Joaquin Delta Of California Research Articles

The Use of Non-targeted Lipidomics and Histopathology to Characterize the Neurotoxicity of Bifenthrin to Juvenile Rainbow Trout (Oncorhynchus mykiss).

Due to the detection frequencies and measured concentrations in surface water, the type I pyrethroid insecticide, bifenthrin, has been of particular concern within the Sacramento-San Joaquin Delta in California. Concentrations have been detected above levels previously reported to impair neuroendocrine function and induce neurotoxicity to several species of salmonids. Metabolomic and transcriptomic studies indicated impairment of cellular signaling within the brain of exposed animals and potential alteration of lipid metabolism. To better understand the potential impacts of bifenthrin on brain lipids, juvenile rainbow trout (Oncorhynchus mykiss) were exposed to mean bifenthrin concentrations of 28 or 48 ng/L for 14 days, and non-targeted lipidomic profiling in the brain was conducted. Brain tissue sections were also assessed for histopathological insult following bifenthrin treatment. Bifenthrin-exposed trout had a concentration-dependent decrease in the relative abundance of triglycerides (TGs) with levels of phosphatidylcholines (PCs) and phosphatidylethanolamines (PEs) significantly altered following 48 ng/L bifenthrin exposure. An increased incidence of histopathological lesions, such as focal hemorrhages and congestion of blood vessels, was noted in the brains of bifenthrin-treated animals, suggesting an association between altered lipid metabolism and neuronal cell structure and integrity.

We Make the Delta, and the Delta Makes us

The Sacramento-San Joaquin Delta of California was largely shaped, and is maintained by, an immense amount of human activity. Evidence of this activity can be felt everywhere in the Delta, from rock-lined levees to the straight channels, from the non-native fish and plant species to the amount of water that flows through the Delta and where that water goes. How the Delta looks, feels, smells, and functions also impacts the people who live, work, and play in the Delta, and who drink or eat crops grown with Delta water. This article will explore how people have made the Delta and how the Delta influences people’s lives, both within and beyond this unique region.

Restoring wetlands on intensive agricultural lands modifies nitrogen cycling microbial communities and reduces N2O production potential

The concentration of nitrous oxide (N2O), an ozone-depleting greenhouse gas, is rapidly increasing in the atmosphere. Most atmospheric N2O originates in terrestrial ecosystems, of which the majority can be attributed to microbial cycling of nitrogen in agricultural soils. Here, we demonstrate how the abundance of nitrogen cycling genes vary across intensively managed agricultural fields and adjacent restored wetlands in the Sacramento-San Joaquin Delta in California, USA. We found that the abundances of nirS and nirK genes were highest at the intensively managed organic-rich cornfield and significantly outnumber any other gene abundances, suggesting very high N2O production potential. The quantity of nitrogen transforming genes, particularly those responsible for denitrification, nitrification and DNRA, were highest in the agricultural sites, whereas nitrogen fixation and ANAMMOX was strongly associated with the wetland sites. Although the abundance of nosZ genes was also high at the agricultural sites, the ratio of nosZ genes to nir genes was significantly higher in wetland sites indicating that these sites could act as a sink of N2O. These findings suggest that wetland restoration could be a promising natural climate solution not only for carbon sequestration but also for reduced N2O emissions.

Lateral Carbon Exports From Drained Peatlands: An Understudied Carbon Pathway in the Sacramento‐San Joaquin Delta, California

AbstractDegradation of peatlands via drainage is increasing globally and destabilizing peat carbon (C) stores. The effects of drainage on the timing and magnitude of lateral C losses from degraded peatlands remains understudied. We measured spatial and temporal variability in lateral C exports from three drained peat islands in the Sacramento‐San Joaquin Delta in California across the 2017 and 2018 water years using measurements of dissolved inorganic C (DIC), dissolved organic C (DOC), and suspended particulate organic C (POC) concentration combined with discharge. These measurements were supplemented with stable isotope data (δ13C‐DIC, δ13C‐POC, δ15N‐PON, and δ2H‐H2O values) to provide insight into hydrological and biogeochemical controls on lateral C exports from drained peatlands. Drainage DOC and DIC concentrations were seasonally variable with the highest values in the winter rainy season, when discharge was also elevated. Seasonal differences in the mobilization of dissolved C appeared to result from changing water sources and water table levels. Peat island drainage C contributions to surrounding waterways were also greatest during the winter. Although temporal variability in C cycling processes and trends were generally similar across islands, baseline drainage DIC, DOC, and POC concentrations were spatially variable, likely a result of sub‐island‐scale differences in soil organic matter content and hydrology. This spatial variability complicates system‐wide assessments of C budgets. Net lateral C exports were water year dependent and comparable to previously published vertical C emission rates for this system. This work highlights the importance of including lateral C exports from drained peatlands in local and regional C budgets.

Trapping of Suspended Sediment by Submerged Aquatic Vegetation in a Tidal Freshwater Region: Field Observations and Long-Term Trends

Widespread invasion by non-native, submerged aquatic vegetation (SAV) may modify the sediment budget of an estuary, reducing the availability of inorganic sediment required by marshes to maintain their position in the tidal frame. The instantaneous trapping rate of suspended sediment in SAV patches in an estuary has not previously been quantified via field observations. In this study, flows of water and suspended sediment through patches of invasive SAV were measured at three tidally forced, freshwater sites, all located within the Sacramento-San Joaquin Delta in California. An acoustic Doppler current profiler deployed from a roving vessel provided velocity and backscatter data used to quantify fluxes of both water and suspended sediment. Sediment trapping efficiency, defined as instantaneous net trapped flux divided by incident flux, was positive in 24 of 29 cases, averaging + 5%. Coupled with 3 years of measured sediment flux data at one site, this suggests that trapping averages 3.7 kg m−2 year−1. This estimate compares favorably with the mean mass accumulation rate of 3.8 kg m−2 year−1 estimated from dated sediment cores collected at the study sites. Long-term measurements made upstream reveal a strong negative trend (− 1.8% year−1) in suspended sediment concentration, and intra-annual changes in both suspended sediment concentration and percent fines. The large footprint and high spatial density of invasive SAV coupled with declining sediment supply are diminishing downstream suspended sediment concentrations, potentially reducing the resiliency of marshes in the Delta and lower estuary to future sea-level rise.

Development of extraction and detection method for fluridone in water and sediment by HPLC-UV

Fluridone is widely used as a herbicide for controlling invasive aquatic plants such as hydrilla in surface water bodies. When applied on surface waters fluridone can attach to bed sediment, requiring rigorous extraction methods prior to analysis. Currently, very limited information exists in terms of fluridone residue detection in delta sediment. In this study, we researched fluridone detection in both water and sediment. To extract fluridone from sediment, here we have tested two extraction methods: (1) a rotavapor method (RM); and (2) a quick, easy, cheap, effective, rugged and safe (QuEChERS) method (QM). The extraction results of RM were compared with those of QM. To quantify fluridone concentrations in extracts, a high-performance liquid chromatography (HPLC)-UV detector was used. HPLC separation was achieved using an Allure C18 5 µm 150 × 4.6 mm column with a mobile phase composed of acetonitrile and water (60:40, v/v). The UV detector was operated at 237 nm. The method was tested and validated using a series of water and sediment samples taken from Sacramento–San Joaquin Delta in California. The average recovery of fluridone was 73% and 78% using RM and QM respectively. The proposed method can be used for testing fluridone in water and sediment samples.

Assessing the carbon and climate benefit of restoring degraded agricultural peat soils to managed wetlands

Restoring degraded peat soils presents an attractive, but largely untested, climate change mitigation approach. Drained peat soils used for agriculture can be large greenhouse gas sources. By restoring subsided peat soils to managed, impounded wetlands, significant agricultural emissions are avoided, and soil carbon can be sequestered and protected. Here, we synthesize 36 site-years of continuous carbon dioxide and methane flux data from a mesonetwork of eddy covariance towers in the Sacramento-San Joaquin Delta in California, USA to compute carbon and greenhouse gas budgets for drained agricultural land uses and compare these to restored deltaic wetlands. We found that restored wetlands effectively sequestered carbon and halted soil carbon loss associated with drained agricultural land uses. Depending on the age and disturbance regime of the restored wetland, many land use conversions from agriculture to restored wetland resulted in emission reductions over a 100-year timescale. With a simple model of radiative forcing and atmospheric lifetimes, we showed that restored wetlands do not begin to accrue greenhouse gas benefits until nearly a half century, and become net sinks from the atmosphere after a century. Due to substantial interannual variability and uncertainty about the multi-decadal successional trajectory of managed, restored wetlands, ongoing ecosystem flux measurements are critical for understanding the long-term impacts of wetland restoration for climate change mitigation.

Evaluation of vegetation dynamics and climatic oscillations in the Sacramento-san Joaquin delta of California during the Holocene

Evaluation of vegetation dynamics and climatic oscillations in the Sacramento-san Joaquin delta of California during the Holocene

State estimation in large-scale open channel networks using sequential Monte Carlo methods: Optimal sampling importance resampling and implicit particle filters

[1] This article investigates the performance of Monte Carlo-based estimation methods for estimation of flow state in large-scale open channel networks. After constructing a state space model of the flow based on the Saint-Venant equations, we implement the optimal sampling importance resampling filter to perform state estimation in a case in which measurements are available at every time step. Considering a case in which measurements become available intermittently, a random-map implementation of the implicit particle filter is applied to estimate the state trajectory in the interval between the measurements. Finally, some heuristics are proposed, which are shown to improve the estimation results and lower the computational cost. In the first heuristics, considering the case in which measurements are available at every time step, we apply the implicit particle filter over time intervals of a desired size while incorporating all the available measurements over the corresponding time interval. As a second heuristic method, we introduce a maximum a posteriori (MAP) method, which does not require sampling. It will be seen, through implementation, that the MAP method provides more accurate results in the case of our application while having a smaller computational cost. All estimation methods are tested on a network of 19 tidally forced subchannels and 1 reservoir, Clifton Court Forebay, in Sacramento-San Joaquin Delta in California, and numerical results are presented.

Integrated Risk Assessment for the Natomas Basin (California) Analysis of Loss of Life and Emergency Management for Floods

This article assesses the risk to life for the Natomas Basin, a low-lying, rapidly urbanizing region in the Sacramento-San Joaquin Delta in California. Using an empirical method, the loss of life is determined for a flood (high water), seismic, and sunny-day levee breach scenario. The analysis indicated that more than 1000 fatalities may occur in the flood scenario and that there is a high flood risk compared to similar systems (such as dams and flood-prone areas in the Netherlands). Findings show that risk to life highly depends on evacuation effectiveness. The evacuation and emergency management system (EEM) was further analyzed through interviews with regional emergency managers and training exercise evaluation reports. Using an analytic framework, critical factors that affect EEM performance and reliability were identified. Results indicate a need to assess EEM performance to improve preparedness and reduce the risk to life. Findings from the investigation contribute to more integrated risk analyses of both the technical and management components for engineered systems.

Greenhouse gas (CO2, CH4, H2O) fluxes from drained and flooded agricultural peatlands in the Sacramento-San Joaquin Delta

The Sacramento-San Joaquin Delta in California was drained and converted to agriculture more than a century ago, and since then has experienced extreme rates of soil subsidence from peat oxidation. To reverse subsidence and capture carbon there is increasing interest in converting drained agricultural land-use types to flooded conditions. Rice agriculture is proposed as a flooded land-use type with CO2 sequestration potential for this region. We conducted two years of simultaneous eddy covariance measurements at a conventional drained and grazed degraded peatland and a newly converted rice paddy to evaluate the impact of drained to flooded land-use change on CO2, CH4, and evaporation fluxes.We found that the grazed degraded peatland emitted 175–299g-Cm−2yr−1 as CO2 and 3.3g-Cm−2yr−1 as CH4, while the rice paddy sequestered 84–283g-Cm−2yr−1 of CO2 from the atmosphere and released 2.5–6.6g-Cm−2yr−1 as CH4. The rice paddy evaporated 45–95% more water than the grazed degraded peatland. Annual photosynthesis was similar between sites, but flooding at the rice paddy inhibited ecosystem respiration, making it a net CO2 sink. The rice paddy had reduced rates of soil subsidence due to oxidation compared with the drained peatland, but did not completely reverse subsidence.

Dynamic Properties of Highly Organic Soils from Montezuma Slough and Clifton Court

The nonlinear dynamic properties of highly organic soils from two levee sites in the Sacramento-San Joaquin Delta in California are described. Cyclic triaxial, resonant column and torsional shear tests were performed on thin-walled tube samples obtained from beneath levee crests, beneath adjacent berms, and in the free field such that the in situ vertical effective stresses ( σ vo ′ ) ranged from about 16 to 67 kPa . These highly organic soils had considerably different organic characteristics from those used in previous studies of dynamic properties. The tested samples had organic contents of 14 to 61%, initial water contents ( wo ) of 88 to 496%, shear wave velocities ( Vs ) of 20 to 130 m∕s , and organic components that ranged from highly fibrous to highly decomposed and amorphous. Secant shear modulus (G) , normalized secant shear modulus (G∕ Gmax ) , and equivalent damping ratio (ξ) versus cyclic shear strain amplitude ( γc ) relations are presented, and their dependence on variables such as consolid...

Two new methods for Regime Change Analyses

There is currently a good deal of concern about a recently recognized decline in the numbers of several pelagic fish species in the Sacramento-San Joaquin Delta in California, USA. Several research groups are investigating possible reasons for this decline. One part of this study addresses whether the decline is the result of some recent regime change in the ecosystem, and more generally whether one or more regime changes have occurred since regular sampling of fish, zooplankton and mysids shrimps began in 1967. There are many statistical methods of analysis that have been proposed to detect regime changes. These are reviewed, but it is noted that none of them is immediately suitable for analysing the basic data collected from the Sacramento-San Joaquin Delta, which consists of counts from trawl hauls and other sampling gears used in the field. Two new methods are therefore proposed for this type of data, which is commonly collected. One method searches for times when the mean level and trend in the abundance of an organism changed, assuming that in the absence of a regime change the abundances will exhibit a linear trend with time. The other method assumes that in the absence of a regime change the abundances will exhibit a polynomial trend in time, and searches for times when the mean level changed significantly. Both methods rely on bootstrap resampling of the data for assessing the significance of apparent regime changes. Simulation studies to verify the properties of the proposed analyses are described, and also some examples of the results of the analyses on the Sacramento-San Joaquin data.

Nonlinear Dynamic Properties of a Fibrous Organic Soil

The nonlinear dynamic properties of a fibrous peaty organic soil beneath a levee in the SacramentoSan Joaquin Delta in California are described herein. Thin-walled tube samples were obtained from f...

Histopathology, blood chemistry, and physiological status of normal and moribund striped bass (Morone saxatilis) involved in summer mortality (’die‐off‘) in the Sacramento‐San Joaquin Delta of California

Summer mortality (’die‐off‘) is common in striped bass, Morone saxatilis (Walbaum), in the San Francisco Bay‐Delta region. Tissue and blood samples of moribund and healthy striped bass collected during the summers of 1986–1988 were analysed. Sixteen moribund and 25 healthy reference fish from the Carquinez Strait area and eight fish caught in the Pacific Ocean were studied. Moribund fish plasma was invariably yellow‐orange; most of the moribund fish had discoloured livers with haemorrhagic regions, and approximately one‐third had haemorrhagic intestines. Piasma levels of aspartale aminotransferase, uric acid, alkaline phosphatase and cortisol were significantly higher than in reference fish from Carquinez Strait and the Pacific Ocean, whereas cholesterol, sodium, chloride, triiodothyronine and glucose levels were significantly lower. Hepatic heavy metal concentrations and bacterial content were similar in moribund and reference fish. Gill Na.+, K+ ‐ATPase activity was significantly lower in moribund fish. Liver, kidney, intestine, and thyroid follicles of moribund fish displayed various histopathological changes, and corticosteroidogenic (interrenal) tissue could not be identified positively in moribund fish. These findings are discussed in relation to recent work on the chemical burdens (industrial and agricultural hydrocarbons) found in livers from some of the fish examined in this study.

Histopathology, blood chemistry, and physiological status of normal and moribund striped bass (Morone saxatilis) involved in summer mortality ('die-off') in the Sacramento-San Joaquin Delta of California

Histopathology, blood chemistry, and physiological status of normal and moribund striped bass (Morone saxatilis) involved in summer mortality ('die-off') in the Sacramento-San Joaquin Delta of California

Irrigation water quality options for corn on saline, organic soils

Corn production on the organic soils of the Sacramento-San Joaquin Delta of California was affected by the salinity of the irrigation water and the adequacy of salt leaching. Full production was achieved on soils that were saline the previous year, provided the electrical conductivity of the irrigation water (ECi) applied by sprinkling was less than about 2 dS/m and leaching was adequate from either winter rainfall or irrigation to reduce soil salinity (ECMSW) below the salt tolerance threshold for corn (3.7 dS/m). For subirrigation, an ECi up to 1.5 dS/m did not decrease yield if leaching had reduced ECMSW below the threshold. If leaching was not adequate, even nonsaline water did not permit full production. In agreement with previous results obtained in a greenhouse, surface irrigation with water of an electrical conductivity of up to 6 dS/m after mid-season (end of July) did not reduce yield below that of treatments where the salinity of the irrigation water was not increased at mid-season. Results also reconfirm the salt tolerance relationship established in the previous three years of the field trial. The earlier conclusion that the irrigation method (sprinkler or subirrigation) does not influence the salt tolerance relationship was also confirmed.

Subsidence of Peat in California and Florida

Subsidence of reclaimed peaty sediments in warm climate is mostly caused by biochemical oxidation and is relatively little known to engineering geologists. Two examples of such subsidence located in areas with major peat deposits, one in the Sacramento-San Joaquin Delta in California and the second one in Florida9s Everglades, described in the paper are good illustrations of the potentially enormous economic impacts of such subsidence. In the 2,835 km 2 Delta, subsidence of original freshwater tidal marsh peat locally exceeded 10–15 m. Initially flat Delta islands became saucer like depressions with surface submerged below the sea level and protected from flooding by some 1,125 km of man-made levees. Levee breaks and inundations of islands already caused multimillion dollar damages and costly repairs and costly pumplift dewatering of flooded islands. With progressing subsidence unavoidable future collapses of levees built frequently with poor materials and on poor foundations in a highly seismic area will cause irreversible flooding of the Delta. Both “soaking” of salt water from the San Francisco Bay and increased evaporation from flooded islands will increase water salinity in the Delta and jeopardize existing giant water conveyance from the Delta to the southern portion of the state. This will endanger the major agroindustry in the arid San Joaquin Valley which depends on importation of surface irrigation water. The annual crop value of the valley is about 7.5 billion dollars. In the Bell Glade area well studied subsidence caused by agricultural drainage of peat locally exceeds 3 m. Subsidence destroys highly valuable agricultural land and damages buildings, roads, and utilities. Data collected in Bell Glade indicates that such subsidence can be minimized by restriction of drainage, i.e., by properly designed agricultural technique. Engineering geologists should be aware of possibility of biochemical subsidence in organic soil and suggest 1) its proper monitoring using compaction recorders and common bench marks, and 2) its control and/or arresting by proper design of drainage or restriction of oxidation by blanketing of organic material.

Salination of organic soils in the sacramento-San Joaquin Delta of California

The Delta is an important agricultural area containing organic soils that are threatened by salinity. To aid in water allocation and management decisions, the maximum salinity level in irrigation water that preserves agricultural production was estimated from data gathered in a field trial to establish the salt tolerance of corn. All of the physical properties measured indicated that the soil under study was typical of organic soils in the Delta and elsewhere. Differences in soil sample preparation were shown to influence salinity measurements from the subsoil. Samples brought to saturation without either grinding or drying gave electrical conductivity measurements in agreement with those for soil water extracted by suction cups. Above average rainfall and water table control during the winter effectively leached the upper soil profile. The ratio between the average electrical conductivity of the soil water in the root zone ( $$\overline {EC}$$ sw ) and the salinity of the irrigation water (EC i) was found to be a function of EC i and not constant. Under present conditions of low EC i (0.2 to 0.8 dS/m) and with normal winter rainfall $$\overline {EC}$$ sw /EC i is about 8. As EC i increases, however, the ratio decreases. At the soil water salinity threshold for corn grain (3.7 dS/m), the average ratio is 1.7 which results in a maximum value of 2.2 dS/m for EC i without yield loss under normal conditions. With subirrigation and below normal rainfall, as in 1981, the maximum value of EC i would be 0.8 dS/m.

The State Water Plan and Salinity Control in the Sacramento-San Joaquin Delta of California

The State Water Plan and Salinity Control in the Sacramento-San Joaquin Delta of California