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The Delta Smelt is a largely zooplanktivorous, endangered fish endemic to the San Francisco Estuary (the estuary). High flows increase the availability of fresh and brackish water habitat for Delta Smelt, but also may mobilize contaminants, potentially increasing toxicological stress. Here, we examine the association between contaminants and Delta Smelt health across contrasting water year types and flow-related management actions. Our study spanned the fall season of three years: 1 dry year (2018) bracketed by 2 wet years (2017 and 2019) and coincided with several management actions meant to benefit Delta Smelt. We collected field water from six sites in the estuary that encompass the freshwater and low-salinity habitat of Delta Smelt and analyzed the water for contaminant concentrations. After a 96-hour exposure to the field water, we assessed cultured Delta Smelt survival and the histopathological condition of the gill and liver. Insecticides, particularly fipronil metabolites, were the most prevalent contaminants detected in 2017 and 2018, and a variety of contaminants associated with the rice harvest were detected in 2019. No acute toxicity was observed during any exposure, but we observed negative effects in the livers of Delta Smelt exposed to agricultural water from the Toe Drain and Cache Slough during a 2019 pulse flow action, which coincided with elevated detections and concentrations of organic pesticides. Other noteworthy sub-lethal effects, likely occurring in response to contaminant mixtures, included severe gill lesions in Delta Smelt exposed to Decker Island water in 2019. In the drier year of 2018, lesions were generally mild or absent. Thus, the trade-offs between increased habitat availability and contaminant loading may provide one explanation for why Delta Smelt abundance does not consistently respond positively to outflow. [ABSTRACT FROM AUTHOR]

Assessing habitat quality is a major goal of conservationists and restoration practitioners, but to associate habitat quality with biomarkers of vagile animals, the biomarkers must respond rapidly. Here, we identified a biomarker capable of rapidly detecting food limitation in the imperiled Delta Smelt (Hypomesus transpacificus), a pelagic fish endemic to the San Francisco Estuary (SFE). We conducted an experiment with fed and unfed treatments of hatchery-raised, sub-adult Delta Smelt that were sampled at 12 time points: 0, 1, 2, 3, 4, 5, 6, 7, 9, 11, 14, and 21 days. We then compared four biomarkers using Day 21 fish: RNA/DNA in liver, triglycerides in liver, glycogen in liver, and glycogen in muscle. Of the liver endpoints, glycogen had the largest difference between treatments at Day 21, so we compared it to muscle glycogen across all time points. Liver glycogen declined by 60% after 1 day of fasting and remained depressed in the fasting treatment across all subsequent time points. Muscle glycogen also responded rapidly, taking only 2 days to decline by 39% in the fasting treatment, but the difference was inconsistent across subsequent time points. When applied to hatchery-released Delta Smelt collected from the SFE, liver glycogen concentrations were less than half that of the fed hatchery fish, consistent with the hypothesis of food limitation in the wild, but also several other potential causes. This study highlights the utility of liver glycogen as an indicator of recent foraging success in Delta Smelt. [ABSTRACT FROM AUTHOR]

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left–right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals. [ABSTRACT FROM AUTHOR]

Temperature and salinity often define the distributions of aquatic organisms. This is at least partially true for Delta Smelt, an imperiled species endemic to the upper San Francisco Estuary. While much is known about the tolerances and distribution of Delta Smelt in relation to these parameters, little is known regarding the temperature and salinity preferences of the species. Therefore, the temperature and salinity preferences of sub-adult Delta Smelt were investigated across a wide range of thermal (8–28 °C) and salinity (0–23 ppt) conditions. Replicates of ten fish were allowed to swim between two circular chambers with different temperature or salinity, and the distribution of fish between the chambers was recorded. We found that Delta Smelt showed no temperature preference below 15 °C, a modest aversion to the warmer tank from 15 to 28 °C, and a strong aversion to the warmer tank with elevated mortality at temperatures above 28 °C. Delta Smelt also preferred lower salinities, and this preference became more pronounced as salinity increased toward 23 ppt. These results indicate that Delta Smelt can tolerate high temperatures and salinities for a short time, and that their preferences for lower temperature and salinity strengthens as these variables increase. [ABSTRACT FROM AUTHOR]

Understanding reproductive biology and performance of fish is essential to formulate effective conservation and management programs. Here, we studied reproductive strategies of female Delta Smelt Hypomesus transpacificus, an endangered fish species in the State of California, the United States, focusing on (1) better understanding their distribution pattern during the winter and spring spawning season at very fine scale to predict their possible spawning grounds and (2) assessing impacts of a recent, severe drought on their reproductive performance. We formulated our hypotheses as follows; (1) female Delta Smelt migrate to particular locations for spawning so that mature females can be frequently found in those locations throughout the spawning season and (2) reproductive performance of individual female fish declined during the drought. To test the first hypotheses, we analyzed relationships between water quality parameters and maturity/distribution pattern of Delta Smelt. Salinity better explained the distribution pattern of Delta Smelt at subadult and adult stages compared with water temperature or turbidity. Although there are some freshwater locations where mature Delta Smelt can frequently be found during the spawning season, Delta Smelt at the final maturation stage (Stage 5: hydration) and post spawners appeared to be widespread in the area where salinity was below 1.0 during the spawning season. Therefore, Delta Smelt could theoretically spawn in any freshwater locations, with more specific spawning requirements in the wild (e.g., substrate type and depth) still unknown. Delta Smelt, which experienced dry and critically dry conditions (the 2013 and 2014 year-classes), showed smaller oocytes, and lower clutch size and gonadosomatic index compared with the fish caught in a wet year (2011 year-class) at the late vitellogenic stage (Stage 4 Late), suggesting reproductive performance was negatively affected by environmental conditions during the drought. [ABSTRACT FROM AUTHOR]

Condition indices are key predictors of health and fitness in wild fish populations. Variation in body condition, therefore, can be used to identify stressful conditions that may impact endangered species, such as California's endemic Delta Smelt (Hypomesus transpacificus McAllister, 1963). Here, we examined spatiotemporal variation in the condition indices of > 1600 Delta Smelt collected over nine years (2011–2019), a period characterized by tremendous variability in hydrodynamic and water quality conditions. The population exhibited low hepatosomatic index (HSI) and condition factor (CF) during September/October/November (fall), and both condition indices declined over the nine-year study during fall. HSI was positively correlated with indicators of pelagic productivity (e.g., Chlorophyll a, zooplankton biomass, and proximity to tidal wetlands), whereas CF was negatively correlated with temperature, peaking at a relatively cool 10–13 °C. In sum, seasonal and interannual variation in body condition corresponded most strongly with pelagic productivity and water temperature, with little correlation to freshwater outflow. Management actions that increase pelagic productivity, restore and freshen productive wetlands during late summer-fall, and reduce water temperatures overall are likely to benefit condition indices and, therefore, fitness of the Delta Smelt population. [ABSTRACT FROM AUTHOR]

Polyunsaturated fatty acids are metabolized into regulatory lipids important for initiating inflammatory responses in the event of disease or injury and for signaling the resolution of inflammation and return to homeostasis. The epoxides of linoleic acid (leukotoxins) regulate skin barrier function, perivascular and alveolar permeability and have been associated with poor outcomes in burn patients and in sepsis. It was later reported that blocking metabolism of leukotoxins into the vicinal diols ameliorated the deleterious effects of leukotoxins, suggesting that the leukotoxin diols are contributing to the toxicity. During quantitative profiling of fatty acid chemical mediators (eicosanoids) in COVID-19 patients, we found increases in the regioisomeric leukotoxin diols in plasma samples of hospitalized patients suffering from severe pulmonary involvement. In rodents these leukotoxin diols cause dramatic vascular permeability and are associated with acute adult respiratory like symptoms. Thus, pathways involved in the biosynthesis and degradation of these regulatory lipids should be investigated in larger biomarker studies to determine their significance in COVID-19 disease. In addition, incorporating diols in plasma multi-omics of patients could illuminate the COVID-19 pathological signature along with other lipid mediators and blood chemistry. [ABSTRACT FROM AUTHOR]

There is an extensive literature establishing, validating, and quantifying a wide range of responses of fishes to fasting. Our study complements this work by comparing fed and unfed treatments of hatchery-raised Delta Smelt (Hypomesus transpacificus)—an imperiled fish that is endemic to the San Francisco Estuary and its tributaries in California, USA—across a diverse suite of endpoints over a two-month time series. The experiment was conducted at 15.9°C, and individuals were sampled at 12 time points as starvation became increasingly severe. We found that hepatosomatic index and condition factor were relatively sensitive to starvation, becoming significantly depressed at Day 4 and 7, respectively. Histological analysis of liver showed elevated cytoplasmic inclusion bodies at Day 7, followed by increased glycogen depletion, single cell necrosis, and hydropic vacuolar degeneration at Day 14, 21, and 28, respectively. Of four antioxidants measured, glutathione decreased at Day 4, superoxide dismutase increased at Day 14, catalase increased at Day 56, and glutathione peroxidase was not affected by starvation. The net result was a ~2-fold increase in lipid peroxidation (malondialdehyde) in fasted fish that was highly inconsistent through time. RNA to DNA ratio and triglycerides in muscle were relatively insensitive to starvation, only consistently decreasing with fasting after mortality began increasing in the 'No Feeding' treatment, at Day 21. Together, these results suggest that Delta Smelt mobilize hepatic energy stores far more rapidly than lipids in muscle when subjected to fasting, leading to rapid atrophy of liver and the development of cytoplasmic inclusion bodies—possibly autophagosomes—in hepatocytes. [ABSTRACT FROM AUTHOR]

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The herbicides glyphosate, imazamox and fluridone are herbicides, with low toxicity towards fish and invertebrates, which are applied to waterways to control invasive aquatic weeds. However, the effects of these herbicides on natural isolates of phytoplankton and cyanobacteria are unknown. Three species of microalgae found in the San Francisco Estuary (SFE)/Sacramento-San Joaquin River Delta (Delta) (Microcystis aeruginosa, Chlamydomonas debaryana, and Thalassiosira pseudonana) were exposed to the three herbicides at a range of concentrations in 96-well plates for 5–8 days. All three algal species were the most sensitive to fluridone, with IC50 of 46.9, 21, and 109 µg L−1 for M. aeruginosa, T. pseudonana and C. debaryana, respectively. Imazamox inhibited M. aeruginosa and T. pseudonana growth at 3.6 × 104 µg L−1 or higher, and inhibited C. debaryana growth at 1.0 × 105 µg L−1 or higher. Glyphosate inhibited growth in all species at ca. 7.0 × 104 µg L−1 or higher. Fluridone was the only herbicide that inhibited the microalgae at environmentally relevant concentrations in this study and susceptibility to the herbicide depended on the species. Thus, the application of fluridone may affect cyanobacteria and phytoplankton community composition in water bodies where it is applied. [ABSTRACT FROM AUTHOR]

The San Francisco Estuary (California, USA) had abundant pelagic fish in the late 1960s, but has few pelagic fish today. A primary cause for this decline in fish is thought to be a trophic cascade, triggered by declining phytoplankton. Here, we describe the changes in pelagic community structure of the San Francisco Estuary. Then, we examine whether changes in hydrodynamics due to freshwater exports, which increased exponentially beginning in 1967, in addition to the 1986 invasion by the clam Potamocorbula amurensis, explain the phytoplankton loss. Hydrodynamic variables were reconstructed back to 1956 using statistical models fit to, and cross-validated against, output from a hydrodynamic model. Then, we regressed mean summer/fall chlorophyll a—the season with the largest phytoplankton decline—against the reconstructed hydrodynamic variables and the presence/absence of P. amurensis for 1969–2014. The regression model, which explained 78% of the interannual variation in chlorophyll a, was then used to quantify the influence of P. amurensis and exports on chlorophyll a. Based on monitoring data, chlorophyll a declined 22-fold from 1969–2014, zooplankton declined 32-fold from 1972–2014, and pelagic fish declined 92-fold from 1968–2014. Averaged over 1990–2014, the chlorophyll a model ascribed an 88% decline in chlorophyll a to P. amurensis, a 74% decline to exports (at minimum), and a 97% decline to the combined influence of P. amurensis and exports (at minimum). Thus, the decline in pelagic productivity in the San Francisco Estuary has occurred largely due to the combined impacts of the P. amurensis invasion and increased freshwater exports. [ABSTRACT FROM AUTHOR]

Delta smelt (Hypomesus transpacificus), an annual fish endemic to the San Francisco Estuary (SFE), is imperiled. One recovery strategy is to restore tidal wetlands, thereby increasing productivity and prey abundance. However, the link between tidal wetlands and foraging of delta smelt is not yet established. Using GIS, we quantified the area of tidal wetlands (km2) within a 2-km radius around sampling stations from which 1380 delta smelt were collected over 4 years (2011–2015). We quantified stomach fullness, a metric of foraging success, for each fish and regressed it against tidal wetland area, turbidity, water temperature, and other factors known to influence foraging success of delta smelt. Stomach fullness increased with both increasing tidal wetland area and increasing water temperature and was reduced at turbidities > 80 NTU. Model estimates show that stomach fullness increased twofold from the minimum (0 km2) to the maximum (4.89 km2) tidal wetland area. Of this increase, 60% was due to increased predation on larval fish, while 40% was due to increased predation on zooplankton. Delta smelt collected from areas with the highest tidal wetland area were six times more likely to have a larval fish in their guts than those collected from areas with the lowest. Thus, tidal wetland appears to confer substantial benefits to the foraging success of delta smelt, mainly via increased predation on larval fish. [ABSTRACT FROM AUTHOR]

Blooms of Microcystis and other harmful cyanobacteria can degrade water quality by producing cyanotoxins or other toxic compounds. The goals of this study were (1) to facilitate understanding of community structure for various aquatic microorganisms in brackish water and freshwater regions with emphasis on cyanobacteria, and (2) to test a hypothesis that Microcystis genotypes that tolerate higher salinity were blooming in brackish water environments during the severe drought, 2014. Shotgun metagenomic analysis revealed that cyanobacteria dominated the brackish water region while bacteria dominated the freshwater region. A group of cyanobacteria (e.g., Aphanizomenon, Microcystis, Planktothrix, Pseudanabaena), bacteria (e.g., Bacillus, Porphyrobacter), and diatoms (Phaeodactylum and Thalassiosira) were abundant in the brackish water region. In contrast, Hassallia (cyanobacteria) and green algae (Nannochloropsis, Chlamydomonas, and Volvox) were abundant in the landward freshwater region. Station variation was also apparent. One landward sampling station located downstream of an urbanized area differed substantially from the other stations in terms of both water chemistry and community structure, with a higher percentage of arthropods, green algae, and eukaryotes. Screening of the Microcystis internal transcribed spacer region revealed six representative genotypes, and two of which were successfully quantified using qPCR (Genotypes I and VI). Both genotypes occurred predominantly in the freshwater region, so the data from this study did not support the hypothesis that salinity tolerant Microcystis genotypes bloomed in the brackish water region in 2014. [ABSTRACT FROM AUTHOR]

Abstract: Pyrethroid insecticides are commonly used in pest control and are present at toxic concentrations in surface waters of agricultural and urban areas worldwide. Monitoring is challenging as a result of their high hydrophobicity and low toxicity thresholds, which often fall below the analytical methods detection limits (MDLs). Standard daphnid bioassays used in surface water monitoring are not sensitive enough to protect more susceptible invertebrate species such as the amphipod Hyalella azteca and chemical loss during toxicity testing is of concern. In the present study, we quantified toxicity loss during storage and testing, using both natural and synthetic water, and presented a tool to enhance toxic signal strength for improved sensitivity of H. azteca toxicity tests. The average half‐life during storage in low‐density polyethylene (LDPE) cubitainers (Fisher Scientific) at 4 °C of 5 pyrethroids (permethrin, bifenthrin, lambda‐cyhalothrin, cyfluthrin, and esfenvalerate) and one organophosphate (chlorpyrifos; used as reference) was 1.4 d, and piperonyl butoxide (PBO) proved an effective tool to potentiate toxicity. We conclude that toxicity tests on ambient water samples containing these hydrophobic insecticides are likely to underestimate toxicity present in the field, and mimic short pulse rather than continuous exposures. Where these chemicals are of concern, the addition of PBO during testing can yield valuable information on their presence or absence. Environ Toxicol Chem 2018;37:462–472. © 2017 SETAC [ABSTRACT FROM AUTHOR]

Diadromy affords fish access to productive ecosystems, increasing growth and ultimately fitness, but it is unclear whether these advantages persist for species migrating within highly altered habitat. Here, we compared the foraging success of wild Delta Smelt—an endangered, zooplanktivorous, annual, semi-anadromous fish that is endemic to the highly altered San Francisco Estuary (SFE)—collected from freshwater (<0.55 psu) and brackish habitat (≥0.55 psu). Stomach fullness, averaged across three generations of wild Delta Smelt sampled from juvenile through adult life stages (n = 1,318), was 1.5-fold higher in brackish than in freshwater habitat. However, salinity and season interacted, with higher fullness (1.7-fold) in freshwater than in brackish habitat in summer, but far higher fullness in brackish than freshwater habitat during fall/winter and winter/spring (1.8 and 2.0-fold, respectively). To examine potential causes of this interaction we compared mesozooplankton abundance, collected concurrently with the Delta Smelt, in freshwater and brackish habitat during summer and fall/winter, and the metabolic rate of sub-adult Delta Smelt acclimated to salinities of 0.4, 2.0, and 12.0 psu in a laboratory experiment. A seasonal peak in mesozooplankton density coincided with the summer peak in Delta Smelt foraging success in freshwater, and a pronounced decline in freshwater mesozooplankton abundance in the fall coincided with declining stomach fullness, which persisted for the remainder of the year (fall, winter and spring). In brackish habitat, greater foraging ‘efficiency’ (prey items in stomachs/mesozooplankton abundance) led to more prey items per fish and generally higher stomach fullness (i.e., a higher proportion of mesozooplankton detected in concurrent trawls were eaten by fish in brackish habitat). Delta Smelt exhibited no difference in metabolic rate across the three salinities, indicating that metabolic responses to salinity are unlikely to have caused the stomach fullness results. Adult migration and freshwater spawning therefore places young fish in a position to exploit higher densities of prey in freshwater in the late spring/summer, and subsequent movement downstream provides older fish more accessible prey in brackish habitat. Thus, despite endemism to a highly-altered estuary, semi-anadromy provided substantial foraging benefits to Delta Smelt, consistent with other temperate migratory fish. [ABSTRACT FROM AUTHOR]

Early colonising ecosystem engineers modify habitats and alter the abundance of basal resources following disturbances. These changes can have profound effects on ecosystem recovery via facilitative or inhibitory effects on subsequent colonists., We quantified how black fly larvae, which can be pioneer species during secondary succession in streams, influence initial community recovery following a simulated drying disturbance., Black fly larvae anchor themselves to the stream substratum with silk, and diatoms adhere to the silk of black flies. Therefore, we hypothesised that black flies speed community recovery following disturbances by increasing the accrual rate of basal resources with their silk., We compared algal and detrital resource abundance and invertebrate community recovery on recently submerged cobbles across three treatments: increased black fly abundance, added black fly silk plus ambient black fly abundance and ambient black fly abundance (control)., After 24 h, the increased black fly treatment had more chlorophyll a, detritus and greater invertebrate abundance and richness, and replicates had more self-similar communities than the control treatment., The added silk treatment responded similarly to the increased black fly treatment, supporting the hypothesis that black flies increase the rate of basal resource accrual with their silk, increasing the colonisation rates of other invertebrate species., Our study suggests that black flies are akin to other organisms that facilitate recovery following disturbance (e.g. alders fixing nitrogen following glacial retreat). Further research is needed to determine the effect of black flies on long-term patterns of recovery and the applicability of our results to natural disturbances in streams. [ABSTRACT FROM AUTHOR]

A key attribute of riverine food webs is the downstream movement of invertebrates via the water column, or invertebrate drift. Causes of drift include benthic predation, food limitation, and perhaps passive entry, which may occur when invertebrates lose their purchase on stream substrate. However, the relative importance of drift causes is unknown, as is whether the relative importance of drift causes varies across space. Combining observational data on invertebrate herbivore and predator guild densities with in-stream experiments, we evaluated the relative importance of benthic predation, food limitation, and passive entry as proximate causes of drift for the herbivore guild across the canopy gradient of a montane stream. We found that 1) benthic predation and food limitation were both more important as causes of herbivore drift than passive entry; 2) drift caused by food limitation did not vary with riparian canopy, whereas herbivore density decreased with increasing riparian canopy, and 3) per capita drift increased linearly with increasing density, while per capita drift decreased in a negative hyperbolic fashion with increasing food, indicating that herbivore drift is proportional to herbivore density, and inversely proportional to food. We conclude that invertebrate herbivore drift was overwhelmingly an active process to improve fitness, and that herbivore food did not vary across the canopy gradient, likely because increased herbivory from larger herbivore populations at sunnier sites prevented food from accumulating. [ABSTRACT FROM AUTHOR]

Harmful cyanobacterial blooms compromise human and environmental health, mainly due to the cyanotoxins they often produce. Microcystins (MCs) are the most commonly measured group of cyanotoxins and are hepatotoxic, neurotoxic, and cytotoxic. Due to MCs ability to covalently bind to proteins, quantification in complex matrices is difficult. To analyze bound and unbound MCs, analytical methods were optimized for analysis in sediment and clam tissues. A clean up step was incorporated to remove lipids, improving percent yield. This method was then applied to sediment and clam samples collected from the Sacramento–San Joaquin River Delta (Delta) in the spring and fall of 2017. Water samples were also tested for intracellular and extracellular MCs. These analyses were used to quantify the partitioning of MCs among sediment, clams, and water, and to examine whether MCs persist during non-summer months. Toxin analysis revealed that multiple sediment samples collected in the Delta were positive for MCs, with a majority of the positive samples from sites in the San Joaquin River, even while water samples from the same location were below detection limit. These data highlight the importance of analyzing MCs in complex matrices to accurately evaluate environmental risk. [ABSTRACT FROM AUTHOR]