Delivering Food to Hungry Fish in the San Francisco Estuary

The San Francisco Estuary is home to an important endangered fish called delta smelt. Delta smelt eat small, nutritious animals called zooplankton to survive and grow. In turn, zooplankton grow by eating microscopic plant-like organisms called phytoplankton. In the past, the Estuary was full of plankton and delta smelt. Because people have removed water from the Estuary and invasive species now live there, the Estuary no longer has enough plankton to feed delta smelt, making it difficult for them to survive. Scientists have found a unique place in the Estuary, the Yolo Bypass, that has lots of fish food. The problem is that delta smelt do not live in the Yolo Bypass year-round. Scientists are working to solve this problem by sending river or farm water through the Yolo Bypass, to move fish food downstream to feed the hungry delta smelt and other fish species.

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Crime Scene San Francisco: Who Is Responsible for the Disappearance of Delta Smelt?

Frontiers for Young Minds ◽

10.3389/frym.2021.612548 ◽

2021 ◽

Vol 9 ◽

Author(s):

Mallory E. Bedwell ◽

Craig Stuart ◽

Melinda R. Baerwald

Keyword(s):

San Francisco ◽

Fish Species ◽

Native Species ◽

Crime Scene ◽

San Francisco Estuary ◽

Invasive Fish ◽

Delta Smelt

Delta smelt are becoming harder and harder to find in the San Francisco Estuary. Some of the suspects in their disappearance are invasive fish species that were introduced from other places into the Estuary. These invasive fish can impact their new habitat by eating the native species that were originally there. However, it is hard to understand what the invasive fish are eating. We found that we can use the DNA in the stomachs of invasive fish to figure out what they have eaten. We caught a common invasive fish in the Estuary, called the Mississippi silverside, and analyzed the DNA from their stomachs to see if it matched delta smelt DNA. We discovered that some Mississippi silversides had delta smelt DNA in their stomachs! We therefore believe that Mississippi silversides are one of the culprits causing the disappearance of delta smelt.

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Multidecadal trends for three declining fish species: habitat patterns and mechanisms in the San Francisco Estuary, California, USA

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/f07-048 ◽

2007 ◽

Vol 64 (4) ◽

pp. 723-734 ◽

Cited By ~ 107

Author(s):

Frederick Feyrer ◽

Matthew L Nobriga ◽

Ted R Sommer

Keyword(s):

Water Quality ◽

San Francisco ◽

Striped Bass ◽

Fish Species ◽

Habitat Suitability ◽

Specific Conductance ◽

San Francisco Estuary ◽

Delta Smelt ◽

Threadfin Shad

We examined a 36-year record of concurrent midwater trawl and water quality sampling conducted during fall to evaluate habitat trends for three declining fish species in the San Francisco Estuary, California, USA: delta smelt (Hypomesus transpacificus), striped bass (Morone saxatilis), and threadfin shad (Dorosoma petenense). Generalized additive modeling revealed that Secchi depth and specific conductance were important predictors of occurrence for delta smelt and striped bass, while specific conductance and water temperature were important for threadfin shad. Habitat suitability derived from model predictions exhibited significant long-term declines for each species; the southeastern and western regions of the estuary exhibited the most dramatic changes. Declines in habitat suitability were associated with anthropogenic modifications to the ecosystem. For delta smelt, an imperiled annual species endemic to the estuary, the combined effects of fall stock abundance and water quality predicted recruit abundance during recent years of chronically low food supply. Our results are consistent with existing evidence of a long-term decline in carrying capacity for delta smelt and striped bass and demonstrate the utility of long-term data sets for evaluating relationships between fish and their habitat.

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A Fish Story: Hot Water and Dangerous Behavior!

Frontiers for Young Minds ◽

10.3389/frym.2021.612015 ◽

2021 ◽

Vol 9 ◽

Author(s):

Brittany E. Davis ◽

Ted Sommer ◽

Nann A. Fangue ◽

Anne E. Todgham

Keyword(s):

Climate Change ◽

San Francisco ◽

San Francisco Estuary ◽

Hot Water ◽

Delta Smelt ◽

Endangered Fish ◽

Dangerous Behavior ◽

The World ◽

The Future ◽

Rare And Endangered

Climate change is warming up water all over the world, including in the San Francisco Estuary. This has caused fish who live there to change their behavior in unexpected ways. All animals, including fish, have regular and specialized behaviors that help them to survive. Fish swim, by themselves or in groups, to move to safer habitats, to find food or mates, or just to avoid danger. Scientists worry that changes to these behaviors brought on by warming water will make estuaries less safe for rare and endangered fish like the delta smelt. In the San Francisco Estuary, we found that warmer waters caused delta smelt to swim faster and further away from their neighbors, and to be eaten more often by predators. All these changes could hurt the ability of delta smelt to survive in the future.

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Modeling the Influence of Outflow and Community Structure on an Endangered Fish Population in the Upper San Francisco Estuary

Water ◽

10.3390/w11061162 ◽

2019 ◽

Vol 11 (6) ◽

pp. 1162 ◽

Cited By ~ 2

Author(s):

Gonzalo C. Castillo

Keyword(s):

San Francisco ◽

Fish Population ◽

San Francisco Estuary ◽

Delta Smelt ◽

Endangered Fish ◽

Population Responses ◽

Low Salinity ◽

Salinity Zone ◽

Community Modeling ◽

Community Variables

The aim of this community modeling study was to evaluate potential mechanisms by which freshwater outflow in the upper San Francisco Estuary, CA, controls the fall habitat and abundance of subadult delta smelt Hypomesus transpacificus and its community. Through analyses of the community matrix, community stability and the direction of change of community variables were qualitatively and quantitatively modeled under four outflow–input scenarios. Three subsystems were modeled in the low salinity zone (1–6 psu), each overlapping the location corresponding to the distance from the mouth of the estuary to upstream positions where the near-bottom 2 psu isohaline (X2) is at 74, 81, and 85 km (corresponding to high-, mid-, and low-outflows). Results suggested communities were qualitatively stable at each X2 position, but simulations showed the percent of stable models decreased from low- to high-X2 positions. Under all outflow–input scenarios, the predicted qualitative population responses of delta smelt were: (1) consistently positive for the low X2 position, and (2) uncertain under both mid- and high-X2 positions. Qualitative predictions were generally consistent with quantitative simulations and with the relations between relative abundance of delta smelt and X2. Thus, high outflow seems beneficial to subadult delta smelt when X2 reaches 74 km during fall.

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What Does Not Kill Can Weaken: How Herbicides Impact Fish In The San Francisco Estuary

Frontiers for Young Minds ◽

10.3389/frym.2021.612966 ◽

2021 ◽

Vol 9 ◽

Author(s):

Khiet Huynh ◽

Tomofumi Kurobe ◽

Marie Stillway ◽

Chelsea Lam ◽

Swee Teh

Keyword(s):

San Francisco ◽

Human Activities ◽

San Francisco Estuary ◽

Food Crops ◽

Delta Smelt ◽

The Past

Farmers in the San Francisco Estuary have been using increasing amounts of weed killers, also called herbicides, on their farms. Herbicides kill unwanted weeds without hurting food crops. However, did you know that herbicides can hurt fish as well, especially those that live in the Estuary, like delta smelt? Delta smelt are small, translucent fish that only occur in the San Francisco Estuary. In the past, delta smelt could be found everywhere in the Estuary. However, they are currently threatened with extinction, largely due to human activities. In this study, we tested the toxicity of fluridone, a commonly used herbicide found in the San Francisco Estuary, on delta smelt. None of the fish died from fluridone, but we found that it weakened them, even after as little as 6 h of exposure!

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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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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.ch8 ◽

2004 ◽

Keyword(s):

Life History ◽

San Francisco ◽

Early Life ◽

Oncorhynchus Tshawytscha ◽

San Francisco Estuary ◽

Sacramento River ◽

Yolo Bypass ◽

Species Abundances ◽

Native Fishes ◽

Rotary Screw

Abstract.—We examined assemblage patterns of early life stages of fishes for two major tributaries of the upper San Francisco Estuary: (1) Sacramento River channel, and (2) Yolo Bypass, the river’s seasonal floodplain. Over four hydrologically diverse years (1999–2002), we collected 15 species in Yolo Bypass egg and larval samples, 18 species in Yolo Bypass rotary screw trap samples, and 10 species in Sacramento River egg and larval samples. Fishes captured included federally listed species (delta smelt Hypomesus transpacificus and splittail Pogonichthys macrolepidotus) and several game species (American shad Alosa sapidissima, striped bass Morone saxatilis, crappie Pomoxis spp., and Chinook salmon Oncorhynchus tshawytscha). As in other regions of the estuary, alien fish comprised a large portion of the individuals collected in Yolo Bypass (40–93% for egg and larval net samples; 84–98% for rotary screw trap samples) and Sacramento River (80–99% for egg and larval net samples). Overall ranks of species abundances were significantly correlated for Yolo Bypass and Sacramento River, suggesting that each assemblage was controlled by similar major environmental factors. However, species diversity and richness were higher in Yolo Bypass, likely because of a wider variety of habitat types and greater hydrologic variation in the floodplain. In both landscapes, we found evidence that timing of occurrence of native fishes was earlier than aliens, consistent with their life history and our data on adult migration patterns. We hypothesize that Yolo Bypass favors native fishes because the inundation of seasonal floodplain typically occurs early in the calendar year, providing access to vast areas of spawning and rearing habitat with an enhanced food web. Conclusions from this analysis have implications for the management of aquatic biodiversity of tributaries to the San Francisco Estuary and perhaps to other lowland rivers.

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