Assessments at multiple levels of biological organization allow for an integrative determination of physiological tolerances to turbidity in an endangered fish species

Evaluating environmental DNA detection of a rare fish in turbid water using field and experimental approaches

Detection sensitivity of aquatic species using environmental DNA (eDNA) generally decreases in turbid water but is poorly characterized. In this study, eDNA detection targeted delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish associated with turbid water. eDNA sampling in the field was first paired with a trawl survey. Species-specific detection using a Taqman qPCR assay showed concordance between the methods, but a weak eDNA signal. Informed by the results of field sampling, an experiment was designed to assess how turbidity and filtration methods influence detection of a rare target. Water from non-turbid (5 NTU) and turbid (50 NTU) estuarine sites was spiked with small volumes (0.5 and 1 mL) of water from a delta smelt tank to generate low eDNA concentrations. Samples were filtered using four filter types: cartridge filters (pore size 0.45 μm) and 47 mm filters (glass fiber, pore size 1.6 μm and polycarbonate, pore sizes 5 and 10 μm). Prefiltration was also tested as an addition to the filtration protocol for turbid water samples. eDNA copy numbers were analyzed using a censored data method for qPCR data. The assay limits and lack of PCR inhibition indicated an optimized assay. Glass fiber filters yielded the highest detection rates and eDNA copies in non-turbid and turbid water. Prefiltration improved detection in turbid water only when used with cartridge and polycarbonate filters. Statistical analysis identified turbidity as a significant effect on detection probability and eDNA copies detected; filter type and an interaction between filter type and prefilter were significant effects on eDNA copies detected, suggesting that particulate-filter interactions can affect detection sensitivity. Pilot experiments and transparent criteria for positive detection could improve eDNA surveys of rare species in turbid environments.

Shoaling behaviour in response to turbidity in three-spined sticklebacks

Many fresh and coastal waters are becoming increasingly turbid because of human activities, which may disrupt the visually mediated behaviours of aquatic organisms. Shoaling fish typically depend on vision to maintain collective behaviour, which has a range of benefits including protection from predators, enhanced foraging efficiency and access to mates. Previous studies of the effects of turbidity on shoaling behaviour have focussed on changes to nearest neighbour distance and average group-level behaviours. Here, we investigated whether and how experimental shoals of three-spined sticklebacks (Gasterosteus aculeatus) in clear (<10 Nephelometric Turbidity Units [NTU]) and turbid (~35 NTU) conditions differed in five local-level behaviours of individuals (nearest and furthest neighbour distance, heading difference with nearest neighbour, bearing angle to nearest neighbour and swimming speed). These variables are important for the emergent group-level properties of shoaling behaviour. We found an indirect effect of turbidity on nearest neighbour distances driven by a reduction in swimming speed, and a direct effect of turbidity which increased variability in furthest neighbour distances. In contrast, the alignment and relative position of individuals was not significantly altered in turbid compared to clear conditions. Overall, our results suggest that the shoals were usually robust to adverse effects of turbidity on collective behaviour, but group cohesion was occasionally lost during periods of instability.

Effects of turbidity, temperature and predation cue on the stress response of juvenile delta smelt

The San Francisco Estuary (SFE) is one of the most degraded ecosystems in the United States, and organisms that inhabit it are exposed to a suite of environmental stressors. The delta smelt (Hypomesus transpacificus), a small semi-anadromous fish endemic to the SFE and considered an indicator species, is close to extinction in the wild. The goal of this study was to investigate how environmental alterations to the SFE, such as reductions in turbidities, higher temperatures and increased prevalence of invasive predators affect the physiology and stress response of juvenile delta smelt. Juvenile delta smelt were exposed to two temperatures (17 and 21°C) and two turbidities (1-2 and 10-11 NTU) for 2 weeks. After the first week of exposure, delta smelt were exposed to a largemouth bass (Micropterus salmoides) predator cue at the same time every day for 7 days. Fish were measured and sampled on the first (acute) and final (chronic) day of exposures to predator cues and later analyzed for whole-body cortisol, glucose, lactate, and protein. Length and mass measurements were used to calculate condition factor of fish in each treatment. Turbidity had the greatest effect on juvenile delta smelt and resulted in reduced cortisol, increased glucose and lactate, and greater condition factor. Elevated temperatures reduced available energy in delta smelt, indicated by lower glucose and total protein, whereas predator cue exposure had negligible effects on their stress response. This is the first study to show reduced cortisol in juvenile delta smelt held in turbid conditions and adds to the growing data that suggest this species performs best in moderate temperatures and turbidities. Multistressor experiments are necessary to understand the capacity of delta smelt to respond to the multivariate and dynamic changes in their natural environment, and results from this study should be considered for management-based conservation efforts.

Reproductive strategy of Delta Smelt Hypomesus transpacificus and impacts of drought on reproductive performance

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.

Monitoring Turbidity in San Francisco Estuary and Sacramento-San Joaquin Delta Using Satellite Remote Sensing

This study utilizes satellite data to investigate water quality conditions in the San Francisco Estuary and its upstream delta, the Sacramento-San Joaquin River Delta. To do this, this study derives turbidity from the European Space Agency satellite Sentinel-2 acquired from September 2015 to June 2019 and conducts a rigorous validation with in situ measurements of turbidity from optical sensors at continuous monitoring stations. This validation includes 965 matchup comparisons between satellite and in situ sensor data across 22 stations, yielding R ² = 0.63 and 0.75 for Nephelometric Turbidity Unit and Formazin Nephelometric Unit (FNU) stations, respectively. This study then applies remote sensing to evaluate patterns in turbidity during the Suisun Marsh Salinity Control Gates Action ("Gates action"), a pilot study designed to increase habitat access and quality for the endangered Delta Smelt. The basic strategy was to direct more freshwater into Suisun Marsh, creating more low salinity habitat that would then have higher (and more suitable) turbidity than upstream river channels. For all seven acquisitions considered from June 29 to September 27, 2018, turbidity conditions in Bays and Sloughs subregions were consistently higher (and more suitable) (26-47 FNU) than what was observed in the upstream River region (13-25 FNU). This overall pattern was observed when comparing images acquired during similar tidal stages and heights.

A case study of factors controlling water quality in two warm monomictic tropical reservoirs located in contrasting agricultural watersheds

The integration of internal (e.g., stratification) and external (e.g., pollution) factors on a comprehensive assessment of reservoir water quality determines the success of ecosystem restoration initiatives and aids watershed management. However, integrated analyses are scarcer than studies addressing factors separately. Integration is likely more efficient in studies of small well-characterized (experimental) reservoir watersheds, because the isolation of factor contributions is presumably clearer. But those studies are uncommon. This work describes the water quality of two small 5.5 m-deep reservoirs (MD-Main and VD-Voçoroca dams) located in Pindorama Experimental Center, state of São Paulo, Brazil, considering the interplay between reservoir dimension, seasonal thermal stratification, chemical gradients, erosive rainfall events, presence of natural biofilters, and land uses and landscape patterns around the reservoirs and within the contributing watersheds. The monitoring of agricultural activities and water quality parameters occurred in October 2018-July 2019. A 4 °C thermal stratification occurred in October (difference between surface and bottom water temperature), which decreased until disappearance in January (VD) or April (MD). The longer stratification period of MD was justified by its larger area relative to VD (≈10×). Thermal stratification triggered hypoxia at the bottom of both reservoirs (DO ≈ 1 mg/L), more prolonged and severe in MD. Hypoxia activated Ec and TDS peaks in January likely explained by bottom-sediment nutrient releases, presumably phosphorus. The Ec peak reached 560 μS/cm in MD and 290 μS/cm in VD. The smaller VD peak was probably explained by the action of macrophytes. In March, a 240 NTU turbidity peak occurred in MD, caused by precedent erosive rainfall and the lack of vegetation protection alongside the south border. As expected, the study accomplished clear isolation of factor contributions, verified by Factor and Cluster analyses. Our results can subsidize studies on larger reservoir watersheds requiring restoration, where the isolation of factors is more challenging.

Impacts of suspended sediment and metal pollution from mining activities on riverine fish population-a review

Mining activities are responsible for the elevated input levels of suspended sediment and hazardous metals into the riverine ecosystem. These have been shown to threaten the riverine fish populations and can even lead to localized population extinction. To date, research on the effects of mining activities on fish has been focused within metal contamination and bioaccumulation and its threat to human consumption, neglecting the effects of suspended sediment. This paper reviews the effects of suspended sediment and metal pollution on riverine ecosystem and fish population by examining the possibilities of genetic changes and population extinction. In addition, possible assessments and studies of the riverine fish population are discussed to cope with the risks from mining activities and fish population declines.

Effects of water turbidity and different temperatures on oxidative stress in caddisfly (Stenopsyche marmorata) larvae

Anthropogenic water turbidity derived from suspended solids (SS) is caused by reservoir sediment management practices such as drawdown flushing. Turbid water induces stress in many aquatic organisms, but the effects of turbidity on oxidative stress responses in aquatic insects have not yet been demonstrated. Here, we examined antioxidant responses, oxidative damage, and energy reserves in caddisfly (Stenopsyche marmorata) larvae exposed to turbid water (0 mg SS L^-1, 500 mg SS L^-1, and 2000 mg SS L^-1) at different temperatures. We evaluated the combined effects of turbid water and temperature by measuring oxidative stress and using metabolic biomarkers. No turbidity level was significantly lethal to S. marmorata larvae. Moreover, there were no significant differences in antioxidant response or oxidative damage between the control and turbid water treatments at a low temperature (10 °C). However, at a high temperature (25 °C), turbid water modulated the activity of the antioxidant enzymes superoxide dismutase and catalase and the oxygen radical absorbance capacity as an indicator of the redox state of the insect larvae. Antioxidant defenses require energy, and high temperature was associated with low energy reserves, which might limit the capability of organisms to counteract reactive oxygen species. Moreover, co-exposure to turbid water and high temperature caused fluctuation of antioxidant defenses and increased the oxidative damage caused by the production of reactive oxygen species. Furthermore, the combined effect of high temperature and turbid water on antioxidant defenses and oxidative damage was larger than the individual effects. Therefore, our results demonstrate that exposure to both turbid water and high temperature generates additive and synergistic interactions causing oxidative stress in this aquatic insect species.

A macrophysiology approach to watershed science and management

Freshwaters are among the most imperiled ecosystems on the planet such that much effort is expended on environmental monitoring to support the management of these systems. Many traditional monitoring efforts focus on abiotic characterization of water quantity or quality and/or indices of biotic integrity that focus on higher scale population or community level metrics such as abundance or diversity. However, these indicators may take time to manifest in degraded systems and delay the identification and restoration of these systems. Physiological indicators manifest rapidly and portend oncoming changes in populations that can hasten restoration and facilitate preventative medicine for degraded habitats. Therefore, assessing freshwater ecosystem integrity using physiological indicators of health is a promising tool to improve freshwater monitoring and restoration. Here, we discuss the value of using comparative, longitudinal physiological data collected at a broad spatial (i.e. watershed) scale (i.e. macrophysiology) as a tool for monitoring aquatic ecosystem health within and among local watersheds to develop timely and effective management plans. There are emerging tools and techniques available for rapid, cost-effective, and non-lethal physiological sampling and we discuss how these can be integrated into management using fish as sentinel indicators in freshwater. Although many examples of this approach are relatively recent, we foresee increasing use of macrophysiology in monitoring, and advocate for the development of more standard tools for consistent and reliable assessment.

Foraging and metabolic consequences of semi-anadromy for an endangered estuarine fish

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.

Fine sediment as environmental stressor affecting freshwater mussel behavior and ecosystem services

Fine sediment pollution is considered a major stressor for aquatic ecosystems and their biodiversity. In particular, fine sediments have been suggested to play a crucial role in the declines of freshwater mussels which are considered keystone fauna of streams and rivers. Whereas the effects of deposited fine sediments on recruitment failure are well known, effects of suspended fine sediments on adult mussel behavior are less studied. Therefore the aim of this study was to investigate the effects of fine sediment exposure on freshwater mussel behavior and on mussel-dependent ecosystem services. Unio pictorum mussels were used to test three behavioral endpoints: Hall activity, transition frequency and relative water clearance rate. Mussels were exposed to fine sediments of different particle size classes (<45μm, 45-63μm, 63-125μm) and different concentration (0-10gL(-1)) of the smallest particle size class. Hall sensor technology and turbidity measurements were used to detect mussel behavior in presence of suspended sediments. Results revealed that mussels improve clearance of suspended particles out of the water column by 35%, independent of particle size class and concentration. Transition frequency was determined an unsuitable behavioral endpoint for non-soluble substances. Contrary to previous studies, we could demonstrate that fine sediments do not interfere with filtration by mussels and that mussels have a great influence on water purification, providing a valuable ecosystem service.