Geology topics

Research about California

Source-linked reports with geographic coverage including California.

At least 415 records · Page 23Linked to original sources

USGS2024

Influence of irrigation water and soil on annual mercury dynamics in Sacramento Valley rice fields

Methylmercury (MeHg) is a human and environmental toxin produced in flooded soils. Little is known about MeHg in rice ( Oryza Sativa L.) fields in Sacramento Valley, California. The objectives of this study were to quantify mercury fractions in irrigation water and within rice fields and to determine their mercury pools in surface water, soil, and grain. Soil, grain, and surface water (dissolved and particulate) MeHg and total mercury (THg) were monitored in six commercial rice fields throughout a winter fallow season and subsequent growing season. Both dissolved and particulate mercury fractions were higher in fallow season rice field water. Total suspended solids and particulate mercury concentrations were positively correlated ( r = 0.99 and 0.98 for THg and MeHg, respectively), suggesting that soil MeHg was suspended in the water column and potentially exported. Dissolved THg and MeHg concentrations were positively correlated with absorbance at 254 nm ( r = 0.47 and 0.58, respectively) in fallow season field water. In the growing season, fields with higher irrigation water MeHg concentrations (due to recycled water use) had elevated field-water MeHg ( r = 0.86) and grain MeHg concentrations ( r = 0.96). Based on a mass balance analysis, soil mercury pools were orders of magnitude larger than surface water or grain mercury pools; however, fallow season drainage and grain harvest were the primary pathways for MeHg export. Based on these findings, reducing (1) discharge when water is turbid, (2) straw inputs, and (3) use of recycled irrigation water could help reduce mercury exports in rice field drainage water.

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USGS2024

The influence of anthropogenic regulation and evaporite dissolution on earthquake-triggered ground failure

Remote sensing observations of Searles Lake following the 2019 moment magnitude 7.1 Ridgecrest, California, earthquake reveal an area where surface ejecta is arranged in a repeating hexagonal pattern that is collocated with a solution-mining operation. By analyzing geologic and geotechnical data, here we show that the hexagonal surface ejecta is likely not a result of liquefaction. Instead, we propose dissolution cavity collapse (DCC) as an alternative driving mechanism. We support this theory with pre-event Interferometric Synthetic Aperture Radar data, which reveals differential subsidence patterns and the creation of subsurface void space. We also find that DCC is likely triggered at a lower shaking threshold than classical liquefaction. This and other unknown mechanisms can masquerade as liquefaction, introducing bias into liquefaction prediction models that rely on liquefaction inventories. This paper also highlights the opportunities and drawbacks of using remote sensing data to disentangle the complex factors that influence earthquake-triggered ground failure.

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USGS2024

Potential use of poultry farms by wild waterfowl in California's Central Valley varies across space, times of day, and species: implications for influenza transmission risk

Interactions between wildlife and livestock can lead to cross-species disease transmission, which incurs economic costs and threatens wildlife conservation. Wild waterfowl are natural hosts of avian influenza viruses (AIVs), are often abundant near poultry farms, and have been linked to outbreaks of AIVs in poultry. Interspecific and seasonal variation in waterfowl movement and habitat use means that the risk of disease transmission between wild birds and poultry inevitably varies across species, space, and time. Here, we used GPS telemetry data from 10 waterfowl species in and near California's Central Valley, a region where both wild waterfowl and domestic poultry are abundant, to study selection of poultry farms by waterfowl across diel, seasonal, and annual cycles. We found that waterfowl selected for wetlands, open water, protected areas, and croplands, which meant that they generally avoided habitats that were likely to be used for poultry farming. These selection patterns were linked to species' ecology and diel behavioral patterns, such that avoidance of poultry habitats was stronger for local or partial migrants than for long-distance migrants, and stronger during daytime than at night. We then combined these habitat selection results with data on poultry farm locations to map risk of waterfowl–poultry contact across the Central Valley. Average selection strength at poultry farms was low, suggesting that current placement of poultry farms is generally effective for limiting risk of contact with wild birds. When we combined these habitat selection results with data on species' abundances and AIV infection prevalence, we found dramatic variation in potential AIV transmission risk among species. These results could be used to prioritize surveillance and biosecurity efforts for regions and times of relatively high risk. More generally, these results highlight that fine-scale movement data can help identify interspecific, seasonal, and diel patterns in animal behaviors that affect wildlife and poultry health.

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USGS2024

A comprehensive assessment of submarine landslides and mass wasting processes offshore southern California

It is critical to characterize submarine landslide hazards near dense coastal populations, especially in areas with active faults, which can trigger slope failure, subsequent tsunamis, and damage seabed infrastructure during earthquake shaking. Offshore southern California, numerous marine geophysical surveys have been conducted over the past decade, and high-resolution bathymetric and subsurface data now cover about 60 percent of the total region between Point Conception and the United States-Mexico border from the California coast out to the base of Patton Escarpment ∼200 km offshore. In a comprehensive compilation and interpretive mapping effort, we find evidence of seafloor failure throughout offshore southern California with nearly 1,500 submarine landslide-related features, including 63 discrete slide deposits with debris and >1,400 slide-related scarps. In our analysis, we highlight new mapping of submarine landslides in Catalina Basin, the Del Mar slide, the San Gabriel slide complex, and the 232 km 2 San Nicolas slide, the largest area of any known submarine landslide mass offshore southern California. Analysis of the spatial distribution of submarine landslide features suggests that most mapped slide features are located relatively near coastal sediment sources, particularly during sea-level lowstand conditions, which underscores the importance of sediment supply and sediment accumulation on low-gradient slopes as failure preconditioning processes. Tectonically driven uplift at shelf edges and along basin flanks is another key preconditioning factor, and our results also suggest that earthquakes along active faults trigger mass wasting, especially for repeated, small-scale failures on tectonically steepened slopes.

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USGS2024

Long-term occupancy monitoring reveals value of moderate disturbance for an open-habitat specialist, the Stephens' kangaroo rat (Dipodomys stephensi)

For species of conservation concern, long-term monitoring is vital to properly characterize changes in population distribution and abundance over time. In addition, long-term monitoring guides management decisions by informing and evaluating the efficacy of management actions. A long-term monitoring initiative for the federally threatened Stephens' Kangaroo rat ( Dipodomys stephensi, SKR) was established in 2005, across 628 hectares within Marine Corps Base Camp Pendleton (MCBCP), San Diego, California, USA. From 2005 to 2018, we tracked trends in area occupied by SKR, trends in relative SKR densities within occupied habitat, and modeled probabilities of SKR occupancy, colonization, extinction, with habitat, climate, and disturbance covariates. Area occupied by SKR increased almost 2-fold from 2005 to 2018 on MCBCP, while density in occupied habitat increased almost 3-fold. Increased area occupied was correlated with increases in estimated density among years, indicating SKR population growth occurs by expansion into suitable habitat patches, as well as increases in numbers within occupied habitat. SKR occupancy was positively associated with gentle slopes (<10%) and moderate open ground (40–80%) and forb cover (>40%). They were more likely to colonize previously unoccupied habitat when there were moderate levels of open ground (40–80%) and low shrub cover (<20%), while more likely to go locally extinct in areas with high slopes (>10%), less open ground (<20%), and increased non-native grass cover (>40%). Additionally, probabilities of SKR occupancy and colonization were higher in areas with moderate levels of disturbance, which was positively associated with open ground and forb cover. We conclude that long-term occupancy and density monitoring is effective in informing status and trends of spatially dynamic species and that moderate habitat-based disturbance is compatible with the management of SKR.

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USGS2024

The noise is the signal: Spatio-temporal variability of production and productivity in high elevation meadows in the Sierra Nevada mountain range of North America

There are expectations that increasing temperatures will lead to significant changes in structure and function of montane meadows, including greater water stress on vegetation and lowered vegetation production and productivity. We evaluated spatio-temporal dynamics in production and productivity in meadows within the Sierra Nevada mountain range of North America by: (1) compiling Landsat satellite data for the Normalized Difference Vegetation Index (NDVI) across a 37-year period (1985–2021) for 8,095 meadows >2,500 m elevation; then, (2) used state-space models, changepoint analysis, geographically-weighted regression (GWR), and distance-decay analysis (DDA) to: (a) identify meadows with decreasing, increasing or no trends for NDVI; (b) detect meadows with abrupt changes (changepoints) in NDVI; and (c) evaluate variation along gradients of latitude, longitude, and elevation for eight indices of temporal dynamics in annual production (mean growing season NDVI; MGS) and productivity (rate of spring greenup; RSP). Meadows with no long-term change or evidence of increasing NDVI were 2.6x more frequent as those with decreasing NDVI (72% vs. 28%). Abrupt changes in NDVI were detected in 48% of the meadows; they occurred in every year of the study and with no indication that their frequency had changed over time. The intermixing of meadows with different temporal dynamics was a consistent pattern for monthly NDVI and, especially, the eight annual indices of MGS and RSP. The DDA showed temporal dynamics in pairs of meadow within a few 100 m of each other were often as different as those hundreds of kilometers apart. Our findings point strongly toward a great diversity of temporal dynamics in meadow production and productivity in the SNV. The heterogeneity in spatial patterns indicated that production and productivity of meadow vegetation is being driven by interplay among climatic, physiographic and biotic factors at basin and meadow scales. Thus, when evaluating spatio-temporal dynamics in condition for many high elevation meadow systems, what might often be considered “noise” may provide greater insight than a “signal” embedded within a large amount of variability.

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USGS2024

Top-predator recovery abates geomorphic decline of a coastal ecosystem

The recovery of top predators is thought to have cascading effects on vegetated ecosystems and their geomorphology 1,2 , but the evidence for this remains correlational and intensely debated 3,4 . Here we combine observational and experimental data to reveal that recolonization of sea otters in a US estuary generates a trophic cascade that facilitates coastal wetland plant biomass and suppresses the erosion of marsh edges—a process that otherwise leads to the severe loss of habitats and ecosystem services 5,6 . Monitoring of the Elkhorn Slough estuary over several decades suggested top-down control in the system, because the erosion of salt marsh edges has generally slowed with increasing sea otter abundance, despite the consistently increasing physical stress in the system (that is, nutrient loading, sea-level rise and tidal scour 7,8,9 ). Predator-exclusion experiments in five marsh creeks revealed that sea otters suppress the abundance of burrowing crabs, a top-down effect that cascades to both increase marsh edge strength and reduce marsh erosion. Multi-creek surveys comparing marsh creeks pre- and post-sea otter colonization confirmed the presence of an interaction between the keystone sea otter, burrowing crabs and marsh creeks, demonstrating the spatial generality of predator control of ecosystem edge processes: densities of burrowing crabs and edge erosion have declined markedly in creeks that have high levels of sea otter recolonization. These results show that trophic downgrading could be a strong but underappreciated contributor to the loss of coastal wetlands, and suggest that restoring top predators can help to re-establish geomorphic stability.

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USGS2024

Chytrid infections exhibit historical spread and contemporary seasonality in a declining stream-breeding frog

Species with extensive geographical ranges pose special challenges to assessing drivers of wildlife disease, necessitating collaborative and large-scale analyses. The imperilled foothill yellow-legged frog ( Rana boylii ) inhabits a wide geographical range and variable conditions in rivers of California and Oregon (USA), and is considered threatened by the pathogen Batrachochytrium dendrobatidis (Bd). To assess drivers of Bd infections over time and space, we compiled over 2000 datapoints from R. boylii museum specimens (collected 1897–2005) and field samples (2005–2021) spanning 9° of latitude. We observed a south-to-north spread of Bd detections beginning in the 1940s and increase in prevalence from the 1940s to 1970s, coinciding with extirpation from southern latitudes. We detected eight high-prevalence geographical clusters through time that span the species' geographical range. Field-sampled male R. boylii exhibited the highest prevalence, and juveniles sampled in autumn exhibited the highest loads. Bd infection risk was highest in lower elevation rain-dominated watersheds, and with cool temperatures and low stream-flow conditions at the end of the dry season. Through a holistic assessment of relationships between infection risk, geographical context and time, we identify the locations and time periods where Bd mitigation and monitoring will be critical for conservation of this imperilled species.

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USGS2024

Fault activity in the San Gabriel Mountains, southern California, USA: Insights from landscape morphometrics, erosion rates, and fault-slip rates

Many studies use landscape form to determine spatial patterns of tectonic deformation, and these are particularly effective when paired with independent measures of rock uplift and erosion. Here, we use morphometric analyses and 10 Be catchment-averaged erosion rates, together with reverse slip rates from the Sierra Madre−Cucamonga fault zone, to reveal patterns in uplift, erosion, and fault activity in the range front of the San Gabriel Mountains in southern California, USA. Our analysis tests two prevailing hypotheses: (1) the range front of the San Gabriel Mountains is at steady state, in which rock uplift balances erosion and topographic elevations are stable throughout time, and (2) that west-to-east increases in elevation, relief, erosion rate, and stream-channel steepness across the interior of the massif reflect a parallel reverse-slip rate gradient on the range-bounding Sierra Madre−Cucamonga fault zone. We show that although deviations from steady state occur, the range-front hillslopes and stream channels are typically both well-connected and adjusted to patterns in Quaternary uplift driven by motion on the range-front fault network. Accordingly, landscape morphometrics, 10 Be erosion rates, and model erosion rates effectively image spatial and temporal patterns in uplift. Interpreted jointly, these data reveal comparable peak slip rates on the Sierra Madre−Cucamonga fault zone and show that they do not monotonically increase from west to east. Thus, the eastward-increasing gradients developed within the interior of the massif are not solely related to reverse slip on the range-front faults. Evaluated on shorter length scales (<10 km), morphometric data corroborate earlier descriptions of the Sierra Madre−Cucamonga fault zone as multiple individual faults or fault sections, with slip rates tapering toward fault tips. We infer that these patterns imply the predominance of independent fault or fault section ruptures throughout the Quaternary, though data cannot rule out the possibility of large, connected Sierra Madre−Cucamonga fault zone ruptures. Deeper in the hanging wall of the Sierra Madre−Cucamonga fault zone, secondary faults accommodate range-front uplift. Motion on these faults may contribute to active uplift of the highest topography within the massif, in addition to partly reconciling differences between geologic and geodetic Sierra Madre−Cucamonga fault zone reverse-slip rates. This study provides a new, unified perspective on tectonics and landscape evolution in the San Gabriel Mountains.

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USGS2024

Modeling the response of an endangered rabbit population to RHDV2 and vaccination

Rabbit hemorrhagic disease virus 2 (RHDV2), recently detected in the western United States, has the potential to cause mass mortality events in wild rabbit and hare populations. Currently, few management strategies exist other than vaccination. We developed a spatially explicit model of RHDV2 for a population of riparian brush rabbits ( Sylvilagus bachmani riparius ), a subspecies of brush rabbit classified as endangered in the United States, on a subsection of the San Joaquin River National Wildlife Refuge. The goal of our model was to provide guidance regarding vaccination strategies for an endangered rabbit species. Our model predicts that increased interactions between rabbits (a proxy for landscape connectivity) and disease transmission rates among susceptible hosts (individual brush rabbits and conspecifics) have the greatest influence on the outcome of a potential vaccination campaign. Our model projects that across a range of parameter estimates (given an RHDV2 incursion), the median estimated population size with a 0%–10% vaccination rate after 1 year is 538 rabbits (95% Confidence Interval [C.I.] 69–1235), approximately 36% of the expected size of the study population of 1470 rabbits without an RHDV2 introduction. With a 10%–20%, 20%–30%, or 30%–40% vaccination rate, the median estimated population size increased to 628 rabbits (95% C.I. 130–1298), 723 rabbits (95% C.I. 198–1317), and 774 rabbits (95% C.I. 228–1410), respectively. These estimates represent 43%, 49%, and 53% of the expected population size without an RHDV2 introduction. Overall, a 1% increase in vaccination rate was associated with a six rabbit (95% C.I. 5–7) increase in total remaining population size. This result is dependent on assumptions regarding environmental transmission, home range size (and contact rates of rabbits). Given the relatively short lifespan of rabbits and the potential need for boosters, vaccination programs are most likely to be successful for small target populations where relatively high vaccination rates can be maintained.

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USGS2024

Scattered tree death contributes to substantial forest loss in California

In recent years, large-scale tree mortality events linked to global change have occurred around the world. Current forest monitoring methods are crucial for identifying mortality hotspots, but systematic assessments of isolated or scattered dead trees over large areas are needed to reduce uncertainty on the actual extent of tree mortality. Here, we mapped individual dead trees in California using sub-meter resolution aerial photographs from 2020 and deep learning-based dead tree detection. We identified 91.4 million dead trees over 27.8 million hectares of vegetated areas (16.7-24.7% underestimation bias when compared to field data). Among these, a total of 19.5 million dead trees appeared isolated, and 60% of all dead trees occurred in small groups ( ≤ 3 dead trees within a 30 × 30 m grid), which is largely undetected by other state-level monitoring methods. The widespread mortality of individual trees impacts the carbon budget and sequestration capacity of California forests and can be considered a threat to forest health and a fuel source for future wildfires.

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USGS2024

Wetland geomorphology and tidal hydrodynamics drive fine-scale fish community composition and abundance

Effective restoration of tidal wetlands for fish communities requires clear goals and mechanistic understanding of the ecosystem drivers which affect fish distribution and abundance. We examined fish community responses to abiotic habitat features in two adjacent but dissimilar freshwater tidal wetlands in the Sacramento-San Joaquin Delta, CA, USA, each of which represents a potential restoration configuration. The first wetland was characterized by a broad, intertidal basin with relatively high hydrodynamic exchange with surrounding waterways. The second wetland was characterized by a dendritic network of shallow subtidal channels with relatively low hydrodynamic exchange. Fish community composition significantly differed between the two wetlands, based on permutational analysis of variance. Fish abundance within and among the two wetlands was also highly affected by specific geomorphic and hydrodynamic characteristics: distance from connection with the main external waterway, bed elevation, and water surface elevation. The physical configuration of a restored tidal wetland, in conjunction with the way tides move across the restored landscape, has strong implications for local fishes. Manipulating these elements to create a landscape mosaic of habitat configurations can be an effective tool for targeting desired restoration outcomes, such as specific fish communities or target fish densities.

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USGS2024

Upper crustal seismic velocity structure of the Hayward fault zone, San Francisco Bay, California, USA: Results from the 2016 East Bay Seismic Experiment (EBSI-16)

We developed Vp, Vs, Vp / Vs ratio, and Poisson’s ratio models of the uppermost crust (<4 km depth) from the eastern San Francisco (SF) Bay (California, USA) to near the Calaveras fault along a 15-km-long, linear profile. Upper crustal velocities are highly variable beneath, west, and well east of the Hayward fault. We observe eight notable features, from west to east: (1) Near San Francisco Bay, there is an ~2-km-wide structure with high Vp / Vs ratios (up to 5) and Poisson’s ratios (up to 0.48) extending from the surface to the base of our model, which we suggest the structure is a near-vertical fault that lies along a straight-line projection between the Silver Creek fault to the south and the Point Richmond fault to the north. The structure may be part of an ~90-km-long fault along the eastern SF Bay. (2) The western East Bay Plain, the lower lying area between the bay and the hills, includes up to 800 m of low-velocity sediments ( Vp ~1600–3000 m/s, Vs ~500 m/s to ~1000 m/s), underlain by higher velocity basement rocks ( Vp ~3000–5800 m/s; Vs ~1000–1500 m/s). (3) Between ~1 km and 3 km east of the Bay shoreline, sediments thin in a series of steps (likely faults) toward the Hayward fault. (4) Between ~3 km west and ~1 km east of the Hayward fault (at the East Chabot fault) at depths greater than 1 km, basement Vp (up to 6000 m/s) and Vs (up to 2800 m/s) are high, and Vp / Vs ratios (<2) and Poisson’s ratios (<0.3) are low, suggesting crystalline rocks. Furthermore, a near-vertical zone of low Vp / Vs ratios and Poisson’s ratios is between near-surface traces of the Hayward and East Chabot faults, likely corresponding to the San Leandro Gabbro of Ponce et al. (2003) . (5) Eastward of the East Chabot fault in the upper 1.5 km, basement Vp (~3000 m/s to ~4200 m/s) and Vs (~1200–2000 m/s) are lower than those west of the fault. (6) In the eastern Hayward/Oakland Hills, there are zones of laterally varying, high- and low-velocity ( Vp ~2500–3000 m/s) Jurassic–Cretaceous and Tertiary sediments in the shallow subsurface that likely extend much deeper than imaged. (7) Seismic energy that propagates westward from sources east of the Hayward fault (HF) appear weaker than energy that propagates eastward from sources west of the HF, suggesting that the HF acts as a partial barrier to shallow seismic energy propagation into the more populated eastern SF Bay area. (8) Unlike many fault zones, it appears that the active trace of the Hayward fault (in our study area) is not cored by a prominent, low-velocity zone relative to rocks to the east and west of the active trace. However, the active trace does mark a prominent change from relatively higher velocities to the west and lower velocities to the east.

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USGS2024

National shoreline change—Summary statistics of shoreline change from the 1800s to the 2010s for the coast of California

Rates of shoreline change have been updated for the open-ocean sandy coastline of California as part of studies conducted by the U.S. Geological Survey. Shorelines from the original assessment (1800s through 1998 or 2002), as well as additional shoreline position data from 2009 to 2011, 2015, and 2016 extracted from light detection and ranging (lidar) data, were used to compute long-term rates (approximately 150 years) that incorporate the proxy-datum bias on a transect-by-transect basis. The proxy-datum bias accounts for the unidirectional onshore bias of proxy-based high water line shorelines relative to datum-based mean high water shorelines. In areas where the methods for delineating shorelines did not make it possible to compute a bias correction, the rates are reported without that correction. In this study, the coasts of northern and central California exhibited the highest average rates of erosion, whereas southern California exhibited the highest average rate of accretion. The maximum erosion rate was in San Mateo County in central California. The maximum rate of accretion was in Humboldt County in northern California. Rates were calculated at 19,063 transect locations. Shoreline positions from the mid-1800s through 2016 were used to update shoreline change rates in California using the Digital Shoreline Analysis System (DSAS) software.

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USGS2024

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

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USGS2024

A machine learning tool for design of behavioral fish barriers in the Sacramento-San Joaquin River Delta

Executive Summary Survival of out-migrating juvenile salmonids ( Oncorhynchus spp.) through the Sacramento-San Joaquin River Delta averages less than 33 percent, depending on water flow through the delta, and is partially governed by the distribution of fish among three Sacramento River distributaries: Sutter, Steamboat, and Georgiana sloughs. Behavioral altering structures in the junctions of the distributaries can effectively increase entrainment into favorable routes, thereby increasing through-delta (Verona to Chips Island, California) survival. The effectiveness of these structures, hence forth called “behavioral barriers,” are dependent on shape, length, location, barrier type, and water velocity, which is governed by Sacramento River discharge (hereinafter referred to as “flow”). We developed a machine learning tool to optimize behavioral barrier designs at up to three junctions within the Sacramento-San Joaquin Delta for improving through-delta survival of juvenile winter-run Chinook salmon ( Oncorhynchus tshawytscha ). This barrier optimization tool (BOT) works by evolving barrier solutions in one to three junctions by repeatedly simulating survival of populations of Sacramento River origin fish as they pass through the Delta. Over approximately 6,000 simulations per junction, the BOT converges on barrier designs that result in the greatest average survival given simulated environmental conditions. Survival at each iteration of the model is simulated using a modified version of the salmon travel time and routing simulation (STARS) model. In the BOT, STARS is modified by replacing probabilistic route determinations with an individual based model (IBM) that simulates fish behavior to predict the entrainment rates in each junction. The IBM allows the flexibility to explore how entrainment changes with evolving barrier designs. We used juvenile winter-run-sized Chinook salmon catch data collected at Knights Landing from 1997 to 2011 to create realistic arrival and spatial distributions of simulated fish within the BOT that varied among water years (hereafter years). We demonstrated the capabilities of the BOT by comparing optimized barrier solutions and their resulting simulated improvement in survival among three scenarios that differed in the number of junctions with barriers (Georgiana Slough, Steamboat Slough, or both) and the barrier operational period (early: November 1–March 15, or late: January 1–April 30). In this initial demonstration of the BOT we only considered a bioacoustic fish fence (BAFF) at Georgiana Slough and a floating fish guidance structure (FFGS) at Steamboat Slough. The increase in simulated through-delta fish survival ranged from 1.0 to 6.3 percent among the optimized barrier designs. The most effective Georgiana Slough barrier design predicted improved survival by 6.3 percent and was chosen by the California Department of Water Resources (DWR) as the Georgiana Slough salmon migratory barrier planned for operation annually from 2023 to 2030 at Georgiana Slough in response to the 2020 California Department of Fish and Wildlife’s (CDFW) Incidental Take Permit Minimization Measure 8.9.1 (California Department of Fish and Wildlife [CDFW], 2020). When barriers were simulated in both junctions, the percentages of simulated winter-run Chinook salmon interacting with a barrier at Steamboat or Georgiana sloughs were 95 percent given the early operational period and 48 percent given the late operational period. When barriers were simulated at both sloughs, the optimal barrier at Steamboat Slough effectively routed fish into the Sacramento River. This is because the Georgiana Slough barrier reduced routing into Georgiana Slough where survival is low, which resulted in higher survival for fish routed down the Sacramento River at Steamboat Slough than fish routed down Steamboat Slough. Whereas when no barrier was simulated at Georgiana Slough, the optimized barrier at Steamboat Slough routed fish into Steamboat Slough. This is because survival was higher through Steamboat Slough than the Sacramento River and Georgiana Slough combined. The greatest improvement in survival (6.3 percent) was predicted over the earlier operational period with only a barrier at Georgiana Slough.

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USGS2024

Mafic alkaline magmatism and rare earth element mineralization in the Mojave Desert, California: The Bobcat Hills connection to Mountain Pass

Occurrences of alkaline and carbonatite rocks with high concentrations of rare earth elements (REE) are a defining feature of Precambrian geology in the Mojave Desert of southeastern California. The most economically important occurrence is the carbonatite stock at Mountain Pass, which constitutes the largest REE deposit in the United States. A central scientific goal is to understand the genesis of the carbonatite ore body in the context of widespread REE-rich igneous activity. A swarm of mafic alkaline (shonkinite) dikes has been mapped and sampled at Bobcat Hills, 65 km southeast of the Mountain Pass mine. Whole-rock geochemistry and zircon geochronology demonstrate a clear affinity to the ca. 1.4 Ga Mountain Pass intrusive system. Bobcat Hills dikes have comparably high REE concentrations (La ∼1,000× chondritic) and an error-weighted mean 207 Pb/ 206 Pb zircon crystallization age of 1,426 ± 2 Ma (2 σ ). Unlike the alkaline intrusions at Mountain Pass, which have abundant inherited zircon from Paleoproterozoic basement rocks and crustally influenced oxygen isotope compositions (δ 18 O zircon = 6.5–7.5‰), the Bobcat Hills dikes lack any evidence of crustal assimilation and have oxygen isotope values that overlap a mantle range (Bobcat Hills average δ 18 O zircon = 5.6 ± 0.3‰). The dikes were a high-temperature, early center of mafic alkaline magmatism in the Mojave Desert that serve as a snapshot of melt generation from a spatially extensive, metasomatized mantle source. We propose that modification of the crust over many tens of Myr at Mountain Pass created an environment that favored crustal assimilation and enabled ascent of late-stage, REE-rich carbonatite magmas.

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USGS2024

Land-use interactions, Oil-Field infrastructure, and natural processes control hydrocarbon and arsenic concentrations in groundwater, Poso Creek Oil Field, California, USA

Like many hydrocarbon production areas in the U.S., the Poso Creek Oil Field in California includes and is adjacent to other land uses (agricultural and other developed lands) that affect the hydrology and geochemistry of the aquifer overlying and adjacent to oil development. We hypothesize that the distributions of hydrocarbons and arsenic in groundwater in such areas will be controlled by complex interactions between mixed land uses, oil-field infrastructure, and natural processes. In 2020–2021, samples of groundwater and surface water were collected and analyzed for a large suite of inorganic and organic chemicals and isotope and gas tracers to test this hypothesis. Those data are supplemented with ancillary data on historical geochemistry, hydrology, geology, and oil-field infrastructure. Hydrocarbons in groundwater (e.g., methane through pentane gases and benzene) are associated with natural processes (e.g., fault offsets or transition in sediment depositional environment) and oil-field infrastructure (e.g., fluid-migration pathways associated with uncemented annulus in oil wells or unlined pits). Arsenic concentrations >10 μg per liter (μg/L; maximum concentration 12.9 μg/L) are associated with natural processes in old, high-pH groundwater, and more recent recharge of water from natural and/or engineered recharge processes. Along the southwest margin of the oil field, pumping for drinking-water and irrigation supplies in combination with engineered groundwater recharge produce a depression in groundwater elevations where groundwater with elevated sulfate concentrations from agricultural areas and groundwater with hydrocarbons from the oil field mix to produce a zone of sulfate reduction that removes hydrocarbons and arsenic from groundwater but produces elevated sulfide (S 2- ) concentrations (maximum concentration 29 mg per liter, mg/L). In this study, multiple approaches were required to resolve the overlapping effects of land uses, oil-field infrastructure, and natural processes on the distributions of hydrocarbons and arsenic in groundwater. The combined use of geographic, historical, physical, chemical, isotopic, and other information to constrain processes could be a useful approach for studies in other hydrocarbon-production areas. This is particularly important where land uses affect aquifer hydrology to an extent that causes mixing of groundwaters with different chemical compositions.

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