Geology topics

Frederick V. Feyrer

Publications and source records attributed to Frederick V. Feyrer.

At least 19 recordsLinked to original sources

USGS2025

Environmental characteristics of select managed ponds in the Sacramento–San Joaquin Delta—Implications for native fish conservation and research

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpose of our study was to examine the physiochemical and biological characteristics of select managed ponds in the Delta to determine if they would be suitable habitats for research involving the conservation of delta smelt ( Hypomesus transpacificus ). We studied 10 managed ponds distributed across the central part of the Delta situated on Bacon Island and Bouldin Island in San Joaquin County, and Holland Tract and Webb Tract islands in Contra Costa County. The managed ponds had a diversity of physical habitat configurations and were not directly connected to waterways surrounding the islands and, therefore, not affected by tides. We studied the managed ponds from approximately November 2021 to December 2023 to assess water quality, zooplankton, fish, and pesticide metrics. Water levels in the managed ponds were managed to varying degrees and were mostly independent of climate-driven wet-dry seasonality. Water quality conditions varied among ponds and were independent of geographic location. Overall, mean monthly chlorophyll a concentration ranged from 15 to 57 (mean=30) micrograms per liter (μg/L), dissolved oxygen concentration ranged from 4 to 9 (mean=7) milligrams per liter (mg/L), pH was 8, salinity was 1 practical salinity units (PSU), specific conductance ranged from 1,202 to 1,839 (mean=1,471) microsiemens per centimeter (μS/cm), and turbidity ranged from 13 to 24 (mean=19) Formazin Nephelometric Units (FNU). Water temperature thresholds that contribute to stress (21 degrees Celsius [°C]) and mortality (28 °C) of delta smelt were often exceeded during summer and fall, though vertical stratification contributed to lower bottom temperatures in the deepest managed ponds, which could potentially provide thermal refugia for delta smelt so long as dissolved oxygen concentrations are suitable. Zooplankton populations were broadly similar among managed ponds and included calanoid and cyclopoid copepods that would be suitable prey for delta smelt. Overall average total zooplankton biomass, as measured with a Schindler-Patalas trap, was 0.6 μg/L (min=0, max=63.6) and peaked during spring at more than 4 μg/L. Fish populations highly varied among the managed ponds with potential predators of delta smelt such as largemouth bass ( Micropterus salmoides ) and black crappie ( Pomoxis nigromaculatus ) present in several of the managed ponds; predator distribution among ponds seemed to have been driven primarily by deliberate stocking to facilitate local fisheries. Measured pesticide concentrations were below U.S. Environmental Protection Agency Aquatic Life Benchmarks except for exceedances of three compounds (diuron [herbicide], clothianidin [insecticide], and deltamethrin [pyrethroid insecticide]) in samples collected from ponds on Bouldin Island and Webb Tract. Overall, most managed ponds seemed suitable to support delta smelt, though physical control of potential predators and summer temperature might be needed. The results provide guidance on how to engineer and manage new managed ponds to support research and conservation efforts for delta smelt and other native fishes.

California↗

USGS2024

Anthropogenic and environmental risk factors of salmonid predation in a tidal freshwater delta

Water diversions that support agricultural and municipal use result in fish mortality through entrainment and impingement. Additionally, this infrastructure may attract both predators and prey fishes, thereby increasing predation rates and prey mortality near these anthropogenic contact points. The Sacramento–San Joaquin Delta (the Delta) in California's Central Valley is a tidal freshwater ecosystem that exports large volumes of water for municipal and agricultural use while at the same time providing valuable migratory and rearing habitat for imperilled fishes. Emigrating juvenile salmonids experience high mortality in the Delta, with predation by non-native fishes contributing substantially. Therefore, this study had three main objectives. First, we determined if small water diversions aggregated piscivorous fishes like other similar structures in freshwater ecosystems. Second, we determined how small diversions may influence juvenile salmon predation risk in conjunction with other known predation risk factors (e.g. predator abundance, temperature and depth). Third, we assessed the predator assemblage, abundance and distribution to determine the likely predator composition in objectives one and two. Throughout the spring of 2021, we used ARIS (adaptive resolution imaging sonar; Sound Metrics) sonars to compare piscivore abundance at 30 water diversions in the north Delta to shorelines adjacent to diversions that did not contain these structures. We used predation event recorders (PERs) to assess the predation risk juvenile salmonids were exposed to, with linear distance (m) from diversions, and other predation risk factors in the north Delta. Finally, we used a boat electrofishing survey to determine the piscivore assemblage and compare spatial trends in black bass ( Micropterus spp.) CPUE and relative abundance throughout these waterways. Piscivore abundance was greater near small water diversions than at adjacent shorelines and the predation risk of juvenile salmonids increased with diversion proximity. Additionally, predation risk increased with increasing piscivore abundance and decreasing water depth. The north Delta predator assemblage was dominated by black basses ( Micropterus spp.), which likely drove the negative relationship of predation risk with water depth, given habitat requirements of these species. Furthermore, increasing smallmouth ( Micropterus dolomieu ) and spotted bass ( Micropterus punctulatus ) abundance in our northern study sites may have weakened temperature effects on predation, given metabolic requirements of these species. Our work demonstrated that small water diversions are likely to increase mortality of endangered salmonids, and that the north Delta predator assemblage was different than recorded by previous work in this system, changing predation risk factors. Although more work is needed to determine the population level impacts of diversions, the ubiquitous distribution of these structures warrants management solutions to reduce mortality from this source. These results indicate that in addition to entrainment and impingement, water diversions may increase mortality of small-bodied fishes by attracting predators and elevating predation risk. Given the continual human demand for freshwater, predator–prey interactions should be considered along with entrainment and impingement when assessing intake infrastructure mitigation, especially when diversions co-occur along migratory routes and essential habitat of imperilled fishes.

California↗

USGS2024

Estimating the benefits of floodplain restoration to juvenile Chinook salmon in the upper San Francisco Estuary, United States, under future climate scenarios

Many river systems within the Central Valley of California have been disconnected from their floodplains, hypothesized to be partially responsible for declining Chinook salmon populations ( Oncorhynchus tshawytscha ). The primary floodplain of the system, Yolo By-Pass (known regionally as “Yolo Bypass”), offered an opportunity to examine whether improved connectivity between the floodplain and river could limit negative climate change effects on salmon populations. Specifically, the top of the floodplain (Fremont Weir) is being modified to provide Sacramento River Chinook salmon better access to floodplain rearing habitat. We estimated restoration effects on the Yolo By-Pass flood regime now and under future climate scenarios using flow rating curves. Additionally, we used temperature and flow-specific effects on Chinook salmon population dynamics within the Yolo By-Pass and Sacramento River complex to describe how the restoration project and climate change may interact to affect juvenile Chinook salmon biomass production. Our results indicate that the Fremont Weir restoration project will extend the frequency, timing, and duration of Yolo By-Pass flooding. Our production model indicates that the modification will result in greater salmon entrainment rates into the Yolo By-Pass, where salmon growth rates, survival rates, and biomass production were higher when compared to the Sacramento River main stem. The project appears to benefit all regional runs of Chinook salmon, which should help support life history diversity. Our results suggest that the weir modification should benefit native fish from the Central Valley that use floodplain habitat and that these benefits may be resilient to challenges created by a changing climate.

California↗

USGS2024

Climate change scenarios for air and water temperatures in the upper San Francisco Estuary: Implications for thermal regimes and Delta Smelt

Climate projections and their effects in the San Francisco Estuary have been evaluated as part of the US Geological Survey’s CASCaDE2 project. Understanding the ecological effects of climate change can help manage and maintain the ecological health and productivity of the San Francisco Estuary. In this study, we assessed downscaled air temperature data from 10 global climate models (GCMs) under two representative concentration pathway (RCP) trajectories for greenhouse gas concentrations for three regions of the San Francisco Estuary: Sacramento–San Joaquin Delta, Suisun and Grizzly bays, and Suisun Marsh. We also used previously derived regression models to estimate future water temperatures at 16 locations in the upper San Francisco Estuary. We used a thermal regime approach to summarize water temperature projections to investigate changes to the thermal regime of the upper San Francisco Estuary, and used the Delta Smelt (Hypomesus transpacificus) to demonstrate the effects that a warming climate may have on the habitat needs of this fish species. Our results suggested there were no major differences in the extent of air-temperature warming among the three regions. Annual average air temperatures were projected to increase approximately 2.0 °C and 4.7 °C by the end of the century for the low and high RCP scenarios, respectively. We found timing, frequency, and magnitude metrics varied by period and RCP scenario, while duration and variability metrics varied by space for water-temperature thermal regimes. For example, the spawning window for Delta Smelt (thermal-regime duration metric) is projected to expand in the future, with spawning starting earlier for both RCP scenarios for most sites. Although our thermal-regime analysis focused on the life history of Delta Smelt, similar approaches could be used to assess climate-change threats to a wide array of native and invasive terrestrial and aquatic species found in San Francisco Estuary.

California↗

USGS2024

The influence of time, tide, and place on fine scale nekton distribution: Insights from the San Francisco Estuary

The location of estuarine organisms varies based on geophysical cycles and environmental conditions, which can strongly bias understanding of organism abundance and distribution. In the San Francisco Estuary, California, extensive monitoring surveys have provided insight into the life history and ecology of certain commercially important or legislatively protected fish species. However, there remains substantial uncertainty in factors influencing the vertical and lateral distributions of many other nekton species in the San Francisco Estuary, including longfin smelt Spirinchus thaleichthys , for whom such distributional information may highly influence interpretation of existing data. We carried out paired sampling using surface and demersal gears to address three questions: (1) Does diel phase influence the vertical position of nekton (e.g., surface versus demersal)? (2) Do environmental conditions, specifically turbidity, influence the vertical and lateral positions of nekton (e.g., center channel versus peripheral shoal)? (3) Does tidal variability influence vertical and lateral distributions of nekton? We documented variability in sampled nekton densities across diel phase (day/night), vertical position (surface/bottom), and lateral position (channel/shoal). Tidal phase and turbidity concentration influenced vertical and lateral distributions for some species at certain locations. Although infrequently encountered, we documented associations of longfin smelt with the lower water column and shoal habitats, with some evidence for upward vertical shifts in low light conditions brought about by nightfall or elevated turbidity. Observed habitat associations provide insight into how interacting geophysical and environmental factors may influence the distribution of nekton and thus the vulnerability of individual species to detection by sampling gears.

California↗

USGS2024

Variability in coastal habitat available for Longfin Smelt Spirinchus thaleichthys in the northeastern Pacific Ocean

An understanding of oceanographic conditions and processes important to marine animal ecology is fundamental to the development of effective management and conservation actions. Longfin Smelt ( Spirinchus thaleichthys ) is a pelagic forage fish found in coastal and estuarine waters along the Pacific coast of North America from Alaska to central California. Substantial population declines in California’s San Francisco Estuary, where Longfin Smelt are protected under California’s Endangered Species Act, have prompted extensive study of estuarine factors associated with the decline. However, coastal factors that affect up to two-thirds of the Longfin Smelt life cycle are poorly understood and may be important drivers of population dynamics. We compiled coastal observations from numerous sources to estimate the range-wide coastal marine distribution of Longfin Smelt and assess habitat factors affecting distribution in the northeast Pacific Ocean. Based on maximum entropy species distribution models, Longfin Smelt distribution was correlated with depth, distance from the nearest estuary, sea surface temperature, and sea surface chlorophyll. Longfin Smelt were found in shallow, higher productivity coastal waters closer to estuaries, with depth and temperature the most consistent factors influencing distribution. Habitat suitability was highly variable at the southern extent of the range, particularly off the California coast, and was largely driven by habitat contractions associated with warm-water conditions. Study results provide insights into the habitat and range-wide distribution of an at-risk estuarine-reliant forage fish and are the first step toward identifying processes that affect the marine portion of the Longfin Smelt life cycle.

Frontiers in Marine Science↗

USGS2024

Wetland geomorphology and tidal hydrodynamics drive fine-scale fish community composition and abundance

Effective restoration of tidal wetlands for fish communities requires clear goals and mechanistic understanding of the ecosystem drivers which affect fish distribution and abundance. We examined fish community responses to abiotic habitat features in two adjacent but dissimilar freshwater tidal wetlands in the Sacramento-San Joaquin Delta, CA, USA, each of which represents a potential restoration configuration. The first wetland was characterized by a broad, intertidal basin with relatively high hydrodynamic exchange with surrounding waterways. The second wetland was characterized by a dendritic network of shallow subtidal channels with relatively low hydrodynamic exchange. Fish community composition significantly differed between the two wetlands, based on permutational analysis of variance. Fish abundance within and among the two wetlands was also highly affected by specific geomorphic and hydrodynamic characteristics: distance from connection with the main external waterway, bed elevation, and water surface elevation. The physical configuration of a restored tidal wetland, in conjunction with the way tides move across the restored landscape, has strong implications for local fishes. Manipulating these elements to create a landscape mosaic of habitat configurations can be an effective tool for targeting desired restoration outcomes, such as specific fish communities or target fish densities.

California↗

USGS2024

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

California↗

USGS2023

Etiology of a fish kill, Including the endangered Tidewater Goby (Eucyclogobius newberryi), in a northeastern pacific coastal lagoon

Ecological disturbances such as fish kills can negatively impact ecosystem processes in coastal lagoons. To gain an understanding of factors causing fish kills, we examined conditions associated with a summertime fish kill in a northeastern Pacific coastal lagoon (Rodeo Lagoon, CA, USA). Examination of available data indicated the fish kill was likely caused by hypoxia involving the following etiology: (1) strong onshore winds (up to 12 m/s) mixed a stratified water column, (2) water column mixing transported nutrients from near the bed into the photic zone, (3) increased nutrient concentrations in the photic zone (> 200%) together with high solar irradiance fueled a phytoplankton bloom, (4) death and decomposition of phytoplankton (72% decrease in abundance) contributed to biological oxygen demand that led to (5) hypoxic conditions (as low as 0.6 mg/L) that caused the fish kill. The event resulted in the death of an estimated 3677 Tidewater Goby ( Eucyclogobius newberryi ), a species listed as endangered under the US Endangered Species Act, and numerous (but not enumerated) Threespine Stickleback ( Gasterosteus aculeatus ), unidentified sculpins (Cottidae), and macroinvertebrates (primarily Amphipoda). The processes contributing to the event are likely re-occurring phenomena responsible for observed periodic fish kills. Coastal lagoons with limited freshwater inflows and connection to the Pacific Ocean may retain nutrients and be susceptible to similar events.

California↗

USGS2023

Hydrodynamics and habitat interact to structure fish communities within terminal channels of a tidal freshwater delta

Terminal channels were historically a common feature of tidal delta ecosystems but have become increasingly rare as landscapes have been modified. Tidal hydrodynamics are a defining feature in tidal terminal channel ecosystems from which native aquatic communities have evolved. However, few studies have explored the relationship between fish community structure and hydrodynamics in these tidal terminal channel ecosystems. We sampled fish communities throughout a network of terminal channels within the northeasternmost region of the San Francisco Estuary to determine the relationship between fish community structure and hydrodynamics within these environments. We collected two years (2017 and 2018) of fish community samples using gill nets and analyzed data using multivariate community analyses and count models. We found metrics of fish diversity and counts of native fishes to be greatest upstream (farthest from tidal influence) of the tidal excursion within terminal channels. Counts of non-native fishes were less affected by this hydrodynamic feature of terminal channels and more tightly correlated to local habitat conditions (e.g., water temperature, depth). Our results suggest that channel hydrodynamics plays a role in structuring fish communities within terminal channels, particularly native fishes. These results indicate that hydrodynamics in tidal delta ecosystems may be able to be altered in ways that benefit native fishes without the cost of water pumping.

California↗

USGS2022

Habitat-specific foraging by striped bass (Morone saxatilis) in the San Francisco Estuary, California: Implications for tidal restoration

Non-native predatory fish strongly impact aquatic communities, and their impacts can be exacerbated by anthropogenic habitat alterations. Loss of natural habitat and restoration actions reversing habitat loss can modify relationships between non-native predators and prey. Predicting how these relationships will change is often difficult because insufficient information exists on the habitat-specific feeding ecology of non-native predators. To address this information gap, we examined diets of non-native Striped Bass ( Morone saxatilis ; 63 to 671 mm standard length; estimated age 1-5 yrs) in the San Francisco Estuary during spring and summer in three habitat types – marsh, shoal, and channel – with the marsh habitat type serving as a model for ongoing and future restoration. Based on a prey-specific index of relative importance, Striped Bass diets were dominated by macroinvertebrates in spring and summer (amphipods in spring, decapods and isopods in summer). In spring, diets were relatively consistent across habitats. In summer, marsh diets were dominated by sphaeromatid isopods and shoal/channel diets by idoteid amphipods and decapods. Striped Bass consumed a variety of native and non-native fishes, primarily Prickly Sculpin ( Cottus asper ) and Gobiidae. The highest importance of fish prey was in the marsh in spring (~40% prey weight), and fish prey comprised less than 25% prey weight in all other season/habitat combinations. Linear discriminant analyses suggested that marsh foraging was prevalent in Striped Bass collected in other habitats, mostly due to the predominance of marsh-associated invertebrates found in the stomachs of individual Striped Bass collected outside of the marsh. Striped Bass diets differ across habitats, with marsh foraging important to Striped Bass regardless of collection location. This information can be used to forecast the potential utilization of restored habitats by this non-native piscivore.

California↗

USGS2022

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. Selectivity curves are provided for each species to inform researchers about population characteristics of fishes sampled with similar gill nets.

California↗

USGS2022

Underwater videographic observations of domesticated Delta smelt in field enclosures

The delta smelt ( Hypomesus transpacificus ) is a small, euryhaline fish species endemic to the Sacramento–San Joaquin Delta; it is protected under the U.S. and California Endangered Species Acts, and because of declines in population abundance, the delta smelt may be vulnerable to extinction. The California Department of Water Resources (DWR) is conducting studies to test the viability of using domesticated fish to supplement the wild population of delta smelt. These studies have focused on examining the health and survival of domesticated delta smelt placed inside enclosures (circular cages that are approximately 1.5 meters tall by 1 meter in diameter) into the wild. We completed two parts within this study using underwater cameras inside the enclosures to observe fish behavior and their responses to certain stimuli. In both parts of the study, delta smelt behaviors were broadly categorized into two basic categories: (1) normal and (2) alarm. Normal behavior was characterized as calm, non-polarized, and docile swimming behavior. Alarm behavior was characterized by sudden and rapid darting, polarized frantic swimming activity, and tighter schooling polarization of individuals. The first part of the study took place in a semi-controlled agricultural pond on the campus of the University of California, Davis. At this agricultural pond, we developed methods of observation and documented how fish behaved in response to enclosure disturbances associated with routine cleaning and service that is required during extended field deployments of the enclosures. We observed that delta smelt behavior changed from normal to alarm at the onset of an enclosure service and from alarm to normal within about 2 minutes after the service ended. The second part of the study was completed in cooperation with the DWR. In October 2019, DWR deployed three enclosures in the Sacramento River near Rio Vista, California. To monitor survival rate of delta smelt, DWR permitted us to deploy cameras in one enclosure to document the frequency and duration of alarm behaviors exhibited by delta smelt and the frequency, duration, and intensity of three types of disturbances: (1) noise generated from passing boats, (2) noise generated from the enclosure moving in response to wave energy, and (3) vertical movements of the enclosure generated from wave energy. Alarm behaviors averaged about 2 minutes in duration and occurred most frequently during the evening compared to midday or morning. Each disturbance variable exhibited substantial variability in duration and intensity and occurred least frequently during the morning and evening compared to midday. Alarm behaviors appeared to be most associated with high intensity enclosure noises and vertical movements; however, limited replicate samples prohibited developing a statistical relation. Alarm behaviors did not directly contribute to injury or mortality of individual delta smelt; however, indirect or sublethal effects of alarm behaviors were not examined.

California↗

USGS2022

Climate change and fishes in estuaries

This chapter provides an overview of the main drivers of change in estuarine systems, their expected causes and impacts on estuarine fish and fisheries. An analysis of global, regional and local patterns of estuarine fish and how climate-induced change may impact estuarine systems and their fish communities is provided. We also examine the main environmental, climatic and biological stressors likely to impact estuarine fish and associated fisheries. A set of case studies is used to illustrate the differences in potential impacts associated with various global regions and types of estuaries. An understanding of climate change in estuaries will support estuarine ecosystem resilience, inform management and facilitate adaptation.

Book chapter↗

USGS2022

Ocean connectivity drives trophic support for consumers in an intermittently closed coastal lagoon

Estuarine food webs are complex, as marine, freshwater, and terrestrial inputs combine and contribute variable amounts of organic material. Seasonal fluctuations in precipitation amplify the dynamism inherent to estuarine food webs, particularly in lagoonal estuaries, which can be seasonally closed and disconnected from the ocean in low-runoff periods (bar-built lagoons). Despite their abundance along coastlines in Mediterranean climates, the organic matter sources fueling bar-built lagoon food webs are poorly understood, particularly with respect to seasonal hydrologic variability, episodic marine connections, and internal nutrient cycling. In this study, we evaluate the food web of a bar-built lagoon with respect to seasonal differences in lagoon water quality, the sources of organic matter which support consumers, and the trophic ecology of resident fishes. Observed water quality conditions reflected biogeochemical processes associated with salinity-driven stratification and high lagoon residence times and were associated with strong seasonal differences in the contribution of different organic matter sources to lagoon consumers. A variety of organic matter sources supported consumers; marine inputs were important to lagoon food webs in spring when the lagoon was open, while summer food webs were largely driven by phytoplankton which was likely fueled by internal nutrient cycling. Fish diets were largely comprised of crustaceans and fish eggs, with clearly defined trophic niches in spring but high overlap in summer. This study demonstrates that the seasonal changes in bar-built lagoon food webs are largely dependent on ocean connectivity and internal cycling within the lagoon, rather than watershed processes as is typical for many estuaries.

California↗

USGS2022

Eye lenses reveal ontogenetic trophic and habitat shifts in an imperiled fish, Clear Lake hitch (Lavinia exilicauda chi)

Stable isotopes recorded in fish eye lenses are an emerging tool to track dietary shifts coincident with use of diverse habitats over the lifetime of individuals. Eye lenses are metabolically inert, sequentially deposited, archival tissues that can open avenues to chronicle contaminant exposures, diet histories, trophic dynamics and migratory histories of individual fishes. In this study, we demonstrated that trophic histories reconstructed using eye lenses can resolve key uncertainties regarding diet and trophic habitat shifts. Clear Lake hitch ( Lavinia exilicauda chi ), a threatened cyprinid, inhabits a single lake (Clear Lake, Lake County, California) and utilizes tributary streams for reproduction. Bayesian mixing models applied to δ 13 C and δ 15 N recorded in eye lenses uncovered ontogenetic diet shifts that corresponded with shifts in occupation of habitats providing spawning (tributary streams), rearing (littoral lake), and growth (pelagic lake) functions. The reconstruction of size-structured trophic and habitat information can provide vital information needed to manage and conserve imperiled species such as the Clear Lake hitch.

California↗

USGS2021

Disentangling stationary and dynamic estuarine fish habitat to inform conservation: Species-specific responses to physical habitat and water quality in San Francisco Estuary

Estuaries represent critical aquatic habitat that connects surface water distributed between Earth’s landmasses and oceans. They are dynamic transitional ecosystems, which provide important habitat for fishes and other aquatic organisms. Effective conservation of species inhabiting estuaries requires knowledge of the habitat features that drive their abundance and distribution. We sought to elucidate how stationary (i.e., wetlands, shoals, and channels) and dynamic (i.e., salinity, temperature, turbidity, and chlorophyll concentration) habitat features interact to drive distributions of individual fish species. The Pacific coast of the conterminous United States has over 400 estuaries of various types. The largest (historical surface area) is San Francisco Estuary, California. We conducted extensive field observations of fishes in the central San Francisco Estuary among stationary habitat types (i.e., wetland, shoal, and channel) over a 19-month period encompassing substantial variability in dynamic water quality conditions. Most of the species observed, especially native species of special management interest, were associated with tidal wetland habitat. Few species exhibited associations with water quality conditions driven by seasonal (temperature) or a combination of broad- and fine-scale ecosystem processes (salinity and turbidity). Our study provides (1) an empirical demonstration of how researchers can deal with the complex and dynamic expressions of habitat in estuarine systems to address urgent natural resource problems and (2) a clear demonstration of the urgent need for habitat restoration and its likely outcome in systems such as San Francisco Estuary. Restoration of suitable tidal wetland habitat on the West Coast of the United States is likely to be an effective conservation tool to support estuarine fishes given that over 90% of historical tidal wetland habitat in San Francisco Estuary and 85% of vegetated wetland habitat along the Pacific coast of the United States has been lost due to human modification.

California↗

USGS2021

Recruitment dynamics of non-native largemouth bass within the Sacramento-San Joaquin delta

Largemouth bass (LMB; Micropterus salmoides ) recruitment is limited by a critical developmental period during early life stages, but this mechanism may be less important within non-native habitats. We conducted boat electrofishing surveys in four tidal lakes of California’s Sacramento–San Joaquin Delta (SSJD) from 2010 to 2011 to describe introduced LMB recruitment dynamics. We evaluated growth, proximate composition, and health indices of young-of-the-year (YOY) LMB among tidal lakes and developed an integrated count model to determine how factors known to affect LMB recruitment shape SSJD population structure. Our results show a mismatch among growth, nutrition, and YOY abundance, where the tidal lake with the most abundant and fastest-growing LMB had the poorest nutritional status. The warm winter water temperatures and lack of a hatching-cohort growth advantage suggests overwinter starvation plays a less important role in SSJD LMB recruitment than in many native LMB habitats. Collectively, our results suggest that habitat characteristics (submerged aquatic vegetation) and not overwinter mortality shapes SSJD LMB population structure, a mechanism consistent with contemporary hypotheses about the altered fish community structure of the SSJD.

California↗