Bay Delta Research Articles

Evaluating the effects of climate change on managed lowland rivers in the California Bay Delta Watershed

Water that is released from reservoirs can affect the downstream thermal regimes of rivers. During the summer months, these flow releases can lower the river temperature downstream of dams in an extension that mainly depends on the volume and temperature of these releases and the energy exchange with the overlying atmosphere. The benefit of this cooling effect has been suggested as an approach to mitigate the effects of climate change in downstream-regulated rivers. However, anticipated climate change conditions may weaken these cooling benefits, especially in managed lowland rivers (MLRs), as they are subjected to large withdrawals, are shallow, and convey clear water. Here, we show that MLRs in the California Bay Delta Watershed are vulnerable to water temperature increases, especially during future summer months subjected to a future high-emission greenhouse scenario. Low-flow conditions exacerbate this vulnerability, especially at locations downstream of high-flow diversions. By using a physical energy balance model (FLUVIAL-EB) paired with a downscaled climate regional model (CRCM5-RCP8.5), we found that for summer months between 2030 and 2100, longwave and latent heat fluxes will contribute to water temperature increases, while absorbed solar radiation will likely decrease under future climate scenarios. Despite the warming effects of climate change on MLRs in the California Bay Delta Watershed, our findings suggest that increasing the release of hypolimnetic water from reservoirs during summer months can be a viable solution to mitigate the river temperature increase.

Implementing Superresolution of Nonstationary Tides with Wavelets: An Introduction to CWT_Multi

Abstract Tides are often nonstationary due to nonastronomical influences. Investigating variable tidal properties implies a trade-off between separating adjacent frequencies (using long analysis windows) and resolving their time variations (short analysis windows). Previous continuous wavelet transform (CWT) tidal methods resolved tidal species. Here, we present CWT_Multi, a MATLAB code that 1) uses CWT linearity (via the “response coefficient method”) to implement superresolution, i.e., resolving tidal constituents beyond the Rayleigh criterion; 2) provides a Munk–Hasselmann constituent selection criterion appropriate for superresolution; and 3) introduces an objective, time-variable form of inference (“dynamic inference”) based on time-varying data properties. CWT_Multi resolves tidal species on time scales of days, and multiple constituents per species with fortnightly filters. It outputs astronomical phase lags and admittances, analyzes multiple records, and provides power spectra of the signal(s), residual(s), and reconstruction(s); confidence limits; and signal-to-noise ratios. Artificial data and water levels from the Lower Columbia River Estuary (LCRE) and San Francisco Bay Delta (SFBD) are used to test CWT_Multi and compare it to harmonic analysis programs NS_Tide and UTide. CWT_Multi provides superior reconstruction, detiding, dynamic analysis utility, and time resolution of constituents (but with broader confidence limits). Dynamic inference resolves closely spaced constituents (like K1, S1, and P1) on fortnightly time scales, quantifying impacts of diel power peaking (with a 24-h period, like S1) on water levels in the LCRE. CWT_Multi also helps quantify the impacts of high flows and a salt barrier closing on tidal properties in the SFBD. On the other hand, CWT_Multi does not excel at prediction, and results depend on analysis details, as for any method applied to nonstationary data. Significance Statement Ocean tides, especially in coastal and estuarine systems, are often nonstationary, in the sense that the mean and standard deviation of tidal properties vary over time, usually in response to some nontidal process. We introduce here a MATLAB code, CWT_Multi, that uses wavelet transforms to resolve both tidal species and constituents on time scales from a few days to months. Our code accommodates multiple scalar time series and has typical tidal analysis features like constituent selection and inference, plus two forms of uncertainty analyses. It is flexible, allowing the user to adapt analysis properties to diverse datasets. CWT_Multi is applicable to many problems involving time-variable tides, including sea level rise, compound flooding, sediment transport, and wetland habitat analyses. Application to vector data is a straightforward extension, but further development of our uncertainty analysis is merited. Because nonstationary tidal analysis is rapidly advancing, we also define the features of a “well-formed” analysis code.

Evaluating Habitat Suitability and Tidal Wetland Restoration Actions With ECOSTRESS

AbstractAs temperatures rise, it is increasingly important to monitor changes in habitat conditions for aquatic species and mitigate emerging stressors. The ECOsystem Spaceborne Thermal Radiometer Experiment on Space Station (ECOSTRESS) instrument provides temperature products at a spatial and temporal scale not previously available. Here, we utilize ECOSTRESS temperature products to assess fluctuations in thermal habitat suitability for an endangered fish species and we also demonstrate the utility of the data set to assess water surface and bulk temperature changes following completion of two tidal wetland restoration efforts in the San Francisco Estuary and Sacramento–San Joaquin River Delta (Bay Delta). During all hours of the day throughout the 2018–2022 study period, key Delta Smelt habitat areas including Honker Bay, West Suisun Bay, and Mid Suisun Bay had greater than 75% of their areas suitable; there were several instances during which less than 25% of the area was thermally suitable generally coinciding with heatwave events. Overall, midday hours are less frequently suitable than morning and evening hours. Early evidence from ECOSTRESS indicates that there may be a decrease in surface water temperature of up to several degrees in tidal restoration areas, but more data is needed to show statistically significant outcomes. The ECOSTRESS record began in summer of 2018, and a longer record is needed to fully capture temperature changes associated with wetland processes and restoration efforts. Future applications of ECOSTRESS products can the capacity to help further understand ecosystem conditions and how restoration efforts affect water temperature, informing decisions that benefit Delta Smelt and other at‐risk aquatic species.

Resilience of riparian vegetation productivity to early 21st century drought in northern California, USA

AbstractDrought and intensive land use can interact as stressors on riparian vegetation, especially along rivers flowing through seasonally dry landscapes. Knowledge of past riparian vegetation response to drought and land use change can provide land managers with a better understanding of changes induced by upstream management actions, climate change, and chronic stressors. To investigate the response of riparian vegetation productivity to drought and land use, we developed a 21‐year time series (2000–2020) of growing season vegetation dynamics using near‐infrared reflectance of vegetation (NIRV) derived from satellite data across 30 watershed subbasins that drain into the San Francisco Bay Delta in central California, USA. We observed a strong response of riparian vegetation to drought, but rapid recovery and very few long‐term declines in productivity. At a local level, vegetation communities' response to drought and post‐drought productivity dynamics were highly variable across biophysical settings and land use gradients. Most of the riparian areas with long‐term declines in NIRV were located in the lower elevation Coast Range on the western side of the study area where there is little to no water engineering or agricultural irrigation runoff to subsidize riparian vegetation. Riparian areas with the greatest long‐term increase were along rivers draining the higher elevation Sierra Nevada range to the east. Our results suggest that river systems with a high proportion of water originating as snowmelt may be more buffered against long‐term drought‐driven declines in productivity than those dependent exclusively on winter rainfall. The long‐term increase in NIRV in the vast majority of riparian areas within our study area may also have been driven in part by increasing atmospheric CO2 concentrations, which have been shown to increase plant water use efficiency.

Status, Trends, and Drivers of Harmful Algal Blooms Along the Freshwater-to-Marine Gradient in the San Francisco Bay–Delta System

Harmful algal blooms (HABs) are on the rise worldwide. Known drivers for the proliferation and intensification of HAB events include increasing nutrient pollution, climate change, regulation and modification of hydrological flow, and the combined effect of climate drivers and nutrient pollution. The San Francisco Bay–Delta system has largely been immune to severe or acute HAB events, but there is both a potential and realized threat which has been underestimated and under-reported, in part because of the lack of coordinated sampling and data reporting. There is also increasing evidence that HABs must be considered in the context of a freshwater-to-marine continuum, and that the physical and political boundaries separating components of the Bay–Delta system are porous barriers to HABs and their toxins. Much remains to be learned about the ecology and physiology of HAB organisms in this system, but five primary environmental drivers can be identified: temperature, salinity, irradiance, nutrients, and stratification/residence time. All these drivers are responding rapidly to climate change, but nutrients are the primary variable that is largely under human control. Plans for the development of a comprehensive monitoring, prediction, and mitigation strategy across the freshwater-to-marine continuum have been documented; effectively following through on these plans provides a roadmap toward identifying the drivers and threats—and reducing the potential consequences now and in the future. While HABs alone are not a sufficient motivator for potentially costly and extensive mitigation efforts, there is strong evidence that decreasing nutrient loads, maintaining hydrological connectivity while minimizing stagnant regions, and managing the biota to maintain biodiversity of the Bay–Delta system will result in multiple co-benefits, including reduction of the HAB threat potential.

Incorporating expanded sampling into an alternative abundance index for the Fall Midwater Trawl survey

The Fall Midwater Trawl (FMWT) Survey has been conducted near continuously since 1967 to assess the abundance and distribution of pelagic fish species throughout the San Francisco Bay/Sacramento-San Joaquin estuary (Bay Delta). For most of this period, sampling 100 core stations provided data for abundance and distribution analyses. Another 22 (non-core) stations were added to the FMWT 8 to 28 years ago to supplement the original 100 (core) stations. However, relative abundance indices are published annually from only the data collected at the core stations. Here we incorporate data from non-core stations along with core station data to calculate an alternative index that also integrates modern estimates of water volume within the Bay Delta into an index calculation. The use of data from non-core stations in calculating the alternative index was particularly useful for American Shad (Alosa sapidissima) and Threadfin Shad (Dorosoma petenense). Consistently high catches at non-core stations for a couple species and modest catches for a couple additional species highlight the value of these additional catch data for our understanding of how fishes are distributed in the estuary.

Wakasagi in the San Francisco Bay Delta Watershed: Comparative Trends in Distribution and Life-History Traits with Native Delta Smelt

Intentional introductions of non-native fishes can severely affect native communities. Wakasagi (Hypomesus nipponensis, referred to as Japanese Pond Smelt) are native to Japan and were once separated from their non-native congener the endangered Delta Smelt (Hypomesus transpacificus) of the San Francisco Estuary (hereon “estuary”) of California. Wakasagi were introduced into California reservoirs in the 20th century as forage fish. Wakasagi have since expanded their distribution downstream to the estuary, but less is known about Wakasagi’s current distribution status, biology in the estuary, and negative influences on Delta Smelt. In this study, we took a comparative approach by synthesizing long-term field monitoring surveys, modeling environmental associations, and quantifying phenology, growth, and diets of Wakasagi and Delta Smelt to describe abundance and range, trends of co-occurrence, and shared ecological roles between smelt species. We found Wakasagi in greatest abundance in the upper watershed below source reservoirs, and in the northern regions of the estuary with the most co-occurrence with Delta Smelt; however, their range extends to western regions of the estuary, and we found evidence of an established population that annually spawns and rears in the estuary. We found these smelt species have similar ecological roles demonstrated by overlaps in habitat use (e.g., an association with higher turbidities and higher outflow), phenology, growth, and diets. Despite similarities, earlier hatching and rearing of Wakasagi during cooler months and reduced growth during warmer drought years suggest this species is unlike typical non-natives (e.g., Centrarchids), and they exhibit a similar sensitivity to environmental variability as Delta Smelt. This sensitivity may be why Wakasagi abundance remains relatively low in the estuary.

Patterns of Water Use in California

Recent patterns of water use and supply in California are presented based on a new data set compiled from the California Department of Water Resources water balance data for 2002 through 2016. The water use and supply include surface water and groundwater, although groundwater reporting has been incomplete. These data are used to support the Water Plan released every 3 to 5 years and are the most comprehensive and finest spatial- and temporal-scale data set for California water resources. First, using the Bay–Delta watershed as a case example, we show that recent fluctuations in water use are highly correlated with variations in precipitation. Developed water supplies and use show these fluctuations, but they are modified by reservoir inflows and releases, groundwater supplies, and Delta outflows. Second, although the annually precipitated water supply in the Bay–Delta varies by about 30%, the developed water supply damps this considerably. The water management system maintained nearly constant agricultural water use even in periods of intense drought, with year-to-year variation of about 7%. Variability in urban water use is higher (∼20%), largely from conservation during periods of drought. Finally, this information can help improve water resource management because it connects regional-scale data to meaningful policy decision-making at county and sub-county levels. At a time when water policy and management are being re-evaluated across the American West in the light of changing climate, decision-making informed by science and data is urgently needed. The statewide water balance data provide the means to establish a consistent, quantitative framework for water resource analysis throughout the state.

Toxic Meals for Seabirds and Seals: Monitoring Mercury in the San Francisco Bay

Mercury is a metal pollutant that travels thousands of miles through air and water. It flows along rivers to lakes, estuaries, and the sea, cycling between animals and their environments. Extensive mercury mining during the Gold Rush left lasting impacts on the San Francisco Bay Delta, one of California’s largest wetland habitats and home to thousands of species. Burning fossil fuels in cities like San Francisco also releases mercury, leading to its buildup in local food chains. Mercury accumulates from plankton to fish to top predators like sharks and seals, where it reaches potentially harmful levels. Mercury never fully breaks down and continues cycling in ecosystems, even reaching migratory animals living offshore in the Pacific Ocean. Scientists collect samples from wildlife to uncover clues about mercury sources and threats to human health. This article explains the mercury problem and why we track this invisible pollutant in the San Francisco Bay.

High aqueous salinity does not preclude germination of invasive Iris pseudacorus from estuarine populations

AbstractEstuarine ecosystems are threatened by climate change and biological invasions. Among global changes, sea‐level rise is broadly impacting tidal wetlands, through increases in salinity and alteration of inundation regimes. Extant freshwater plant species are often presumed to be limited to reaches of estuaries with low salinity and narrow tidal ranges. However, the potential for invasive freshwater species (e.g., Iris pseudacorus) to persist and spread with increased salinity and flooding is poorly understood and can jeopardize native biodiversity and other wetland ecosystem services. The successful establishment of invasive plants will be dependent on their tolerance to salinity and inundation, starting with the germination life stage. Changes to abiotic estuarine gradients may alter the germination process of tidal wetland plant species that underlies significant patterns of plant community composition and biodiversity. We explored germination responses of seeds from two invasive I. pseudacorus populations from freshwater and brackish tidal sites in California’s San Francisco Bay–Delta Estuary. We tested germination dynamics under salinity levels ranging from freshwater to seawater (0, 12.5, 25, and 45 dS/m) and two hydrological conditions (moist and flooded). Salinity levels >12.5 dS/m inhibited germination of seeds from both populations, consistent with viviparism and seedling emergence recorded at field sites. However, seeds exposed to seawater for 55 d germinated once exposed to freshwater. Germination velocity and seed buoyancy differed between populations, likely due to differences in seed coat thickness. Our results demonstrate that after 55 d in seawater, buoyant seeds of I. pseudacorus retain their ability to germinate, and germinate quickly with freshwater exposure. This suggests that invasive populations of I. pseudacorus can colonize new sites following potentially long‐distance dispersal of buoyant seeds with tidal currents. These findings inform risk assessments and highlight the need to prioritize the management of invasive I. pseudacorus in estuarine ecosystems impacted by rising sea level.

The effects of temperature and salinity on the endocrinology in two life stages of juvenile rainbow/steelhead trout (Oncorhynchus mykiss)

The San Francisco Bay Delta is experiencing seasonally warmer waters and saltwater intrusion into historically freshwater ecosystems due to climate change. Steelhead/rainbow trout (Oncorhynchus mykiss) are resident in the Bay-Delta from juvenile development through the smoltification process. Due to increases in sea level, premature seawater (SW) acclimation may co-occur with increased temperatures on pre-smolt juveniles. To evaluate the interactive effects of salinity and temperature on juvenile life stages of salmonids, rainbow trout alevin (3 days post-hatching) were exposed to 13, 16.4 and 19°C for 10 days and then challenged for 24 h to 18 parts per thousand SW. Similarly, fry (4 weeks post-hatching) were exposed to 13, 16.4 and 19°C for 2 weeks (14 days) and then challenged to SW. Estradiol-17β (E2 ), cortisol, triiodothyronine (T3 ) and thyroxine (T4 ) were measured in whole animal homogenates and muscle tissue using enzyme-linked immunosorbent assays. Transcripts of gill Na+ /K+ ATPase β (NKAα1b), brain growth hormone I (gh1) and brain gonadotropin-releasing hormone receptor 2 (gnrh2) were also measured. Alevin exhibited a significant temperature-dependent decrease in survival, and fry showed a temperature-dependent decrease in condition factor. The gene expression of NKAα1b, gh1 and gnrh2 significantly decreased in all SW-challenged alevin, and a significant decrease in gnrh2 expression was observed in fry with temperature. Alevin T3 and T4 concentrations significantly increased with increasing temperature. There was a temperature-dependent increase in E2 of fry but not of alevin. The results of this study demonstrate that increasing temperature and SW exposure may adversely affect the survival and SW acclimation of alevin and fry stages of salmonids and that the tolerances of younger juvenile stages should be considered when assessing the response of salmonid populations to climate change stressors.

Salinity Changes the Dynamics of Pyrethroid Toxicity in Terms of Behavioral Effects on Newly Hatched Delta Smelt Larvae.

Salinity can interact with organic compounds and modulate their toxicity. Studies have shown that the fraction of pyrethroid insecticides in the aqueous phase increases with increasing salinity, potentially increasing the risk of exposure for aquatic organisms at higher salinities. In the San Francisco Bay Delta (SFBD) estuary, pyrethroid concentrations increase during the rainy season, coinciding with the spawning season of Delta Smelt (Hypomesus transpacificus), an endangered, endemic fish. Furthermore, salinity intrusion in the SFBD is exacerbated by global climate change, which may change the dynamics of pyrethroid toxicity on aquatic animals. Therefore, examining the effect of salinity on the sublethal toxicity of pyrethroids is essential for risk assessments, especially during the early life stages of estuarine fishes. To address this, we investigated behavioral effects of permethrin and bifenthrin at three environmentally relevant concentrations across a salinity gradient (0.5, 2 and 6 PSU) on Delta Smelt yolk-sac larvae. Our results suggest that environmentally relevant concentrations of pyrethroids can perturb Delta Smelt larvae behavior even at the lowest concentrations (<1 ng/L) and that salinity can change the dynamic of pyrethroid toxicity in terms of behavioral effects, especially for bifenthrin, where salinity was positively correlated with anti-thigmotaxis at each concentration.

Exposure to permethrin or chlorpyrifos causes differential dose- and time-dependent behavioral effects at early larval stages of an endangered teleost species.

Pyrethroid and organophosphate pesticides are two of the most commonly used classes of insecticide worldwide. At sublethal concentrations, permethrin (a pyrethroid) and chlorpyrifos (an organophosphate) impact behavior in model fish species. We investigated behavioral effects of environmentally relevant concentrations of permethrin or chlorpyrifos on early larval delta smelt Hypomesus transpacificus, a Critically Endangered teleost species endemic to the San Francisco Bay Delta, California, USA. Using a photomotor behavioral assay of oscillating light and dark periods, we measured distance moved, turn angle, meander, angular velocity, rotations, thigmotaxis (time spent in the border versus center), and swim speed duration and frequency. The lowest concentrations of permethrin used in the tests (0.05 and 0.5 μg l−1) caused significant increases in distance moved at 72 and 96 h, respectively. At 48, 72, and 96 h of exposure, 5 μg l−1 of permethrin caused a hyperactive state in which the larvae significantly decreased thigmotaxis, quickly turning in short bouts of activity, characterized by significant increases in rotations and freezing events. Larvae exposed to 0.05 μg l−1 chlorpyrifos significantly increased thigmotaxis at 72 and 96 h. In response to 5 μg l−1 chlorpyrifos, larvae significantly increased velocity at 72 h exposure, and significantly increased freezing events at 96 h. Behavioral data on larval delta smelt exposed to contaminants present in their limited habitat have the potential to aid evaluations of the suitability of spawning and rearing habitats for this endangered species, thus improving conservation management strategies focused on this sensitive life stage.

Response of Lower Sacramento River phytoplankton to high-ammonium wastewater effluent

Since the 1980s, the San Francisco Bay Delta ecosystem has experienced large declines in primary production. Hypothesized reasons for this decline include (1) suppression of nitrate (NO3−) uptake, and thus phytoplankton growth, due to high concentrations of ammonium (NH4+), and (2) wastewater NH4+-induced changes in phytoplankton community composition away from large-celled diatoms. These twin hypotheses implicate NH4+ loading from the Sacramento Regional Wastewater Treatment Plant effluent outfall in explaining declines in primary production in the region. They have been controversial within the water resources management community and have stimulated a lengthy public scientific and regulatory debate. Here, in an effort to resolve this debate, we present results from a 48-h incubation experiment with surface water from both upstream and downstream of the Sacramento Regional Wastewater Treatment Plant effluent outfall, a major source of NH4+ loading to the ecosystem. We amended this water with either NH4+, NO3−, or full wastewater effluent. All assays were incubated under high light (52% of incident irradiance) or low light (6% of incident irradiance). NO3− uptake rates were suppressed to near zero in all treatments with either added NH4+, added wastewater effluent, or high in situ NH4+ concentrations. Yet, phytoplankton uniformly grew well on all dissolved inorganic nitrogen sources, including effluent and NH4+. Diatom species were the most abundant taxa at all stations, and diatom cell abundances increased at greater rates than all other taxa over the course of the experiment. Among all treatments, the light treatment had the greatest effects on chlorophyll a accumulation and phytoplankton growth rates. Our results suggest that high NH4+ loading is not a driver of the lower productivity in the San Francisco Bay Delta. Although phytoplankton preferred NH4+ to NO3− when both were available in our experiment, the form of dissolved inorganic nitrogen had no effect on growth rates or species composition.

Large‐Scale Flow Management Action Drives Estuarine Ecological Response

AbstractResource managers rely on large‐scale flow and habitat enhancement actions to support sensitive species in the San Francisco Bay–Delta. The effects of these actions on target species and ecosystems are largely unknown. In 2018, we implemented an ecosystem‐scale experiment to reduce salinity and improve access to high‐quality habitat in Suisun Marsh, California, for Endangered Species Act‐listed Delta Smelt Hypomesus transpacificus. The action included a release of approximately 46 million m3 of additional flow in conjunction with the operation of a novel water management facility, the Suisun Marsh Salinity Control Gates. This experimental action resulted in more low‐salinity habitat in Suisun Marsh than would have been present as compared to similar historical low‐flow summer conditions. We evaluated the effect of decreasing salinity on the species assemblage in Suisun Marsh using a combination of ordination analyses and circular statistics. We focused this analysis on long‐term monitoring data collected within Suisun Marsh during July and August and found that the aquatic community changed significantly in small sloughs but not large‐slough habitat in response to the Suisun Marsh action. The assemblage shift from July to August 2018 differed from historical trends in both slough sizes, albeit not significantly in large‐slough habitat. Specifically, we observed (1) a shift in California bay shrimp Crangon franciscorum and Striped Bass Morone saxatilis abundance like that occurring in low‐salinity, wet water year types; and (2) an uncharacteristic seasonal decline in Black Sea jellyfish Maeotias marginata. We posit that the observed community changes were driven by a combination of behavioral responses to lower‐salinity conditions and physical displacement by directional flow resulting from the flow management action.

How to Respond? An Introduction to Current Bay–Delta Natural Resources Management Options

Abstracts are not presented with Essays. -The SFEWS Editors

Bifenthrin exposure causes hyperactivity in early larval stages of an endangered fish species at concentrations that occur during their hatching season

Bifenthrin is a pyrethroid insecticide commonly used in agricultural and urban sectors, and is found in watersheds worldwide. As a sodium channel blocker, at sublethal concentrations it causes off-target effects, including disruption of calcium signaling and neuronal growth. At the whole organism level, sublethal concentrations of bifenthrin cause behavioral effects in fish species, raising concerns about the neurotoxic properties of the compound on fish populations. Here we describe the application of a high-throughput behavioral system to evaluate contaminant impacts on the sensitive early-life stages of Delta smelt (Hypomesus transpacificus), a critically endangered teleost species endemic to the San Francisco Bay Delta (SFBD), California, USA.Leveraging the natural behavior of early-larval Delta smelt, whereby they increase movement in bright light and decrease movement in the dark, we developed a test using a cycle of light and dark periods in a closed chamber to test hyper- or hypoactivity for this species. We show that early-larval Delta smelt have a significant preference to move toward light, and utilized the behavioral test to evaluate the impact of exposure to bifenthrin at concentrations found in habitats where Delta smelt reportedly spawn, ranging up to concentrations detected in tributaries to these habitats. All tested concentrations of bifenthrin (nominal 2, 10, or 100 ng/L) caused hyperactivity, over a 96 h exposure, with noted significance determined during the light period of the test. To further understand the impact of bifenthrin exposure, expression of a suite of genes relevant to neurodevelopment, the mechanistic target of rapamycin (mTOR) signaling pathway, and biotransformation in exposed larvae were also measured. Following exposure to picomolar concentrations of bifenthrin, expression of genes in the mTOR signaling and neurogenesis pathways were altered alongside behavior. This study demonstrates how light and dark cycle behavioral tests can be used to assess sensitive alterations in swimming activity in Delta smelt at early developmental stages and how gene expression can complement these assays. This approach can be used to assess the impact of multiple compounds that occur within the restricted habitat of Delta smelt, thus having the potential to greatly inform conservation management strategies for this critically sensitive life stage.

Improving the Transferability of Suspended Solid Estimation in Wetland and Deltaic Waters with an Empirical Hyperspectral Approach

The deposition of suspended sediment is an important process that helps wetlands accrete surface material and maintain elevation in the face of sea level rise. Optical remote sensing is often employed to map total suspended solids (TSS), though algorithms typically have limited transferability in space and time due to variability in water constituent compositions, mixtures, and inherent optical properties. This study used in situ spectral reflectances and their first derivatives to compare empirical algorithms for estimating TSS using hyperspectral and multispectral data. These algorithms were applied to imagery collected by NASA’s Airborne Visible/Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG) over coastal Louisiana, USA, and validated with a multiyear in situ dataset. The best performing models were then applied to independent spectroscopic data collected in the Peace–Athabasca Delta, Canada, and the San Francisco Bay–Delta Estuary, USA, to assess their robustness and transferability. A derivative-based partial least squares regression (PLSR) model applied to simulated AVIRIS-NG data showed the most accurate TSS retrievals (R2 = 0.83) in these contrasting deltaic environments. These results highlight the potential for a more broadly applicable generalized algorithm employing imaging spectroscopy for estimating suspended solids.

Geospatial Tools for the Large-Scale Monitoring of Wetlands in the San Francisco Estuary: Opportunities and Challenges

Author(s): Taddeo, Sophie; Dronova, Iryna | Abstract: Significant wetland losses and continuing threats to remnant habitats have motivated extensive restoration efforts in the San Francisco Bay–Delta estuary of California, the largest in the western United States. Consistent monitoring of ecological outcomes from this restoration effort would help managers learn from past projects to improve the design of future endeavors. However, budget constraints and challenging field conditions can limit the scope of current monitoring programs. Geospatial tools and remote sensing data sets could help complement field efforts for a low-cost, longer, and broader monitoring of wetland resources. To understand where geospatial tools could best complement current field monitoring practices, we reviewed the metrics and monitoring methods used by 42 wetland restoration projects implemented in the estuary. Monitoring strategies within our sample of monitoring plans relied predominantly on field surveys to assess key aspects of vegetation recovery while geospatial data sets were used sparingly. Drawing on recent publications that focus on the estuary and other wetland systems, we propose additional geospatial applications to help monitor the progress made toward site-specific and regional goals. These include the use of ecological niche models to target on-the-ground monitoring efforts, the up-scaling of field measurements into regional estimates using remote sensing data, and the analysis of time-series to detect ecosystem shifts. We discuss challenges and limitations to the broad-scale application of remote sensing data in wetland monitoring. These notably include the need to find a venue to store and share computationally intensive data sets, the often cumbersome pre-processing effort needed for long-term analyses, and multiple confounding factors that can obscure the signal of remote sensing data sets.

Developmental staging and salinity tolerance in embryos of the delta smelt, Hypomesus transpacificus

Delta smelt (Hypomesus transpacificus) is a critically endangered species endemic to the San Francisco Bay Delta (SFBD). Important for the conservation of this species is understanding the physiological and ecological impacts contributing to their population decline, and current studies lack information on embryonic development. Changes in patterns of salinity across the SFBD may be a particularly important environmental stressor contributing to the recruitment and survival of the species. Throughout their ontogeny, delta smelt may exhibit unique requirements and tolerances to environmental conditions including salinity. Here, we describe 22 stages of embryonic development of delta smelt that characterize early differentiation from the fertilized egg until hatching, allowing the identification of critical morphological features unique to this species. Additionally, we investigated aspects of physiological tolerance to environmental salinity during development. Embryos survived incubation at salinity treatments between 0.4 and 20 ppt, yet had lower hatch success at higher salinities. Prior to hatching, embryos exposed to higher salinities had increased osmolalities and reduced fractions of yolk implying that the elevated external salinity altered the physiology of the embryo and the environment internal to the chorion. Lastly, egg activation and fertilization appear to also be impacted by salinity. Altogether, we suggest that any potential tolerance to salinity during embryogenesis, a common feature in euryhaline teleost species, impacts life cycle transitions into, and out of, embryonic development. Results from this investigation should improve conservation and management practices of this species and further expand our understanding of the intimate relationship between an embryo and its environment.