Injury and mortality assessment of pumping on a small, sensitive fish species

Studying rare and sensitive species is a challenge in conservation biology. The problem is exemplified by the case of the imperiled delta smelt Hypomesus transpacificus, a small delicate fish species endemic to the San Francisco Estuary, California. Persistent record-low levels of abundance and relatively high sensitivity to handling stress pose considerable challenges to studying delta smelt in the wild. To attempt to overcome these and other challenges we have developed the SmeltCam, an underwater video camera codend for trawled nets. The SmeltCam functions as an open-ended codend that automatically collects information on the number and species of fishes that pass freely through a trawled net without handling. We applied the SmeltCam to study the fine-scale distribution of juvenile delta smelt in the water column in the upper San Francisco Estuary. We learned that during flood tides delta smelt were relatively abundant throughout the water column and that during ebb tides delta smelt were significantly less abundant and occurred only in the lower half and sides of the water column. The results suggest that delta smelt manipulate their position in the water column to facilitate retention in favorable habitats. With the application of the SmeltCam we increased the survival of individual delta smelt by 72% compared to using a traditional codend, where all of the fish would have likely died due to handling stress. The SmeltCam improves upon similar previously developed silhouette photography or video recording devices and demonstrates how new technology can be developed to address important questions in conservation biology as well as lessen the negative effects associated with traditional sampling methods on imperiled species.

The effects of water temperature on individual and group movement behaviour in prey fish can affect ecological interactions such as competition and predation, but how variability in temperature influence fish behaviour is less understood. Of particular concern is how increased warming in tidally fluctuating estuaries may impact the native and endangered delta smelt (Hypomesus transpacificus, Osmeridae). To help address this issue, we tested the effects of increased water temperature (fluctuating [17–21°C] and warm [21°C] acclimated treatments) on juvenile delta smelt individual and group behaviour, response to chemical alarm and predator cues, as well as capacity to evade predation. In addition, predation of delta smelt was tested in the presence of a dominant invasive competitor, Mississippi silversides (Menidia beryllina, Atherinopsidae), as well as comparative predation mortality on Mississippi silversides when isolated. After 7 days of increased temperature treatments, delta smelt in the warm treatment increased swimming velocity, decreased turning angle, and altered group structure with larger inter‐individual distances compared to fish in the control (17°C) and fluctuating temperature treatments. Following conspecific and predator chemical alarm cues, delta smelt showed anti‐predator responses. Control and fluctuating treatment fish responded to conspecific cues with increased swimming speeds, decreased inter‐individual distances and near‐neighbour distances, and, after 15 min, fish recovered back to baseline behaviours. In contrast, fish in the warm treatment had not recovered after 15 min, and swimming speeds were maintained at roughly 25 cm/s, close to maximum capabilities. Fish in control and fluctuating treatments showed minimal responses to predator cues, whereas delta smelt exposed to warm conditions significantly increased swimming speeds and decreased turning angle. Predation of delta smelt by largemouth bass (Micropterus salmoides, Centrarchidae) was greatest under the warm treatment, correlating with altered behaviours of delta smelt; however, predation of Mississippi silversides was greater than delta smelt, independent of temperature. This study provides novel insight into the group behaviour of delta smelt, their response to predation, and how prolonged exposure to elevated temperature may induce negative individual and group behaviours causing alterations in predator–prey dynamics. This work highlights the importance of testing ecologically realistic temperature fluctuations in experiments as delta smelt had significantly altered responses to elevated temperature, dependent on variability of warming.

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.

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.

Coastal estuaries are among the most heavily impacted ecosystems worldwide with many keystone fauna critically endangered. The delta smelt (Hypomesus transpacificus) is an endangered pelagic fish species endemic to the Sacramento-San Joaquin Estuary in northern California, and is considered as an indicator species for ecosystem health. This ecosystem is characterized by tidal and seasonal gradients in water parameters (e.g., salinity, temperature, and turbidity), but is also subject to altered water-flow regimes due to water extraction. In this study, we evaluated the effects of turbidity and salinity on feeding performance and the stress response of delta smelt because both of these parameters are influenced by water flows through the San Francisco Bay Delta (SFBD) and are known to be of critical importance to the completion of the delta smelt's life cycle. Juvenile delta smelt were exposed to a matrix of turbidities and salinities ranging from 5 to 250 nephelometric turbidity units (NTUs) and 0.2 to 15 parts per thousand (ppt), respectively, for 2 h. Best statistical models using Akaike's Information Criterion supported that increasing turbidities resulted in reduced feeding rates, especially at 250 NTU. In contrast, best explanatory models for gene transcription of sodium-potassium-ATPase (Na/K-ATPase)-an indicator of osmoregulatory stress, hypothalamic pro-opiomelanocortin-a precursor protein to adrenocorticotropic hormone (expressed in response to biological stress), and whole-body cortisol were affected by salinity alone. Only transcription of glutathione-S-transferase, a phase II detoxification enzyme that protects cells against reactive oxygen species, was affected by both salinity and turbidity. Taken together, these data suggest that turbidity is an important determinant of feeding, whereas salinity is an important abiotic factor influencing the cellular stress response in delta smelt. Our data support habitat association studies that have shown greater delta smelt abundances in the low-salinity zone (0.5-6.0 ppt) of San Francisco Bay, a zone that is also understood to have optimal turbidities. By determining the responses of juvenile delta smelt to key abiotic factors, we hope to aid resource managers in making informed decisions in support of delta smelt conservation.

Successful aquaculture operations strive to produce high-quality, healthy fish while minimizing costs. One way to do this is to wean fish off live feed as soon as possible to a formulated dry feed. In this study, Delta Smelt Hypomesus transpacificus were weaned onto a dry feed diet at three life stages: early larval (14 days posthatch [dph]), late larval (60 dph), and juvenile (105 dph), and compared to a control group of fish receiving live prey to 160 dph according to current practices. Delta Smelt did not have high survival or growth when dry feed was introduced at 14 dph, and showed significant increases in growth but low survival when the weaning process was started at 60 dph. Fish going through the experimental weaning process starting at 105 dph showed higher growth and survival rates than the control regime, indicating that this is a more optimal time to wean them off the live prey diet. Our findings suggest that Delta Smelt production methods could be improved by weaning fish earlier than the 160 dph currently implemented at the conservation hatchery.

Most of the research on marking of aquatic organisms has been done using large organisms since they tend to have better retention rates, their swimming behaviour is less affected by the size of the tag, they have less trauma due to injectable tags or from the injector itself and they are easier to handle and able to withstand the stress of tagging and recapture. The development of small tags has grown from a necessity to study smaller fish species, earlier life stages of fish and to study other small aquatic organisms. As an endangered species, delta smelt (Hypomesus transpacificus) are being intensively studied in the upper San Francisco Estuary (CA, USA). A crucial part of many of these studies is tracking delta smelt, which requires a distinctive mark on each individual or group of fish. Unfortunately, many of the experimental fish suffer inadvertent mortality, as delta smelt are very sensitive to environmental and handling stress. The purpose of this review was to synthesize the different tagging and marking studies on small fish and aquatic organisms and to evaluate the advantages and disadvantages of each method for applications on sensitive species such as delta smelt. This review suggests the most effective methods for tracking delta smelt are visible implant alphanumeric (VIA) tagging and adipose fin clips for subadult to adult fish and calcein marks for young life stages. Among these methods, only VIA tagging currently provides individual organism identification.

Research into the effects of contaminants on fishes is often conducted on well- studied model test species, whose responses may be different than those of endangered species. We developed an oligonucleotide microarray consisting of 12 595 genes to examine the effects of the pesticide permethrin on an endangered fish in California, USA, the delta smelt Hypomesus transpacificus. The microarray was used in combination with quantitative PCR (qPCR) assess- ments. We exposed larval delta smelt to permethrin for 96 h at concentrations of 0.69, 1.37, 2.56, 4.84, 12.88 and 24.94 µg l �1 , and compared the responses to a control group. The 96 h 50% lethal concentration (LC50) was 4.07 µg l �1 , which is lower than those reported for model test species and similar to other endangered species. With increasing exposure concentration, we detected the dif- ferential expression of 3342 microarray features with elevated expression of genes involved in protein degradation and apoptosis, and decreased expression of immune function genes. Func- tional analysis indicated that genes involved in protein degradation, immune function, an unfolded protein response, meta bolism and cell signaling cascades were affected by exposure to permethrin. Many of the gene responses in the 0.69 µg l �1 treatment group differed in their direc- tional change in expression from those at higher exposure concentrations, suggesting a potential mechanistic threshold of sub-lethal toxicity at concentrations below the lowest observed effect concentration (LOEC) of 2.56 µg l �1 . These results are consistent with non-monotonic response patterns to contaminants, and demonstrate the effects on a sensitive fish species of a widely used pyrethroid pesticide at concentrations below those that affect model test species.

Delta Smelt Hypomesus transpacificus, is an endangered fish endemic to the California San Francisco Bay-Delta, USA. Extreme declines of the wild Delta Smelt population have prompted use of cultured fish to supplement the wild population since 2021 to prevent the extinction of the species. However, evidence of adaptation to captivity in the conservation hatchery has raised concerns about the use of captive-bred fish for supplementation and how these fish may differ from wild Delta Smelt. We conducted a study over two consecutive years to investigate the effects of varying levels of captive ancestry on the growth and survival of cultured Delta Smelt from two different domestication index (DI) groups, capturing high DI and low DI values. Fish growth and survival were monitored in the hatchery from larval to adult life-stages to determine differences between DI groups. Our findings indicate that DI can have a significant influence as we observed reduced growth and survival of low DI fish at multiple life-stages. The results suggest that the DI of released hatchery-reared Delta Smelt may affect the performance of their offspring in the natural environment. Further studies might be necessary to develop a better management strategy on the released fish to enhance the conservation efforts.

We used a combination of published literature and field survey data to synthesize the available information about habitat use by delta smelt Hypomesus transpacificus, a declining native species in the San Francisco Estuary. Delta smelt habitat ranges from San Pablo and Suisun bays to their freshwater tributaries, including the Sacramento and San Joaquin rivers. In recent years, substantial numbers of delta smelt have colonized habitat in Liberty Island, a north Delta area that flooded in 1997. The species has a more upstream distribution during spawning as opposed to juvenile rearing periods. Post-larvae and juveniles tend to have a more downstream distribution during wetter years. Delta smelt are most common in low-salinity habitat (<6 psu) with high turbidities (>12 NTU) and moderate temperatures (7 °C to 25 °C). They do not appear to have strong substrate preferences, but sandy shoals are important for spawning in other osmerids. The evidence to date suggests that they generally require at least some tidal flow in their habitats. Delta smelt also occur in a wide range of channel sizes, although they seem to be rarer in small channels (<15 m wide). Nonetheless, there is some evidence that open water adjacent to habitats with long water-residence times (e.g. tidal marsh, shoal, low-order channels) may be favorable. Other desirable features of delta smelt habitat include high calanoid copepod densities and low levels of submerged aquatic vegetation (SAV) and the toxic algae Microcystis. Although enough is known to plan for large-scale pilot habitat projects, these efforts are vulnerable to several factors, most notably climate change, which will change salinity regimes and increase the occurrence of lethal temperatures. We recommend restoration of multiple geographical regions and habitats coupled with extensive monitoring and adaptive management. An overall emphasis on ecosystem processes rather than specific habitat features is also likely to be most effective for recovery of the species.

Urban rivers are socioecological systems, and restored habitats may be attractive to both sensitive species and recreationists. Understanding the potential conflicts between ecological and recreational values is a critical issue for the development of a sustainable river-management plan. Habitat models are very promising tools for the ecological evaluation of river restoration projects that are already concluded, ongoing, or even to be planned. With our paper, we make a first attempt at integrating recreational user pressure into habitat modeling. The objective of this study was to analyze whether human impact is likely to hinder the re-establishment of a target species despite the successful restoration of physical habitat structures in the case of the restoration of the Isar River in Munich (Germany) and the target fish species Chondostroma nasus L. Our analysis combined high-resolution 2D hydrodynamic modeling with mapping of recreational pressure and used an expert-based procedure for modeling habitat suitability. The results are twofold: (1) the restored river contains suitable physical habitats for population conservation but has low suitability for recruitment; (2) densely used areas match highly suitable habitats for C. nasus. In the future, the integrated modeling procedure presented here may allow ecological refuge for sensitive target species to be included in the design of restoration and may help in the development of visitor-management plans to safeguard biodiversity and recreational ecosystem services.

We examined predation by nonnative Mississippi Silversides Menidia audens, other small fishes, and invertebrates on the early life stages of the endangered Delta Smelt Hypomesus transpacificus, which is endemic to the Sacramento–San Joaquin Delta in California. Mississippi Silversides and other putative predators were collected primarily via boat electrofishing in the northern reaches of the upper San Francisco Estuary, an area targeted for substantial tidal wetland restoration to enhance habitat for Delta Smelt and other endangered fishes. Predators’ digestive tracts were removed and analyzed for the presence of Delta Smelt DNA by using quantitative PCR TaqMan assays. Across all sites, 69 of 550 Mississippi Silversides tested positive for Delta Smelt DNA. The number of sampled Mississippi Silversides that were positive for Delta Smelt DNA was significantly greater in offshore habitats than in nearshore habitats. Delta Smelt DNA detection data indicated that a wide variety of other species were also predators of Delta Smelt. Additionally, we used generalized linear modeling to analyze the relationship between Delta Smelt predation detections in Mississippi Silversides and concurrently collected habitat parameters. Turbidity was identified as a significant predictor of predation, as Delta Smelt DNA was detected more often in Mississippi Silverside samples from clearer water. These results suggest that restoration efforts designed to increase turbidity in the estuary may be beneficial in reducing Mississippi Silversides’ predatory impacts on Delta Smelt.Received August 24, 2015; accepted February 3, 2016 Published online June 15, 2016

This study uses Landsat 5, 7, and 8 level 2 collection 2 surface temperature to examine habitat suitability conditions spanning 1985-2019, relative to the thermal tolerance of the endemic and endangered delta smelt (Hypomesus transpacificus) and two non-native fish, the largemouth bass (Micropterus salmoides) and Mississippi silverside (Menidia beryllina) in the upper San Francisco Estuary. This product was validated using thermal radiometer data collected from 2008 to 2019 from a validation site on a platform in the Salton Sea (RMSE = 0.78 °C, r = 0.99, R2 = 0.99, p < 0.01, and n = 237). Thermally unsuitable habitat, indicated by annual maximum water surface temperatures exceeding critical thermal maximum temperatures for each species, increased by 1.5 km2 yr-1 for the delta smelt with an inverse relationship to the delta smelt abundance index from the California Department of Fish and Wildlife (r = -0.44, R2 = 0.2, p < 0.01). Quantile and Theil-Sen regression showed that the delta smelt are unable to thrive when the thermally unsuitable habitat exceeds 107 km2. A habitat unsuitable for the delta smelt but survivable for the non-natives is expanding by 0.82 km2 yr-1. Warming waters in the San Francisco Estuary are reducing the available habitat for the delta smelt.

The establishment of nonnative predatory fish species is a worldwide phenomenon often having adverse effects on native species. Trophic interactions are complex, and uncertainty is a common theme in discussions of nonnative predator management. Several fishes of the San Francisco Estuary have experienced significant declines in recent decades due to multiple factors, including habitat alteration and predation. The role of predation as a direct cause of mortality remains an open question, as does whether habitat conditions play a role in promoting predation on species of concern. Recent studies using visual identification of prey have found little to no evidence of predation on species listed under the Endangered Species Act such as Delta Smelt Hypomesus transpacificus and juvenile Chinook Salmon Oncorhynchus tshawytscha. To increase the likelihood of detecting predation, this study employed a genetic approach. We combined this technique with habitat and water quality data to investigate the role that habitat may be playing on incidence of predation. This study focused on detection of predation on Chinook Salmon and Delta Smelt, six other native fish species, and six nonnative fish species by Striped Bass Morone saxatilis and other piscivores. Unlike previous studies in the region, the proportion of predators with no prey detected in their gut contents was high (47–81%). The study detected Delta Smelt in 1.3% of Striped Bass—considerably higher than other contemporary predation studies in the Sacramento–San Joaquin Delta. In April 2014, 6.6% of Striped Bass were positive for Chinook Salmon—substantially higher than observed in recent visual diet studies. Interestingly, native species comprised a relatively high proportion of Striped Bass prey (60%). Water temperature and conductivity were identified as significant predictors of Chinook Salmon presence in Striped Bass gut contents. This research also suggests that predation on soft-bodied prey may be an overlooked segment of the diets of piscivores.

Understanding reproductive behavior of sensitive species is crucial for their conservation. The Delta Smelt Hypomesus transpacificus is a federally threatened, state‐endangered fish whose reproductive behavior is poorly understood. We used genetic techniques to investigate the spawning behavior of cultured Delta Smelt in a conservation hatchery. We conducted a natural tank‐spawning experiment in a total of four separate tanks during two spawning seasons. Delta Smelt were allowed to spawn in order to investigate spawning patterns using genetic parentage analysis of larvae produced. In total, 2,474 larvae were assigned two parents with &gt;80% likelihood. Of the adults that had larvae assigned to them, males spawned on average 2.8 times and females 1.7 times. The mean number of larvae produced by females was 40.7, while males produced a mean number of 19.2 larvae during a single spawning season. Genetic diversity was reduced from the parent population to the offspring population, as indicated by a small but significant reduction in heterozygosity. Finally, we found no evidence that Delta Smelt preferred to mate with unrelated individuals.