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Generating geochemical and mineralogy distributions of soil in the conterminous United States using Bayesian hierarchical spatial models

Characterizing geochemical and mineralogical soil distributions across large spatial extents is essential for understanding mineral resources, ecosystem processes, and environmental risks. Rasters of soil geochemical distributions for the conterminous United States, however, are limited. We present a Bayesian modeling workflow and tool for generating predictive geochemical and mineralogy distribution maps for the conterminous United States using integrated nested Laplace approximation (INLA) with the stochastic partial differential equation approach. By modeling soil geostatistical data with environmental covariates (soil properties, topography, climate, and land cover), we generate predictive distributions of soil geochemistry that can be mapped or extracted for further analyses. As an example, we model the spatial distribution of trace elements in soil relevant to vertebrate health (cobalt, copper, iron, manganese, selenium, and zinc) and provide a workflow that can be used to generate and visualize predictive distributions of 39 other major and trace elements and 21 minerals of the soil survey, supporting a variety of ecological, environmental, and agricultural applications.

MethodsX

Automated, near real-time ground-motion processing at the U.S. Geological Survey

We describe automated ground‐motion processing software named gmprocess that has been developed at the U.S. Geological Survey (USGS) in support of near‐real‐time earthquake hazard products. Because of the open‐source development process, this software has benefitted from the involvement and contributions of a broad community and has been used for a wider range of applications than was initially envisioned. Here, we give an overview and introduction to the software, including how it has leveraged other open‐source libraries. We highlight some key features that gmprocess provides, compare response spectra calculated with the automated processing approach of gmprocess to the response spectra provided by the Next Generation Attenuation projects, and summarize projects that have utilized gmprocess. These use‐cases demonstrate that this software development effort has been successfully leveraged in earthquake research activities both within and outside the USGS.

Seismological Research Letters

Climate-driven sulfate export in alpine watersheds may stimulate methylmercury production

Climate change is increasing sulfate export and changing wetland extent in mountain regions. These changes may increase microbially mediated production of the neurotoxic substance methylmercury due to enhanced sulfate metabolism in mountain environments. Here, we assess methylmercury concentrations and formation rates across high-elevation wetlands in the Colorado Rocky Mountains. We also investigate sulfate controls on methylmercury production within subalpine peatlands by amending soils with sulfate to mimic increased stream export of sulfate from the alpine zone and measuring methylmercury formation rates for different sulfate treatments. We found that subalpine peatlands have statistically significant higher methylmercury concentrations and formation rates compared to alpine, mineral-soil wetlands. Methylmercury production in subalpine peatlands also increased significantly ( p < 0.05) following sulfate additions; the highest rates occurred in sediments with intermediate extractable sulfate concentrations (∼0.60–1.4 mg sulfate g −1 dry soil). Our study is the first to identify soil sulfate-related thresholds for methylmercury production and sulfate-limitation of methylmercury production in subalpine peatlands. These findings highlight important linkages between climate-driven mineral weathering and mercury cycling in mountain regions globally.

Colorado

Shallow lake, strong shake: Record of seismically triggered lacustrine sedimentation from the 1959 M7.3 Hebgen Lake earthquake within Henrys Lake, Idaho

We investigate a shallow lake basin for evidence of a large historic intraplate earthquake in western North America. Henrys Lake, Idaho is an atypical candidate for a lacustrine paleoseismic study given its shallow depth (~7 m) and low relief (≤2° slopes ). Here, we test the earthquake-recording capacity of this basin type by showing sedimentological evidence of the 1959 M7.3 Hebgen Lake earthquake within sediment cores, using anthropogenically produced 137 Cs activity to constrain timing. In addition to expanding the morphologic range of basins targeted for lacustrine paleoseismic studies, this work has implications for sediment response in dam-enhanced basins. Lack of sedimentological evidence for other earthquakes coupled with radiocarbon chronology reveals that the 1959 event is the only clearly recorded earthquake within Henrys Lake since the mid-Holocene. Henrys Lake offers a proxy for paleo-earthquake signatures within similar lacustrine environments and underscores the importance of further paleoseismic studies in the region.

Idaho

Evaluation of an open earthquake early warning system in Mexico, and laboratory tests of their sensors

Microelectromechanical system (MEMS) accelerometers are useful for seismological and engineering applications because of their ability to record unsaturated large seismic signals. Recent advances in MEMS technologies enable the design of instruments with improved capabilities that also allow the recording of small signals. As a result, MEMS can be useful across a broad dynamic range and for both major earthquakes and smaller magnitude events. Here, we analyze the performance of a MEMS‐based accelerometer with the capability of real‐time data transmission. We discuss the self‐noise level, dynamic range, and sensitivity, along with the timing precision and data transmission latency, and compare these parameters to other MEMS‐based instruments. We also summarize observations from a regional network deployed in southern Mexico over a period of 3+ yr for the purpose of earthquake early warning. In addition to the sensor evaluation, we present a large, openly available data set of strong motion data from the Mexican network that comprises continuous ground‐motion records from 24 accelerometers in the period between 2017 and 2022.

Seismological Research Letters

Uppermost Oligocene and Miocene diatom biostratigraphy of Ocean Drilling Program Sites 682 and 688 from the Peru Margin

The diatom biochronology of ODP (Ocean Drilling Program) Holes 682A and 688E provides a detailed framework for refiningMiocene diatom zonation in the East Pisco Basin of southern Peru, establishing both a nearly complete offshore reference section and a correlation tool for the fragmentary onshore vertebrate-bearing deposits. This new biostratigraphic record documents a complete succession of low latitude and/or northeastern Pacific Miocene diatom zones, with two notable exceptions: a dissolution and/or hiatus interval (*16.5–14 Ma) during the Middle Miocene Climatic Optimum and a likely earliest Miocene hiatus (*23.4–21.8 Ma). Although eastern equatorial Pacific diatom zones characterize the Upper Oligocene and Lower Miocene strata, an increased abundance of cool-water diatoms that lived during the Middle and Late Miocene allows better application of northeast Pacific diatom zones, except during the Messinian (7–6 Ma) when warm-water diatoms predominate. The effects of eustatic sea level and tectonics on depositional sequences in the EPB and in offshore cores off central Peru are discussed.

Stratigraphy

A crosswalk of the 2015 World Terrestrial Ecosystems to the International Union for the Conservation of Nature Global Ecosystem Typology Framework

To support ecosystem mapping and accounting applications, we aligned the 2015 U.S. Geological Survey/Esri/The Nature Conservancy-World Terrestrial Ecosystems (WTEs) with the International Union for Conservation of Nature Global Ecosystem Typology (GET) framework. This process, known as “crosswalking,” enabled the development of a global map of GET level 3 Ecosystem Functional Groups (EFGs) at a 250-meter spatial resolution. Crosswalking involved manually assigning 1,781 biogeographically stratified WTEs to their most probable EFG based on similarities in climate, terrain, vegetation, and geographic distribution. We compared attributes of the WTE dataset with summary characteristics of the EFGs. The resulting crosswalked global map of International Union for Conservation of Nature GET ecosystems is intended to be useful for standardizing ecosystem classification and reporting under frameworks such as the Kunming-Montreal Global Biodiversity Framework and the United Nations System of Environmental-Economic Accounting. We discuss key challenges in reconciling non-identical classifications, such as many-to-one relationships and variation in data quality.

Open-File Report

The role of groundwater in contributing to surface water salinization in the Upper Colorado River Basin

Freshwater salinization impacts the availability of water for human use and ecosystem needs worldwide. It has been estimated that total dissolved solids (TDS) in the Colorado River Basin cause $350 million/year in damages and substantial resources are devoted to reducing TDS loading to streams. This study describes the development and application of coupled watershed models that enable TDS source tracking through the subsurface and across the landscape at a seasonal timestep for 35 years in the Upper Colorado River Basin. Results indicate that, on average, 75% of TDS loading to streams originates as baseflow, and 50% of loading is lagged in delivery by longer than one season. Snowmelt was identified as a dominant process controlling the transport of lagged TDS to streams. This approach informs when and where TDS mitigation efforts may be effective in a watershed that serves as a critical water supply for the southwestern United States.

Arizona, Colorado, New Mexico, Utah, Wyoming

Insights and strategic opportunities from the USGS 2024 Per- and Polyfluoroalkyl Substances (PFAS) Interagency Workshop

Introduction In 2021, the U.S. Geological Survey (USGS) published Circular 1490 titled, “Integrated Science for the Study of Perfluoroalkyl and Polyfluoroalkyl Substances (PFAS) in the Environment: A Strategic Science Vision for the U.S. Geological Survey” (Tokranov and others, 2021). Circular 1490 was created to be a resource for USGS scientists prioritizing and planning research related to per- and polyfluoroalkyl substances (PFAS) and to be a guide for developing partnerships with other scientists, State and Federal agencies, and stakeholders engaged in PFAS research and management and mitigation of the environmental and human-health effects of PFAS. This USGS PFAS Strategic Science Vision document was intended to be the foundation for a “living strategic vision,” periodically providing updates on the state of USGS PFAS research, emerging PFAS data gaps and needs, and progress on interagency and stakeholder PFAS partnerships and priorities. To meet this objective, the USGS planned to host an Interagency and Stakeholder PFAS Workshop every 2–3 years. During September 10–12, 2024, the USGS hosted the first Interagency and Stakeholder PFAS Workshop in Reston, Virginia. The Workshop brought together experts from other Federal agencies (U.S. Environmental Protection Agency, National Institute of Environmental Health Sciences, Food and Drug Administration, Department of Defense [Air Force, Army]), State agencies (Washington Fish and Wildlife, Virginia Department of Transportation), and academia (Harvard University, University of Maryland) to address key challenges relating to the measurement and modeling of PFAS and the implications for environmental health. Participants engaged in in-depth discussions centered around six pivotal topics related to PFAS: (1) sampling protocols, methods and interpretation; (2) environmental sources, source apportionment, and occurrence; (3) environmental fate and transport; (4) human and wildlife exposure routes and risk; (5) bioconcentration, bioaccumulation, and biomagnification; and (6) ecotoxicology and effects. Each topic had three breakout sessions. A recurrent theme of workshop discussions was how data on a nationwide scale for PFAS occurrence in various environmental matrices, including air, water, food crops, biota, soil, and streambed sediment could help to advance scientific understanding. Participants noted significant geospatial data gaps, particularly in the midwestern and southern United States and the Pacific Northwest. PFAS data collection tends to be more robust along the eastern seaboard and in California. Participants stressed how enhancing the integration of large and small datasets across various agencies could help to support national scale understanding of PFAS. To address these gaps, attendees suggested leveraging datasets from Federal entities like the USGS and the U.S. Department of Defense, State agencies, and municipal utility services to develop predictive contaminant detection and transport models. Improved coordination between water quality programs and USGS research could help to facilitate access to valuable data, leading to comprehensive databases that inform PFAS point (wastewater treatment plants and landfills) and nonpoint (runoff from land, atmospheric deposition, food packaging) sources, environmental transport mechanisms, environmental detection and concentrations, potential exposure routes, and health effects on different biota, including humans. A specific request was made to develop a map demarking the depth of modern (1953 or later) groundwater, which is susceptible to surface-derived anthropogenic (that is, human-made) contamination, based on tritium-age dating. Emphasis was placed on incorporation of hydrology, groundwater flow paths, groundwater–surface water interactions, and landscape factors in predictive statistical models as a step to improve contaminant source identification and tracking. Molecular fingerprinting approaches garnered attention as techniques to link specific PFAS mixtures detected in a sample to environmental sources and levels in biota (Dávila-Santiago and others, 2022). Integrating data from abiotic (that is, water, soil, and air) and biotic (that is, living organisms) systems identified as a research opportunity. For example, understanding the composition of soils and sediments, which include a mixture of mineral, plant, and animal components, could advance understanding of exposure pathways. The discussions highlighted opportunities to explore and understand the potential redistribution and biotic exposures of PFAS from biosolid and wastewater treatment plant effluent land application practices, in addition to atmospheric releases and discharges from landfill and wastewater treatment plants. Participants identified research gaps surrounding how these sources may contribute to contamination and may affect surrounding ecosystems, including a better definition of anthropogenic background concentrations. Moving forward, the collection of co-occurrence data was noted as a means to improve understanding of complex mixtures and to leverage companion modeling efforts focused on areas with high and low contamination levels to identify areas of concern and unaffected resources. Participants emphasized how centralized USGS databases and the establishment of sample-metadata archives can help to ensure that samples are preserved and accessible for future research. In conclusion, the workshop participants identified opportunities to bridge data gaps and improve measurement techniques, modeling frameworks, databases, and communication, to enhance the understanding of PFAS and their effects on environmental and human health. Upon completion of the workshop, participants indicated an interest in developing strategic data collection, modeling, and analytical approaches to address these challenges.

Open-File Report

A geographic dataset of rocky reefs habitat areas of particular concern for the United States West Coast

The United States National Marine Fisheries Service determines “essential fish habitat (EFH)” for federally managed species in coordination with regional fishery management councils, considers adverse effects to those habitats, and provides information to further habitat conservation and enhancement. Identifying discrete subsets of EFH as “habitat areas of particular concern (HAPC)” can help focus conservation, management, and research efforts. In 2006, the Pacific Fishery Management Council designated rocky reefs along the United States (U.S.) West Coast as HAPCs for groundfishes because of their ecological significance, sensitivity to human impacts, and relative rarity. To better understand where rocky reefs occur, we (1) located rocky reef areas that were not included in the 2006 rocky reef dataset, and (2) incorporated best available data into a refined geographic dataset that enables visualization. Our update shows that rocky reefs are distributed throughout the U.S. West Coast continental margin, are patchier than previously known, and comprise 8% of the extent of all data inputs. This updated dataset will inform resource management decisions in coastal and marine environments.

California, Oregon, Washington

Tracking diagenetic alteration of magnetic susceptibility in thrust ridge and slope basin sediments of the Cascadia margin (ODP Sites 1249 and 1252; IODP Site U1325)

We investigated sediment core records from the Cascadia Margin (Ocean Drilling Program Sites 1249 and 1252 at Hydrate Ridge; Integrated Ocean Drilling Program Site U1325 offshore Vancouver Island) using a Zr/Rb heavy mineral proxy from X-ray fluorescence (XRF) core scanning to identify intervals of primary detrital magnetic susceptibility (κ) and predict intervals where diagenesis caused magnetite dissolution by hydrogen sulfide. We also measured total sulfur (TS) content, grain size distributions, total organic carbon (TOC) content, and the magnetic mineral assemblage to further constrain the role of diagenesis on κ. Understanding how κ can be used to better characterize the varied effects of detrital and diagenetic signals in marine settings is important for understanding biogeochemical cycling and records of paleoenvironmental change. The upper 100 m of slope basin Site 1252 contains multiple intervals (> 90 m total) of decreased κ correlated with elevated TS content, consistent with dissolution of magnetite and precipitation of pyrite, iron monosulfides, and/or elemental sulfur. Similarly at the other slope basin site, Site U1325, κ is lower and TS is elevated in the interval between 24 and 51 mbsf, due to sulfide formation. At both slope basin sites, these low κ intervals correspond with high TOC, suggesting the possibility that organoclastic sulfate reduction (OSR) is likely a major driver of diagenetic alteration of κ at these sites. High TS:TOC ratios at Site U1325 suggests anaerobic oxidation of methane (AOM) during sulfate-methane transition zone (SMTZ) migration may have contributed to alteration of κ. In contrast, within the upper 90 m of Site 1249, a methane seep site at the summit of Hydrate Ridge, κ is almost entirely altered by diagenetic processes, with much of the low κ explained by a high degree of iron sulfide formation, while some intervals are affected by precipitation of magnetic iron sulfides that maintain or even increase κ. The presence of abundant methane seepage and gas hydrate as well as chemosynthetic seafloor fauna at this site, suggests that sulfide is released to the water column and AOM, rather than OSR, drives diagenetic alteration of κ at this site. Overall, the slope basin sites show episodic variation of κ that is influenced by TOC content, likely driven by changes in marine primary productivity and sedimentation rate, while the seep site shows consistently altered κ with lower TS content and no correlation with TOC. Methane seep environments likely experience loss of hydrogen sulfide to the water column and oxidation of hydrogen sulfide by seafloor seep fauna, which limits the amount of solid phase sulfur (pyrite, iron monosulfides, elemental sulfur) that can be precipitated within the sediments. In contrast, the migration of a buried SMTZ at slope basin sites results in enhanced sulfur precipitation within the sediments. This integrated magnetic and geochemical approach reveals the diagenetic production pathway and residence time of sulfide with the sediment column ultimately controls the style and degree of diagenetic loss of κ in marine sediments. This approach works best in environments with unaltered reference intervals/sites, consistent magnetic mineralogy, and clay-to-silt grain sizes.

Cascadia margin, Pacific Ocean

A 481 m-high landslide-tsunami in a cruise ship-frequented Alaska fjord

Early in the morning of 10 August 2025, a >64 × 10 6 –cubic meter landslide struck Tracy Arm fjord in Alaska. The landslide was preconditioned by glacial retreat caused by climate change. The resulting 481-meter runup megatsunami followed an initial 100-meter-high breaking wave traveling at >70 meters per second. The landslide was preceded by several days of microseismicity, which increased in rate and magnitude until ~1 hour before failure. The landslide produced globally observed long-period seismic waves equivalent in size to a moment magnitude 5.4 earthquake. A long-period (~66 second) global seismic signal, produced by a landslide-induced seiche trapped within the fjord, persisted for up to 36 hours, the second time a days-long seiche had thus been observed. With fjord regions increasingly visited by cruise ships, and climate change making similar events more likely, this unanticipated, near-miss event highlights the growing risk from landslides and tsunamis in coastal environments.

Alaska

Increasing artificial light at night enhances salmonid predator foraging efficiency in an urbanized lake

Artificial light at night (ALAN) poses a threat to ecosystems globally. It includes both direct and indirect light, or skyglow, which occurs when ALAN scatters in the atmosphere, extending beyond its original source. We analyzed ALAN trends in Lake Washington, WA, from 2014 to 2023 using Visible Infrared Imaging Radiometer Suite (VIIRS) nighttime light measurements, evaluated the relationship between in situ and satellite measurements, and modeled predator search volumes for a juvenile salmon predator, cutthroat trout ( Oncorhynchus clarki ), as a function of ambient light and turbidity conditions. Open water regions experienced significant increases in ALAN, while nearshore areas primarily showed no or negative trends, revealing the role of skyglow in shaping open water light environments. Using a visual foraging model for cutthroat trout, we found that juvenile salmon at the shallow southern pelagic site experienced light 28 times brighter, resulting in a 168% greater predation vulnerability than those at the northern site. In the Ship Canal, a narrow corridor for outmigrating salmon, predator search volumes were 249% higher than at the southern site. These contrasts in predation vulnerability demonstrate how local conditions influence predator–prey dynamics and provide critical insight for targeting mitigation of both nearshore and distant light sources.

Washington

Estimating paleotemperature using stable isotopes of soil-formed phyllosilicates from paleosols: A review

Fossilized soils, or paleosols, contain soil-formed phyllosilicates whose stable isotopic compositions may be used to calculate paleotemperature and thus reconstruct ancient terrestrial environments. Though paleosols are common in the geologic record, the use of phyllosilicates as paleotemperature proxies is limited in the literature owing to difficulties with selecting optimal paleosols, isolation from non-clay minerals and organic materials, mixtures of phyllosilicates in natural samples, wide variations of chemical compositions for phyllosilicates, and limited to undefined equilibrium fractionation factors between phyllosilicates-water. Here, we address these challenges by examining and comparing methods used for sample selection, mineral isolation, pretreatments, mineral identification, conventional and developing methods for oxygen and hydrogen isotopic analyses, and determination of phyllosilicate-water equilibrium fractionation factors, concluding with recommendations for best approaches for paleotemperature estimation. Additionally, we discuss how to identify and avoid detrital phyllosilicates, the impacts of diagenesis, comparison of stable isotope and non-isotope paleosol paleotemperature proxies, and challenges and opportunities for broadly using paleosols as paleoclimate archives. With ongoing efforts to refine this multi-faceted paleotemperature approach, the stable isotope geochemistry of soil-formed phyllosilicates continues to be an invaluable proxy system, enhancing our understanding of terrestrial paleoenvironments and paleoclimate.

Kansas

Teach me how to pycap: A high-capacity well decision support tool using analytical solutions in Python

Regulatory agencies in humid temperate environments rely on timely evaluations of streamflow depletion and drawdown to protect aquatic ecosystems and existing water users. Numerical models offer detailed insights, but their complexity and time demands often preclude their practical use in rapid decision-making. We present pycap-dss, an open-source Python package that implements a suite of analytical solutions for estimating streamflow depletion and drawdown. The tool supports superposition of multiple wells and time-varying pumping, enabling cumulative impact assessments in situations with multiple wells and streams. The software is modular and extensible, allowing users to interchange solutions or add new analytical methods. A YAML-based configuration supports batch processing of multiple wells, and an optional AnalysisProject class facilitates integration with regulatory workflows. Rigorous unit and regression testing ensures computational reliability, and continuous integration supports ongoing development. We demonstrate deterministic examples of drawdown where multiple solutions are readily compared and streamflow depletion with multiple wells in the Central Sands region of Wisconsin. We also show the value of Monte Carlo analyses of streamflow depletion in the same Central Sands example, leveraging computational efficiency to evaluate the uncertainty of individual and cumulative streamflow depletion calculations from over 200 high-capacity wells.

Wisconsin

Self-guided decision support groundwater modelling with Python

The GMDSI tutorial notebooks repository provides learners with a comprehensive set of tutorials for self-guided training on decision-support groundwater modelling using Python-based tools. Although targeted at groundwater modelling, they are based around model-agnostic tools and readily transferable to other environmental modelling workflows. The tutorials are divided into three parts. The first covers fundamental theoretical concepts. These are intended as background reading for reference on an as-needed basis. Tutorials in the second part introduce learners to some of the core concepts parameter estimation in a groundwater modelling context, as well as providing a gentle introduction to the PEST, PEST++ and pyEMU software. Lastly, the third part demonstrates how to implement highly-parameterized applied decision-support modelling workflows. The tutorials aim to provide examples of both “how to use” the software as well as “how to think” about using the software. A key advantage to using notebooks in this context is that the workflows described run the same code as practitioners would run on a large-scale real- world application. Using a small synthetic model facilitates rapid progression through the workflow.

Journal of Open Source Education

Microbial ecology of permafrost soils: Populations, processes, and perspectives

Permafrost microbial research has flourished in the past decades, due in part to improvements in sampling and molecular techniques, but also the increased focus on the permafrost greenhouse gas feedback to climate change and other ecological processes in high latitude and alpine permafrost soils. Permafrost microorganisms are adapted to these extreme environments and remain active at low temperatures and when resources are limited. They are also an important component of global elemental cycles as they regulate organic matter turnover and greenhouse gas production, particularly as permafrost thaws. Here we review the permafrost microbiology literature coupled with an exploration of its historical aspects, with a particular focus on a new understanding advanced by molecular biology techniques. We further identify knowledge gaps and ways forward to improve our understanding of microbial contributions to ecosystem biogeochemistry of permafrost-affected systems.

Permafrost and Periglacial Processes

A soil velocity model for improved ground motion simulations in the U. S. Pacific Northwest

Near-surface seismic velocity structure may significantly impact the intensity, duration, and frequency content of ground shaking during an earthquake. In this study, we compile 649 shear wave velocity (Vs) profiles throughout the U.S. Pacific Northwest and southern British Columbia (PNW) and use these measured profiles to develop a representative soil velocity model for four major Holocene soil provinces: Puget Lowlands, Willamette Valley, fill and alluvium, and `other' soils. The resulting soil velocity model shows good agreement to measured data for a wide range of site conditions, with variability between different geologic domains reflecting fundamental differences in depositional environments. We then show that using this regional soil velocity model in simulations of the 2001 M6.8 Nisqually, Washington earthquake improves the fit to observed high-frequency (≥ 0.5 Hz) ground motions in the Puget Sound region compared to simulations that do not incorporate shallow (≤ 200 m) seismic velocity structure. Overall, this work shows that incorporating localized soil velocity profiles into seismic velocity models is important for accurately estimating high-frequency ground motion and regional seismic hazard in earthquake simulations. Future earthquake simulations and hazard studies in the PNW could incorporate these soil velocity profiles to capture the region's distinct site response characteristics.

Washington