Sacramento-San Joaquin River Delta Research Articles

Clams on stilts: a phytoplankton bioassay investigating effects of wastewater effluent amendments and Corbicula fluminea grazing

Shallow-water habitats are being restored in the Sacramento-San Joaquin River Delta with the goal of enhancing phytoplankton production and food availability for higher trophic levels. However, elevated grazing pressure from the non-native freshwater clam Corbicula fluminea and localized depletions of dissolved inorganic nitrogen may limit phytoplankton biomass accumulation in restored habitats. To evaluate interactions between nutrients and grazing on phytoplankton productivity and biomass accumulation, Sacramento River water high or low in phytoplankton biomass was amended with wastewater effluent, presence of C. fluminea, or both, in 48 h in situ incubations. We measured changes in chl a concentration, phytoplankton community composition, and photosynthetic efficiency as well as carbon and nitrogen uptake rates as indicators of phytoplankton responses. Diatoms dominated phytoplankton communities before and after incubation. Chl a concentrations increased 0.7 and 7.4 times in the high and low phytoplankton biomass controls, respectively, and 4.5 and 14 times in the high and low phytoplankton biomass effluent-added treatments, respectively. In the clam treatments, chl a accumulation was suppressed to near zero regardless of effluent additions or initial phytoplankton biomass. In treatments with clams and effluent combined, phytoplankton photosynthetic efficiency was nearly 50% lower than in the effluent-only treatments, suggesting phytoplankton were stressed in the presence of clams. This experiment demonstrated that the presence of clams can prevent the accumulation of phytoplankton biomass, both directly by clam filtering and indirectly by depressing phytoplankton photosynthetic efficiency and rate of growth. We recommend that future wetland restoration projects promoting increased phytoplankton biomass assess clam settlement likelihood as well as nutrient availability.

A Simple Approach to Modeling Light Attenuation in the Sacramento–San Joaquin Delta Using Commonly Available Data

The diffuse attenuation coefficient of photosynthetically active radiation (KdPAR) is commonly used to predict light attenuation in aquatic productivity models, but obtaining measurements of PAR to compute KdPAR is difficult. In situ calculations of KdPAR require multiple measurements of PAR through the water column, and these measurements are infeasible for real-time recording. Instead, predictive models using surface-water measurements may be used. Traditional KdPAR models are based on open-ocean habitats and rely on chlorophyll—as a proxy measurement for phytoplankton abundance—as the main predictive parameter. However, elevated suspended sediments and dissolved organic materials may also affect KdPAR values of inland water bodies and estuaries. In this study, we leverage KdPAR calculations derived from in situ light measurements collected along with surface-water-quality parameters across the Sacramento-San Joaquin River Delta in California, USA (the Delta). Sampling occurred between January of 2013 and May of 2014. We also explored regional and seasonal effects, but these did not clearly affect the model. Ultimately, the best-performing model included surface-level turbidity only (R2 = 0.91). The simplicity of the model facilitates use of KdPAR estimates for a variety of purposes throughout the Delta, including euphotic depth calculations, and as inputs to primary-productivity and habitat-suitability models. We demonstrate the model’s usability with two open-sources data sets (one spatially dense, and one temporally dense), and estimate KdPAR, euphotic depth, and primary productivity within the Delta. We provide calculations for each estimation, allowing users to easily adopt these models and apply them to their own data or with open-sourced data, which are abundant.

Multiple trophic pathways support fish on floodplains of California's Central Valley.

We used compound-specific isotope analysis of carbon isotopes in amino acids (AAs) to determine the biosynthetic source of AAs in fish from major tributaries to California's Sacramento-San Joaquin river delta (i.e., the Sacramento, Cosumnes and Mokelumne rivers). Using samples collected in winter and spring between 2016 and 2019, we confirmed that algae are a critical component of floodplain food webs in California's Central Valley. Results from bulk stable isotope analysis of carbon and nitrogen in producers and consumers were adequate to characterize a general trophic structure and identify potential upstream and downstream migration into our study site by American shad Alosa sapidissima and rainbow trout Oncorhynchus mykiss, respectively. However, owing to overlap and variability in source isotope compositions, our bulk data were unsuitable for conventional bulk isotope mixing models. Our results from compound-specific carbon isotope analysis of AAs clearly indicate that algae are important sources of organic matter to fish of conservation concern, such as Chinook salmon Oncorhynchus tshawytscha in California's Central Valley. However, algae were not the exclusive source of energy to metazoan food webs. We also revealed that other sources of AAs, such as bacteria, fungi and higher plants, contributed to fish as well. While consistent with the well-supported notion that algae are critical to aquatic food webs, our results highlight the possibility that detrital subsidies might intermittently support metazoan food webs.

Floodplain trophic subsidies in a modified river network: managed foodscapes of the future?

ContextCross-boundary subsidies create important growth opportunities for a range of taxa. In modified river systems, remnant patches of floodplain and flood bypasses become ephemeral hotspots of zooplankton production, however, the extent to which these prey items are (or could be) transported downstream is unclear.ObjectivesWe investigated the diet of juvenile salmon under varying hydroclimatic conditions to assess the importance of floodplain-produced prey subsidies in an otherwise food-scarce region.MethodsJuvenile salmon (n = 3033) and zooplankton were sampled across the California Central Valley Sacramento-San Joaquin River Delta in 2014–2018, incorporating a range of climatic conditions including drought and flood. Salmon stomach fullness and diet composition, and ambient zooplankton densities were used to assess spatiotemporal patterns in prey production and consumption.ResultsFloodplain-produced cladocerans provided ephemeral food pulses to juvenile salmon in downstream riverine habitats. Salmon had the fullest stomachs in wetter years (2016–2017) and the emptiest stomachs in the final year of a multi-year drought (2015). Cladoceran abundances in the water column and salmon diets were highest during wet periods and below floodplains, and decreased with increasing distance downstream, consistent with flow-mediated trophic subsidies.ConclusionsThese data emphasize the importance of maintaining diverse, interconnected habitats to support resilient fish populations and the potential for managing floodplains to boost prey production and delivery. Here, the inundation of a flood bypass (or lack of) played a pivotal role shaping the juvenile salmon foodscape. As freshwater ecosystems are increasingly transformed by large-scale engineering, it is important to coordinate infrastructure, habitat and flow modifications to maximize climate resilience and trophic benefits to target species.

RURAL TURTLES: ESTIMATING THE OCCUPANCY OF NORTHWESTERN POND TURTLES AND NON-NATIVE RED-EARED SLIDERS IN AGRICULTURAL HABITATS IN CALIFORNIA'S SACRAMENTO VALLEY AND SACRAMENTO-SAN JOAQUIN RIVER DELTA

The Northwestern Pond Turtle (Actinemys marmorata; WPT) was once widespread throughout the Sacramento Valley and the Sacramento-San Joaquin River Delta. Much of its historical range has been converted into agricultural land, reducing and altering aquatic habitat and surrounding uplands. Red-eared Sliders (Trachemys scripta elegans; RES) have been introduced throughout much of the existing WPT range, particularly near urban centers, potentially competing with WPT for resources. Previous surveys for turtles in central California have primarily focused on rivers, lakes, and protected wetlands. Little is known about where WPT and RES occur in the vast expanses of agricultural land across the Sacramento Valley and Sacramento-San Joaquin River Delta. Using aquatic hoop nets, we surveyed 142 locations (102 irrigation canal sites, 39 wetlands, 1 tidally influenced slough) across 8 counties during the summers of 2018 and 2019. Both species were detected in agricultural habitats. Using occupancy modeling, we estimated that WPT occur at 44 (95% CRI = 38–53) of our trapping sites and RES occur at 51 (41–66) sampled sites. Co-occurrence of these 2 species was rare; the species were found together at only 6 sites. RES were primarily found in restored wetlands near major roads and the Sacramento metropolitan area, whereas WPT were more commonly found farther from urban areas in wider canals. Our work provides a picture of how WPT and RES occupy this modified agroecosystem that can inform future conservation efforts.

Integrating monitoring and optimization modeling to inform flow decisions for Chinook salmon smolts

Monitoring is usually among the first actions taken to help inform recovery planning for declining species, but these data are rarely used formally to inform conservation decision making. For example, Central Valley Chinook salmon were once abundant, but anthropogenic activities have led to widespread habitat loss and degradation resulting in significant population declines. Monitoring data suggest survival through the southern Sacramento-San Joaquin River Delta, in particular, may be a limiting factor for juvenile Chinook salmon outmigrating from the San Joaquin River and its tributaries. However, survival and routing monitoring data have not been formally used to inform water management in a decision analytic framework. Here, we illustrate how estimates derived from disjunct monitoring data can be used to inform water management and as a basis for adaptively managing flows. We aggregated a meta-analysis of Chinook salmon smolt survival and routing estimates through the south Delta with other sources of data to develop a survival and routing simulation model to estimate optimal flows for the San Joaquin River during smolt outmigration from February–May. We found that large flow pulses at predictable times during the spring are projected to be optimal for increasing Chinook salmon smolt survival to the San Francisco Bay and that optimal scenarios differed somewhat with water year type. Sensitivity analysis revealed temperature and smolt outmigration timing are driving optimal pulse distribution and that water allocation changes little with parameter uncertainty. This case study highlights the utility of the decision-analytic framework for solving conservation problems.

Biological control of water hyacinth, Pontederia crassipes (C. Mart.) Solms (Pontederiaceae), in California: release and re-distribution of biological control agents 1987–2006

Water hyacinth, Pontederia crassipes (C. Mart.) Solms (Pontederiaceae), is a serious aquatic weed in lakes, ponds, and waterways in California and around the world. Three insects, the weevils Neochetina eichhorniae Warner, 1970, Neochetina bruchi Hustache, 1926 (Coleoptera: Brachyceridae), and a leaf moth Niphograpta albiguttalis (Warren, 1889) (Lepidoptera: Crambidae) were released at four sites in 1982–1987 for the biological control of water hyacinth in the Sacramento-San Joaquin River Delta. Here we report on statewide efforts to distribute the biological control agents outside the Delta and subsequent surveys to determine insect establishment. From 1987–2006, the three insects were redistributed to seven locations in five counties (Fresno, Los Angeles, Merced, Sacramento, and Santa Cruz) in California. Surveys in 2018–2020 found both Neochetina weevils at two locations in Merced County and one location in Sacramento County. No weevils were found at release locations in the upper San Joaquin River and associated waterways in western Fresno County or at the release location in Santa Cruz County. Plants at the release locations in Los Angeles County and eastern Fresno County had been eradicated and not sampled in this survey. These recoveries expand the known locations of Neochetina weevils in central California. The hyacinth moth, N. albiguttalis, was not recovered.

Assessing the distribution and abundance of larval Longfin Smelt: What can a larval monitoring program tell us about the distribution of a rare species?

Following its listing as threatened under the California Endangered Species Act in 2009, Longfin Smelt (Spirinchus thaleichthys) became a focus of resource managers in the San Francisco Estuary. Water exports were identified as one of the factors affecting Longfin Smelt abundance, and managers were challenged with balancing freshwater flows through the Sacramento-San Joaquin River Delta between human and ecosystem needs. This balance becomes especially challenging during the winter and spring when Longfin Smelt are spawning. Resource managers identified that the impact associated with entrainment of larval Longfin Smelt in the winter was uncertain, and to understand and manage this risk, new data was needed. In 2009 the Smelt Larva Survey was implemented and has since sampled newly hatched larvae from January–March. Here, I analyze this data and ask specific questions regarding distribution and densities of the larvae throughout five regions of the Upper Estuary – Napa River, Suisun, Confluence, Northern Delta, and Southern Delta – with the goal of understanding the spatial and temporal patterns of larval distribution since 2009. I found that larvae were most prevalent in the Suisun, Confluence, and Northern Delta regions, and less common in the Southern Delta and Napa River regions. Larval Longfin Smelt densities changed following a recent drought and record low population abundances. Median per-station averaged densities ranged from 154 to 274 fish per 1,000 m3 between 2009 and 2013 but declined to 1 to 65 fish per 1,000 m3 from 2014 to 2019. This survey data demonstrates that Longfin Smelt reproductive output has declined since their listing in 2009 and that their distribution into the Southern Delta is low relative to the rest of the Upper Estuary. These results reaffirm the species’ continued decline since its listing, and that improving the abundance of spawning adults is one of the many important steps needed for long-term recovery and resilience.

Performance and Feasibility of Drone-Mounted Imaging Spectroscopy for Invasive Aquatic Vegetation Detection

Invasive plants are non-native species that can spread rapidly, leading to detrimental economic, ecological, or environmental impact. In aquatic systems such as the Sacramento-San Joaquin River Delta in California, USA, management agencies use manned aerial vehicles (MAV) imaging spectroscopy missions to map and track annual changes in invasive aquatic plants. Advances in unmanned aerial vehicles (UAV) and sensor miniaturization are enabling higher spatial resolution species mapping, which is promising for early detection of invasions before they spread over larger areas. This study compared maps made from UAV-based imaging spectroscopy with the manned airborne imaging spectroscopy-derived maps that are currently produced for monitoring invasive aquatic plants in the Sacramento-San Joaquin Delta. Concurrent imagery was collected using the MAV mounted HyMap sensor and the UAV mounted Nano-Hyperspec at a wetland study site and classification maps generated using random forest models were compared. Classification accuracies were comparable between the Nano- and HyMap-derived maps, with the Nano-derived map having a slightly higher overall accuracy. Additionally, the higher resolution of the Nano imagery allowed detection of patches of water hyacinth present in the study site that the HyMap could not. However, it would not be feasible to operate the Nano as a replacement to HyMap at scale despite its improved detection capabilities due to the high costs associated with overcoming area coverage limitations. Overall, UAV-based imaging spectroscopy provides comparable or improved capability, and we suggest it could be used to supplement existing monitoring programs by focusing on target areas of high ecologic or economic priority.

Abiotic and biotic influences on the performance of two biological control agents, Neochetina bruchi and N. eichhorniae, in the Sacramento-San Joaquin River Delta, California (USA)

Variability in the effectiveness of biological control programs can be due to a myriad of abiotic and biotic interactions. Here, we explore these interactions in relation to the suboptimal biological control on the invasive water hyacinth, Pontederia (=Eichhornia) crassipes, by two weevils, Neochetina bruchi and N. eichhorniae, in the Sacramento-San Joaquin River Delta in California, USA (Delta). We conducted monthly surveys from 2015 to 2017 throughout 1667 km2 to analyze the impacts of temperature, nutrients, river flow, pathogens and genetic variation in relation to the performance of these biological control agents. Weevils (predominantly N. bruchi) demonstrated a positive numerical response to increased nitrogen content in water hyacinth crown and roots. Weevil densities and water hyacinth biomass declined significantly during periods of high river flow. We found negative impacts of cooler temperatures on weevil performance, with a significant lagged-response of weevil densities in the field to water temperature from three months prior and a lack of population growth under laboratory conditions simulating winter air temperatures in the Delta (3.9–13.9 °C). We confirmed the presence of a microsporidian pathogen, with 10.7% average prevalence of infection across four seasons and low infection loads. In addition, we found low genetic diversity of N. bruchi in the Delta compared to native populations, low population genetic structure and a lack of genetic isolation by distance among metapopulations. Overall we conclude that cooler temperatures and periods of high river flow are likely the main factors limiting the current biological control program in the Delta.

Analysis of Covalently Bound Microcystins in Sediments and Clam Tissue in the Sacramento-San Joaquin River Delta, California, USA.

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.

Toxicity of herbicides to cyanobacteria and phytoplankton species of the San Francisco Estuary and Sacramento-San Joaquin River Delta, California, USA

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.

Invasive perennial forb effects on gross soil nitrogen cycling and nitrous oxide fluxes depend on phenology.

Invasive plants can increase soil nitrogen (N) pools and accelerate soil N cycling rates, but their effect on gross N cycling and nitrous oxide (N2 O) emissions has rarely been studied. We hypothesized that perennial pepperweed (Lepidium latifolium) invasion would increase rates of N cycling and gaseous N loss, thereby depleting ecosystem N and causing a negative feedback on invasion. We measured a suite of gross N cycling rates and net N2 O fluxes in invaded and uninvaded areas of an annual grassland in the Sacramento-San Joaquin River Delta region of northern California. During the growing season, pepperweed-invaded soils had lower microbial biomass N, gross N mineralization, dissimilatory nitrate reduction to ammonium (DNRA), and denitrification-derived net N2 O fluxes (P<0.02 for all). During pepperweed dormancy, gross N mineralization, DNRA, and denitrification-derived net N2 O fluxes were stimulated in pepperweed-invaded plots, presumably by N-rich litter inputs and decreased competition between microbes and plants for N (P<0.04 for all). Soil organic carbon and total N concentrations, which reflect pepperweed effects integrated over longer time scales, were lower in pepperweed-invaded soils (P<0.001 and P=0.04, respectively). Overall, pepperweed invasion had a net negative effect on ecosystem N status, depleting soil total N to potentially cause a negative feedback to invasion in the long term.

Invasive Aquatic Vegetation Management in the Sacramento–San Joaquin River Delta: Status and Recommendations

Author(s): Ta, Jenny; Anderson, Lars W.J.; Christman, Mairgareth A.; Khanna, Shruti; Kratville, David; Madsen, John D.; Moran, Patrick J.; Viers, Joshua H. | Abstract: https://doi.org/10.15447/sfews.2017v15iss4art5 Widespread growth of invasive aquatic vegetation is a major stressor to the Sacramento-San Joaquin River Delta, a region of significant recreational, economic, and ecological importance. Total invaded area in the Delta is increasing, with the risk of new invasions a continual threat. However, invasive aquatic vegetation in the Delta remains an elusive ecosystem management challenge despite decades of directed scientific research and prioritized policy recognition. In this paper, we summarize the current state of knowledge of the history, status, and potential future directions for coordinated research, management actions, and policy based on topics discussed at symposium head on invasive aquatic vegetation on September 15, 2015. Remote sensing technology, mechanical, chemical, and biological control, as well as community science networks have all been shown to be effective management tools, but overall effectiveness has been hindered by complex regulatory structure, the lack of a consistent monitoring program, regulations that restrict treatments in space and time, and funding cuts. In addition, new management options depend on continued research and development of new active ingredients for chemical control and testing of biological control agents. The ongoing development and implementation of new strategies for adaptive, integrated management of aquatic weeds, using currently-available management tools, new knowledge derived from remote sensing and plant growth models, and an area-wide, ecosystem-based approach, is showing promise to achieve improved management outcomes and enhance protection of the Delta’s water resources.

Spatial and temporal variation of biological control agents associated with Eichhornia crassipes in the Sacramento-San Joaquin River Delta, California

The invasive water hyacinth (Eichhornia crassipes) severely limits the ecosystem services provided by the Sacramento-San Joaquin River Delta in California, USA. As part of the biological control program in the Delta, two weevils, Neochetina bruchi and N. eichhorniae (Coleoptera: Curculionidae) and a moth, Niphograpta albiguttalis (Lepidoptera: Pyralidae), were released in the 1980s. Additionally, a planthopper, Megamelus scutellaris (Hemiptera: Delphacidae) was released in 2011. We conducted monthly surveys for one year at 16 sites throughout 1667km2 of the Delta to determine the resulting establishment, abundance and distribution of these introduced herbivores. Morphological identifications, and partial sequencing of the mitochondrial cytochrome oxidase subunit 1 gene determined that 96.6% of the examined weevils were N. bruchi. N. eichhorniae was only recovered from two sites in the southern Delta tributaries. Densities (larvae and adult weevils per destructively sampled plant) varied spatially and temporally. Peak mean densities (averaged across August–November) decreased with increasing distance from the original release sites. Peak mean densities ranged from 0.31 to 6.31 weevils per plant. Densities averaged across sites were the lowest in June 2015 (0.54 weevils), increasing in August to 5.35 weevils, and peaking in November at 6.22 weevils. The proportion of damaged leaf area from weevil feeding increased concomitantly with weevil densities. Although N. albiguttalis was not recovered, M. scutellaris remained established at its original release site but has not dispersed into the other surveyed regions. We propose hypotheses to explain patterns in species establishment and distribution, with potential mechanisms for improved future biological control.

Erosion characteristics and horizontal variability for small erosion depths in the Sacramento-San Joaquin River Delta, California, USA

Erodibility of cohesive sediment in the Sacramento-San Joaquin River Delta (Delta) was investigated with an erosion microcosm. Erosion depths in the Delta and in the microcosm were estimated to be about one floc diameter over a range of shear stresses and times comparable to half of a typical tidal cycle. Using the conventional assumption of horizontally homogeneous bed sediment, data from 27 of 34 microcosm experiments indicate that the erosion rate coefficient increased as eroded mass increased, contrary to theory. We believe that small erosion depths, erosion rate coefficient deviation from theory, and visual observation of horizontally varying biota and texture at the sediment surface indicate that erosion cannot solely be a function of depth but must also vary horizontally. We test this hypothesis by developing a simple numerical model that includes horizontal heterogeneity, use it to develop an artificial time series of suspended-sediment concentration (SSC) in an erosion microcosm, then analyze that time series assuming horizontal homogeneity. A shear vane was used to estimate that the horizontal standard deviation of critical shear stress was about 30% of the mean value at a site in the Delta. The numerical model of the erosion microcosm included a normal distribution of initial critical shear stress, a linear increase in critical shear stress with eroded mass, an exponential decrease of erosion rate coefficient with eroded mass, and a stepped increase in applied shear stress. The maximum SSC for each step increased gradually, thus confounding identification of a single well-defined critical shear stress as encountered with the empirical data. Analysis of the artificial SSC time series with the assumption of a homogeneous bed reproduced the original profile of critical shear stress, but the erosion rate coefficient increased with eroded mass, similar to the empirical data. Thus, the numerical experiment confirms the small-depth erosion hypothesis. A linear model of critical shear stress and eroded mass is proposed to simulate small-depth erosion, assuming that the applied and critical shear stresses quickly reach equilibrium.

LC- and GC-QTOF-MS as Complementary Tools for a Comprehensive Micropollutant Analysis in Aquatic Systems.

Efficient strategies are required to implement comprehensive suspect screening methods using high-resolution mass spectrometry within environmental monitoring campaigns. In this study, both liquid and gas chromatography time-of-flight mass spectrometry (LC-QTOF-MS and GC-QTOF-MS) were used to screen for >5000 target and suspect compounds in the Sacramento-San Joaquin River Delta in Northern California. LC-QTOF-MS data were acquired in All-Ions fragmentation mode in both positive and negative electrospray ionization (ESI). LC suspects were identified using two accurate mass LC-QTOF-MS/MS libraries containing pesticides, pharmaceuticals, and other environmental contaminants and a custom exact mass database with predicted transformation products (TPs). The additional fragment information from the All-Ions acquisition improved the confirmation of the compound identity, with a low false positive rate (9%). Overall, 25 targets, 73 suspects, and 5 TPs were detected. GC-QTOF-MS extracts were run in negative chemical ionization (NCI) for 21 targets (mainly pyrethroids) at sub-ng/L levels. For suspect screening, extracts were rerun in electron ionization (EI) mode with a retention time locked method using a GC-QTOF-MS pesticide library (containing exact mass fragments and retention times). Sixteen targets and 42 suspects were detected, of which 12 and 17, respectively, were not identified by LC-ESI-QTOF-MS. The results highlight the importance of analyzing water samples using multiple separation techniques and in multiple ionization modes to obtain a comprehensive chemical contaminant profile. The investigated river delta experiences significant pesticide inputs, leading to environmentally critical concentrations during rain events.

Measuring landscape-scale spread and persistence of an invaded submerged plant community from airborne remote sensing.

Processes of spread and patterns of persistence of invasive species affect species and communities in the new environment. Predicting future rates of spread is of great interest for timely management decisions, but this depends on models that rely on understanding the processes of invasion and historic observations of spread and persistence. Unfortunately, the rates of spread and patterns of persistence are difficult to model or directly observe, especially when multiple rates of spread and diverse persistence patterns may be co-occurring over the geographic distribution of the invaded ecosystem. Remote sensing systematically acquires data over large areas at fine spatial and spectral resolutions over multiple time periods that can be used to quantify spread processes and persistence patterns. We used airborne imaging spectroscopy data acquired once a year for 5years from 2004 to 2008 to map an invaded submerged aquatic vegetation (SAV) community across 2220km2 of waterways in the Sacramento-San Joaquin River Delta, California, USA, and measured its spread rate and its persistence. Submerged aquatic vegetation covered 13-23km2 of the waterways (6-11%) every year. Yearly new growth accounted for 40-60% of the SAV area, ~50% of which survived to following year. Spread rates were overall negative and persistence decreased with time. From this dataset, we were able to identify both radial and saltatorial spread of the invaded SAV in the entire extent of the Delta over time. With both decreasing spread rate and persistence, it is possible that over time the invasion of this SAV community could decrease its ecological impact. A landscape-scale approach allows measurements of all invasion fronts and the spatial anisotropies associated with spread processes and persistence patterns, without spatial interpolation, at locations both proximate and distant to the focus of invasion at multiple points in time.

Anadromous Salmonids in the Delta: New Science 2006-2016

As juvenile salmon enter the Sacramento–SanJoaquin River Delta (“the Delta”) they disperse among its complex channel network where they are subject to channel-specific processes that affect their rate of migration, vulnerability to predation, feeding success, growth rates, and ultimately, survival. In the decades before 2006, tools available to quantify growth, dispersal, and survival of juvenile salmon in this complex channel network were limited.Fortunately, thanks to technological advances such as acoustic telemetry and chemical and structural otolith analysis, much has been learned over the past decade about the role of the Delta in the life cycle of juvenile salmon. Here, we review new science between 2006and 2016 that sheds light on how different life stages and runs of juvenile salmon grow, move, and survive in the complex channel network of the Delta. One of the most important advances during the past decade has been the widespread adoption of acoustic telemetry techniques. Use of telemetry has shed light on how survival varies among alternative migration routes and the proportion of fish that use each migration route. Chemical and structural analysis of otoliths has provided insights about when juveniles left their natal river and provided evidence of extended rearing in the brackish or saltwater regions of the Delta. New advancements in genetics now allow individuals captured by trawls to be assigned to specific runs. Detailed information about movement and survival in the Delta has spurred development of agent-based models of juvenile salmon that are coupled to hydrodynamic models. Although much has been learned, knowledge gaps remain about how very small juvenile salmon (fry and parr) use theDelta. Understanding how all life stages of juvenile salmon grow, rear, and survive in the Delta is critical for devising management strategies that support a diversity of life history strategies.

The nature of organic carbon in density-fractionated sediments in the Sacramento-San Joaquin River Delta (California)

Abstract. Rivers are the primary means by which sediments and carbon are transported from the terrestrial biosphere to the oceans but gaps remain in our understanding of carbon associations from source to sink. Bed sediments from the Sacramento-San Joaquin River Delta (CA) were fractionated according to density and analyzed for sediment mass distribution, elemental (C and N) composition, mineral surface area, and stable carbon and radiocarbon isotope compositions of organic carbon (OC) and fatty acids to evaluate the nature of organic carbon in river sediments. OC was unevenly distributed among density fractions. Mass and OC were in general concentrated in mesodensity (1.6–2.0 and 2.0–2.5 g cm−3) fractions, comprising 84.0 ± 1.3 % of total sediment mass and 80.8 ± 13.3 % of total OC (TOC). Low-density (&lt; 1.6 g cm−3) material, although rich in OC (34.0 ± 2.0 % OC) due to woody debris, constituted only 17.3 ± 12.8 % of TOC. High-density (&gt; 2.5 g cm−3) organic-poor, mineral-rich material made-up 13.7 ± 1.4 % of sediment mass and 2.0 ± 0.9 % of TOC. Stable carbon isotope compositions of sedimentary OC were relatively uniform across bulk and density fractions (δ13C −27.4 ± 0.5 ‰). Radiocarbon content varied from Δ14C values of −382 (radiocarbon age 3800 yr BP) to +94 ‰ (modern) indicating a mix of young and old OC. Fatty acids were used to further constrain the origins of sedimentary OC. Short-chain n-C14–n-C18 fatty acids of algal origin were depleted in 13C (δ13C −37.5 to −35.2 ‰) but were enriched in 14C (Δ14C &gt; 0) compared to long-chain n-C24–n-C28 acids of vascular plant origins with higher δ13C (−33.0 to −31.0 ‰) but variable Δ14C values (−180 and 61 ‰). These data demonstrate the potentially complex source and age distributions found within river sediments and provide insights about sediment and organic matter supply to the Delta.