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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

Development of a hydrogeologic visualization model for western Sarpy County, Nebraska

Population in western Sarpy County, Nebraska, has steadily increased over the last several decades and has led to increased groundwater use for domestic purposes. To meet the increase in demand, the Papio-Missouri River Natural Resources District is seeking to use all available sources of groundwater in western Sarpy County. Additionally, elevated groundwater nitrate plus nitrite as nitrogen concentrations were detected, indicating the need to better understand the groundwater quality of the area. Although the general geology of the area is understood, the area does not have detailed information on the extent of the various aquifers, particularly the Dakota aquifer. To characterize these aquifers, the Papio-Missouri River Natural Resources District invested in airborne electromagnetic surveys of the area to better understand the subsurface geology. Although these surveys improved understanding of the groundwater systems in the area, the Papio-Missouri River Natural Resources District wanted to integrate the subsurface information with available water-quality and groundwater-level data. In response, the U.S. Geological Survey, in cooperation with the Papio-Missouri River Natural Resources District, the Nebraska Natural Resources Commission, and the Nebraska Department of Natural Resources, assembled geologic, hydrogeologic and nitrate plus nitrite as nitrogen information for the selected area into a three-dimensional visualization computer software package called GeoScene3D. The completed GeoScene3D project was assembled to provide a visualization of the groundwater systems and associated water-quality results in Sarpy County and to provide the Papio-Missouri River Natural Resources District managers with information that can be used to make more informed groundwater resource-planning decisions in the future. This report details the development of a three-dimensional model created within GeoScene3D to visualize the subsurface, particularly the Dakota Sandstone in western Sarpy County.

Nebraska

Paleomagnetic correlation of surface and subsurface basalt flows in the central and southwestern part of the Idaho National Laboratory, Idaho

The U.S. Geological Survey, in cooperation with the U.S. Department of Energy, used paleomagnetic data from 22 coreholes to construct 3 fence diagrams of subsurface basalt flows in the southern part of the Idaho National Laboratory. These diagrams provide comprehensive descriptions of the horizontal and vertical distribution of basalt flows and sediment layers beneath the surface, aiding geological studies and contributing valuable data to numerical models of groundwater flow and contaminant transport. The correlations established though these diagrams include spatial correlations between basalt flows found in multiple coreholes. Correlations were identified by matching average paleomagnetic inclinations and confirming or denying these correlations using petrology, geochemistry and radiometric ages. The fence diagrams aid in identifying potential locations of subsurface vents, volcanic vents that have been buried by more recent volcanic activity, associated to subsurface basalt flows. By tracing the subsurface flows and analyzing where the greatest thickness occurs, the locations of buried vents can be inferred. Some subsurface flows exhibit correlations across several coreholes and may indicate yet unidentified surface or buried vents, thereby enhancing our understanding of the volcanic history and subsurface geology of the region.

Idaho

Gulf Coast Basin CORE-CM initiative final report

The Bureau of Economic Geology at the University of Texas at Austin (UT-BEG) is leading the Gulf Coast Carbon Ore, Rare Earth, and Critical Minerals (CORE-CM) Initiative to assess the potential to produce critical minerals (CMs), including rare earth elements (REEs) from coal, coal ash, and produced water related to oil and gas production, and related materials (alumina processing waste [red mud], heavy mineral sands, graphite, and zeolite) within the Gulf Coast Basin. This project represents the first phase in a long-term program and provides reconnaissance data that will be foundational for future work by assessing resources and suggesting plans to be conducted in future work and expanding stakeholder engagement. The project includes several tasks designed to identify, characterize, and assess several necessary aspects for development of CMs and REEs in the Gulf Coast Basin.

Gulf Coast basin

A time-space model of graphite mineral systems

Increasing demand for graphite in energy storage systems warrants review of graphite ore genesis in a mineral systems framework. Orogenic graphite encompasses the metamorphic and orogenic mineral systems that produce flake graphite and hydrothermal vein (lump and chip) graphite deposits, respectively. A common feature of orogenic graphite deposits is an association with upper amphibolite- to granulite-facies metasedimentary rocks in continent-continent or continent-island arc collisional orogens. Orogenic flake graphite deposits form primarily through graphitization of organic carbon during regional metamorphism, but strain localization and partial melting of pelitic protoliths are likely important processes for graphite grade and quality enrichment. Orogenic vein graphite deposits precipitate from hydrothermal fluids, possibly derived from metamorphism or anatexis at depth. Decarbonation reactions in mixed calcareous-carbonaceous metasedimentary sequences are the most likely carbon sources for the veins. In contrast, intrusion-related graphite includes magmatic-hydrothermal and metamorphic mineral systems that form primarily in continental arc settings via the interaction of magmas with carbonaceous sedimentary packages. Magmatic-hydrothermal flake graphite deposits are hosted in plutonic and volcanic rocks, and result from the exsolution of CO 2 -CH 4 -rich fluids from melts contaminated by such packages. Contact metamorphism of carbonaceous sedimentary rocks by plutons produces some microcrystalline (amorphous) graphite deposits, including many in China. Compilation of geologic data from known graphite deposits globally suggests that pulses of carbon deposition in the Paleoproterozoic, Mesoproterozoic, and Neoproterozoic provided source carbon material. Subsequent supercontinent orogenesis at ca. 2,100 to 1,700 Ma (Columbia), ca. 1,300 to 1,000 Ma (Rodinia), and ca. 650 to 500 Ma (Gondwana) resulted in the genesis of orogenic flake and vein graphite deposits, where favorable geologic components overlapped with organic ± carbonate carbon-rich strata. Cryogenian deposition of graphite protoliths and Cryogenian – Cambrian metamorphic mineralization account for nearly 75% of all known resources globally and coincide with profound carbon isotope excursions and climate variability, implying a link with the global carbon budget. Comparatively few graphite deposits are associated with Pangea-forming orogens, attributed to less exhumation and/or denudation. High-temperature metasedimentary belts containing organic carbon-rich protoliths are most favorable for hosting orogenic flake graphite deposits, whereas sequences that also contain carbonate protoliths are favorable for orogenic graphite veins. Continent-scale orogenic belts may host both deposit types along with vanadium deposits. Use of a time-space mineral systems framework for graphite deposits can improve exploration models needed to ensure future supply of this critical mineral and provide insights into Earth’s long-term carbon cycle.

Mineralium Deposita

To heal or not to heal?: 1. The effect of pore fluid pressure on the frictional healing behavior of lithologies in Oklahoma

The competition between fault healing (i.e., re-strengthening) and fault loading determines the timing and magnitude of fault failure within the seismic cycle. Repeating earthquakes can give observational estimates of fault healing rates, however, it is difficult to link laboratory studies of frictional healing and observed healing rates from repeating earthquakes in part because of uncertainty in lithology at depth. Due to well-constrained and relatively simple geology, earthquakes in Oklahoma can be linked to the granitic basement rock and to the Arbuckle Group, which is primarily composed of dolomite at earthquake depths. Here, we conduct friction experiments to measure healing rates of the two earthquake-bearing lithologies at confining pressures representative of earthquake depths and pore pressures ranging from 0% to 80% of the confining pressure. We measure frictional healing by executing slide-hold-slide tests with hold times ranging from 3 s to 3000 s. The friction experiments on the Troy Granite indicate that pore fluid pressure does not greatly affect healing rate. On the other hand, the dolomite of the Arbuckle Group exhibits decreased healing with increased pore fluid pressure, with weakening at the highest pore pressure. We hypothesize that this is due to an increase in dissolution of dolomite at high pore pressures/low effective normal stress. These healing rates are used in the companion paper to understand the moment-recurrence time behavior of repeating earthquakes in Prague, Oklahoma. This work has implications for possible enhanced dissolution and weakening behavior of the Arbuckle Group during wastewater injection activities.

Oklahoma

A spatial analysis of the groundwater emergence flood hazard in Long Island, New York and near coastal areas surrounding Long Island Sound in New York, Connecticut, and Rhode Island

Long Island, New York and near coastal areas surrounding Long Island Sound are densely populated and, like other coastal areas, are susceptible to flooding from several potential sources, including stormwater from precipitation events, tidal flooding and storm surge, and groundwater inundation or groundwater emergence flooding. The latter refers to the intersection of a rising water table with land surface or critical infrastructure. Many studies of flood drivers either neglect or only briefly discuss how shallow groundwater conditions may contribute to or exacerbate flood conditions. As part of a comprehensive study of compound flood hazards in the near coastal areas surrounding Long Island and Long Island Sound, a spatial analysis was completed, in cooperation with the Environmental Protection Agency’s Long Island Sound Study, using available regional datasets to characterize the potential hazard for groundwater emergence flooding. The approximately 3,100 square mile study area was subdivided into 11,407 900-meter by 900-meter (approximately 3,000-feet by 3,000-feet) grid cells, for the purposes of integrating the spatial datasets to calculate and map the groundwater emergence flood hazard. The depth to the water table, hydrologic soil groups, and National Land Cover Database were harmonized to the common grid. A groundwater emergence flood hazard rank was calculated for each grid cell for current average conditions following a set of rules accounting for the depth to the water table and the percent of area within each cell with slow infiltrating soils. A higher sea level position scenario was also calculated for the Long Island part of the study area. The calculated groundwater emergence flood hazard rank was reviewed in concert with the National Land Cover Data Base to identify developed areas and associated infrastructure that may be at risk to groundwater emergence flooding. Study results indicate that the groundwater emergence flood hazard is highest in coastal areas and near surface water where the water table is close to ground surface. Inland areas away from surface water bodies are not likely to be exposed to groundwater emergence flooding. For Long Island, under a scenario with higher sea level position, a greater groundwater emergence flood hazard is calculated in some locations closer to the coast and where land is submerged. Away from the coast and surface-water drainage, the groundwater emergence flood hazard is similar between the current average sea level condition and a higher sea level position scenario.

EarthArXiv

Factors regulating the potential for freshwater mineral soil wetlands to function as natural climate solutions

There are increasing global efforts and initiatives aiming to tackle climate change and mitigate its impacts via natural climate solutions (NCS). Wetlands have been considered effective NCS given their capacity to sequester and retain atmospheric carbon dioxide (CO 2 ) while also providing a myriad of other ecosystem functions that can assist in mitigating the impacts of climate change. However, wetlands have a dual impact on climate, influencing the atmospheric concentrations of both CO 2 and methane (CH 4 ). The cooling effect associated with wetland CO 2 sequestration can be counterbalanced by the warming effect caused by CH 4 emissions from wetlands. The relative ability of wetlands to sequester CO 2 versus emit CH 4 is dependent on a suite of interacting physical, chemical, and biological factors, making it difficult to determine if/which wetlands are considered important NCS. The fact that wetlands are embedded in landscapes with surface and subsurface hydrological connections to other wetlands (i.e., wetlandscapes) that flow over and through geochemically active soils and sediments adds a new layer of complexity and poses further challenges to understanding wetland carbon sequestration and greenhouse gas fluxes at large spatial scales. Our review demonstrates how additional scientific advances are required to understand the driving mechanisms associated with wetland carbon cycling under different environmental conditions. It is vital to understand wetland functionality at both wetland and wetlandscape scales to effectively implement wetlands as NCS to maximize ecological, social, and economic benefits.

Wetlands

Sources and risk factors for nitrate, pathogens, and fecal contamination of private wells in rural southwestern Wisconsin, USA

Household well water can be degraded by contaminants from the land's surface, but private well owners lack means to protect the source water from neighboring disturbances. Rural residents of southwestern Wisconsin, USA, rely on private well water, and the combination of land use and fractured carbonate bedrock makes groundwater vulnerable to contamination. To identify the extent, sources, and risk factors of private well contamination, randomly selected wells sampled during two-day periods in fall (n = 301) and spring (n = 529) were analyzed for nitrate and indicator bacteria, and a subset (n = 138) was sampled across four seasonal events for analysis of pathogens and microbial source tracking markers by quantitative polymerase chain reaction. Risk factors representing land use, hydrology, geology, and well construction were analyzed for associations with contamination in multivariable models. The importance of risk factors varied by contaminant, illustrating the multifaceted nature of rural groundwater quality. Nitrate contamination was associated with agricultural land use, and wells with casings that extended below a shale aquitard accessed less contaminated water than those drawing water from above it. Human fecal microbes were detected in 64 wells (46%), and rainfall was the key risk factor for contamination, indicating that wastewater from septic systems was available to contaminate wells when transport conditions were favorable. Manure microbes from cattle/ruminants and pigs were detected in 33 and 13 wells, respectively, and concentrations increased with the hectarage of cultivated land near wells. Pathogen genes for viruses, bacteria, and protozoa were detected in 66 wells (48%), including more detections of zoonotic than human-specific pathogens, and human Bacteroides , an indicator of wastewater, was an equivocal predictor of pathogen presence in private wells. Characterizing important elements of the setting, like geology, and identifying sources and risk factors for contaminants can inform landscape-level policies to protect groundwater quality.

Wisconsin

Distributed volcanic fields—Patterns, products, processes, and plumbing

Distributed volcanic fields—also referred to as “monogenetic fields” or simply “volcanic fields”—are found on every continent, on the seafloors, and in every tectonic setting on Earth. Yet, our understanding of what constitutes a distributed volcanic field, and our knowledge of the common products, spatiotemporal patterns in activity, and plumbing systems of these fields, are commonly poor and (or) debated. Here we provide an overview of the current understanding of distributed volcanic fields (DVFs) through review and compilation of published data, with an emphasis on understanding the characteristics of fields that are essential to prepare for future hazardous volcanic activity. Distributed fields can erupt restricted to variable magma compositions. Activity in these fields produces nearly all types of volcanoes, including scoria and spatter cones, maars, low shields, lava fields, stratovolcanoes, and calderas, but monogenetic volcanoes are the defining characteristic of DVFs. The number of vents and lifespans of DVFs vary greatly; vent numbers range from 2 to greater than 1,000, and fields can remain active for 150,000 to 10 million years. Some characteristics of DVFs appear field dependent. Although the volumes of single monogenetic eruptions within DVFs globally are variable (from less than 0.1 to a few cubic kilometers), each field may have a characteristic range in eruption volumes. Eruptions within distributed volcanic fields can have a random distribution and timing, but spatial and (or) temporal vent clustering and alignment are common, and eruptions may be time or volume predictable. Average eruption recurrence intervals in DVFs span over an order of magnitude, from less than 3 to greater than 100 thousand years. Exposures of the shallow portions of older systems reveal that many magma batches end their ascent before reaching the surface, with some dikes stopping within only meters of the surface. Petrologic insights into the deeper plumbing systems of DVF volcanoes indicate variable depths of magma crystallization and (or) stalling, and that magma transport and storage systems may be unique to a particular DVF and its underlying crustal structure. Both seismic and petrologic data for mafic DVF eruptions corroborate intrusions of magma into storage systems in the months to years before eruption, as well as variable ascent rates through the crust (days to weeks). Few distributed fields are closely monitored, as they erupt infrequently, but these observations imply that the amount of time available to install monitoring instrumentation after the first felt seismicity may be short, as precursory activity is frequently on the order of days to months for modern DVF eruptions. Satellite-based geodesy may provide useful warning in such cases. This chapter concludes with outstanding questions and areas for future research that will aid in our understanding and preparedness for future DVF eruptions.

Professional Paper

Critical minerals in mine waste

Introduction Critical minerals are commodities with vulnerable supply chains that play a vital role in supporting the United States’ economy, national defense and security, emerging technologies, and energy independence. The prosperity of our Nation depends on generating a resilient supply of domestic critical minerals; mine waste may be an untapped source of these commodities. Mine waste from centuries of legacy mining persist on the landscape and may contain critical minerals and other valuable commodities previously deemed uneconomic to recover. At modern mines, the financial viability of recovering byproduct critical minerals, which are not the primary target, may be marginal and can ultimately destine them to mine waste. Further, mine waste can be a liability for the mining company or, at legacy mines, the taxpayer because of its effect on the landscape. The U.S. Geological Survey (USGS) has several initiatives to evaluate critical mineral resources in various types of waste. This factsheet highlights studies of mine waste carried out by USGS scientists at the Geology, Energy & Minerals Science Center in collaboration with other science centers funded through the USGS Mineral Resources Program. Recovery of critical minerals from mine waste can aid in remediation efforts and increase domestic supply of vital mineral resources.

Fact Sheet

The Mammoth magnetic anomaly, Pinal County, Arizona

A high-resolution Earth Mapping Resources Initiative airborne geophysical survey was flown in the southwest North American porphyry copper province to improve bedrock geologic maps and to identify areas that have unrecognized critical mineral resource potential. During the review of the aeromagnetic data, a distinctly monopolar-shaped, negative magnetic anomaly was observed at a flight elevation of 200 m above the ground with a maximum amplitude of –9500 nT. We have named this the Mammoth magnetic anomaly (MMA) because it is centered 12 km northeast of the town of Mammoth, Arizona, USA. The total field anomaly (TFA) contour of –500 nT enclosing the MMA defines an elongate shape measuring 2.5 km long by 1 km wide that trends northwest–southeast. Given the striking nature of this negative, monopolar-shaped magnetic anomaly, we conducted a ground campaign in May 2025 to determine its authenticity and potential relationship to critical mineral endowment. The MMA was confirmed on the ground with a TFA approaching –46,000 nT. Total magnetic intensity (TMI) observations routinely fell below the 18,000 nT operating floor of an industry-standard cesium-vapor total field magnetometer, and extremely low TMI measurements were corroborated along coincident traverse lines using two high dynamic range, but lower sensitivity, smartphone vector magnetometers. The lowest TMI values recorded by both smartphone magnetometers were 1000 nT and confirmed with multiple adjacent and crossing lines. Field observations suggest that this magnetic feature is caused by strong remanent magnetization within fine-grained magnetite hosted within locally altered Pinal Schist.

Arizona

Regional variations in sea ice and primary productivity in the Bering Sea during Marine Isotope Stage 11

Marine Isotope Stage (MIS) 11 (424-374 ka) has long been an analog for Holocene climate, because it is the most recent interglacial period with similar orbital conditions. However, there is significant global and regional variability in the climate response to MIS 11 warmth. Here, we review sediment core records from across the Bering Sea to investigate changes in paleoceanographic conditions during Marine Isotope Stages 12-10. Sea ice was present over much of the Bering Sea during MIS 11, but today, none of the sites investigated are ever ice-covered. This suggests that sea ice regimes in the Bering Sea during MIS 11 were different to those of the Holocene. There are also regional differences in the response of sea ice to MIS 11 warming. At the Umnak Plateau, Southeastern Bering Sea, sea ice concentrations decline during deglaciation, but they remain high at the slope sites until Peak MIS 11. Sea ice re-advances over the Umnak Plateau during peak interglacial warmth, at the same time that it declines over the slope sites. Late MIS 11 is characterized by high concentrations of seasonal sea ice at the Umnak Plateau, whilst sea ice at the slope sites fluctuates between consolidated and unconsolidated ice cover. This east-west dichotomy may be explained by changes in the behavior of the Aleutian Low. Productivity increases dramatically during deglaciation due to increased upwelling and sea level rise bringing fresh nutrients into the oceans. This is characterized by increased diatom productivity, increased terrestrial carbon deposition, and laminations at all sites.

Alaska

Detecting hidden sedimentary geothermal systems in the Upper Colorado River Basin

Geothermal resources exist in sedimentary rock where circulation of water for efficient extraction or storage of heat is possible. Except in rare instances where hot water is expressed at the land surface, sedimentary geothermal resources are hidden, so the identification of these systems is optimally accomplished using predictive subsurface modeling. An integrated approach using detailed paleogeographic interpretations, subsurface geologic mapping, and numerical modeling has produced regional geologic and temperature models for the Upper Colorado River Basin, a large watershed in central North America that contains many sedimentary basins. These models identify areas of hidden sedimentary geothermal resource potential in low temperature (<90°C), moderate temperature (90–150°C), and high temperature (>150°C) fairways across the study area. These models incorporate maps of key horizons in outcrop and the subsurface to create a robust structural framework that can be used to target favorable geology for natural or engineered permeability. This framework is populated with lithologies derived from detailed palaeogeographical maps and over 40,000 bottom hole temperature (BHT) values were used to create a calibrated three-dimensional (3D) temperature model across the region. The resulting maps serve as a regional sedimentary geothermal play fairway screening tool for evaluating different grades of sedimentary geothermal resources and for identifying areas of interest where more detailed, prospect-scale studies can be undertaken.

Arizona, Colorado, New Mexico, Utah, Wyoming

Stratigraphy, structure, and geomorphology of the central Appalachians across the North Mountain fault zone near Harrisonburg, Virginia, USA

This field trip focuses on the geology of the central Appalachian Valley and Ridge province near Harrisonburg, Virginia, USA. Recent geologic mapping utilizing 1-m resolution lidar data has revealed new insights into the Paleozoic stratigraphy, structural geology, and Neogene landscape evolution of the region. The detailed mapping reveals the presence of the Big Spring Station Member and multiple thrombolite zones in the Cambrian Conococheague Formation extending as far south as the Briery Branch 7.5 min quadrangle, providing insights into Late Cambrian sea-level fluctuations. Multiple outcrop exposures in the study area of this guidebook confirm recent work in Pennsylvania, USA, showing that the Ordovician Reedsville Shale overlies the Martinsburg Formation and that the two are distinct and mappable as separate formations rather than laterally equivalent units as previously interpreted. Our work extends the Silurian Williamsport Sandstone into Shenandoah County, Virginia, and describes its facies relationships with the Bloomsburg Formation along strike and across the Adams Run anticline. Mapping within the thick Devonian siliciclastic sequence reveals the presence of the Mahantango Formation on the western limb of Supin Lick syncline and illustrates its complex facies relationship with the Millboro Shale. In addition, we highlight new mapping criteria for the Brallier and Foreknobs Formations and demonstrate how the specific changes to the placement of the contact between them addresses previous challenges in their differentiation. We present cosmogenic burial ages of broad alluvial fan sediments in the Shenandoah Valley near Timberville and Briery Branch, Virginia, and erosion rates estimated for the Briery Branch stream basin. Both analyses provide new constraints on the timing of landscape evolution and karst development since the middle Pliocene. This field guide also highlights some significant structural features within the North Mountain fault zone, such as evidence of imbricated thrust sheets cut by cross-strike faults that have been exploited by Eocene igneous intrusions. Map-scale horses of Silurian and Ordovician rocks hold up ridges that are oblique to the regional strike. Deformation internal to one of these horse blocks is shown to be non-coaxial with respect to the main regional northwest directed transport.

Virginia