scholarly journals Estuaries, A Happy Place For Fish

2021 ◽  
Vol 9 ◽  
Author(s):  
Pedro Morais ◽  
Ester Dias
Keyword(s):  
San Francisco ◽  
Fish Species ◽  
San Francisco Estuary ◽  
Estuarine Species ◽  
Special Places

Anchovies, salmon, sardines, gobies, mullets, flounder, bass, barbels, eels, shad, and even sharks—what do they have in common? Well, at certain points in their lives you may find them in estuaries, the final sections of rivers before they meet the ocean. Some fish live in estuaries their entire lives. However, some fish species prefer living in the freshwater parts of estuaries, others only live close to the ocean, and a few others spread throughout the estuary. Some species prefer living close to the bottom, some in marshes, and some constantly swim around in the estuary. Some prefer eating other fish, while other species like worms, or insects, or microscopic animals. Unfortunately, many estuarine species are in danger, and all because of humans. In this article, we will tell you why estuaries are such special places for fish and describe some of the species that call the San Francisco Estuary their home.

scholarly journals Fish Misidentification and Potential Implications to Monitoring Within the San Francisco Estuary, California

2018 ◽  
Vol 9 (2) ◽  
pp. 467-485
Author(s):  
Joseph E. Kirsch ◽  
Julie L. Day ◽  
James T. Peterson ◽  
David K. Fullerton
Keyword(s):  
San Francisco ◽  
Fish Species ◽  
False Positive ◽  
Juvenile Fish ◽  
Monitoring Program ◽  
San Francisco Estuary ◽  
Full Time ◽  
Monitoring Programs ◽  
Observer Experience ◽  
Fish Monitoring

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.

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

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.

scholarly journals Delivering Food to Hungry Fish in the San Francisco Estuary

2021 ◽  
Vol 9 ◽  
Author(s):  
Laura Twardochleb ◽  
Leela Dixit ◽  
Mallory Bedwell ◽  
Brittany Davis ◽  
Jared Frantzich
Keyword(s):  
Invasive Species ◽  
San Francisco ◽  
Fish Species ◽  
San Francisco Estuary ◽  
Fish Food ◽  
Yolo Bypass ◽  
Delta Smelt ◽  
Endangered Fish ◽  
The Past

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.

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

2007 ◽  
Vol 64 (4) ◽  
pp. 723-734 ◽  
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.

scholarly journals Can Plants Be Engineers?

2021 ◽  
Vol 9 ◽  
Author(s):  
J. Louise Conrad
Keyword(s):  
San Francisco ◽  
Water Flow ◽  
Fish Species ◽  
Aquatic Ecosystems ◽  
Native Species ◽  
Ecosystem Engineer ◽  
Water Clarity ◽  
Ecosystem Engineers ◽  
San Francisco Estuary ◽  
Native Fish

When we think of engineers, we think of making a machine, like a car. Are there engineers for ecosystems? When an organism can make big changes to its environment, we call it an ecosystem engineer. In aquatic ecosystems like the San Francisco Estuary, underwater plants can be important ecosystem engineers because they can change water flow and water clarity. In the Estuary, a plant called Brazilian waterweed, which was introduced by humans, is one of the most important ecosystem engineers. With its leaves and stems, this plant traps tiny particles floating in the water, making the water clearer. Clearer water has made it easier for more plants to grow and these changes helped some non-native fish species to increase in number, while some native species declined. Introduction of Brazilian waterweed has led to an entirely different ecosystem, which has also affected how people use and take care of the Estuary.

scholarly journals 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 ◽  
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.

scholarly journals Managed Wetlands Can Benefit Juvenile Chinook Salmon in a Tidal Marsh

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.

Atmospheric Concentrations and Fluxes of Organic Compounds in the Northern San Francisco Estuary

2002 ◽  
Vol 36 (22) ◽  
pp. 4741-4747 ◽  
Author(s):  
Pam Tsai ◽  
Rainer Hoenicke ◽  
Donald Yee ◽  
Holly A. Bamford ◽  
Joel E. Baker
Keyword(s):  
Organic Compounds ◽  
San Francisco ◽  
San Francisco Estuary ◽  
Atmospheric Concentrations
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