential exposure of delta smelt during their early life stages to dissolved pesticides. For 3 years (1998–2000), water samples from the Sacramento–San Joaquin Delta were collected during April–June in coordination with the California Department of Fish and Game’s delta smelt early life stage monitoring program. Samples were analyzed for pesticides using solid-phase extraction and gas chromatography/mass spectrometry. Water samples contained multiple pesticides, ranging from 2 to 14 pesticides in each sample. In both 1999 and 2000, elevated concentrations of pesticides overlapped in time and space with peak densities of larval and juvenile delta smelt. In contrast, high spring outflows in 1998 transported delta smelt away from the pesticide sampling sites so that exposure could not be estimated. During 2 years, larval and juvenile delta smelt were potentially exposed to a complex mixture of pesticides for a minimum of 2–3 weeks. Although the measured concentrations were well below short-term (96-h) LC50 values for individual pesticides, the combination of multiple pesticides and lengthy exposure duration could potentially have lethal or sublethal effects on delta smelt, especially during early larval development.

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Comparing and Integrating Fish Surveys in the San Francisco Estuary: Why Diverse Long-Term Monitoring Programs are Important

San Francisco Estuary and Watershed Science ◽

10.15447/sfews.2020v18iss2art4 ◽

2020 ◽

Vol 18 (2) ◽

Author(s):

Dylan Stompe ◽

Peter Moyle ◽

Avery Kruger ◽

John Durand

Keyword(s):

Survey Data ◽

San Francisco ◽

Monitoring Program ◽

San Francisco Estuary ◽

Data Sets ◽

Data Set ◽

Monitoring Programs ◽

Long Term Monitoring ◽

Term Monitoring

Many fishes in the San Francisco Estuary have suffered declines in recent decades, as shown by numerous long-term monitoring programs. A long-term monitoring program, such as the Interagency Ecological Program, comprises a suite of surveys, each conducted by a state or federal agency or academic institution. These types of programs have produced rich data sets that are useful for tracking species trends over time. Problems arise from drawing conclusions based on one or few surveys because each survey samples a different subset of species or reflects different spatial or temporal trends in abundance. The challenges in using data sets from these surveys for comparative purposes stem from methodological differences, magnitude of data, incompatible data formats, and end-user preference for familiar surveys. To improve the utility of these data sets and encourage multi-survey analyses, we quantitatively rate these surveys based on their ability to represent species trends, present a methodology for integrating long-term data sets, and provide examples that highlight the importance of expanded analyses. We identify areas and species that are under-sampled, and compare fish salvage data from large water export facilities with survey data. Our analysis indicates that while surveys are redundant for some species, no two surveys are completely duplicative. Differing trends become evident when considering individual and aggregate survey data, because they imply spatial, seasonal, or gear-dependent catch. Our quantitative ratings and integrated data set allow for improved and better-informed comparisons of species trends across surveys, while highlighting the importance of the current array of sampling methodologies.

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Introduction of Bluefin Killifish (Lucania goodei) into the Sacramento–San Joaquin Delta

San Francisco Estuary and Watershed Science ◽

10.15447/sfews.2020v18iss2art3 ◽

2020 ◽

Vol 18 (2) ◽

Author(s):

Brian Mahardja ◽

Andrew Goodman ◽

Alisha Goodbla ◽

Andrea Schreier ◽

Catherine Johnston ◽

...

Keyword(s):

San Francisco ◽

Juvenile Fish ◽

Ecological Impact ◽

Monitoring Program ◽

San Francisco Estuary ◽

Native Fish ◽

Close Relative ◽

Proactive Management ◽

Lucania Goodei ◽

Bluefin Killifish

Biological invasion by non-native species has been identified as one of the major threats to native fish communities worldwide. The fish community of San Francisco Estuary is no exception, as the estuary has been recognized as one of the most invaded on the planet and the system has been impacted significantly by these invasions. Here, we summarize the introduction and probable establishment of a new species in the Sacramento–San Joaquin Delta, the Bluefin Killifish (Lucania goodei), as discovered by the US Fish and Wildlife Service Delta Juvenile Fish Monitoring Program (DJFMP). The DJFMP has conducted a large-scale beach seine survey since 1976, and it is the longest-running monitoring program in the San Francisco Estuary that extensively monitors the shallow-water nearshore habitat. Possibly introduced as discarded aquarium fish within the vicinity of the Delta Cross Channel, Bluefin Killifish is a close relative of the Rainwater Killifish (Lucania parva), another non-native fish species that has been present in the San Francisco Estuary system for decades. Studies in their native range suggest that Bluefin Killifish will fill a similar niche to Rainwater Killifish, albeit with a more freshwater distribution. The potential ecological impact of Bluefin Killifish remains unclear in the absence of additional studies. However, we have been able to track the spread of the species within the Sacramento–San Joaquin Delta through the existence of long-term monitoring programs. Our findings demonstrate the value of monitoring across various habitats for the early detection and proactive management of invasive species.

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Supporting Restoration Decisions through Integration of Tree-Ring and Modeling Data: Reconstructing Flow and Salinity in the San Francisco Estuary over the Past Millennium

Water ◽

10.3390/w13152139 ◽

2021 ◽

Vol 13 (15) ◽

pp. 2139

Author(s):

Paul H. Hutton ◽

David M. Meko ◽

Sujoy B. Roy

Keyword(s):

San Francisco ◽

Tree Ring ◽

San Francisco Estuary ◽

Salinity Intrusion ◽

Estuarine Ecosystem ◽

Freshwater Flow ◽

The Past ◽

Decadal Scale ◽

Tree Ring Data ◽

Past Millennium

This work presents updated reconstructions of watershed runoff to San Francisco Estuary from tree-ring data to AD 903, coupled with models relating runoff to freshwater flow to the estuary and salinity intrusion. We characterize pre-development freshwater flow and salinity conditions in the estuary over the past millennium and compare this characterization with contemporary conditions to better understand the magnitude and seasonality of changes over this time. This work shows that the instrumented flow record spans the range of runoff patterns over the past millennium (averaged over 5, 10, 20 and 100 years), and thus serves as a reasonable basis for planning-level evaluations of historical hydrologic conditions in the estuary. Over annual timescales we show that, although median freshwater flow to the estuary has not changed significantly, it has been more variable over the past century compared to pre-development flow conditions. We further show that the contemporary period is generally associated with greater spring salinity intrusion and lesser summer–fall salinity intrusion relative to the pre-development period. Thus, salinity intrusion in summer and fall months was a common occurrence under pre-development conditions and has been moderated in the contemporary period due to the operations of upstream reservoirs, which were designed to hold winter and spring runoff for release in summer and fall. This work also confirms a dramatic decadal-scale hydrologic shift in the watershed from very wet to very dry conditions during the late 19th and early 20th centuries; while not unprecedented, these shifts have been seen only a few times in the past millennium. This shift resulted in an increase in salinity intrusion in the first three decades of the 20th century, as documented through early records. Population growth and extensive watershed modification during this period exacerbated this underlying hydrologic shift. Putting this shift in the context of other anthropogenic drivers is important in understanding the historical response of the estuary and in setting salinity targets for estuarine restoration. By characterizing the long-term behavior of San Francisco Estuary, this work supports decision-making in the State of California related to flow and salinity management for restoration of the estuarine ecosystem.

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Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh

Estuaries and Coasts ◽

10.1007/s12237-020-00880-4 ◽

2021 ◽

Author(s):

Nicole M. Aha ◽

Peter B. Moyle ◽

Nann A. Fangue ◽

Andrew L. Rypel ◽

John R. Durand

Keyword(s):

San Francisco ◽

Growth Rates ◽

Chinook Salmon ◽

Oncorhynchus Tshawytscha ◽

Nursery Habitat ◽

San Francisco Estuary ◽

Rice Fields ◽

Fish Growth ◽

Juvenile Chinook Salmon ◽

Juvenile Chinook

AbstractLoss of estuarine and coastal habitats worldwide has reduced nursery habitat and function for diverse fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Underutilized off-channel habitats such as flooded rice fields and managed ponds present opportunities for improving rearing conditions and increasing habitat diversity along migratory corridors. While experiments in rice fields have shown enhanced growth rates of juvenile fishes, managed ponds are less studied. To evaluate the potential of these ponds as a nursery habitat, juvenile Chinook salmon (~ 2.8 g, 63 mm FL) were reared in cages in four contrasting locations within Suisun Marsh, a large wetland in the San Francisco Estuary. The locations included a natural tidal slough, a leveed tidal slough, and the inlet and outlet of a tidally muted managed pond established for waterfowl hunting. Fish growth rates differed significantly among locations, with the fastest growth occurring near the outlet in the managed pond. High zooplankton biomass at the managed pond outlet was the best correlate of salmon growth. Water temperatures in the managed pond were also cooler and less variable compared to sloughs, reducing thermal stress. The stress of low dissolved oxygen concentrations within the managed pond was likely mediated by high concentrations of zooplankton and favorable temperatures. Our findings suggest that muted tidal habitats in the San Francisco Estuary and elsewhere could be managed to promote growth and survival of juvenile salmon and other native fishes.

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