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Floodplain rearing of juvenile Chinook salmon: evidence of enhanced growth and survival
Abstract
In this study, we provide evidence that the Yolo Bypass, the primary floodplain of the lower Sacramento River (California, U.S.A.), provides better rearing and migration habitat for juvenile chinook salmon (Oncorhynchus tshawytscha) than adjacent river channels. During 1998 and 1999, salmon increased in size substantially faster in the seasonally inundated agricultural floodplain than in the river, suggesting better growth rates. Similarly, coded-wire-tagged juveniles released in the floodplain were significantly larger at recapture and had higher apparent growth rates than those concurrently released in the river. Improved growth rates in the floodplain were in part a result of significantly higher prey consumption, reflecting greater availability of drift invertebrates. Bioenergetic modeling suggested that feeding success was greater in the floodplain than in the river, despite increased metabolic costs of rearing in the significantly warmer floodplain. Survival indices for coded-wire-tagged groups were somewhat higher for those released in the floodplain than for those released in the river, but the differences were not statistically significant. Growth, survival, feeding success, and prey availability were higher in 1998 than in 1999, a year in which flow was more moderate, indicating that hydrology affects the quality of floodplain rearing habitat. These findings support the predictions of the flood pulse concept and provide new insight into the importance of the floodplain for salmon.
... Salmon. This reduction forces them into faster, colder, and deeper main stem channels and away from warmer, slow moving, and shallow offchannel habitat which often allows for increased growth rates (McCullough, 1999;Sommer et al., 2001;Jeffres et al., 2008;Limm & Marchetti, 2009). Discharge is also directly related to the drift delivery of invertebrate prey for salmon (Leung et al., 2009;T. ...
... The dominance of oligochaetes and similar pollution-tolerant collector and gatherer species (e.g. some Chironomidae, Amphipoda) is well documented in the Central Valley (Leland & Fend, 1998;Merz, 2001;Sommer et al., 2001;Griffith et al., 2003;Bacey & Spurlock, 2007;Utz et al., 2012). The dominance of these taxa is generally indicative of high levels of fine depositional material (fine benthic material), anoxic environments, and heavy agricultural impacts (Bacey & Spurlock, 2007;Walters et al., 2009). ...
... Equally important is that increased flow would likely result in increased floodplain and off-channel habitat. It is likely that this habitat would provide a warmer water refuge for salmonids, although velocities would likely be lower, allowing for increased growth potential (Sommer et al., 2001;Ahearn et al., 2006;Jeffres et al., 2008;Limm & Marchetti, 2009). ...
Salmon fisheries managers often use models to determine the growth of individuals and populations for a variety of management objectives. Most models of juvenile salmon growth during their freshwater residency only incorporate activity costs for drift foraging when making growth assessments and predictions. I propose that fish may need to include a searching foraging strategy to meet their energy needs under certain situations, such as when prey are scarce, difficult to find, or if low water velocities do not promote high drift delivery. To investigate this I tested how the growth derived from otoliths collected from a cohort of wild juvenile Chinook Salmon (Onchorhyncus tschawytscha) in the San Joaquin River compared to predictions of growth derived from the individual based model inSTREAM. Model predictions of search foraging events were confirmed by stable isotope analyses, which suggested that a significant portion of total consumed biomass was derived from oligochaetes. The model was then used to simulate a variety of discharge and prey production scenarios to investigate their effects on growth and survival. Results from these scenarios suggest that prey production has the most significant effect on growth and survival, while all discharge levels above Critical Low are beneficial for growth and survival.
... During their seaward migration, they rear in a variety of freshwater and estuarine habitats in and around the SSJD. These populations have life histories adapted to exploit high invertebrate production on seasonally inundated floodplains during freshwater emigration Sommer et al., 2001, Jeffres et al., 2008, Corline et al., 2017. Secondary production on floodplains is conventionally thought to be supported primarily by 'green' pathways: phytoplankton and attached algae . ...
... Utilization of off-channel habitats has been identified as an important factor in juvenile salmon growth and success (Jeffres et al., 2008;Katz et al., 2017;Sommer et al., 2001). High densities of invertebrates and relatively warm temperature on the floodplains compared to the river channel provide opportunities for high growth rates in juvenile fishes (Corline et al., 2017;Grosholz & Gallo, 2006;Jeffres et al., 2020;Sommer et al., 2001). ...
... Utilization of off-channel habitats has been identified as an important factor in juvenile salmon growth and success (Jeffres et al., 2008;Katz et al., 2017;Sommer et al., 2001). High densities of invertebrates and relatively warm temperature on the floodplains compared to the river channel provide opportunities for high growth rates in juvenile fishes (Corline et al., 2017;Grosholz & Gallo, 2006;Jeffres et al., 2020;Sommer et al., 2001). ...
We used compound specific isotope analysis of carbon isotopes in amino acids to determine the biosynthetic source of amino acids in fish from major tributaries to California's Sacramento-San Joaquin river delta (i.e., Sacramento, Cosumnes, and Mokelumne rivers). Using samples collected in Winter and Spring between 2016 and 2019, we confirmed that algae are a critical component of floodplain food webs in California's Central Valley. Results from bulk stable isotope analysis of carbon and nitrogen in producers and consumers were adequate to characterize a general trophic structure and identify potential upstream and downstream migration into our study site by American shad Alosa sapidissima and rainbow trout Oncorhynchus mykiss, respectively. However, owing to overlap and variability in source isotope compositions, our bulk data were unsuitable for conventional bulk isotope mixing models. Our results from compound specific carbon isotope analysis of amino acids clearly indicate that algae are important sources of organic matter to fish of conservation concern such as Chinook salmon Oncorhynchus tshawytscha in California's Central Valley. But, algae were not the exclusive source of energy to metazoan food webs. We also revealed that other sources of amino acids such as bacteria, fungi, and higher plants contributed to fish as well. While consistent with the well-supported notion that algae are critical to aquatic food webs, our results highlight the possibility that detrital subsidies might intermittently support metazoan food webs. This article is protected by copyright. All rights reserved.
... Despite limited marine input, some bar-built estuaries remain highly productive and have high juvenile salmonid growth rates throughout summer months for more thermally tolerant species (Oncorhynchus mykiss in Bond et al. 2008). When closed, bar-built estuaries may inundate surrounding marsh or floodplains, increasing terrestrial input and drift invertebrates (Sommer et al. 2001;Behrens et al. 2013). While mouth closure may be reducing marine prey, this phenomenon may also increase productivity ...
... Increasing contribution of the estuary type life history requires improving growth and survival in the estuary. Expanding floodplain and estuary habitats has notably increased the growth and smolt-to-adult survival of juveniles in other watersheds (Sommer et al. 2001;Bottom et al. 2005). Improving estuarine growth would increase their size towards the thresholds required to survive overwinter. ...
... Although restoration in the watershed has primarily been focused on reducing sediment input upstream (Madej and Ozaki 2009), the value of restoring the estuary is recognized among managers in the watershed. Removing dikes and levees confining estuaries have expanded floodplains and salt marshes and increased estuarine use in other watersheds(Sommer et al. 2001;Bottom et al. 2005). These habitats provide higher growth for juveniles than mainstem freshwater habitats, but whether they also provide higher survival while rearing is less apparent(Sommer et al. 2001;Hayes et al. 2008;Johnston et al. 2018). ...
Estuaries are commonly touted as nurseries for outmigrating salmonids, providing higher prey availability than streams, a physiological transition zone, and refugia from marine predators. Yet the diversity of estuaries makes it difficult to generalize the effect they have on salmonid recruitment. In bar-built estuaries, sandbars form at the mouth of rivers during periods of low flow, closing access to the ocean and disrupting outmigration. In this thesis, I evaluated how residency in a bar-built estuary affects the growth, survival, and ultimately recruitment of Chinook salmon (Oncorhynchus tshawytscha) in Redwood Creek, California. I conducted a mark-recapture experiment on outmigrating juveniles during the summer of 2018 to determine estuary abundance, growth, and survival. I used scales and sagittal otoliths collected from spawning adult carcasses to quantify the contribution of different juvenile life histories to the adult population. I then integrated these data and monitoring data collected from spawning ground surveys, rotary screw traps, and estuary seines to create a stage-structured matrix model. iii Juveniles that remained in the estuary after the mouth closed were larger at ocean entry than ocean rearing juveniles that entered the ocean earlier in the spring. However, estuary rearing juveniles grew less and ultimately were smaller than ocean rearing juveniles prior to winter. Despite having a larger ocean entry size, estuary rearing juveniles had lower survival from river outmigration to adult return than ocean rearing juveniles and contributed disproportionately less to the spawning population. Lack of marine influence and low river flow are common attributes of bar-built estuaries that may lower food availability and deteriorate conditions in these estuaries. Levees constructed in lower Redwood Creek prevent flooding and establishment of marsh and floodplain habitat, potentially majorly limiting the productivity of the estuary and salmonid growth. Restoration efforts designed to address limitations to growth in the estuary such as low food availability and high temperatures are needed to increase the ocean survival and ultimately contribution of estuary juveniles to the population. iv ACKNOWLEDGEMENTS
... The stability and resiliency of salmon populations depends partially on a juvenile salmon's ability to access and utilize suitable freshwater rearing habitats during emigration to the ocean. Juvenile salmon often utilize a diverse mosaic of habitat types off the main migratory corridor-such as shallow-water wetlands, tidal marshes, and floodplains-which can provide increased feeding opportunities (Sommer et al. 2001;Williams 2006;Jeffres et al. 2008;Limm and Marchetti 2009). This habitat diversity increases growth opportunities for juvenile salmon in freshwater habitats (Brennan et al. 2019), which is critical for age class success because early growth during freshwater residence can significantly affect marine survival (Woodson et al. 2013). ...
... Regardless of their migratory behavior, all naturally produced juvenile California Central Valley fall run use the Delta as a migration corridor. While juvenile fall run experience increased growth in shallow-water wetlands and floodplains in the Delta (Sommer et al. 2001), access to these habitats is limited because urban development, levee construction, and increased agricultural activities have replaced more than 95% of the historical Delta rearing habitat (Williams 2006;Robinson et al. 2014). Alongside the extensive habitat loss and associated reduction in local food production, juvenile fall run can experience high mortality in the Delta as a result of the combined effect of high temperatures, contaminant loads, and increased predation (Kjelson et al. 1982;Marine and Cech 2004;Grossman 2016;Michel et al. 2020 Yet, otolith chemistry reconstructions of adult Chinook Salmon indicate that fry emigrants can successfully rear in the Delta (Miller et al. 2010;Sturrock et al. 2015;Phillis et al. 2018;Sturrock et al. 2020). ...
... In particular, the "habitat" defined here isotopically as "the Delta" comprises fastflowing, leveed channels (Robinson et al. 2014) as well as productive patches of relict, restored and managed wetland and floodplain habitats, such as Liberty Island, Yolo Bypass, Sherman Island, and Browns Island. Furthermore, during wet years like 2017, the lower American River inundates Discovery Park (Cannon and Kennedy 2006) creating a large, ephemeral floodplain within the natal stream that likely would have supported increased food production and growth (Sommer et al. 2001). ...
Historically, Chinook Salmon in the California Central Valley reared in the vast wetlands of the Sacramento–San Joaquin Delta. However, more than 95% of floodplain, riparian, and wetland habitats in the Delta have become degraded because of anthropogenic factors such as pollution, introduced species, water diversions, and levees. Despite pronounced habitat loss, previous work using otolith reconstructions has revealed that some juvenile salmon continue to successfully rear for extended periods in the Delta. However, the extent to which the Delta functions to promote salmon growth relative to other habitats remains unknown. In this study, we integrated otolith microstructure (daily increment count and width) and strontium isotope (87Sr/86Sr) records to fill this critical knowledge gap by comparing the growth of natural-origin fall-run Chinook Salmon from the American River that reared in the Delta with those that remained in their natal stream. Using generalized additive models, we compared daily otolith growth rates among rearing habitats (Delta vs. American River) and years (2014 to 2018), encompassing a range of hydrologic conditions. We found that juvenile Chinook Salmon grew faster in the Delta in some years (2016), but slower in the Delta during drought conditions (2014 to 2015). The habitat that featured faster growth rates varied within and among years, suggesting the importance of maintaining a habitat mosaic for juvenile salmonids, particularly in a dynamic environment such as the California Central Valley. Linking otolith chemistry with daily growth increments provides a valuable approach to explore the mechanisms governing interannual variability in growth across habitat types, and a useful tool to quantify the effects of large-scale restoration efforts on native fishes.
... Within the Sacramento River watershed, the Yolo Bypass, an ephemerally inundated agricultural floodplain, represents an important rearing habitat for threatened juvenile Chinook salmon, Oncorhynchus tshawytscha (Sommer et al., 2001a). Previous studies have demonstrated that juvenile Chinook salmon rearing in floodplain habitats exhibit increased growth and body condition relative to fish rearing in the channelized Sacramento River (Jeffres et al., 2008;Sommer et al., 2001b). However, the potential for differential pesticide exposure and bioaccumulation between fish residing in the two habitats has not been directly determined. ...
... The Yolo Bypass floodplain is an important rearing habitat for threatened juvenile Chinook salmon populations, with previous studies suggesting that floodplain rearing confers a host of benefits including increased growth, survival and prey availability compared to rearing in the mainstem Sacramento River (e.g. Jeffres et al., 2008;Sommer et al., 2001b). However, the findings of the present study suggest the potential for greater organochlorine exposure in fish rearing in the floodplain compared to the Sacramento River. ...
... A large number of studies have focused on the potential benefits of floodplain restoration for improving outcomes for rearing endangered salmonids (Bellmore et al., 2013;Goertler et al., 2018), however the influence of contaminants is rarely considered. The findings of the present study suggest that fish rearing on the floodplain, a habitat known to confer benefits for growth and survival (Sommer et al., 2001a(Sommer et al., , 2001b, may be exposed to elevated concentrations of organochlorines compared to those fish rearing in adjacent riverine habitats, and that pesticide exposure may be exacerbated under high-flow conditions. Consequently, the findings of the present study should be used to support management decisions and restoration actions aimed at improving the health of threatened salmonid populations. ...
The Sacramento River watershed, California, provides important rearing and migratory habitat for several species of conservation concern. Studies have suggested significant benefits for juvenile fish rearing in floodplain habitats of the watershed compared to the mainstem Sacramento River. However, the potential for contaminant exposure in each of these two habitats is poorly understood. Consequently, the present study aimed to determine the distribution and occurrence of bioavailable pesticides within two known salmon habitats using a suite of approaches including exhaustive chemical extraction, single-point Tenax extraction (SPTE) and ex situ passive sampling. Sediment samples were collected from sites within both habitats twice annually in 2019 and 2020, with inundation of the floodplain and high flows for both areas in 2019 and low flow conditions observed in 2020. Sediment characteristics including total organic carbon, black carbon and particle size distribution were determined to elucidate the influence of physical characteristics on pesticide distribution. Using exhaustive extractions, significantly greater sediment concentrations of organochlorines were observed in the floodplain compared to the Sacramento River in both years, with bioaccessible organochlorine concentrations also significantly greater in the floodplain (ANOVA, p < 0.05). Using both SPTEs and exhaustive extractions, significantly fewer pesticides were detected across both sites under low flow conditions as compared to high flow conditions (Poisson regression, p < 0.05). Sediment characteristics including percent fines and black carbon had significant positive relationships with total and bioaccessible pyrethroid and organochlorine concentrations. Fewer analytes were detected using low-density polyethylene (LDPE) passive samplers as compared to SPTEs, suggesting greater sensitivity of the Tenax technique for bioavailability assessments. These findings suggest that threatened juvenile fish populations rearing on the floodplain may have greater exposure to organochlorines than fish inhabiting adjacent riverine habitats, and that pesticide exposure of resident biota may be exacerbated during high-flow conditions.
... Directly upstream of the mouth of the Sacramento lies the adjacent Yolo Bypass, an important seasonal floodplain (Fig. 1). Out-migrating fall-run Chinook salmon inhabit either the Sacramento River mainstem channel or the bypass, the latter of which provides fertile rearing habitat especially when inundated Goertler et al., 2018;Sommer et al., 2001Sommer et al., , 2020. Previous studies have indicated that juvenile salmon residing in the bypass may grow faster and larger than fish rearing in the mainstem Sacramento River channel Katz et al., 2017;Sommer et al., 2001;Takata et al., 2017), due to an increase in habitat complexity, prey availability and quality Jeffres et al., 2020). ...
... Out-migrating fall-run Chinook salmon inhabit either the Sacramento River mainstem channel or the bypass, the latter of which provides fertile rearing habitat especially when inundated Goertler et al., 2018;Sommer et al., 2001Sommer et al., , 2020. Previous studies have indicated that juvenile salmon residing in the bypass may grow faster and larger than fish rearing in the mainstem Sacramento River channel Katz et al., 2017;Sommer et al., 2001;Takata et al., 2017), due to an increase in habitat complexity, prey availability and quality Jeffres et al., 2020). However, there is also evidence that the basal energy sources of Chinook salmon and their principal prey differ between the river and bypass (Goertler et al., 2018;Sommer et al., 2001), which could potentially cause different routes of exposure of hydrophobic pesticides to resident biota, as these compounds tend to concentrate in the sediments of aquatic systems (Fong et al., 2016;Weston et al., 2013). ...
... Previous studies have indicated that juvenile salmon residing in the bypass may grow faster and larger than fish rearing in the mainstem Sacramento River channel Katz et al., 2017;Sommer et al., 2001;Takata et al., 2017), due to an increase in habitat complexity, prey availability and quality Jeffres et al., 2020). However, there is also evidence that the basal energy sources of Chinook salmon and their principal prey differ between the river and bypass (Goertler et al., 2018;Sommer et al., 2001), which could potentially cause different routes of exposure of hydrophobic pesticides to resident biota, as these compounds tend to concentrate in the sediments of aquatic systems (Fong et al., 2016;Weston et al., 2013). Studies of juvenile Chinook salmon stomach contents have suggested that fish rearing in the bypass feed primarily on benthic macroinvertebrates as compared to a greater consumption of pelagic prey items by fish rearing in the Sacramento River (Sommer et al., 2001), though recent studies have suggested this may vary with hydrological conditions and changes to prey availability (Goertler et al., 2018). ...
Juvenile Chinook salmon (Oncorhynchus tshawytscha) of the Sacramento River system encounter many anthropogenically-induced stressors while rearing and migrating to the Pacific Ocean. Located in a prominent agricultural region, the watershed serves as a source of notable contaminants including pesticides. Salmon rearing in riverine and floodplain areas are potentially exposed to these compounds via dietary exposure, which can vary based on selected food webs. Previous studies have suggested that juvenile Chinook salmon rearing in riverine and floodplain environments of the Sacramento River watershed are characterized by different dietary preferences, with potential for contrasting pesticide exposure between habitats. To examine the potential for pesticide exposure, juvenile Chinook salmon and known dietary items were collected in the mainstem Sacramento River and an adjacent floodplain, the Yolo Bypass, in 2019 and 2020, and analyzed for 33 pesticides, including degradates and isomers. Organochlorine pesticides including the DDX group (p,p’-DDT, p,p’-DDD and p,p’-DDE) were prevalent in all examined biota. There was a significantly greater number of total pesticide detections across all classes in zooplankton compared to macroinvertebrates, coupled with higher bifenthrin concentrations in zooplankton across regions and years, which may indicate different exposure potential depending on fish dietary preferences. Detection frequencies and concentrations of organochlorines were higher in prey items during flooding than in drought conditions, suggesting resuspension of legacy compounds. Significantly higher concentrations of organochlorines were recorded in floodplain rearing fish compared to the Sacramento River. These findings suggest that within these habitats, juvenile Chinook salmon feeding primarily on zooplankton within the water column may be exposed to a greater range of pesticides than those feeding on benthic macroinvertebrates, and that the benefits of floodplain rearing may come at a cost of increased organochlorine exposure.
... Consequently, valuable habitat for larval and juvenile fishes has been lost, either directly through the upstream diversion of water and construction of levees to prevent or limit river flooding or indirectly through the loss of connectivity between habitat types (e.g., via river channelization; Mount 1995, Tockner andStanford 2002). Historically, floodplain habitats served as important rearing grounds for the early-life-history stages of migrating anadromous fishes (Brown andHartman 1988, Moyle 2002) , and research has increasingly focused on the role of these habitats in promoting juvenile survival in fishes (i.e., Sommer et al. 2001;Jeffres et al. 2008). For example, outmigrating juvenile Chinook salmon (Oncorhynchus tshawytscha) that have access to the Yolo Bypass floodplain (California, USA) show faster growth (i.e., increased body mass d −1 in rearing area) than those restricted to the main channel of the Sacramento River (Sommer et al. 2001). ...
... Historically, floodplain habitats served as important rearing grounds for the early-life-history stages of migrating anadromous fishes (Brown andHartman 1988, Moyle 2002) , and research has increasingly focused on the role of these habitats in promoting juvenile survival in fishes (i.e., Sommer et al. 2001;Jeffres et al. 2008). For example, outmigrating juvenile Chinook salmon (Oncorhynchus tshawytscha) that have access to the Yolo Bypass floodplain (California, USA) show faster growth (i.e., increased body mass d −1 in rearing area) than those restricted to the main channel of the Sacramento River (Sommer et al. 2001). Similar results have been found for juvenile Chinook smolts in other California rivers using natural floodplains/riparian zones (Jeffres et al. 2008), and Chinook smolts reared on agricultural floodplains have shown growth rates among the highest recorded in freshwater systems in California Jeffres et al. 2020;Katz et al. 2017). ...
... The mechanisms driving increased growth and survival of salmonids within floodplains may be attributed to interactions between abiotic and biotic factors, such as increased water temperatures and productivity (Sommer et al. 2001;Jeffres et al. 2020), or the promotion of phytoplankton and zooplankton densities from reduced water velocities associated with vegetative structure (Jeffres et al. 2008). In northern California, floodplains and their associated riverbanks, flooded riparian zones, and levees can be vegetated with willow (Salix spp., Harris 1987)and other vegetative structure that may facilitate increased growth rates in fishes. ...
Outmigrating, juvenile Chinook salmon Oncorhynchus tshawytscha, with access to floodplains (e.g., Yolo Bypass California, USA), grow faster than those restricted to the main channel of the Sacramento River. How these young salmon might use rooted, vegetative structure (e.g., to decrease energy expenditures) while holding positions in flowing water on floodplains and flooded riparian zones is unknown. We conducted daytime experiments in a large (24.4 m long) flume containing a planted area (9.76 m × 1.22 m) of sandbar willows, Salix interior. Flume water was maintained at 1.5 m depth and 16 °C over a 15–90 cm s⁻¹ test velocity range. Fish were videoed using 19 cameras to determine positional behavior, including their depth, use of vegetation, and tail-beat (body-undulation) frequencies (TBFs). These TBFs were replicated with similarly-sized salmon in a calibrated, Brett-type swimming respirometer, where oxygen consumption rates were measured. Using these laboratory measurements, we estimated their swimming velocities and energetic costs associated with occupying sandbar willow habitats in the flume. As flume velocities increased and the leafy canopies of the willows were bent over from the flow, salmon occupied deeper water, among the thick stems of the willows, and maintained their positions. Even at the highest (90 cm s⁻¹) nominal flume velocities, their estimated swimming velocities were only 35.6 cm s⁻¹, within the bottom 15 cm of the water column. This resulted in unchanged energetic costs, compared with those estimated at lower nominal water velocities. The use of vegetated (e.g., with sandbar willow common to the riparian zone) floodplains, rather than non-vegetated ones, can potentially provide energy-saving, growth-promoting daytime habitat for migrating juvenile salmonids during river-flow periods that include floodplain inundation.
... Juveniles rear in freshwater habitats for 5-10 months before out-migrating to the ocean. They exhibit a diverse rearing history with habitats that include the Sacramento River mainstem, Sutter and Yolo bypasses (Jones and Stokes Associates 1993;Sommer et al., 2001), and other off-channel habitats. Recently, winter-run Chinook have also been found to rear in non-natal tributaries such as the Lassen tributaries (i.e., Deer, Mill and Battle Creeks) and the Feather and American Rivers (Phillis et al., 2018). ...
... Such habitats likely provide diverse rearing conditions and possibly support growth and survival during out-migration (Maslin et al., 1996;Limm and Marchetti 2009). Similarly, seasonal floodplains, such as the Yolo and Sutter bypasses, provide critical rearing habitat where the growth of juvenile salmonids has outperformed congeners reared in the mainstem Sacramento River during the same period (Sommer et al., 2001Jeffres et al., 2008Jeffres et al., , 2020Katz et al., 2017). Sacramento River winter-run Chinook salmon appear to rely on a more diverse set of rearing habitats than previously acknowledged, suggesting expanded conservation opportunities for species recovery (Phillis et al., 2018). ...
... Growth of juveniles in mainstem and tributary habitats was modeled as a constant percent increase in weight per day, due to the lack of field studies documenting prey composition and prey density data. Growth rates were obtained using an average of reported values by scarce existing field studies (Sommer et al., 2001;Jeffres 2016). These studies were based on fall-run Chinook juveniles from end-of-January to mid-March when coexisting winter-run juveniles are greater in length. ...
Reconciliation between water uses and sustaining aquatic species populations requires an effort to identify and quantify essential habitat characteristics for ecosystem health and valuation methods to predict ecosystem response to restoration actions. This process is particularly challenging for anadromous fish species such as California's Sacramento River winter-run Chinook salmon, due to their limited geographic range and diverse life history habitat requirements. Tools, such as life-cycle models, are needed to manage population dynamics and quantify the composite effects of processes across space and time. Nevertheless, complex institutions can hinder result interpretation and communication, and limit model use in decision-making. This paper focuses on the federally endangered and endemic Sacramento River winter-run Chinook (Oncorhynchus tshawytscha) by developing a Winter-Run Habitat-based Population Model (WRHAP). WRHAP is a conceptual, freshwater rearing stage model that includes alternative rearing habitats reported in the literature (e.g., floodplains, off-channel and tributaries), defines rules of habitat use based on instream conditions, and incorporates a juvenile growth module that combines bioenergetics modeling with empirical growth rates. Model outputs reasonably follow observed out-migration patterns and provide a realistic smolt size distribution arriving at the San Francisco Bay. This effort demonstrates the importance of currently “non-critical” habitats (as defined by the Endangered Species Act) for juvenile development, with floodplain habitat contributing to a quarter of out-migrating biomass (despite < 18% availability and <10% of total rearing days), and off-channel growth being one of the most sensitive parameters (explaining ~13% of average juvenile weight variance). The model shows the utility of a simple population model to explore relationships between habitat quality/quantity and juvenile development, and to assist water/environmental management and decision-making processes focused on species recovery.
... Floodplains are critical habitats for many of California's native fishes. Of particular importance are the abundant invertebrate communities typical of these off-channel ephemeral habitats which provide rich trophic resources for native fish (Sommer et al. 2001b, Grosholz and Gallo 2006, Jeffres et al. 2008. Despite their importance, it is estimated that 95% of historic floodplain habitats in the Central Valley have been lost due to hydrologic modification of rivers and urban and agricultural development of floodplains (Hanak et al. 2011). ...
... During flood events, high flows are routed through these managed floodways in order to protect cities and key infrastructure . Previous studies in the Yolo Bypass have demonstrated that inundated bypass lands provide high-quality zooplankton food resources to native fishes such as Sacramento splittail (Pogonichthys macrolepidotus) and Chinook Salmon (Oncorhynchus tshawytscha; Sommer et al. 2001b, Feyrer et al. 2006. Chinook Salmon reared in floodplain and off-channel habitats experience greater growth rates than those in rivers due to the high abundance of zooplankton prey as well as increased water temperatures (Jeffres et al. 2008. ...
... All samples were placed in Whirl-Pak bags (Madison, Wisconsin, USA) and preserved in a solution of 95% ethyl alcohol with rose bengal dye. Zooplankton samples from Sherwood Harbor on the Sacramento River were collected by the California Department of Water Resources using methods from Sommer et al. (2001bSommer et al. ( , 2004. Samples were collected with a 153-lm mesh 0.5 m diameter Clark-Bumpus net equipped with a General Oceanics Flowmeter (Miami, Florida, USA) and preserved in 5% formalin. ...
Abstract Community assembly has been an important topic in ecological research and theory for over a century. Recently, restoration ecologists have emphasized the use of community assembly rules, such as environmental filtering, to better inform management actions. Although there has been a strong call for the use of community assembly rules in terrestrial restoration ecology, few studies have examined their potential use in providing habitat benefits such as food resources to native species in large‐scale managed aquatic ecosystems. In this study, we found evidence of deterministic community assembly mechanisms in zooplankton communities in floodplain and seasonally inundated off‐channel habitats in California’s Central Valley. Additionally, we found that all sampled off‐channel floodplain habitat types had similar zooplankton communities and that assembly in floodplain habitats was governed by variables associated with increased water residence time. This study is the first to determine community assembly rules in floodplain‐river ecosystems in order to assist managers in providing floodplain food‐web benefits to native fish and wildlife species at the landscape scale.
... Autotrophic production is widely recognized as an important source of aquatic food web productivity [10] but a significant portion of the trophic energy transfer in river-floodplain systems may also move through heterotrophic food webs driven by breakdown of plant detritus [12][13][14][15][16]. The abundant floodplain food resources contribute significantly to the diets of juvenile salmonids accessing these off-channel habitats during flood events [17,18] where they grow more quickly than fish confined to adjacent leveed river channels [11,19]. ...
... The largest bypass is the Yolo Bypass, a 24,000 ha floodway adjacent to the city of Sacramento and immediately upstream of the Sacramento-San Joaquin Delta (Fig 1). The Yolo Bypass is extensively farmed during summer and it floods in two out of three winters on average, although flood events are frequently shorter than a week [18]. Substantial areas of the Yolo Bypass are managed as seasonal agricultural floodplain wetlands to support wildlife, and a perennial drainage canal spans much of the eastern edge of the floodplain. ...
... Overall, we found support for our hypotheses that off-channel agricultural wetland habitat generates higher densities of zooplankton and increased growth rates of juvenile salmon as compared to adjacent perennial canal and river channels. While our study design relied on the use of caged hatchery fish and a heavily managed agricultural wetland as part of the habitat comparisons, these results are consistent with observations of zooplankton densities and wild fish growth rates during more natural uncontrolled flood events [18,33,34]. Below we describe some of the habitat attributes that may be responsible for these differences. ...
Similar to many large river valleys globally, the Sacramento River Valley has been extensively drained and leveed, hydrologically divorcing river channels from most floodplains. Today, the former floodplain is extensively managed for agriculture. Lack of access to inundated floodplains is recognized as a significant contributing factor in the decline of native Chinook Salmon (Oncorhynchus tshawytscha). We observed differences in salmon growth rate, invertebrate density, and carbon source in food webs from three aquatic habitat types-leveed river channels, perennial drainage canals in the floodplain, and agricultural floodplain wetlands. Over 23 days (17 February to 11 March, 2016) food web structure and juvenile Chinook Salmon growth rates were studied within the three aquatic habitat types. Zooplankton densities on the floodplain wetland were 53x more abundant, on average, than in the river. Juvenile Chinook Salmon raised on the floodplain wetland grew at 0.92 mm/day, 5x faster than fish raised in the adjacent river habitat (0.18 mm/day). Two aquatic-ecosystem modeling methods were used to partition the sources of carbon (detrital or photosyn-thetic) within the different habitats. Both modeling approaches found that carbon in the floodplain wetland food web was sourced primarily from detrital sources through heterotro-phic pathways, while carbon in the river was primarily photosynthetic and sourced from in situ autotrophic production. Hydrologic conditions typifying the ephemerally inundated flood-plain-shallower depths, warmer water, longer water residence times and predominantly detrital carbon sources compared to deeper, colder, swifter water and a predominantly algal-based carbon source in the adjacent river channel-appear to facilitate the dramatically higher rates of food web production observed in the floodplain. These results suggest that hydrologic patterns associated with seasonal flooding facilitate river food webs to access floodplain carbon sources that contribute to highly productive heterotrophic energy pathways important to the production of fisheries resources. PLOS ONE PLOS ONE | https://doi.org/10.1371/journal.pone.
... Floodplain inundation stimulates aquatic food webs, causing increases in primary production and zooplankton abundance (Ahearn et al., 2006;Corline et al., 2017;Jeffres et al., 2020). Such prey are often consumed by juvenile Chinook salmon, which can show vastly increased growth rates when compared with individuals reared in non-floodplain habitats (Ahearn et al., 2006;Jeffres et al., 2008Jeffres et al., , 2020Sommer et al., 2001). Juvenile salmon that enter the ocean at larger sizes may exhibit improved survival (Unwin, 1997), suggesting that habitats that fuel growth during early life history may improve adult returns. ...
... Here, we examined fish outmigration cues from the Cosumnes River in the Central Valley of California, focusing on emigration and stranding patterns of native and non-native fishes. In light of growing evidence worldwide that floodplain access provides significant benefits to native fishes, there is a critical need for an evaluation of natural dynamics driving patterns of use and movement by those fishes Jeffres et al., 2008;Katz et al., 2017;Sommer et al., 2001). ...
Floodplains are highly productive environments that provide critical rearing habitat and increased growth for diverse native fishes, including juvenile Chinook salmon (Oncorhynchus tshawytscha). Yet, stranding during the flood recession is a potential negative outcome in restored ecosystems where environmental cues are not always present as they were under historical conditions. Outmigration cues of native and non‐native fishes from a restored floodplain were evaluated along the Cosumnes River, CA, USA. This river is the only remaining major unregulated river in the Sierra Nevada that flows into the Central Valley. It remains unclear how native and non‐native fishes utilize spatiotemporally heterogeneous habitats in the Cosumnes River; however, a better understanding of these dynamics could yield insight into how degraded river ecosystems in the region could be rehabilitated to benefit native fishes. In 2018 and 2019, daily fyke net surveys of fish assemblages were conducted within the floodplain and in outmigration corridors, along with the collection of environmental data to identify possible cues. Bayesian modeling showed that temperature increases, along with the rate of floodplain drawdown and the average flow over a rolling seven‐day period, were important triggers for cuing native fishes to exit the floodplain. We conclude that the numerous benefits to the aquatic food web and growth of native fishes justify the risk of stranding that floodplain restoration poses, particularly when supplemented with outmigration cues.
... Chinook salmon use ocean, freshwater, and estuarine habitats to fulfill their life history needs, but observations of low survival (<0.05; Buchanan et al., 2018aBuchanan et al., , 2018bPerry et al., 2018;Buchanan and Skalski, 2020) for juveniles outmigrating through the Sacramento-San Joaquin River Delta (hereafter, Delta), and the importance of this region for water management, has made the Delta a research priority (Sommer et al., 2001;Limm and Marchetti, 2009;Michel et al., 2013;. Every natural-origin juvenile must pass through the Delta to successfully reach the ocean (Newman and Brandes, 2010;Perry et al., 2018;Buchanan and Skalski, 2020). ...
... Juvenile fall-run Chinook salmon can disperse from natal tributaries in early spring as smaller fry and achieve considerable growth for multiple weeks in non-natal waters prior to ocean entry, or they can rear in natal tributaries and leave as larger smolts later in the spring (Limm and Marchetti 2009;Merz et al., 2013;Sturrock et al., 2020;Nobriga et al., 2021). Historically, the Delta was dominated by floodplains and wetlands that could support large numbers of rearing fry, and provide predator and thermal refugia for later outmigrating smolts (Sommer et al., 2001). However, <3% of these habitats remain today and salmon that emigrate early from natal tributaries as fry have low survival (Sturrock et al., 2020). ...
Monitoring is usually among the first actions taken to help inform recovery planning for declining species, but these data are rarely used formally to inform conservation decision making. For example, Central Valley Chinook salmon were once abundant, but anthropogenic activities have led to widespread habitat loss and degradation resulting in significant population declines. Monitoring data suggest survival through the southern Sacramento-San Joaquin River Delta, in particular, may be a limiting factor for juvenile Chinook salmon outmigrating from the San Joaquin River and its tributaries. However, survival and routing monitoring data have not been formally used to inform water management in a decision analytic framework. Here, we illustrate how estimates derived from disjunct monitoring data can be used to inform water management and as a basis for adaptively managing flows. We aggregated a meta-analysis of Chinook salmon smolt survival and routing estimates through the south Delta with other sources of data to develop a survival and routing simulation model to estimate optimal flows for the San Joaquin River during smolt outmigration from February–May. We found that large flow pulses at predictable times during the spring are projected to be optimal for increasing Chinook salmon smolt survival to the San Francisco Bay and that optimal scenarios differed somewhat with water year type. Sensitivity analysis revealed temperature and smolt outmigration timing are driving optimal pulse distribution and that water allocation changes little with parameter uncertainty. This case study highlights the utility of the decision-analytic framework for solving conservation problems.
... Additionally, Jensen and Johnsen (2002) found that growth of Atlantic Salmon Salmo salar decreased in years with higher spring discharges in Norway. Many growth studies focused on larval and juvenile life stages, and important rearing habitats for these life stages are floodplains (Dudley 1974;Schlosser 1991;Sommer et al. 2001;Balcombe et al. 2007;Jeffres et al. 2008). Often, floodplain habitat is only connected to the stream during periods of higher discharges, and the lack of connectivity could influence growth (Sommer et al. 2001). ...
... Many growth studies focused on larval and juvenile life stages, and important rearing habitats for these life stages are floodplains (Dudley 1974;Schlosser 1991;Sommer et al. 2001;Balcombe et al. 2007;Jeffres et al. 2008). Often, floodplain habitat is only connected to the stream during periods of higher discharges, and the lack of connectivity could influence growth (Sommer et al. 2001). These studies provide some evidence that fish growth can be influenced by river hydrology, but there is a need for similar research focused on warmwater sportfish. ...
We examined the influence of variable discharge on hatching and age-0 growth for fluvial specialist and habitat generalist species of black bass Micropterus spp. in two southeastern U.S. rivers, the Flint River, Georgia (unregulated), and the Tallapoosa River, Alabama (regulated by several hydropower dams). Between 2008 and 2010, we collected 285 Largemouth Bass M. salmoides (generalist) and 254 Shoal Bass M. cataractae (specialist) from two reaches of the Flint River. In 2010–2011, we collected 309 Alabama Bass M. henshalli (generalist) and 216 Redeye Bass M. coosae (specialist) from two regulated reaches and one unregulated reach of the Tallapoosa River. Successful hatching of black bass in both rivers generally occurred from late March to early June when water levels were low and stable. Hatching distributions of all black bass were generally unimodal with little evidence of spawning disruption, except for Alabama Bass in the most-regulated reach of the Tallapoosa River, which appeared to be disrupted by large discharge events. Mean growth of both species in the Flint River varied from 0.64 to 0.82 mm/d across reaches and years; Shoal Bass generally grew faster than Largemouth Bass in all reach–year combinations. Largemouth Bass growth was inversely correlated to discharge variation in one reach, but Shoal Bass growth was not correlated to discharge variation in either reach. Alabama Bass and Redeye Bass growth rates in the Tallapoosa River were similar to rates observed for congeners in the Flint River; Alabama Bass grew faster than Redeye Bass. Growth of both species was inversely related to discharge variation in five of six reach–species combinations; the only exception was for Redeye Bass in the less-regulated reach. Results from this study suggest that variable discharge has less influence on successful reproduction of black bass than was reported for other fishes, but growth may be more affected by discharges resulting from anthropogenic sources than those associated with the natural regime.
... Central Valley Chinook Salmon natural production has been greatly reduced due to extensive dam-building and other eco- The survival of Chinook Salmon smolts transiting the Delta generally declines as a function of declining river flow and increasing water temperature, historically reaching nearly zero by the time waters warmed to 20°C (Kjelson & Brandes, 1989). It is within the physiological capacity of local salmon stocks to survive in water of 20°C (Marine & Cech, 2004), and from a bioenergetics perspective, it can be advantageous for them to do so if they have enough food (Sommer et al., 2001). Therefore, low survival at 20°C is widely believed to be caused by predation. ...
... They may be migrating earlier to escape the intensifying threat posed by multiple predators. We consider this worthy of closer research attention given the shallow-water habitat limitation salmon fry often face (Sommer et al., 2001) and evidence for strong density-dependent mortality in natal tributaries under lower flow conditions (Sturrock et al., 2019). ...
• Predator–prey systems face intensifying pressure from human exploitation and a warming climate with implications for where and how natural resource management can successfully intervene. We hypothesized young salmon migrating to the Pacific Ocean face a seasonally intensifying predator gauntlet when warming water temperature intensifies a multiple predator effect (MPE) from Striped Bass Morone saxatilis and Largemouth Bass Micropterus salmoides. We evaluated this hypothesis using data synthesis and simulation modeling.
• Contemporary studies based on acoustically tagged fish reaffirmed older observations that Chinook Salmon smolts must transit the Delta before water temperature reaches 20°C or mortality will be nearly 100%. Striped Bass attack rates on tethered smolts were insensitive to distance from shore and water temperature, whereas Largemouth Bass attack rates were highest near shorelines in warm water, supporting the temporal aspect of the hypothesis. Whether the combined effects of the two predators produce an MPE remains unconfirmed due to limitations on quantifying salmon behavior.
• We used multiple simulation models to try to reconstruct the empirical relationship between smolt survival and water temperature. Simulations reinforced attack rate results, but could not recreate the temperature dependence in smolt survival except at higher than observed temperatures. We propose three hypotheses for why and recommend discerning among them should be a focus of research.
• We found significant linear relationships between monthly mean inflow to the Delta from each of its two largest tributaries and monthly mean water temperatures along associated salmon migration routes, but these relationships can be nonlinear, with most of the correlation occurring at low inflows when water temperature is largely controlled by air temperature and day length. As the global climate warms, changed circumstances in predator–prey relationships may present important challenges when managing species vulnerable to extinction in addition to presently more abundant species.
... Yet it has large tidal excursions (much of the tidal water moving up the Sacramento River channel winds up there), a complex, branching channel pattern, and is a known spawning and rearing area for delta smelt and probably for other native fish as well. It is the outlet for water draining from the Yolo Bypass, with potential major interactions ranging from exporting nutrients to rearing juvenile salmon (Sommer et al., 2001a and2001b). Arguably, this region is most like the historical Delta, although many of its channels have been leveed or otherwise altered. A "natural" levee failure experiment exists there now (Liberty Island, which flooded in 1998) and much of the 1. ...
... The bypass presents some major opportunities for ecosystem manipulation (e.g., by gating the Fremont Weir), which are currently under discussion (Department of Fish and Game, 2006). It is also a major spawning and rearing area for splittail and other native fish, a rearing area for juvenile salmon, and a potential source of nutrients for Delta food webs (Sommer et al., 2001a and2001b). This region could act as a major interface with the Delta ecosystem, especially in the Cache Slough region, a role that will likely grow in importance, both through deliberate manipulations and through the increased frequency of flooding as a result of climate change. ...
... This potential negative influence of in-channel bars on rearing habitat availability at moderately high flows may reverse, however, as discharge continues to increase to higher levels not considered in this study. Any reduction in channel conveyance will encourage floodplain inundation at lower discharges than otherwise, greatly increasing of the availability of productive rearing habitat in overbank areas (Sommer et al. 2001). ...
... Both larval and adult chironomids have been observed to be a common food source and potential source of xenobiotics for a variety of fish, predatory aquatic insects, and bats (Puig Montserrat et al., 2020;Shadrin, et al., 2021). Gut content studies have found that the dominant prey items in juvenile Chinook salmon (Oncorhynchus tshawytscha) in northern California are from the taxon Diptera, primarily members of the family Chironomidae (Sommer et al., 2001b;Goertler et al., 2018). During flooding years, studies have found that dipterans comprise up to 78% of juvenile Chinook diet in the Yolo bypass, dominated by adult chironomids (Sommer et al., 2001a;Anzalone et al., 2022). ...
... The energy density of insects is generally higher than benthic or pelagic prey in the LCRE (Fig 2), making them an optimal prey item. Chinook Salmon grew faster on dipterans in floodplain habitat than on zooplankton from mainstem river habitats [69]. Zooplankton dominated diets of juvenile salmon sampled along exposed shorelines of the mainstem Columbia River, while insects were the important prey in protected backchannel environments [70], suggesting enhanced insect availability near wetland sources. ...
Tidal freshwater wetlands linking terrestrial, riverine, and saline habitats are critical areas for material processing and exchange. Once historically widespread, herbaceous marsh and forested tidal freshwater wetlands especially are now highly degraded worldwide. Additionally, quantitative assessments of hydrology and material exchange from these systems are lacking compared to lotic and estuarine (saltmarsh) habitats. Here we investigate macroinvertebrate and energy export from tidal marsh and forested wetlands and consider potential benefits from this ecological process to endangered Pacific salmon in a large tidal freshwater system, the Columbia River (USA). Macroinvertebrate (salmon prey) concentration, water velocity, and discharge were measured at several wetland habitat types (forested swamp, emergent marsh, and restored marsh). We used these data to compute prey flux and transport metrics. Then, applying literature values to calculate prey energy equivalents and juvenile salmon metabolic requirements, we estimated the potential energy subsidy available to juvenile salmon. Numerically, larval stages of aquatic insects were the predominant type of prey exported from the wetlands, with Diptera chironomid fly abundance exceeding other groups. Energetically, however, non-chironomid dipterans and hemipteran prey comprised most of energy transport due to their higher energetic content (energy density × mean weight). We determined the prey energy transported from the sampled tidal channels was sufficient to meet energetic needs of tens to thousands of juvenile salmon per day, depending on prey production and hydrography. The prey taxonomic composition differed among organisms exiting forested swamp, emergent marsh, and restored marsh habitats with corresponding differences in energy transport, but all habitat types supported similar numbers of juvenile salmon. We conclude that macroinvertebrate prey exported from varied tidal freshwater wetlands likely provide significant benefits to juvenile salmon over a larger ecological footprint than the wetland area would suggest.
... Ряд авторов справедливо отмечают, что далеко не все бентосные организмы в условиях валунных грунтов доступны для молоди лососевых рыб (Ward, 1992;DeWalt, Stewart, 1995). Поскольку эти рыбы основную часть пищевых объектов потребляют из дрифта, то его количественная оценка может дать более точное представление о кормовой базе (Шустов, 1983;Nacano, 1995;Веселов, Калюжин, 2001;Sommer et al., 2001;Есин и др., 2009). Вместе с тем известно, что дрифт беспозвоночных в реках является чрезвычайно динамичным явлением и количество сносимых организмов варьирует в широких пределах в зависимости от времени суток, сезона и даже облачности (Шубина, 1986;Богатов, 1994;Самохвалов, 1995;Hieber et al., 2003;Robinson et al., 2004;Барышев, Веселов, 2007;Есин и др., 2009;Кашеваров, Яковлев, 2015;Богатов, Федоровский, 2017). ...
В монографии обобщены результаты многолетних исследований макрозообентоса водотоков Восточной Фенноскандии, относящихся к водосборным бассейнам Балтийского, Белого и Баренцева морей. Рассмотрено влияние природных и антропогенных факторов на таксономический состав, обилие и трофическую структуру сообществ донных беспозвоночных. Представлены результаты изучения пространственной и сезонной динамики макрозообентоса и дрифта. Показано, что северное расположение,
порожистый характер русла и наличие множества проточных озер в реках Восточной Фенноскандии обусловливают особую структуру макрозообентоса, для которой характерны преобладание литореофильной фауны, качественная обедненность, многократное варьирование количественных показателей по участкам и фрагментированная продольная организация. Значительное влияние оказывают также низкая минерализация и олиготрофный характер речных вод региона, которые определяют чувствительность
структуры сообществ донных беспозвоночных к поступлению биогенных и органических веществ природного и антропогенного происхождения.
Для гидробиологов, ихтиологов, зоологов, экологов и других специалистов, занимающихся вопросами охраны и рационального использования природных ресурсов, а также преподавателей вузов, студентов и аспирантов.
... However, this doesn't explain significant differences in condition between salmon captured at Scout Island and Highway 99. Though there are a multitude of factors that can effect fish growth and condition (Clarke et al. 1981;Morgan and Iwama 1991;Sommer et al. 2001), water temperature is commonly accepted as having a significant impact (Kjelson et al. 1981). Analysis of temperature profiles recorded at each weir site in 2016 indicate a significant interaction between temperature and date (one-way ANCOVA; p < 0.001). ...
San Joaquin River Juvenile Chinook salmon Monitoring 2016, California, USA
... Studies for portions of the Chehalis basin also show that floodplain reconnection in the upper Chehalis and Newaukum Rivers might decrease flood peaks by 3%-16% depending on tributary and flood recurrence interval (Abbe et al., 2016(Abbe et al., , 2020, which is generally half or less of the projected climate change increase. Moreover, off-channel habitats such as alcoves and wetlands afford fish an escape from high-velocity flood flows (Bell et al., 2001;Waples et al., 2009), and such habitats also increase growth and survival throughout winter rearing for a variety of species (Nickelson et al., 1992;Ogston et al., 2015;Sommer et al., 2001). Low flow decreases can be mitigated where water withdrawals can be reduced, or where increased water storage via beaver dams or beaver dam analogs is possible (Kendy et al., 2018;Weber et al., 2017). ...
A pressing question for managing recovery of depressed or declining species is: Can habitat restoration increase resilience to climate change? We addressed this question for salmon populations with varying life histories, where resilience is defined as maintaining or increasing population size despite climate change effects. Previous studies indicate that several interrelated mechanisms may influence salmon resilience to climate change, including improving either habitat capacity or productivity, and ameliorating climate change effects on flood flow, low flow, or stream temperature. Using the Habitat Assessment and Restoration Planning (HARP) model, we first examined the relative importance of each mechanism for increasing salmon population resilience by comparing projected salmon spawner abundance for seven individual restoration action types under current and projected mid‐ and late‐century climates. We found that restoring habitats with the greatest restoration potential most increased resilience for all species, but the most beneficial restoration actions varied among species. Increasing habitat capacity and productivity both contributed to resilience, and ameliorating climate change effects was important in a few subbasins where the restoration opportunity was widespread. Cool‐water climate refuges contributed to resilience of some subpopulations by reducing late‐century declines in spawner abundance even without restoration. We also modeled more complex habitat restoration strategies comprised of several restoration action types at varying restoration intensities and found that the restoration action types and level of restoration effort needed to increase resilience varied among species. Less vulnerable species such as coho salmon responded well to four restoration actions (floodplain reconnection, wood augmentation, increased shade, and increased beaver ponds) applied at low restoration intensity and over a large area. More vulnerable species such as spring Chinook responded to fewer action types (floodplain reconnection, wood augmentation, and increased shade), but at much higher intensity and over a much smaller area. The analysis also identified important locations for each restoration action type for each species, which helps focus habitat restoration effort on areas that are likely to provide the largest increases in resilience.
... Invertebrate communities on these floodplains tend to be dominated by cladocerans, particularly large-bodied species such as Daphnia pulex that thrive in their relatively warm, slow-moving waters (Davidson et al. 2000;Corline et al. 2021). Both of these floodplains support exceptionally high growth rates in juvenile salmon that are experimentally reared on them (Sommer et al. 2001;Jeffres et al. 2008;Katz et al. 2017), resulting in considerable interest in enhancing fish passage opportunities to enable more frequent volitional access to them. However, the extent to which these floodplains subsidize the downstream food web is unknown. ...
Context
Cross-boundary subsidies create important growth opportunities for a range of taxa. In modified river systems, remnant patches of floodplain and flood bypasses become ephemeral hotspots of zooplankton production, however, the extent to which these prey items are (or could be) transported downstream is unclear.
Objectives
We investigated the diet of juvenile salmon under varying hydroclimatic conditions to assess the importance of floodplain-produced prey subsidies in an otherwise food-scarce region.
Methods
Juvenile salmon (n = 3033) and zooplankton were sampled across the California Central Valley Sacramento-San Joaquin River Delta in 2014–2018, incorporating a range of climatic conditions including drought and flood. Salmon stomach fullness and diet composition, and ambient zooplankton densities were used to assess spatiotemporal patterns in prey production and consumption.
Results
Floodplain-produced cladocerans provided ephemeral food pulses to juvenile salmon in downstream riverine habitats. Salmon had the fullest stomachs in wetter years (2016–2017) and the emptiest stomachs in the final year of a multi-year drought (2015). Cladoceran abundances in the water column and salmon diets were highest during wet periods and below floodplains, and decreased with increasing distance downstream, consistent with flow-mediated trophic subsidies.
Conclusions
These data emphasize the importance of maintaining diverse, interconnected habitats to support resilient fish populations and the potential for managing floodplains to boost prey production and delivery. Here, the inundation of a flood bypass (or lack of) played a pivotal role shaping the juvenile salmon foodscape. As freshwater ecosystems are increasingly transformed by large-scale engineering, it is important to coordinate infrastructure, habitat and flow modifications to maximize climate resilience and trophic benefits to target species.
... Offchannel features such as side channels, backwater alcoves and other intermittently connected features have been constructed to mimic naturally occurring conditions common to floodplains. Studies have found that off-channel features provide diverse habitat, such as thermal variability through stratification, diverse food availability, and protection from predation during vulnerable life stages (Jeffres et al. 2008, Sommer et al. 2001. ...
The Trinity River Restoration Program has made efforts to improve juvenile salmonid rearing habitat degraded by legacy hydraulic mining and dam operations through habitat restoration and adaptive flow management. We assessed how restored off-channel habitats benefit the growth of juvenile Chinook Salmon compared to mainstem habitats in locations just downstream of Lewiston Dam and locations farther downstream affected by accretionary flows near Junction City. We hypothesized that 1) juvenile Chinook Salmon growth is greater in off-channel features during spring rearing so much that 2) those off-channel benefits would persist through the summer and fall for greater survival upon historical timing of November through December flow events that reconnect off-channel features to the mainstem and its resources. We compared temperature and juvenile growth in off-channel sites paired with mainstem sites with continuous temperature data collection and four sequential fish length and weight measurements from May to mid-June. Temperature regimes in the mainstem Trinity River are influenced by dam releases and were mostly below the optimal range (13.0–16.5°C) for juvenile growth. Temperatures in off-channel features offered warmer, more thermally diverse conditions into late spring during 2019, with some features maintaining optimal ranges, but some becoming lethally warm for extended durations (>24°C) in spring of 2020. Greater fish growth was observed in mainstem habitats compared to off-channel habitats. Greater fish growth was observed in warmer mainstem sites in downstream locations compared to cooler upstream mainstem locations. However, insufficiently sealed enclosures allowed fish to escape some experimental enclosures, compromising our study design. The loss of data at several sites did not allow for a formal analysis, resulting in a presentation of results as largely descriptive and qualitative. We recommend this study be repeated in a wetter water year to provide contrast to the findings presented herein, particularly with respect to the unexpected lower growth in thermally optimal conditions in off-channel features.
... The coincidence of high flows and emergence can result in lower survival (Jensen & Johnsen, 1999) and may also increase downstream dispersal (Saltveit et al., 1995). Streamflow also controls the accessibility and profitability of floodplain habitats (Baldock et al., 2016), which can provide velocity refuge and enhanced growth opportunities for juvenile salmon (Jeffres et al., 2008;Sommer et al., 2001). Thus, the timing of emergence relative to floodplain inundation may influence habitat use and the benefits floodplains provide to juvenile salmon. ...
Many salmonid‐bearing rivers exhibit thermal and hydrologic heterogeneity at multiple spatial and temporal scales, but how this translates into spatiotemporal patterns of fry emergence is poorly understood. Understanding this variability is important because emergence timing determines the biophysical conditions fish first experience (e.g., temperature, flow, and food supply), thereby influencing growth opportunities and survival during this critical life stage. We predicted spring Chinook Salmon (Oncorhynchus tshawytscha) emergence phenology across four northeastern Oregon subbasins over 5–9 years using empirical spawning and temperature data. We then related interannual emergence timing estimates to juvenile salmon size and growth rates at consistent sampling locations. There were clear longitudinal patterns of predicted emergence timing in each subbasin: The shape of these patterns was consistent among years, but not among subbasins. In two subbasins, emergence occurred progressively later with distance upstream, whereas in the other two subbasins emergence was earliest at upstream sites. Within each year, median emergence dates among sites within each subbasin ranged between 44 and 58 days. This spatial variation was comparable to interannual variation, with median emergence dates for a given location in each subbasin ranging between 47 and 74 days among years. Contrary to our expectations, juvenile salmon were not larger in years with earlier emergence, owing to slower estimated spring and summer growth rates compared to years with later emergence. Despite large interannual variation in estimated emergence dates, these results suggest that other factors (e.g., stream flow, temperature, and density‐dependence) were more important than growth duration in determining juvenile salmon growth rates and size among years. We demonstrated considerable spatial and interannual variation in emergence phenology within these subbasins. Understanding how this variation translates to spatiotemporal patterns of juvenile salmon habitat use, growth, and survival has important implications for guiding restoration efforts and understanding how climate change may impact these populations.
... Compared to current conditions, the historic Delta likely presented a relatively safe migration corridor for Chinook Salmon and Steelhead, with rich and ample floodplain habitat supporting additional growth before the stressful transition to marine waters (Sommer et al. 2001). In contrast, in the modern Delta, much of this floodplain habitat has been reclaimed as agricultural lands, and the remaining waterways are deeper, highly channelized, and inhabited by large populations of non-native predators, including Striped Bass, Black Bass and Catfish (Young et al. 2018;Lindley et al. 2019). ...
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. We use a quantile regression forest approach to create a risk forecasting tool, which can inform adjustments of diversions based on near real-time predictions. Models were trained using historical entrainment data (Water Years 1999–2019) for Sacramento River winter-run Chinook Salmon or Central Valley Steelhead and a suite of environmental and water operations metrics. A range of models was developed; their performance was evaluated by comparison of a quantile loss metric. The models were validated through examination of partial dependence plots, cross-validation procedures, and further evaluated through WY 2019 pilot testing, which integrated real-world uncertainty in environmental parameters into model predictions. For both species, the strongest predictor of loss was the previous week’s entrainment loss. In addition, risk increased with higher water exports and more negative Old and Middle Rivers (OMR) flows. Point estimates of loss were modestly correlated with observations (R2 0.4 to 0.6), but the use of a quantile regression approach provided reliable prediction intervals. For both species, the predicted 75th quantile appears to be a robust and conservative estimator of entrainment risk, with overprediction occurring in fewer than 20% of cases. This quantile balances the magnitude of over- and under-prediction and results in a low probability (< 5% of predictions) of unexpected high-take events. These models, and the web-based application through which they are made accessible to non-technical users, can provide a useful and complementary approach to the current system of managing entrainment risk.
... The geomorphic survey results (i.e., bank height ratio and entrenchment ratio measurements) validate that channelfloodplain connections were restored in Black Slough and Crystal Creek where flows above bankfull discharge spill onto the historical floodplain surfaces. Floodplain inundation at flows greater than the bankfull discharge provides important ecological functions (Opperman et al., 2010) and can be critical for the survival of salmonids and the growth of juvenile salmonids (Junk et al., 1989;Sommer et al., 2001). Increased floodplain inundation has numerous positive effects on stream and floodplain biota, invertebrates, vertebrates, plant communities, nutrients, and inorganic and organic fractions (Junk et al., 1989). ...
In the face of climate change and dwindling water supplies, this long‐term monitoring study examines the effectiveness of restoring two incised and degraded streams (Crystal Creek and Black Slough) to benefit livestock ranching and wild trout populations in a spring creek and wetland complex, central Idaho, USA. By raising the incised streambeds and connecting to historical floodplains, the restoration aimed to raise groundwater levels to create subsurface saturation conditions to sustain grazing forage and hay production without flood irrigation; diverted flows from the Big Wood River previously used for flood irrigation were instead routed through the restored systems. The restoration used natural channel design methods to reconstruct 5.2 km of Black Slough and 8.4 km of Crystal Creek to emulate a downstream reference reach (Willow Creek); within the relic incised channels, off‐channel oxbow ponds and wetlands were created while filling other segments. Additionally, screened gravels were placed in the reconstructed channels. We monitored before–after restoration changes in channel morphology, groundwater levels, wetlands, instream flows, spawning substrates and redds, fish populations, and invertebrates for the restored creeks and reference reach over 10+ years. Following restoration, average groundwater levels increased by 0.35 m, mean annual flows at Willow Creek (receiving stream) increased from 0.64 to 1.11 m3/s, and average days per year that baseflows were below 0.28 m3/s decreased from 44.5 to 5.4 despite a decrease in average annual precipitation (16.97 to 11.53 cm). Moreover, residual pool depths increased (<0.18 to >0.90 m), spawning substrate sizes increased (0.1 to 19.0 mm), and egg‐to‐fry trout survival rates increased from <20% to >90%. Six years after restoration, fish diversity increased from three to seven species, matching reference conditions. We also found dramatic increases in Brown Trout and Rainbow Trout redd counts (7 to 161 and 17 to 143, respectively) and relative abundance (0.013 to 1.166 trout/m and 0.029 to 0.222 trout/m, respectively). Invertebrate indices of restoration effectiveness were positive for both restored streams but negative for the reference reach. Overall, this study exemplifies how restoration reduced consumptive water use, created sustainable streams with hydrological connections and ponds and wetlands, and improved trout populations.
... Together, riverine floodplains and tidal marshes are critical habitats that support splittail populations at different life stages. These shallow wetland habitats, connected by riverine corridors, also provide important foraging (Goertler et al. 2018) and growth opportunities (Sommer et al. 2001) to outmigrating juvenile Chinook salmon (Oncorhynchus tshawytscha), particularly for the numerous small fish that leave their natal stream soon after emergence (Phillis et al. 2018). ...
Ecosystem management and governance of cross-scale dependent systems require integrating knowledge about ecological connectivity in its multiple forms and scales. Although scientists, managers, and policymakers are increasingly recognizing the importance of connectivity, governmental organizations may not be currently equipped to manage ecosystems with strong cross-boundary dependencies. Managing the different aspects of connectivity requires building social connectivity to increase the flow of information, as well as the capacity to coordinate planning, funding, and actions among both formal and informal governance bodies. We use estuaries in particular the San Francisco Estuary, in California, in the United States, as examples of cross-scale dependent systems affected by many intertwined aspects of connectivity. We describe the different types of estuarine connectivity observed in both natural and human-affected states and discuss the human dimensions of restoring beneficial physical and ecological processes. Finally, we provide recommendations for policy, practice, and research on how to restore functional connectivity to estuaries.
... temperature, dissolved oxygen, salinity) that are highly variable in space and time and often different to those of the river channel (Amoros & Bornette, 2002;Tonolla et al., 2010). When compared to the main channel, warmer habitat temperatures on floodplains may enhance growth and hence affect survival and recruitment of some species (Gutreuter et al., 1999;Schramm & Eggleton, 2006;Sommer et al., 2001). During drier, non-flood periods, harsh physical conditions on floodplains can interact with behavioural and physiological traits to reduce the survival rates of some species over others (McNeil & Closs, 2007;Stoffels et al., 2017). ...
Lateral Hydrological Connectivity (LHC) has been extensively fragmented in river–floodplain ecosystems of the world. Uncertainties about how LHC affects fishes are great, impeding the design of effective rehabilitation strategies. Existing conceptual frameworks do not provide sufficient mechanistic detail to support the novel decision problems river managers face. We offer a framework of how LHC affects fishes in river–floodplain ecosystems that is, process‐based, integrates all life‐stages and is spatial; these features, we argue, are required to assess risks and opportunities associated with different LHC rehabilitation strategies. Within river–floodplain segments, LHC affects population processes through five ‘effect‐classes’: effects of floodplain habitat (1) and channel habitat (2); effects of material subsidies from the floodplain to the channel (3) and vice versa (4); and effects of connectivity on lateral dispersal (5). The relative influence of these effect‐classes on processes varies among species and life‐stages. At the scale of the drainage basin, inter‐segment variation in geomorphology generates a longitudinal source‐sink structure to habitat quality and quantity, pointing to a need to better understand fish metapopulation dynamics in river–floodplain ecosystems. Given the significant investment in trying to restore river–floodplain ecosystems, we highlight potentially costly and ineffective LHC management decisions. These include certain heavily engineered LHC rehabilitation strategies that do not promote critical population processes at a local scale, and at basin scales implementing strategies that do not facilitate the metapopulation processes that promote species’ persistence.
... These habitats are engines of productivity that increase food production, allowing fish to feed successfully while minimizing energy expenditures on foraging . Freshwater floodplain habitats above the tidal excursion of the SFE have shown elevated levels of zooplankton biomass and correspondingly high Chinook salmon growth rates compared to local riverine habitats (Sommer et al. 2001;Jeffres et al. 2008;Katz et al. 2017). While these upriver floodplain habitats have been recognized for their benefits to salmon, wetland habitats in the tidal estuarine portion of this large deltaic ecosystem have received less attention. ...
... However, they did not have diking information and were unable to consider floodplain forests and Sumas lake within their estimates. The loss of floodplain habitat may have important implications for salmon productivity in the Lower Fraser system, particularly for coho and Chinook, which rely on these habitats for rearing and gain an advantage in the form of increased growth rates relative to other areas (Brown and Hartman 1988, Sommer et al. 2001. In California, Chinook salmon benefit from the use of seasonally flooded farmlands (Katz et al. 2017) and ephemeral floodplain habitats (Jeffres et al. 2008) in the form of increased growth rates and improved body condition. ...
Loss of connectivity caused by anthropogenic barriers is a key threat for migratory freshwater species. The anadromous life history of salmonids means that barriers on streams can decrease the amount of habitat available for spawning and rearing. To set appropriate targets for restoration, it is important to know how different populations have been impacted in terms of the location and extent of historically available habitat that has been lost or has become inaccessible. Using mapped and predicted barriers to fish passage in streams and diking infrastructure, the amount of both floodplain and linear stream habitat that remains accessible today was estimated for 14 populations of salmon in the Lower Fraser River, British Columbia, Canada’s most productive salmon river. To place these estimates within a historical context, the floodplain area was estimated using vegetation records from the 1850s, and lost streams were estimated using a digital elevation model‐derived stream network. To bolster areas where little mapping has been done, current barrier data were used to predict locations likely to have barriers. Accessibility to floodplain was poor across the entire region with only 15% of the historical floodplain remaining accessible. Linear stream habitat ranged in accessibility from 28% to 99% across populations based on mapped barriers. Inclusion of predicted barriers revealed an additional 33 km of potentially inaccessible stream habitat and the modeled stream network located approximately 1700 km of stream length that has been completely lost. Comparing habitat accessibility and barrier density against the assessed status of populations revealed insights useful for understanding the impact of barriers on spawning and rearing and guiding the allocation of restoration effort. Applying methods for addressing missing data, such as lost streams and unmapped barriers, was essential for estimating the accessibility of habitat within a historical context. While much emphasis has been placed on the role of marine conditions in wild Pacific salmon recovery, the magnitude of habitat loss in the Fraser cannot be ignored and suggests it is a major driver of observed salmon declines.
... Amphibians require water submersion until the completion of their aquatic life history stage in early summer (Trush et al., 2000). Jager (2014) demonstrated that seasonal, floodplain-inundating flow pulses might benefit salmon production through accelerated fish growth, facilitated by higher water temperature and prey availability (see also Opperman et al., 2010;Sommer et al., 2001Sommer et al., , 2005. Although the erosive forces of flood pulses present serious abiotic stressors, native species have adapted to their occurrence (Hering et al., 2004;Marchetti and Moyle, 2001;Valdez et al., 2001;Yarnell et al., 2015). ...
Free-flowing rivers support diverse, complex and dynamic ecosystems, as well as provide societal and economic services. Globally, however, the water flow of many rivers has been regulated by hydropower or other sources. Flow modification affects crucial ecosystem functions and processes, and organism’s capacity to fulfil its life cycle requirements. In light of these widespread effects, it is urgent to mitigate ecological impacts caused by existing water infrastructures. To achieve environmental objectives, as well as to manage water uses in a sustainable way, a thorough understanding of ecological responses to hydrological alterations on different temporal levels (e.g., environmental flow, hydropeaking) is essential. This work aims to establish holistic approaches for restoring flows in modified rivers, and to develop environmental flows able to sufficiently mitigate the ecological effects of short-term and annual flow modifications in fluvial ecosystems.
This thesis disentangles the effects of multiple stressors and shows that flow regulation is a primary predictor of fish populations. Moreover, by assessing flow-ecology relationships on annual, seasonal, and sub-daily levels, this work identifies fundamental principles to implement flow restoration measures in rivers affected by water abstraction and hydropeaking. While more dynamic flows are generally recommended as environmental flows, flow restrictions are needed for hydropeaking mitigation. Regarding the latter, a seasonal framework for hydrological mitigation based on fish life-history stages is established, and thresholds are synthesized.
Overall, this thesis advances the establishment of guidelines for successful flow restoration in river systems affected by competing water uses by establishing holistic flow restoration schemes and by subsuming quantitative and qualitative hydropeaking thresholds. Moreover, this thesis sets the topic of flow restoration into the broader context of hydromorphological river rehabilitation. Hence, this work contributes to a more balanced discussion on trade-offs between societal and environmental water uses.
... threshold, which could be evidence that fish utilizing this alternate route experienced decreased survival compared to fish remaining in the Sacramento River. While flood bypasses are generally considered to be high-quality rearing habitat for juvenile salmon (Sommer et al. 2001), there is little known about the relative survival of fish utilizing these habitats. Travel times for fish above the high threshold were significantly higher and are more widely distributed than for fish just below this threshold (Fig. 8), with fish taking up to 27 d to transit the region of interest. ...
Water is a fundamental resource in freshwater ecosystems, and streamflow plays a pivotal role in driving riverine ecology and biodiversity. Ecologically functional flows, managed hydrographs that are meant to reproduce the primary components of the natural hydrograph, are touted as a potential way forward to restore ecological functions of highly modified rivers, while also balancing human water needs. A major challenge in implementing functional flows will be establishing the shape of the managed hydrograph so as to optimize improvements to the ecosystem given the limited resources. Identifying the shape of the flow–biology relationship is thus critical for determining the environmental consequences of flow regulation. In California's Central Valley, studies have found that increased streamflow can improve survival of imperiled juvenile salmon populations during their oceanward migration. These studies have not explored the potential nonlinearities between flow and survival, giving resource managers the difficult task of designing flows intended to help salmon without clear guidance on flow targets. We used an information theoretic approach to analyze migration survival data from 2436 acoustic‐tagged juvenile Chinook salmon from studies spanning differing water years (2013–2019) to extract actionable information on the flow–survival relationship. This relationship was best described by a step function, with three flow thresholds that we defined as minimum (4259 cfs), historic mean (10,712 cfs), and high (22,872 cfs). Survival varied by flow threshold: 3.0% below minimum, 18.9% between minimum and historic mean, 50.8% between historic mean and high, and 35.3% above high. We used these thresholds to design alternative hydrographs over the same years that included an important component of functional flows: spring pulse flows. We compared predicted cohort migration survival between actual and alternative hydrographs. Managed hydrographs with pulse flows that targeted high survival thresholds were predicted to increase annual cohort migration survival by 55–132% without any additions to the water budget and by 79–330% with a modest addition to the water budget. These quantitative estimates of the biological consequences of different flow thresholds provide resource managers with critical information for designing functional flow regimes that benefit salmon in California's highly constrained water management arena.
... PANPP is estimated potential aquatic net primary production in the Sacramento-San Joaquin Delta comparing historical and modern landscapes and a future landscape after habitat restoration for the wet-year scenario. C flows to herbivores and to detritus production were estimated using median values of the fractions of NPP routed to those pathways from the meta-analysis of Cebrian and Lartigue (2004 salmonids (Sommer et al., 2001). This management action depends upon water availability, and its long-term sustainability is uncertain given projected shifts toward drier spring months as global warming proceeds (Knowles et al., 2018). ...
Humans are changing the Earth's surface at an accelerating pace, with significant consequences for ecosystems and their biodiversity. Landscape transformation has far-reaching implications including reduced net primary production (NPP) available to support ecosystems, reduced energy supplies to consumers, and disruption of ecosystem services such as carbon storage. Anthropogenic activities have reduced global NPP available to terrestrial ecosystems by nearly 25%, but the loss of NPP from wetland ecosystems is unknown. We used a simple approach to estimate aquatic NPP from measured habitat areas and habitat-specific areal productivity in the largest wetland complex on the USA west coast, comparing historical and modern landscapes and a scenario of wetland restoration. Results show that a 77% loss of wetland habitats (primarily marshes) has reduced ecosystem NPP by 94%, C (energy) flow to herbivores by 89%, and detritus production by 94%. Our results also show that attainment of habitat restoration goals could recover 12% of lost NPP and measurably increase carbon flow to consumers, including at-risk species and their food resources. This case study illustrates how a simple approach for quantifying the loss of NPP from measured habitat losses can guide wetland conservation plans by establishing historical baselines, projecting functional outcomes of different restoration scenarios, and establishing performance metrics to gauge success.
... Non-linear increases in marine survival occur when O. mykiss smolts achieve minimum fork lengths of 150 mm . Consequently, rapid growth in intermittent lagoonal estuaries prior to ocean entry is critical for survival, similar to the role that inland floodplains provide to juvenile O. tshawytscha (Sommer et al. 2001. As the productive capacity of rivers and streams degrade, the importance of these stop-over nursery habitats likely increases. ...
In this dissertation I investigate the impacts of artificial and natural watershed disconnection on the management and ecology of valued native California fishes. I explore the subject at regional and local scales and pay particular attention to the consequences of river discontinua on juvenile rearing and habitat use patterns for multiple populations of Pacific salmonids with conservation and economic importance. Scientific inquiry in my study systems was initially motivated by the intention to comprehend the potential direct and indirect links between connectivity loss and collapsed hatchery-supported Chinook salmon (Oncorhynchus tshawytscha) commercial and recreational fisheries and recurring widespread animal mass mortality events involving the take of threatened O. mykiss at one of California's few remaining estuary-saltmarsh habitat complexes. My research coincided with a severe and historic drought and the timing offers a special opportunity to better understand the potential effects of climate change on salmon hatchery management and estuarine fish ecology in California.
... Reestablishing connections between hydrologically disconnected lands and tidal-fluvial systems is a high priority for restoration projects because of the direct (onsite) and indirect (offsite) contributions that shallow water wetland ecosystems provide to food webs supporting juvenile fishes and other wetland-dependent species (Johnson et al., 2018). Hydrologic restoration of floodplain wetlands benefits fish, especially juveniles (e.g., Sommer et al., 2001;Bottom et al., 2005;David et al., 2014). ...
In intertidal wetlands, habitat access by out-migrating juvenile anadromous fishes, such as salmon (Oncorhynchus spp.), is influenced by both physical and biological factors. Physical limits are set by inundation patterns and water quality parameters, while biological bounds are determined by species-specific migration timing and seasonal residency behaviors. We developed a new metric called the fish habitat opportunity index to quantify the total time (h) and volume-time (m³-h) per calendar year that salmon could access a given wetland, based on periods of inundation (volume) and seasonal migration period (time). The basic assumption of the index is that the volume of water inundating a restored wetland and the amount of time the wetland is inundated are both positively related to ecological benefits to juvenile salmon in terms of foraging success, growth, condition, and refuge from predators. We tested this index using data collected at a reconnected tidal freshwater wetland area in the lower Columbia River and estuary during 2006–2009. We found the wetland to be accessible to different salmon species for different lengths of time and periods of the year. On average, Chum Salmon (O. keta) had remarkably consistent opportunities to use wetland marsh habitat over the four years sampled, while opportunities were more variable for Chinook Salmon (O. tshawytscha), and Coho Salmon (O. kisutch). Inundation varied nonlinearly with tidal height. Fish had access to the productive marsh edge for approximately 40–50% of the time during out-migration periods. The fish habitat opportunity index is applicable to wetland systems throughout the tidal-fluvial continuum. It provides a metric for assessing fish habitat opportunity that is more realistic than simple wetted-area calculations or species presence/absence data. Most importantly, the fish habitat opportunity index affords a method for a priori comparison among potential restoration sites to help resource managers predict the likely relative effects on habitat opportunity from restoration aimed at benefiting juvenile anadromous fishes. Maximizing the fish habitat opportunity index should positively affect fish populations that use tidal-fluvial wetlands as vital habitats in their life cycle.
... These habitats are engines of productivity that increase food production, allowing fish to feed successfully while minimizing energy expenditures on foraging . Freshwater floodplain habitats above the tidal excursion of the SFE have shown elevated levels of zooplankton biomass and correspondingly high Chinook salmon growth rates compared to local riverine habitats (Sommer et al. 2001;Jeffres et al. 2008;Katz et al. 2017). While these upriver floodplain habitats have been recognized for their benefits to salmon, wetland habitats in the tidal estuarine portion of this large deltaic ecosystem have received less attention. ...
Loss 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.
... This is consistent with the current understanding that the relatively long-lived Sacramento splittail (Daniels and Moyle 1983) depend on strong year classes that are recruited during wet years when floodplain habitat is available for spawning (Sommer et al. 1997, Moyle et al. 2004. Similarly, Chinook salmon exhibited low resistance and high resilience, likely due to increased survival of juveniles in freshwater in wet years (Michel et al. 2015) and availability of highquality floodplain habitat (Sommer et al. 2001, Goertler et al. 2018. The low resistance and relatively high resilience of the native Longfin Smelt is also expected given the positive influence of freshwater flow on juvenile production Baxter 2007, Nobriga andRosenfield 2016). ...
Many estuarine ecosystems and the fish communities that inhabit them have undergone substantial changes in the past several decades, largely due to multiple interacting stressors that are often of anthropogenic origin. Few are more impactful than droughts, which are predicted to increase in both frequency and severity with climate change. In this study, we examined over five decades of fish monitoring data from the San Francisco Estuary, California, U.S.A, to evaluate the resistance and resilience of fish communities to disturbance from prolonged drought events. High resistance was defined by the lack of decline in species occurrence from a wet to a subsequent drought period, while high resilience was defined by the increase in species occurrence from a drought to a subsequent wet period. We found some unifying themes connecting the multiple drought events over the fifty‐year period. Pelagic fishes consistently declined during droughts (low resistance), but exhibit a considerable amount of resiliency and often rebound in the subsequent wet years. However, full recovery does not occur in all wet years following droughts, leading to permanently lower baseline numbers for some pelagic fishes over time. In contrast, littoral fishes seem to be more resistant to drought and may even increase in occurrence during dry years. Based on the consistent detrimental effects of drought on pelagic fishes within the San Francisco Estuary and the inability of these fish populations to recover in some years, we conclude that freshwater flow remains a crucial but not sufficient management tool for the conservation of estuarine biodiversity.
... The floodplain floods seasonally in approximately 60% of years during winter and spring. The mean depth of the floodplain is generally < 2 m, which creates broad shoal areas and provides better rearing and migration habitat for juvenile chinook salmon (Oncorhynchus tshawytscha) than adjacent river channels (Sommer et al., 2001). During summer and autumn, the Yolo Bypass maintains year-round connectivity to the SFE via a perennial riparian channel, the 'Toe Drain,' along the east side of the leveed floodplain. ...
We measured growth rates of the copepod Pseudodiaptomus forbesi in relation to food, environmental conditions and hydrology in the northern San Francisco Estuary, California, USA. We conducted 38 copepod growth-rate experiments during summers 2015–2017 at four sites in a tidal, freshwater channel that had strong gradients in environmental conditions. Copepod growth rates were measured using the artificial cohort method with an image analysis technique, and seston attributes were measured to investigate the effects of food quantity and quality on copepod growth rates. Growth rates ranging from 0.03 to 0.47 day−1 (median 0.30 day−1) and growth rates, chlorophyll, turbidity and total lipids in the channel decreased with distance downstream. Growth rates had a saturating response to chlorophyll and were generally higher than rates previously measured in larger estuarine channels, presumably because of higher chlorophyll and temperature in our study area. Growth rate was positively associated with biovolume of cyanobacteria but not with that of other major phytoplankton groups, which is consistent with a recent finding of high feeding of P. forbesi on cyanobacteria. This adds to the small but growing literature suggesting that crustacean planktons are able to overcome the nutritional deficiencies of cyanobacteria to grow and reproduce.
... This is consistent with the current understanding that the relatively long-lived Sacramento Splittail (Daniels and Moyle 1983) depend on strong year classes that are recruited during wet years when floodplain habitat is available for spawning (Sommer et al. 1997, Moyle et al. 2004. Similarly, Chinook Salmon exhibited low resistance and high resilience, likely due to increased survival of juveniles in freshwater in wet years (Michel et al. 2015) and availability of high quality floodplain habitat (Sommer et al. 2001, Goertler et al. 2018. The low resistance and relatively high resilience of the native Longfin ...
Many estuarine ecosystems and the fish communities that inhabit them have undergone substantial changes in the past several decades, largely due to multiple interacting stressors that are often of anthropogenic origin. Few are more impactful than droughts, which are predicted to increase in both frequency and severity with climate change. In this study, we examined over five decades of fish monitoring data from the San Francisco Estuary, California, U.S.A, to evaluate the resistance and resilience of fish communities to disturbance from prolonged drought events. High resistance was defined by the lack of decline in species occurrence from a wet to a subsequent drought period, while high resilience was defined by the increase in species occurrence from a drought to a subsequent wet period. We found some unifying themes connecting the multiple drought events over the fifty-year period. Pelagic fishes consistently declined during droughts (low resistance), but exhibit a considerable amount of resiliency and often rebound in the subsequent wet years. However, full recovery does not occur in all wet years following droughts, leading to permanently lower baseline numbers for some pelagic fishes over time. In contrast, littoral fishes seem to be more resistant to drought and may even increase in occurrence during dry years. Based on the consistent detrimental effects of drought on pelagic fishes within the San Francisco Estuary and the inability of these fish populations to recover in some years, we conclude that freshwater flow remains a crucial but not sufficient management tool for the conservation of estuarine biodiversity.
... Moderate rainfall and associated increases in streamflow during the summer months likely increase invertebrate drift (Naman, Rosenfeld, & Richardson, 2016), which could benefit juvenile salmon rearing in main-stem habitats. Moderate increases in flow also allow juveniles to access off-channel habitats, which can confer advantages for growth and survival due to favorable temperatures, high invertebrate production, and cross-ecosystem resource subsidies (Baldock, Armstrong, Schindler, & Carter, 2016;Huntsman & Falke, 2019;Rine, Wipfli, Schoen, Nightengale, & Stricker, 2016;Sommer, Nobriga, Harrell, Batham, & Kimmerer, 2001). At the extreme, however, heavy rains and associated high flows likely increase water velocity, turbidity, or inedible debris densities to levels that reduce drift foraging efficiency (Donofrio, Simon, Neuswanger, & Grossman, 2018;Gregory & Northcote, 1993;Neuswanger, Wipfli, Rosenberger, & Hughes, 2014). ...
The ecosystems supporting Pacific salmon (Oncorhynchus spp.) are changing rapidly as a result of climate change and habitat alteration. Understanding how—and how consistently—salmon populations respond to changes at regional and watershed scales has major implications for fisheries management and habitat conservation. Chinook salmon (O. tshawytscha ) populations across Alaska have declined over the past decade, resulting in fisheries closures and prolonged impacts to local communities. These declines are associated with large‐scale climate drivers, but uncertainty remains about the role of local conditions (e.g., precipitation, streamflow, and stream temperature) that vary among the watersheds where salmon spawn and rear. We estimated the effects of these and other environmental indicators on the productivity of 15 Chinook salmon populations in the Cook Inlet basin, southcentral Alaska, using a hierarchical Bayesian stock‐recruitment model. Salmon spawning during 2003–2007 produced 57% fewer recruits than the previous long‐term average, leading to declines in adult returns beginning in 2008. These declines were explained in part by density dependence, with reduced population productivity following years of high spawning abundance. Across all populations, productivity declined with increased precipitation during the fall spawning and early incubation period and increased with above‐average precipitation during juvenile rearing. Above‐average stream temperatures during spawning and rearing had variable effects, with negative relationships in many warmer streams and positive relationships in some colder streams. Productivity was also associated with regional indices of streamflow and ocean conditions, with high variability among populations. The cumulative effects of adverse conditions in freshwater, including high spawning abundance, heavy fall rains, and hot, dry summers may have contributed to the recent population declines across the region. Identifying both coherent and differential responses to environmental change underscores the importance of targeted, watershed‐specific monitoring and conservation efforts for maintaining resilient salmon runs in a warming world.
Uncertainties affecting the benefits of restoration project design in the Columbia River estuary identified by the Expert Regional Technical Group (ERTG) of the Columbia Estuary Ecosystem Restoration Program.
The size of an organism is an important factor for a variety of physiological and ecological processes. For fishes, larger size can increase long‐term survival and provide a population level benefit. Therefore, threatened and endangered species management often focuses on supporting high quality habitat that provides growth opportunities. There are numerous habitat characteristics that can affect growth, including food availability, temperature, and habitat complexity. Understanding how growth responds to habitat types of different quality is the first step in determining what could lead to increased growth and potentially increased individual survival. We use Bayesian techniques to determine which of the differing methods is best for modeling the effects of habitat type and temperature on growth. To apply this method, we gather data from previous studies of the growth benefits of differing habitats and temperature regimes on Chinook salmon on the Sacramento River, CA, USA. We find a consistent growth benefit of floodplain rearing across multiple studies and show that a Ratkowsky model is the best for modeling this growth data. This information can specifically help managers model and protect the endangered and threatened Chinook populations in this system and more generally understand fish growth across differing habitat types.
Climate change is intensifying the effects of multiple interacting stressors on aquatic ecosystems worldwide. 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). Based on our review, we found that the estuary is experiencing shifting baseline environmental conditions, amplification of extremes, and restructuring of physical habitats and biological communities. We present priority topics for research and monitoring, and a conceptual model of how the estuary currently functions in relation to climate variables. In addition, we discuss four tools for management of climate change effects: regulatory, water infrastructure, habitat development, and biological measures. We conclude that adapting to climate change requires fundamental changes in management.
Floodplains represent critical nursery habitats for a variety of fish species due to their highly productive food webs, yet few tools exist to quantify the extent to which these habitats contribute to ecosystem-level production. Here we conducted a large-scale field experiment to characterize differences in food web composition and stable isotopes (δ¹³C, δ¹⁵N, δ³⁴S) for salmon rearing on a large floodplain and adjacent river in the Central Valley, California, USA. The study covered variable hydrologic conditions including flooding (1999, 2017), average (2016), and drought (2012–2015). In addition, we determined incorporation rates and tissue fractionation between prey and muscle from fish held in enclosed locations (experimental fields, cages) at weekly intervals. Finally, we measured δ³⁴S in otoliths to test if these archival biominerals could be used to reconstruct floodplain use. Floodplain-reared salmon had a different diet composition and lower δ ¹³ C and δ³⁴S (δ¹³C = -33.02±2.66‰, δ³⁴S = -3.47±2.28‰; mean±1SD) compared to fish in the adjacent river (δ¹³C = -28.37±1.84‰, δ³⁴S = +2.23±2.25‰). These isotopic differences between habitats persisted across years of extreme droughts and floods. Despite the different diet composition, δ¹⁵N values from prey items on the floodplain (δ¹⁵N = 7.19±1.22‰) and river (δ¹⁵N = 7.25±1.46‰) were similar, suggesting similar trophic levels. The food web differences in δ ¹³ C and δ³⁴S between habitats were also reflected in salmon muscle tissue, reaching equilibrium between 24–30 days (2014, δ¹³C = -30.74±0.73‰, δ³⁴S = -4.6±0.68‰; 2016, δ¹³C = -34.74 ±0.49‰, δ³⁴S = -5.18±0.46‰). δ³⁴S measured in sequential growth bands in otoliths recorded a weekly time-series of shifting diet inputs, with the outermost layers recording time spent on the floodplain (δ³⁴S = -5.60±0.16‰) and river (δ³⁴S = 3.73±0.98‰). Our results suggest that δ¹³C and δ³⁴S can be used to differentiate floodplain and river rearing habitats used by native fishes, such as Chinook Salmon, across different hydrologic conditions and tissues. Together these stable isotope analyses provide a toolset to quantify the role of floodplains as fish habitats.
Aquatic weed management in the California Sacramen-to-San Joaquin Delta (Delta), and its tributaries has been conducted since 1982 by the California Department of Parks and the Recreation Division of Boating and Waterways (CDBW). The program uses chemical, physical, and biological control methods as a part of integrated pest management (IPM) in the Delta, which is approximately 28,000 ha (68,000 ac) of waterways. The CDBW targets nine invasive aquatic plant species, including water hyacinth [Eichhornia crassipes (Mart.) Solms] and Brazilian waterweed (Egeria densa Planch.). Weed management challenges, such as budget, regulatory requirements, and multiple stakeholder groups, require the program to be flexible and also aim at control of all target weeds in the Delta. An increased number of target invasive plants and trends in target plants and environmental conditions, such as high or low water flow years, have further emphasized the importance of IPM and a flexible toolset to control target invasive plants in the Delta.
This study analysed the spatial–temporal abundance and distribution of exotic Chinook salmon (Onchorynchus tsawytscha) along the shore zone of the Lapataia River in relationship with the presence of non-native brook trout (Salvelinus fontinalis) and brown trout (Salmo trutta), and native small puyen (Galaxias maculatus) during the four seasons of the year. These data were used to detect fish patchiness and spatial overlap and related to environmental characteristics to determine the habitat used by each species. Juvenile Chinook salmon was recorded only in spring and summer, showing a highly aggregated spatial distribution pattern. The native small puyen dominated fish assemblages all over the year, except in winter when brook trout showed the highest abundance. The highest overlap was detected between small puyen and Chinook salmon. Chinook salmon distribution was mainly explained by the occurrence of flood plains. Brown trout distribution was highly related to the presence of woody debris, while small puyen and brook trout showed no preferences for any environment. These results provide little evidence for habitat competition between Chinook salmon and the other native and non-native fish species. In contrast, species habitat preferences are likely shaping the current fish distribution.
Floodplains provide multiple benefits to both resident and migratory fish species, including juvenile Chinook Salmon Oncorhynchus tshawytscha, but direct comparisons of survival during migration through a floodplain versus riverine routes are scarce. The Yolo Bypass is a broad floodplain of the Sacramento River that floods in about 30% of years in response to large, uncontrolled runoff events. We analyzed data from an acoustic telemetry study conducted in winter 2016 to estimate the proportion of tagged juvenile Chinook Salmon entrained from the Sacramento River into the Yolo Bypass and their spatial distribution within the Yolo Bypass. In addition, we compared survival and travel time of Chinook Salmon that migrated through the Yolo Bypass to those migrating via alternative non‐floodplain migration routes at varying stages of a flood event that activated the Yolo Bypass. We found that entrainment into the Yolo Bypass ranged from 1% to 80% among different release groups, with the highest entrainment coinciding with the peak of the March 2016 flooding event. Survival for Chinook Salmon migrating through the Yolo Bypass was similar to survival of those migrating through main‐stem migration routes. At the relatively high flows necessary to enable flooding of the Yolo Bypass, survival estimates varied little among release groups and migration routes. Furthermore, mean daily survival rates for Chinook Salmon migrating through the flooded Yolo Bypass were comparable to those of fish migrating through the other non‐floodplain routes. Median travel times remained relatively constant during various stages of flooding in the Yolo Bypass. This research should help managers to better understand the potential costs and benefits to floodplain restoration and routing of migrating Chinook Salmon into off‐channel habitat.
Monitoring is an essential component in ecosystem management and leveraging existing data sources for multiple species of interest can be one effective way to enhance information when making management decisions. Here we analyzed juvenile Chinook Salmon (Oncorhynchus tshawytscha) bycatch data that has been collected by the recently established Enhanced Delta Smelt Monitoring program (EDSM), a survey designed to estimate the abundance and distribution of the San Francisco Estuary’s (estuary) endangered Delta Smelt (Hypomesus transpacificus). Two key aspects of the EDSM program distinguish it from other fish surveys in the estuary: a stratified random sampling design and the spatial scale of its sampling effort. We integrated the EDSM dataset with other existing surveys in the estuary and used an occupancy model to assess detection probability differences across gear types. We saw no large-scale differences in size selectivity, and while detection probability varied among gear types, cumulative detection probability for EDSM was comparable to other surveys due to the program’s use of replicate tows. Based on our occupancy model and sampling effort in the estuary during spring of 2017 and 2018, we highlighted under-sampled regions that saw improvements in monitoring coverage due to EDSM. Our analysis also revealed that each sampling method has its own benefits and constraints. Although the use of random sites with replicates as conducted by EDSM can provide more statistically robust abundance estimates relative to traditional methods, the use of fixed stations and simple methods such as beach seine may provide a more cost-effective way of monitoring salmon occurrence in certain regions of the estuary. Stronger inference on salmon abundance and distribution can be made by leveraging the strengths of each survey’s method. Careful consideration of these trade-offs is crucial as the management agencies of the estuary continue to adapt and improve their monitoring programs.
Variation in life history traits within and across species is known to reflect adaptations to different environmental drivers through a diversity of mechanisms. Trait variation can also help buffer species and populations against extinction in fluctuating environments and against anthropogenic disturbances. Here, we examine the distribution and drivers of Ocean‐type Chinook salmon (Oncorhynchus tschawytscha) juvenile migratory life histories. We defined alternative migratory strategies according to whether individuals reared in the stream (natal rearing) or left shortly after hatching to rear elsewhere (non‐natal rearing). We then evaluated the frequency of migratory strategies across 16 populations with time series extending up to 25 years and evaluated the environmental variables that influenced variation in migration strategy. We found bimodal migration patterns and abrupt transitions in migrant sizes across all populations, supporting the widespread nature of alternative migratory strategies. Additionally, we found that the amount of freshwater rearing habitat available to juveniles, relative juvenile density and spring flow patterns significantly influenced the overall migration pattern for populations. Smaller streams and higher conspecific densities generally produced more non‐natal rearing migrants and larger streams and lower conspecific densities producing more natal rearing migrants. Our results shed light on previously unexplored patterns of juvenile migratory strategies and encourage broader consideration for how current conservation actions perform at protecting juvenile migratory diversity.
Spatial patterns in the abundance, distribution, and characteristics of organisms are a fundamental feature of all ecosystems. However, achieving a mechanistic understanding of the forces behind these population patterns is a major challenge for ecologists due to the number and diversity of variables and relationships involved. Here, we developed a spatially‐explicit agent‐based model to determine the minimum individual characteristics and environmental relationships necessary to reproduce population patterns observed in the field across habitat quality. We designed the model so each trait and mechanism could be independently included or excluded allowing us to systematically identify their impacts. The model was parameterized and outputs compared to natural population patterns using data collected on an archetypical species, the mud crab Panopeus herbstii – a species that experiences drastic habitat degradation when oyster reefs are harvested or deteriorate. Surprisingly few parameters were required to reproduce field patterns. Food availability was the primary environmental determinant of spatial patterns, as crab abundances increased almost directly proportional to this variable. The main individual level mechanisms were the ability to detect food as well as size‐ and personality‐dependent movement, since proportionally more active individuals aggregated in high quality habitat. Although habitat‐ and size‐dependent mortality influenced the magnitude of differences in population demographics across habitats, these relationships did not impact the nature of the predicted patterns. Our model demonstrates that a few simple rules can underlie complex population patterns and highlights the importance of phenotypic differences, particularly in movement, for shaping populations across heterogenous terrain. The approach used here provides a framework for identifying the roles of multiple mechanisms in structuring complex systems, and demonstrates the importance of sensory limits, movement propensity of individuals, and the availability of limiting resources for producing quantitative predictions of population responses to habitat change, such as degradation or restoration efforts. This article is protected by copyright. All rights reserved.
A marked decline of alewife (Alosa pseudoharengus) in Lake Michigan during 1981-83 led to diet shifts by coho (Oncorhynchus kisutch) and chinook salmon (O. tshawytscha) from feeding primarily on large alewife to eating proportionately more immature alewives and other prey. Diets of lake trout (Salvelinus namaycush) did not change greatly during that period. Population biomass conversion efficiency averaged 24.5% for coho and 16.6% for lake trout. Chinook salmon suffered an apparent 20% decline in gross conversion efficiency of biomass (25.1 to 20.8%) and a 25% decline in average weight of sport-caught fish. We infer that chinook salmon growth was inhibited by insufficient forage available to them. A simulation of chinook salmon feeding on bloater (Coregonus hoyi) at 8-degrees-C suggested that such behavior could lead to further declines in growth rates. Extension of modeling results to include approximations for brown trout (Salmo trutta) and rainbow trout (O. mykiss) revealed peaks in total annual salmonine predation of 71 000 t in 1983 and 76 000 t in 1987. The alewife was 70% of all prey eaten by salmonines in 1987-88. Lakewide gross production by salmonines was 15 300 t (or 0.27 g.m-2) in 1987. Ratios of annual gross production to average monthly population biomass were 1.6 for chinook, 1.15 for coho, and only 0.6 for lake trout.
Populations of native and introduced aquatic organisms in the San Francisco Bay/Sacramento- San Joaquin Delta Estuary ("BayJDelta") have undergone significant declines over the past two decades. De- creased river inflow due to drought and increased freshwater diversion have contributed to the decline of at least some populations. Effective management of the estuary's biological resources requires a sensitive indicator of the response to freshwater inflow that has ecological significance, can be measured accurately and easily, and could be used as a "policy" variable to set standards for managing freshwater inflow. Positioning of the 27~0 (grams of salt per kilogram of seawater) bottom salinity value along the axis of the estuary was examined for this purpose. The 2% bottom salinity position (denoted by X,) has simple and significant statistical relationships with annual measures of many estuarine resources, including the supply of phytoplankton and phytoplankton-derived detritus from local production and river loading; benthic macroinvertebrates (molluscs); mysids and shrimp; larval fish survival; and the abundance of planktivorous, piscivorous, and bottom-foraging fish. The actual mechanisms are understood for only a few of these populations. X, also satisfies other recognized requirements for a habitat indicator and probably can be measured with greater accuracy and precision than alternative habitat indicators such as net freshwater inflow into the estuary. The 2%~ value may not have special ecological significance for other estuaries (in the BayJDelta, it marks the locations of an estuarine turbidity maximum and peaks in the abundance of several estuarine organisms), but the concept of using near-bottom isohaline position as a habitat indicator should be widely applicable. Although X, is a sensitive index of the estuarine community's response to net freshwater inflow, other hydraulic features of the estuary also determine population abundances and resource levels. In particular, di - version of water for export from or consumption within the estuary can have a direct effect on population abundance independent of its effect on X,. The need to consider diversion, in addition to X,, for managing certain estuarine resources is illustrated using striped bass survival as an example. The striped bass survival data were also used to illustrate a related important point: incorporating additional explanatory variables may decrease the prediction error for a population or process, but it can increase the uncertainty in parameter estimates and management strategies based on these estimates. Even in cases where the uncertainty is currently too large to guide management decisions, an uncertainty analysis can identify the most practical direction for future data acquisition.
The ‘flood pulse advantage’ is the amount by which fish yield per unit mean water area is increased by a natural, predictable flood pulse. Evidence for this increase is presented from tropical and temperate fisheries. It is argued that increasing multispecies fish yield by restoring the natural hydrological regime is consistent with increasing production of other trophic levels and with restoration from ecological and aesthetic viewpoints. When applied to a river-floodplain system, this restoration would provide a large, self-sustaining potential for recreation, commercial exploitation, and flood control. An interim ‘natural flood pulse’ restoration approach is proposed for systems modified for navigation. This approach approximates the natural hydrological regime in a river reach and is intended as a first step in the long process of restoring the watershed.
The study examines the relationship between floodplain aquatic macroinvertebrates and sector-scale parameters such as geomorphology and history of regulation. The assemblages of six groups of invertebrates (Molluscs, Crustaceans, Ephemeroptera, Odonata, Trichoptera, and Coleoptera) were compared in various types of former channels from two contrasting but adjacent floodplain sectors: (1) the Jons sector of the Rhǒne River where successive meandering and braiding phases has left diversified fluvial forms in the landscape but where the main river is now embanked, and (2) the unregulated Ain River sector where the river is still actively meandering, although this process is being slowed by incision. The results demonstrate little difference in faunal composition between the two sectors but a significant difference in faunal structure. In the Rhǒne floodplain, there was a clear distinction between the faunal assemblages together with a high taxa richness at the scale of the sector (dominance of the beta diversity). In the Ain floodplain, the faunal assemblages were overlapping and the taxa richness was high at the sample scale (alpha diversity). Sector-scale spatial patterns of the faunal assemblages along former channels were also distinct: between-channel heterogeneity dominated in the Rhǒne, whereas within-channel heterogeneity dominated on the Ain. These results stress the influence of geomorphological and historical determinants on the floodplain communities and, conversely, the relevance of macroinvertebrate assemblages for the assessment, at the landscape scale, of aquatic systems within the floodplains.
The functional value of a restored estuarine wetland as a foraging area for juvenile chum salmon (Oncorhynchus keta) and fall chinook salmon (O. tshawytscha) was evaluated during the spring seaward migrations of each species in 1987 and 1988. During both years, fish foraged selectively.
While temporarily residing in the restored wetland, both salmon selected primarily chironomid insects (midge larvae, pupae,
and adults) over all other organisms considered available prey. A detritus-based food chain (detritus-chironomids-juvenile
chum salmon or chinook salmon) suggests that the restored wetland provides productive foraging habitat for migrating juvenile
chum and fall chinook salmon during their early residency in the estuary. However, the equivalency of foraging in restored
or created estuarine wetlands compared to foraging in altered riverine or natural habitats remains untested.
Movement of fishes onto a fringing floodplain was studied by seining and trapping during five spring floods. We collected 26 species from the inundated floodplain; the known channel fauna is 42 species. Species numerically dominant on the floodplain were Fundulus olivaceus, F notti, Gambusia affinis, Notropis welaka, N. texanus, N. roseipinnis, Lepomis macrochirus, L. cyanellus and L. marginatus. Catch-per-effort in traps was generally greatest on the upper floodplain during the day and greatest nearer the channel at night. Night activity of fishes on the floodplain was apparently low Several species, which we term flood-quiescent forms, were common in the channel (e.g., Lepomis megalotis and Percina nigrofasciata) but did not exploit the floodplain. Activity (as catch per trap-hour) of P nigrofasciata was negatively correlated with flood-induced turbidity A flood-exploitative species, Notropis texanus, had higher population abundance during 3 high-flow years than in 3 low-flow years, suggesting that spring flooding may exert significant control over fish community structure.
Comparisons of growth rates and consumption rates among fish populations are not straightforward and are difficult to interpret in the absence of other information about the populations. Differences in temperature regimes, reproductive timing, activity cost, prey availability, caloric densities of predator and prey, and allometric effects of body size on metabolism are factors that can alter the direct effect of consumption rate on growth rate, We developed a method to elucidate relations between growth and consumption by correcting for allometric weight effects. Bioenergetics model simulations showed that when growth rate is regressed against consumption rate (on either an absolute or a relative basis), the relationship is confounded by the allometric effects of differences in body weight among the populations being compared. Regressing growth rates on the difference between actual and maintenance consumption rate corrects for most of the allometric effects. That regression can be used to determine whether growth rate differences are best explained by consumption (in conjunction with weight allometries), temperature regime differences, variable activity costs, or other factors. Bioenergetics models can be used to evaluate the relative importance of factors limiting growth for fish populations.
A formal statistical model is presented for the release of smolts marked with coded-wire tags (CWTs) in the lower Sacramento River and the subsequent recovery of marked smolts in midwater trawls in the Delta. This model treats survival as a logistic function of water temperature, and the release and recovery of different CWT groups as independent mark-recapture experiments. Iteratively reweighted least squares is used to fit the model to the data, and simulation is used to establish confidence intervals for the fitted parameters. A 95% confidence interval for the upper incipient lethal temperature, inferred from the trawl data by this method, is 23.01 ± 1.08°C. This is in good agreement with experimental results obtained under controlled conditions (24.3 ± 0.1°C and 25.1 ± 0.1°C for chinook acclimatized to 10 and 20°C, respectively). -from Authors
Horizontal zonation of fish reproduction, a lotic-to-lentic succession similar to that seen with increasing stream order,
was evident from the relative abundance of larval and 0 + juvenile fishes in three floodplain spawning and nursery areas (lotic,
semi-lotic, lentic) of the Upper Rhône River, France. Although the lotic and lentic ecosystems provided similar estimates
of standing crop (0 + juveniles), differences were apparent in the reproductive and trophic guild structure of the YOY taxocoenoses
at the three sites. A new sampling approach (Random Point-Abundance Sampling and modified electrofishing) is described for
early-life fish ecology. The electrofishing method employed is mobile, effective for all sizes of larvae and 0 + juveniles
of most species, quantitative, and applicable to a number of freshwater situations; and the punctual data resulting from this
sampling approach are comparable both spatially and temporally.
The objective of this study was to determine if pond permanence and vertebrate predation (by fish and waterfowl) affect invertebrate
community structure in the mudflat habitat of floodplain ponds. Invertebrate communities were studied for 1 year in four Mississippi
River floodplain ponds with different hydroperiods. Pond 1 experienced five dry periods, pond 2 experienced four, pond 3 dried
once, and standing water remained in pond 4 for the entire year. Vertebrate predator exclusion treatments (all access, no
access, small-fish access and cage controls) were placed in all ponds. As pond duration increased, predatory invertebrate
richness and abundance increased while overall invertebrate richness and abundance decreased. With the exception of the cladoceran
Diaphanosoma, all commonly encountered taxa were strongly affected by pond permanence in terms of abundance, biomass and, generally, individual
biomass. Taxa were nearly early divided between those that were more abundant in less permanent ponds and those that were
more abundant in longer-duration ponds. Invertebrate taxa richness, abundance, and total biomass were lower in the all-access
treatment than in the treatments that restricted predator access, and these effects were stronger in the more permanent ponds.
In general, there were no significant differences in responses to the treatments with small-fish access and no access. These
results support models that predict relatively weak effects of predation in frequently disturbed habitats.