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USGS2026

Detecting earthquakes in noisy real-time GNSS data with deep learning for improved PGD magnitude estimation

To disseminate accurate and useful warnings, earthquake early warning (EEW) systems must quickly determine the size and location of an earthquake to estimate expected shaking. Traditional seismic‐based algorithms tend to underestimate the true magnitudes of large earthquakes, a phenomenon known as magnitude saturation. This limitation motivated the recent inclusion of Global Navigation Satellite Systems (GNSS) data into the U.S. Geological Survey’s ShakeAlert EEW system with the Geodetic First Approximation of Size and Time (GFAST) algorithm because GNSS data do not saturate with large ground motions. However, the noise levels of GNSS data are very high compared with traditional seismic data, which obscures P ‐wave arrivals and can result in less accurate magnitude estimations if displacement amplitudes are low, such as for lower magnitude earthquakes or large source–station distances. In this study, we develop a deep‐learning model that detects earthquakes in GNSS data and use the Ridgecrest, California, earthquake sequence as a case study to demonstrate how the model could act as a filter to reduce the amount of low‐quality data that enters an algorithm like GFAST. To preserve our limited real earthquake data for model inference, we generated a training dataset composed of >700,000 synthetic displacement waveforms. We combined the synthetic waveforms with real‐time GNSS noise to produce realistically noisy training waveforms and then tested our model on additional synthetic data and performed inference using the real data that were held back. We discuss the performance of our trained model on both the unseen synthetic data and real inference data. Our model can be used to selectively filter only high‐quality data where an earthquake signal is observed for input into an algorithm like GFAST (outperforming a simple signal‐to‐noise ratio–based filter) to reduce the error in GFAST’s real‐time earthquake magnitude estimations.

California↗
USGS2026

The use of fluorite geochemistry and machine learning to identify critical mineral systems

Fluorite (CaF 2 ) is a potential pathfinder to critical mineral and rare earth element (REE) deposits but its application has been limited to a narrow range of mineralization types. I show that fluorite is a robust recorder of mineralization fertility by applying statistical and machine-learning methods to a new global fluorite geochemical database. Distinct median rare earth and trace element patterns are observed among deposit types and genetic environments. Fluorite associated with carbonatites and REE deposits are relatively enriched in Sr and have minimal Eu anomalies. These characteristics define new bivariate discrimination diagrams that correctly identify 78% of carbonatite-related fluorite and 88% of fluorite from REE deposits. Random forest classifiers were developed for a wide range of mineralization types and genetic settings. Trained solely on rare earth element patterns, these models achieve accuracies of 77–79%. Higher classification accuracies (up to 88–96%) are obtained when including elements such as Sr, highlighting the significance of trace elements for optimal fluorite classification. The recognition of diagnostic fluorite compositional fingerprints, particularly in REE-fertile systems, underscores its potential as a pathfinder and indicator for critical mineral exploration in F-bearing environments.

Mineralium Deposita↗
USGS2026

Global performance of remote sensing-based and reanalysis-driven models to estimate open water evaporation

Evaporation plays an essential role in the water cycle, influencing local and regional climates while directly impacting water availability in lakes. However, directly measuring evaporation over water bodies remains challenging due to the high costs of installing and maintaining the required in situ instrumentation. Although several remote sensing algorithms have been providing evaporation estimates, the lack of a global validation hinders our understanding of their relative uncertainties and performances across different regions. Here, we analyze the performance of a suite of models that leverage satellite data and meteorological reanalysis to estimate evaporation over lakes worldwide. We compare 3 remote sensing-based models, 1 reanalysis-driven model and 1 ensemble approach, using in situ observations from 27 lakes representing a diverse range of geographic and climatic regions. Our results demonstrate that, overall, the ensemble outperformed any individual model in terms of accuracy, with a RMSE and a bias of 1.3 and 0.3 mm day −1 , respectively. These findings highlight the benefits of using an ensemble approach to estimate open water evaporation with satellite-based models at the global scale, leveraging the unique strengths of each model. For the individual models, differences in the representation of heat storage changes and advection effects led to lower values of RMSE and bias, depending on the location and depth of the lakes. This study sets the path for future improvement of open water evaporation algorithms globally, while remote sensing techniques are proven satisfactory to monitoring of water loss in lakes globally, an essential step toward effective large-scale water resources management.

Water Resources Research↗
USGS2026

Velocity-independent dry friction on mica: A realization of ideal Amontons-Coulomb friction

The Amontons-Coulomb friction law assumes that the frictional force between materials is independent of sliding velocity. However, as Coulomb noted, this is a rough approximation, and a second-order dependence of friction on the logarithm of sliding velocity is incorporated in a commonly used ‘rate- and state-dependent’ friction representation. Here we conduct shear experiments on mica, a layer-structured mineral, at temperatures ranging from 25 to 200ºC and under normal stress of 100 MPa. The friction coefficient clearly depends on the logarithmic sliding velocity at 25ºC, but rate sensitivity decreases with increasing temperature until at 200ºC, the friction coefficient is independent of sliding velocity. Our findings could initiate the development of velocity-independent frictional materials, realizing the ideal Amontons-Coulomb friction.

Physical Review Letters↗
USGS2026

Geologic framework, hydrostratigraphy, and ichnology of the Blanco, Payton, and Rough Hollow 7.5-minute quadrangles, Blanco, Comal, Hays, and Kendall Counties, Texas

During 2023, the U.S. Geological Survey, in cooperation with the Edwards Aquifer Authority, revised an initial characterization completed during 2015–16 of the geologic framework, hydrostratigraphy, and ichnology of the Edwards and Trinity aquifers in the Blanco, Payton, and Rough Hollow 7.5-minute quadrangles in Blanco, Comal, Hays, and Kendall Counties, Texas. The purpose of this report is to present the updated geologic framework, hydrostratigraphy, and ichnology of the Trinity and Edwards Groups in those quadrangles. Rocks exposed in the study area are of the Lower Cretaceous Trinity Group and lower part of the Fort Terrett Formation of the Lower Cretaceous Edwards Group. The faulting and fracturing in the study area are part of the Balcones Fault Zone, an extensional system of faults active during the Paleocene to middle Eocene that generally trends southwest to northeast in south-central Texas. Hydrostratigraphically, the rocks exposed in the study area contain a section of the Edwards (Balcones Fault Zone) aquifer, upper zone of the Trinity aquifer, and middle zone of the Trinity aquifer. In the study area, the only hydrostratigraphic units of the Edwards (Balcones Fault Zone) aquifer remaining are (from top to bottom) VII and VIII, which cap several hills. The mapped hydrostratigraphic units of the upper zone of the Trinity aquifer are (from top to bottom) the cavernous, Camp Bullis, upper evaporite, fossiliferous, and lower evaporite. The mapped hydrostratigraphic units of the middle zone of the Trinity aquifer are (from top to bottom) the Bulverde, Little Blanco, Twin Sisters, Doeppenschmidt, Herff Falls (where present), Rust, Honey Creek, Hensell, and Cow Creek hydrostratigraphic units.

Texas↗
USGS2026

Structural evolution of iron coordination in proteins across Earth’s oxygenation history

Protein metal-binding sites support essential biological functions shaped by protein fold, subunit interactions, and cofactor chemistry. Because these sites encode both biochemical function and environmental constraint, they offer a route to connect protein evolution with changes in Earth’s surface environment through time. Of particular interest is iron (Fe), the most widely used metal in biology and a cofactor central to both anaerobic and aerobic metabolism. Here, we systematically compare the immediate chemical environments of functionally essential Fe-binding sites in three-dimensional protein structures to test whether Fe coordination spheres differ across oxygen contexts. Using a curated dataset of experimentally determined structures, we identify a clear shift in the local chemistry of Fe-binding environments from anaerobic to aerobic proteins. Aerobic Fe sites are significantly more hydrophilic than anaerobic ones, and amino-acid composition analyses show reduced cysteine use in aerobic Fe-binding neighborhoods. These patterns suggest that as Earth’s surface environments became more oxygenated, proteins retained Fe as a core redox metal while reconfiguring local coordination chemistry in ways less vulnerable to oxidative damage. More broadly, this study introduces and applies the Coordination Sphere Analysis and Comparison (CSAC) workflow, an open and archived Python workflow for extracting local metal-binding environments from structure datasets, providing a framework for linking metalloprotein structure to evolutionary and geobiological transitions across Earth history.

Discover Life↗
USGS2026

Thermal detectability of subsurface water ice on Mars: A comparative analysis for the Subsurface Water Ice Mapping (SWIM) Project

We have developed a new global map of shallow ground ice distribution, SWIM23, based on Mars Global Surveyor Thermal Emission Spectrometer data and made systematic comparisons between this new map and two similar, previously developed data products. We have explored the origin of differences between the three ice maps by detailing technical and procedural differences in their development, by making global pixel-by-pixel comparisons, and by carrying out a series of one-dimensional thermal simulations to explore fundamental physical limitations of thermal ice-detection techniques. These efforts and the production of a composite thermal ice-consistency map supported integration of multiple geophysical data products relevant to ice detection in the upper meter of the Martian regolith into the larger Mars Subsurface Water Ice Mapping project. Our work also highlights fundamental physical limitations to thermal ice detection as a technique, particularly the rapid fall-off in ice detection sensitivity at depths >30 cm, which produces maximum uncertainty in the presence and depth of ice within regions preferred for potential human landing sites. A future Mars orbiter mission designed to detect ice and support crewed landing site selection in the midlatitude region should give payload priority to an instrument capable of probing the 1–5 m depth range (i.e., a high-frequency radar), over a next-generation thermal spectrometer, which is unlikely to offer clarity on ice table depths or lateral continuity of the ice table in the locations of highest interest.

Planetary Science Journal↗
USGS2026

Hydrogeologic conceptualization of the Arroyos subarea and Northeast Air Force Research Laboratory subarea of the Air Force Research Laboratory, Edwards Air Force Base, Antelope Valley, California, 2017–21

Research and testing within the Air Force Research Laboratory at Edwards Air Force Base in the southwestern Mojave Desert has been conducted since the 1950s. This testing requires large quantities of groundwater for cooling and operations involving hazardous constituents that have entered the groundwater. To better understand the potential movement of contaminants through the groundwater system, the U.S. Geological Survey entered into a cooperative agreement with the U.S. Air Force Civil Engineer Center with the purpose of (1) gaining a more detailed understanding of the hydraulic connection between the unconsolidated basin-fill sediment and the underlying weathered and crystalline bedrock and (2) investigating faults and their potential effect on groundwater flow. This study was specific to the Arroyos subarea and Northeast Air Force Research Laboratory subarea of the Air Force Research Laboratory. The refined hydrogeologic characterization was derived by evaluating surface geologic maps, a regional gravity model, new subsurface geophysical surveys, lithology data from boreholes, and groundwater-level data. Refinement of the hydrogeologic characterization of the study area involved developing a map of basin-fill sediment thickness, estimating the geometry and depth to bedrock, determining the presence of weathered bedrock material, and identifying the location of faults and subsurface structures. The thickness of basin-fill sediment was derived from a regional gravity model. Basin-fill sediment ranges from less than 20 feet (ft) thick to about 150 ft thick and increases substantially toward a deep structural basin in the northwestern part of the study area. The top of bedrock estimated from the new surface geophysical surveys is generally deeper than the top of bedrock from the regional gravity model. These differences in interpreted bedrock tops indicate that there may be a zone of weathered bedrock in the subsurface, overlying crystalline bedrock. Additional subsurface data evaluating the geometry and thickness of weathered bedrock are necessary for a comprehensive evaluation of weathered bedrock in the study area. Previously unmapped extensions of the Leuhman Fault, Spring Fault Zone, and Boron Gate Fault were identified in the new surface geophysical surveys. Evaluation of groundwater flow between bedrock and basin-fill sediment, and the effects of faults on groundwater flow, was done using groundwater-level data from 2020. The groundwater table was in crystalline bedrock throughout most of the Arroyos and Northeast Air Force Research Laboratory subareas, with a few exceptions where it was in basin-fill sediment and weathered bedrock. Basin-fill sediment, and likely weathered bedrock, was partially saturated in parts of the study area where basin-fill sediment was as thick as 150 ft. Weathered bedrock material may be present near the Spring Fault Zone, and if so, was likely saturated in 2020. The groundwater-level data near and within Spring Fault Zone indicate that the Spring Fault Zone acts as a vertical-along-strike conduit for, and as an across-strike impediment to, groundwater flow. In addition, steep groundwater-level gradients in the southeastern part of the study area indicate that a subsurface structure affecting groundwater flow could be related to the Leuhman Fault. Sufficient groundwater-level data were not available to conclusively determine if the Arroyos, Rich, and Boron Gate Faults, and their inferred extensions from the geophysical surveys, affect the movement or direction of groundwater flow.

California↗
USGS2026

Groundwater source water assessment area delineation of public supply wells in the Treasure Valley, western Idaho

The Idaho Department of Environmental Quality (IDEQ) is responsible for assessing the source water for public water supply systems including the delineation of source water assessment areas for wells, which are defined as the subsurface areas contributing water to a well during a period of time. Part of the IDEQ assessment plan is to update source water assessments over time. The U.S. Geological Survey (USGS) developed a new groundwater-flow model for part of the western Snake River Plain aquifer in southwestern Idaho. This groundwater- flow model provided a new opportunity for IDEQ to update source water assessment for public water supply wells within the model boundary. The USGS, in cooperation with IDEQ, used the USGS Treasure Valley Groundwater Flow Model along with a MODPATH particle tracking post-processing program to reassess public-water supply source water assessment areas. The USGS created an automated script that requests a well location, depth, and pumpage rate, and then incorporates that information into the Treasure Valley Groundwater Flow Model combined with the MODPATH model to create 3-, 6-, and 10-year time of travel zones that are output to a geographic information system shapefile. The TVSWA_Delineator script provides a fast, transparent tool for IDEQ to reassess or create new public-water supply source water assessment area delineations based on new and updated information and is available as a Python script and a Windows executable with the compiled script and all necessary components. TVSWA_Delineator utilizes a quadtree approach to rediscretize the Treasure Valley Groundwater Flow Model grid around the pumping well location from 1-mile cell lengths telescoped down to 1/16 mile. This rediscretization increases the source water assessment area delineation resolution near the pumping well and minimizes the effect of weak sinks in the MODPATH model. The stress inputs for each month of the final 10 years (2006 to 2015) of the Treasure Valley Groundwater Flow model historical simulation were averaged for the particle tracking analysis. The MODPATH model used backwards tracking of particles released at each stress period to create the source water assessment area delineations. This report documents the creation of the TVSWA_Delineator Python script, including adaptations made to the Treasure Valley Groundwater Flow Model, creation of a companion MODPATH model, and post-processing results to provide source water assessment areas.

Idaho↗
USGS2026

Groundwater and surface-water interactions in the Waihe‘e-Kahalu‘u watershed, O‘ahu, Hawai‘i—Analysis of historical data and numerical groundwater-model simulations

The Waihe‘e-Kahaluʻu watershed and surrounding areas lie in a dike-impounded groundwater setting of the Ko‘olau Range, O‘ahu, Hawai‘i, where groundwater withdrawal from wells and tunnels have resulted in reductions in streamflow. Resource managers and surface-water users seek information that can be used to balance the needs of competing uses of groundwater and streamflow in the watershed. This study assesses the effects of four groundwater developments in the Waihe‘e-Kahalu‘u watershed—Kahaluu Tunnel, Waihee Tunnel, Kahaluu Well, and Waihee Incline Wells—on Kahalu‘u and Waihe‘e Streams. Analyses of historical streamflow, withdrawal, and rainfall data indicate that base flow (the component of streamflow that is supplied from groundwater discharge) in Kahalu‘u and Waihe‘e Streams decreased in response to withdrawals from wells and tunnels within and outside the watershed. Groundwater-model simulations indicate that shutdown of selected tunnels and wells in the Waihe‘e-Kahaluʻu watershed will result in increases of groundwater discharge, but not all of the increase will occur in streams within the watershed; increases will also occur in streams outside the basin, the ocean, and tunnels other than those that were shut down. The analysis of historical data and model simulations is consistent in showing that the effects of withdrawal changes on streams are not constrained by the topographic boundaries of watersheds. Stream base flows in the Waihe‘e-Kahalu‘u watershed are subject to a complex interaction of multiple withdrawals from wells and tunnels installed at various times within and outside the watershed. The correspondence between withdrawals and base-flow changes is consistent with the conceptual model and understanding of the connection between groundwater and streamflow in the dike-impounded groundwater setting of the Waihe‘e-Kahalu‘u watershed and the Ko‘olau Range.

Hawaii↗
USGS2026

Cruise summary—Samoa Basin abyssal mapping—Box coring leg, Pago Pago, Territory of American Samoa to Pago Pago, American Samoa, April 11– May 1, 2026

Expedition Summary U.S. Geological Survey scientists led a box coring effort to the Samoa Basin to characterize minerals and the surrounding abyssal sediments and fauna. Thirty-eight box cores were deployed between April 13, 2026, and April 28, 2026. Thirty-six box cores recovered sufficient material to determine nodule density, and 35 recovered sufficient material for subcores to be collected. The purpose of this Data Report is to provide a summary of samples collected, initial results that were obtained shipboard, and briefly mention planned future analyses from this expedition.

Data Report↗
USGS2026

Tectonic controls on volcanism and associated hydrothermal activity in a sediment-dominated mid-ocean ridge; Escanaba Trough

Mid-ocean ridges, the Earth's most extensive volcanic system, exhibit unique characteristics in sediment-dominant environments. Thick sediment cover insulates the crust and channels fluid along pathways that can lead to the formation of distinct crustal alteration patterns, exceptionally large mineral deposits, and specialized chemosynthetic ecosystems. This study presents an interdisciplinary investigation into the tectonics of the Escanaba Trough, a heavily sedimented axial valley at the southern Gorda Ridge in the Northeast Pacific Ocean. A primary challenge in such environments is overcoming the masking effect of thick sediments on basement structures that control magmatic and hydrothermal activity. We address this by employing three-dimensional (3D) magnetic modeling of high-resolution near-seafloor magnetic data collected by an autonomous underwater vehicle (AUV). The 2022 surveys with AUV Sentry provided data for 3D magnetic susceptibility models, refining our understanding of the geometry of sub-sediment laccoliths/saucer-shaped sills and hydrothermal alteration. In conjunction with a new 1:100,000 scale lithostratigraphic map, we outline the tectonic controls on the emplacement of Escanaba Trough's three main volcanic centers, characterize the geometry of its spreading segments, and provide volumetric data on the distribution of sub-sediment volcanism in the southern Gorda Ridge.

Escanaba Trough, Pacific Ocean↗
USGS2026

Beaver dam analogs as nature-based solutions to mitigate snowpack loss in northern New Mexico

Reductions in snow have left many streams in northern New Mexico dry or with very low flows during the summer. Base flow, defined as the contribution of groundwater to streamflow, can sustain streamflow during the summer and during drought conditions. Beaver dam analogs can be used to “slow the flow,” or increase the infiltration of rain-based runoff to replenish shallow groundwater reservoirs and increase base flow and potentially increase summertime streamflow.

New Mexico↗
USGS2026

Background and geologic model for the 2024 U.S. Geological Survey assessment of undiscovered conventional petroleum resources in the Norphlet Formation, U.S. Gulf Coast

The Upper Jurassic Norphlet Formation is a stratigraphic unit located in the subsurface of the United States Gulf coastal plain and offshore Gulf of America (Gulf of Mexico). The Norphlet consists of clastic sediments derived from the southern Appalachian highlands, and was deposited in a continental dryland setting on the margins of the early Gulf of America rift basin. The formation contains a variety of sedimentary facies, including facies representing updip alluvial fans, wadis, red beds, and a widespread erg, or eolian sand sea. The erg facies form the primary reservoirs from which hydrocarbons sourced from the overlying Smackover Formation are produced. Development of the Norphlet began in earnest in the late 1960s, with new discoveries, including large fields at Flomaton, Hatters Pond, and Mobile Bay, continuing through the 2000s–2010s with the discovery of major oil fields in the offshore Desoto Canyon area. Onshore, Norphlet hydrocarbon traps typically are faulted salt anticlines, although many fields also have a stratigraphic trapping component because of the preservation of dune-scale bedforms. Thermal maturity across the Norphlet play varies significantly with depth, resulting in oil production transitioning downdip to natural gas liquids production, then dry gas production; production depths reach to greater than 21,000 feet. A 2024 U.S. Geological Survey assessment divided the Norphlet into four conventional assessment units defined by the type and frequency of trapping mechanisms, sedimentology, and thermal maturity of each area, with little potential for hydrocarbon development observed west of the Mississippi River. Although petroleum resources in the Norphlet were revised downward, it is probable that significant resources remain to be discovered.

Alabama, Florida, Mississippi↗
USGS2026

Simulation of groundwater flow in the Silurian aquifer, eastern Iowa, 2020–45

The Silurian aquifer is an important water source for municipalities, industry, and rural households and communities in eastern Iowa, including Johnson County. Increasing demand for groundwater from the aquifer indicated that analytical tools may be beneficial to quantify groundwater resources and inform water-management decisions for the aquifer. The U.S. Geological Survey, in cooperation with the Johnson County Board of Supervisors, developed conceptual and numerical groundwater models to simulate water levels in the Silurian aquifer, determine groundwater budgets, and forecast changes in groundwater levels through 2045. A MODFLOW numerical model was constructed to match water levels for 2020 through 2022. Model performance was assessed by comparing simulated and observed water-level hydrographs at several pumping and monitoring wells. Hydrograph comparison indicates that the model simulates water levels accurately at monitoring wells that are not near areas of pumping and generally overpredicts water levels near pumping wells, while accurately simulating the drawdown trend over time at pumping wells. This transient model framework was then used to predict water levels through 2045 in a scenario of moderate drought and increased groundwater withdrawals. Results from the predictive model indicate as much as 13 meters of additional drawdown in 2045 from 2020 water levels in the area of pumping wells.

Iowa↗
USGS2026

Apatite (U-Th)/He thermochronology from Marsh Creek anticline reconciles Cenozoic and Holocene strain patterns and elucidates the Cenozoic canning displacement zone of Arctic Alaska

The northeastern Brooks Range is a vast fold-thrust belt that records the northernmost expression of Cenozoic deformation in Alaska, likely with complex dynamic linkages to distant tectonic elements. The principal focus of this manuscript is the Marsh Creek anticline (MCA), which is a large and recently active structure within the broader northeastern Brooks Range. The MCA is a complex, polyphase structure mostly buried beneath the Arctic coastal plain. We present apatite (U-Th)/He (AHe) dates from six outcrop samples, all near the structural crest of the anticline, as well as supporting detrital zircon U/Pb (ZUPb) age spectra from five outcrop samples. The AHe sample transect spans ~3 km of structural relief. The four shallowest AHe samples are not reset. However, the two deepest samples exhibit low intrasample variability among replicates and strong date versus grain radius correlations, suggesting post-depositional burial heating to within the AHe partial retention zone. Inverse thermal history modeling of these data resolves a protracted phase of exhumational cooling that began around 33–28 Ma. Detrital ZUPb age spectra from Paleogene strata support an interpretation of diverse inherited thermal histories recorded by the AHe data, and they are also consistent with extant reconstructions of Paleogene sediment dispersal. Placed into regional context, the results constrain a phase of increasing structural relief in the northeastern Brooks Range fold-thrust belt that began by the Eocene. The relief developed in a zone characterized by diminishing structural relief to the west called the Canning displacement zone. Although this zone was active since the Eocene, several structures including the studied part of the MCA were rapidly exhumed in the Oligocene. Lastly, we argue for kinematic compatibility between Cenozoic contraction and active strike-slip in the northeastern Brooks Range, with the temporal change in strain style likely reflecting the increase in structural relief and topography.

Alaska↗
USGS2026

Effects of a low-lipid diet on the gut microbiome and head kidney transcriptome of juvenile Chinook Salmon

Objective Pacific salmon Oncorhynchus spp. reared in production hatcheries are typically fed high-lipid, energy-dense diets to achieve large size and high body condition prior to release. In contrast, juveniles in natural environments tend to consume low-lipid, high-protein diets, and fish reared for research or conservation purposes are sometimes fed diets that are formulated to mimic natural diets and promote wild-like phenotypes. Understanding how these alternative diets affect fish health beyond growth and body condition could ultimately contribute to improving hatchery fish fitness. Methods In this work, we evaluated changes in the fecal microbiome and gene expression of juvenile Chinook Salmon O. tshawytscha on a standard high-lipid hatchery diet versus a low-lipid diet formulated to mimic the nutrition profile of natural-origin fish. To evaluate the time scale at which diet alters the fecal microbiome, we collected longitudinal samples over a 12-week period and switched the diets of a subset of fish twice during the experiment. We used 16S ribosomal RNA gene amplicon sequencing to characterize fecal microbiome differences between fish on the two diets as well as hatchery-reared fish at a production hatchery, hatchery fish that had been captured after release into a stream, and natural-origin, stream-reared fish of similar ages. Additionally, we conducted RNA sequencing on head kidney samples from laboratory-reared fish to evaluate changes in gene expression in this important immune organ. Results We found that the low-lipid diet and the hatchery diet resulted in microbiomes that differed from the microbiome of natural-origin fish and from each other and that diet-driven changes to the microbiome could occur in under 14 d. The low-lipid diet did not result in a microbiome that resembled the microbiome of naturally produced fish. Instead, the low-lipid diet resulted in a microbiome community that was distinct from those of fish reared on the hatchery diet and fish sampled from the wild. The RNA sequencing results indicated differential enrichment of pathways related to immunity, metabolism, and hormone synthesis between fish that were fed the two experimental diets. Conclusions The results suggest that additional environmental factors influence the microbiome more strongly than diet formulation or that the low-lipid diet has a smaller effect on the microbiome than a natural, ­invertebrate-based diet. Given that the gut microbiome and systemic immune function contribute significantly to disease resistance, our findings highlight the importance of understanding how diets fed to fish in captivity may affect fish health beyond growth and body condition metrics.

Journal of Aquatic Animal Health↗