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USGS2024

RegionGrow3D: A deterministic analysis for characterizing discrete three-dimensional landslide source areas on a regional scale

Regional-scale characterization of shallow landslide hazards is important for reducing their destructive impact on society. These hazards are commonly characterized by (a) their location and likelihood using susceptibility maps, (b) landslide size and frequency using geomorphic scaling laws, and (c) the magnitude of disturbance required to cause landslides using initiation thresholds. Typically, this is accomplished through the use of inventories documenting the locations and triggering conditions of previous landslides. In the absence of comprehensive landslide inventories, physics-based slope stability models can be used to estimate landslide initiation potential and provide plausible distributions of landslide characteristics for a range of environmental and forcing conditions. However, these models are sometimes limited in their ability to capture key mechanisms tied to discrete three-dimensional (3D) landslide mechanics while possessing the computational efficiency required for broad-scale application. In this study, the RegionGrow3D (RG3D) model is developed to broadly simulate the area, volume, and location of landslides on a regional scale (≥1,000 km 2 ) using 3D, limit-equilibrium (LE)-based slope stability modeling. Furthermore, RG3D is incorporated into a susceptibility framework that quantifies landsliding uncertainty using a distribution of soil shear strengths and their associated probabilities, back-calculated from inventoried landslides using 3D LE-based landslide forensics. This framework is used to evaluate the influence of uncertainty tied to shear strength, rainfall scenarios, and antecedent soil moisture on potential landsliding and rainfall thresholds over a large region of the Oregon Coast Range, USA.

Journal of Geophysical Research: Earth Surface↗
USGS2026

Evaluating the effects of a multi-modal deterrent on upstream passage by invasive carp and native species

Invasive carp, including Silver Carp ( Hypophthalmichthys molitrix ) and Grass Carp ( Ctenopharyngodon idella ), are increasing their range within the Mississippi River Basin, threatening native fishes and ecosystem function. We conducted a 3-year field test of a multi-modal deterrent that uses sound, bubbles, and light to test its ability to impede upstream passage by invasive carp. The test was performed at a lock and dam on the Cumberland River, Kentucky, USA, using acoustic telemetry to track the movements of Silver Carp, Grass Carp, and several native fish species. When the deterrent was operating, the estimated probability of upstream lock passage was 53% lower (95% CI: 41%–63%) for Silver Carp but 74% higher (95% CI: 3%–190%) for Grass Carp compared to times when the deterrent was not operating. Paddlefish ( Polyodon spathula ) passage was reduced by 43% (95% CI: 71% reduction to 9% increase), although this was not statistically significant. We detected no significant effects on Freshwater Drum ( Aplodinotus grunniens ) or Smallmouth Buffalo ( Ictiobus bubalus ). However, sample sizes were small for these native species, limiting our ability to identify effects. Water temperature, tailwater elevation, and vessel lockages affected passage rates, although this varied among species.

Kentucky↗
USGS2025

Dietary bioavailability of uranium to a model freshwater invertebrate

Uranium (U) mining increases environmental exposures. Understanding how U is taken up by organisms can aid in evaluating the potential for bioaccumulation and toxicity. Although the importance of aqueous geochemical speciation is well recognized for U bioavailability after dissolved exposures, far less is known about the processes controlling U bioavailability after dietary exposures. This study characterizes the biogeochemical drivers of dietary U uptake in the freshwater snail Lymnaea stagnalis in laboratory experiments. Solids tested included benthic diatoms pre-exposed to dissolved U(VI), soils from contaminated U mine sites, and colloidal hydrous ferric oxide (HFO) synthesized in the presence of dissolved U(VI) or with U complexed by natural organic matter (NOM). Results showed that U was bioavailable from all solids. Uranium assimilation efficiency (AE), a proxy for dietary U bioavailability, varied among solids. AE was lowest for the U-contaminated soils (25 ± 17%) and highest for the U-laden diatoms (71 ± 13%). AE varied slightly among HFO preparations, suggesting modest influences of NOM and iron on U bioavailability. Increases in dietary U exposures reduced feeding rates, and the extent of feeding inhibition appeared inversely related to U bioavailability. The high U assimilation and range of bioavailability have implications for toxicity risks inferred without considering dietary uptake.

Environmental Science and Technology↗
USGS2025

Review: The hydrogeology of critical mineral resources relevant to the energy transition

Attaining the goals of the international treaty on climate change (the Paris Agreement) will greatly increase the demand for the critical minerals required to implement clean-energy technologies. This poses both challenges and opportunities to the hydrogeologic community from several perspectives. Here, important insights that the hydrogeological sciences have to offer for mineral exploration, mineral production, and addressing environmental issues related to mining and mine decommissioning are summarized. This study focuses on copper, cobalt, lithium, and rare earths to represent the broad spectrum of critical minerals and illustrate their relevance by referring to projected demands and production rates. The current understanding of the hydrogeologic processes that form major deposits of these minerals are then summarized. Ore is defined as the naturally occurring material from which minerals of economic value can be extracted, where most ore deposits are the products of complex hydrogeologic couplings between fluid flow, heat transport, solute transport, chemical reactions, and mechanical deformation. Exploration models for the discovery of deeper, hidden deposits are potentially informed by hydrogeologic theory and hydrogeochemical processes. Hydrogeologic understanding and methods are also essential to production and recovery. Longstanding challenges are mine dewatering and (conversely) mine water supply, as well as mineral-extraction practices such as spoil heap leaching and in situ mining. New challenges arise from element extraction from subsurface brines. Finally, the quantity of water use and potential environmental impacts of mining on water quality are at the core of ‘social license’: the approval and acceptance of society to mining activities.

Hydrogeology Journal↗
USGS2026

Surface-wave relocation and characterization of the 2024–2025 dyking episode along the Fentale–Dofen segment of the Ethiopian rift

From late-December 2024 to mid-March 2025, a 50-km-long dyke intrusion triggered over 300 earthquakes (magnitude 4 to 5.9) between Fentale and Dofen volcanoes along the Northern Main Ethiopian Rift. Dyke intrusions periodically occur along the Fentale–Dofen magmatic segment and are an expression of ongoing rift extension. Preliminary analyses using interferometric synthetic aperture radar revealed extensive ground deformation (up to 60 cm), which closely matched the temporal and spatial evolution of surface manifestations and earthquake locations from global catalogues. While global catalogues are critical for real-time monitoring, the precision of locations in remote and or sparsely instrumented regions can be low. In this investigation, we present surface-wave relocation results of the dyking episode that began near Fentale volcano in December 2024. We estimate relative locations using differential traveltimes measured from regional-to-teleseismic distance surface-wave observations of earthquakes reported by the U.S. Geological Survey. Relative relocations reduce the initial region of diffuse seismicity to a 50-km-long narrow band bounding the strike of surface manifestations and the zone of maximum surface deformation. We demonstrate the precision of surface-wave relocations over incremental time periods, capturing the progression of dyking from seismic onset through seismic migration and caldera subsidence. Results showcase the utility of surface-wave relocations in the characterization of dyking episodes and provide complementary insights into the current understanding of the Fentale–Dofen volcanic plumbing system.

Geophysical Journal International↗
USGS2023

Slow slip detectability in seafloor pressure records offshore Alaska

In subduction zones worldwide, seafloor pressure data are used to observe tectonic deformation, particularly from megathrust earthquakes and slow slip events (SSEs). However, such measurements are also sensitive to oceanographic circulation-generated pressures over a range of frequencies that conflate with tectonic signals of interest. Using seafloor pressure and temperature data from the Alaska Amphibious Community Seismic Experiment, and sea surface height data from satellite altimetry, we evaluate the efficacy of various seasonal and oceanographic pressure signal proxy corrections and conduct synthetic tests to determine their impact on the timing and amplitude prediction of ramp-like signals typical of SSEs. We find that subtracting out the first mode of the complex empirical orthogonal functions of the pressure records on either the shelf or slope yields signal root-mean-square error (RMS) reductions up to 73% or 80%, respectively. Additional correction with proxies that exploit the depth-dependent spatial coherence of pressure records provides cumulative variance reductions up to 83% and 93%, respectively. Our detectability tests show that the timing and amplitude of synthetic SSE-like ramps can be well constrained for ramp amplitudes ≥4 cm on the shelf and ≥2 cm on the slope, using a fully automated detector. The principal limits on detectability are residual abrupt changes in pressure that occur as part of the transition to and from summer to winter conditions but are not adequately characterized by our seasonal corrections, as well as the inability to properly account for instrumental drift, which is not readily separated from the seasonal signal.

Alaska↗
USGS2026

Hydrological control on soil redox condition and carbon loss of coastal wetland under sea-kevel rise

Coastal wetlands are critical carbon sinks with their biogeochemical and ecological functioning shaped by dynamic hydrological conditions that are increasingly influenced by climate change. A key unresolved question is how hydrologic flow, vegetation response, and rising sea levels interact to regulate soil redox condition and carbon loss in coastal wetlands. Using a field-tested hydrological–biogeochemical–ecological modeling framework, we reveal how the interplay between terrestrial groundwater discharge and tidal fluctuations generates complex groundwater flow patterns at the terrestrial–aquatic interface, and how these patterns modulate soil redox conditions, in turn influencing soil organic matter decomposition and carbon loss. Notably, rising sea levels suppress soil CO 2 emissions while reducing lateral dissolved carbon losses, thereby enhancing litter carbon sequestration under anoxic conditions. As vegetation responds to sea-level rise and carbon inputs diminish, litter carbon subsequently declines. These findings underscore a critical hydrological control on carbon cycling, advancing our understanding of coastal ecosystem resilience in a warming world.

Louisiana↗
USGS2026

Deaf, deafblind, and hard of hearing university student experiences with earthquake early warning in the United States: Evaluating language planning and technology access

The growing literature on deaf and hard of hearing (DHH+) populations and disasters demonstrates that emergency communication (including alerts) is not reaching global DHH + individuals with dangerous impacts for morbidity and mortality. This is the first research study in the U.S. to qualitatively explore the experiences of DHH + persons with earthquake early warning (EEW) through group-based dialogue sessions. The study investigates eight DHH + university students'past earthquake experiences, access to EEW alerts, and perceptions of ShakeAlert Ⓡ , an EEW system for detecting earthquakes and alerting residents of California, Oregon, and Washington. Findings highlight key gaps in disaster alert usability within four thematic areas: lack of messaging in participants' language(s), unclear alert messaging, deficient message delivery mechanisms for deafblind persons, and insufficient access to earthquake information and training that leads to dependence on informal information networks. Weaknesses identified in these four themes reduce DHH + trust in EEW systems and compromise the capacity of alert recipients to take swift protective action or to mentally prepare before shaking starts. The study also underscores structural factors such as insufficient linguistic representation in disaster language planning and technology design, which ignores the linguistic and sensory access needs of DHH + individuals. Building on disaster language planning frameworks, we recommend involving DHH + populations to co-develop EEW alerts. By centering DHH + perspectives, this research contributes to ongoing efforts to ensure that EEW systems reach everyone.

California↗
USGS2025

Uncertainty reduction for subaerial landslide-tsunami hazards

Subaerial rock slopes may generate a tsunami by rapidly moving into the water. Large uncertainty in landslide characteristics propagates into large uncertainty in tsunami hazard, making hazard assessment more difficult for land and emergency managers. Once a potentially tsunamigenic landslide is identified, it may not be clear which landslide characteristics contribute most significantly to uncertainty in the tsunami hazard. Our aim is to document the relative worth of different landslide characteristics (e.g., size, material properties) for reducing uncertainty in landslide-tsunami hazard assessments. Isolating the relative importance of specific landslide characteristics may inform prioritization of data collection and improve efficiency in understanding hazard. To accomplish this, we generated a set of 288 landslide-tsunami simulations in which we systematically varied the size and material properties of possible failure extents at the Barry Arm landslide complex in northwestern Prince William Sound, Alaska, USA. We find that for landslides smaller than the receiving waterbody, the landslide volume has the strongest effect on resulting wave characteristics and thus the highest leverage on reducing uncertainty in tsunami hazard. In contrast, for landslides substantially larger than the waterbody, the duration of rapid movement of the landslide has the highest leverage. Based on our results, we propose a classification scheme for subaerial landslides based on the relative size of the landslide and waterbody. Additionally, our results support the generation of a tsunami height transfer function between existing tide gages and a nearby coastal city. These results have direct implications for the practice of operational early warning.

Alaska↗
USGS2025

Timescales of surface faulting preservation in low-strain intraplate regions from landscape evolution modeling and the geomorphic and historical record

Large surface-rupturing intraplate earthquakes in stable continental regions (SCRs) are uncommon globally and have recurrence intervals of thousands to hundreds of thousands of years based on the paleoseismic and geomorphic record, challenging accurate active fault identification in these regions. To constrain the timescales of preservation for scarps created by surface ruptures from dip-slip earthquakes, we use a two-dimensional scarp diffusion model for typical intraplate settings and explore which parameters influence fault scarp preservation. These parameters include the coseismic vertical surface offset, the recurrence interval of similar magnitude earthquakes, diffusivity (as a proxy for mean annual precipitation rate), and the erodibility of the surficial material. We constrain parameter ranges from a compilation of historical surface ruptures in intraplate settings in a variety of climates, including the Central and Eastern United States, Australia, Europe, Central Asia (Mongolia, China), India, and West Africa. The timescales of scarp preservation from landscape evolution modeling agree well with observations of scarp preservation in low-strain SCR and intraplate tectonic settings, with some notable exceptions for Australian scarps. We find that the erodibility of the surficial material and earthquake recurrence interval have a stronger effect on the timescales of scarp preservation than diffusivity or coseismic vertical surface offset. Our model results may aid in identifying and characterizing subtle, slow-moving active faults in low-strain SCR and intraplate tectonic settings for different tectonic, geomorphic, and climatic characteristics. Accurate fault locations and characterization from the landscape record has implications for both probabilistic seismic and fault displacement hazard analyses.

Journal of Geophysical Research Solid Earth↗
USGS2025

Expression of corticoid-regulatory genes in the gills of Atlantic salmon (Salmo salar) parr and smolt and during salinity acclimation

In teleost fishes, cortisol is the major corticoid and has both glucocorticoid and mineralocorticoid actions. However, how fish tissues discriminate between these distinct corticosteroid actions is unclear. In mammals, the major factors responsible for intracellular corticosteroid regulation are glucocorticoid receptors ( gr s) and the mineralocorticoid receptor ( mr ), but their role in osmoregulation of fish is unclear. 11β-hydroxysteroid dehydrogenases ( hsd11b s) control the levels of intracellular corticosteroids by converting from bioactive forms to inert forms. To investigate how Atlantic salmon ( Salmo salar ) respond to cortisol in different physiological or environmental conditions, we performed comparisons of parr and smolt, and osmotic challenge experiments to examine the physiological responses and gill transcript levels of genes underlying cortisol-signalling, including gr1 , gr2 , mr , hsd11b2 and hsd11b3 . Because cortisol may interact with growth hormone and prolactin during salinity changes, transcript levels encoding growth hormone receptors ( ghr1 , ghr2 ) and the prolactin receptor ( prlr ) were also examined. Hsd11b2 transcript levels in seawater-acclimated fish were consistently lower compared to fish acclimated to fresh water. After transfer to seawater, prlr transcript levels in fish significantly decreased and transcript levels of ghr1 , ghr2 and hsd11b3 showed no change or were slightly higher than those of freshwater control groups. Gr1 , gr2 and mr transcript levels were slightly but consistently higher in fish acclimated to fresh water relative to seawater. Our results indicate that changes in corticosteroid receptor and hsd11b2 transcript levels in the gills may be important mechanisms that regulate corticoid signals to achieve ion homeostasis in Atlantic salmon.

Journal of Fish Biology↗
USGS2025

Estimated average annualized losses from potential building damage and fatalities due to earthquake-generated tsunamis in the United States

Earthquake-generated tsunamis represent substantial economic threats to states and territories in the United States (U.S.), but we are unaware of any effort to quantify potential impacts at the national level. This gap is partially due to the lack of nationally consistent data on tsunamigenic sources and associated return periods. This study addresses this issue and provides estimates of average annualized losses (AAL) for potential residential fatalities and capital stock losses associated with building damage (i.e., structural, non-structural, contents, and inventory damage) in the U.S. by curating tsunami-hazard information based on deterministic scenarios and probabilistic approaches, calculating potential losses, and estimating return periods where necessary. This assessment was done for the U.S. West Coast, Alaska, Hawaii, U.S. Pacific Territories, and U.S. Atlantic Territories. We estimate that earthquake-generated tsunamis that could affect these states and territories collectively represent $1 billion in potential AAL with 79 % of losses due to residential fatalities and 21 % of losses due to capital stock losses from building damage. We identify AAL variations based on county and county equivalents, states and territories, geographic regions, return periods, and departure-delay assumptions for evacuating residents. Results include high AAL values for potential fatalities in Puerto Rico and the U.S. Pacific Northwest region, high AAL values for potential building-related damage in Hawaii and California, and high building- and population-loss ratios for county equivalents in Alaska and U.S. territories.

International Journal of Disaster Risk Reduction↗
USGS2024

Constraining mean landslide occurrence rates for non-temporal landslide inventories using high-resolution elevation data

Constraining landslide occurrence rates can help to generate landslide hazard models that predict the spatial and temporal occurrence of landslides. However, most landslide inventories do not include any temporal data due to the difficulties of dating landslide deposits. Here we introduce a method for estimating the mean landslide occurrence rate of deep-seated rotational and translational slides derived solely from high-resolution (≤3 m) elevation data and globally available estimates of the diffusion coefficient for sediment flux. The method applies a linear diffusion model to the roughest landslide deposits until they reach a representative non-landslide roughness distribution. This estimates the time for a landslide deposit to be unrecognizable in high-resolution digital elevation data, which we term the mean lifetime of the landslide. Using the mean lifetime and number of landslides within an area of interest, we can estimate the mean occurrence rate of landslides over that domain. We validate this approach using a comprehensive temporal inventory of landslides in western Oregon created using age-roughness curves that are calibrated with high-resolution elevation data and radiocarbon data. We find good agreement between our diffusion method and the existing age-roughness-derived estimates, producing mean lifetimes of 4500 and 5200 years (4% difference), respectively. Hazard maps produced using the two methodologies generally agree, with the maximum differences in landslide probability reaching 0.1. Due to the relative abundance of high-resolution elevation data compared with age-dated landslides, our method could help constrain landslide occurrence rates in areas previously considered unfeasible.

Oregon↗
USGS2026

Egg thiamine concentrations reflect dietary differences between four hatchery strains, including two morphotypes, of Lake Trout in Lake Ontario

Objective Test whether dietary differences among hatchery strains of Lake Trout Salvelinus namaycush were associated with variation in egg thiamine concentrations and assess the potential for using strain-specific traits to mitigate thiamine deficiency complex (TDC) in Lake Ontario restoration efforts. Methods Stomach content analysis and stable isotope mixing models were used to compare diets among four hatchery strains of Lake Trout, representing lean and humper morphotypes. Egg thiamine concentrations were measured to test whether dietary differences correlated with susceptibility to TDC. Results Significant differences in diet and egg thiamine concentrations were observed among Lake Trout strains. A humper-like morphotype strain exhibited elevated thiamine levels, which were associated with reduced consumption of prey known to degrade thiamine levels when consumed, Alewife Alosa pseudoharengus and Rainbow Smelt Osmerus mordax , and increased reliance on Round Goby Neogobius melanostomus or sculpin species (Slimy Sculpin Cottus cognatus and Deepwater Sculpin Myoxocephalus thompsonii ). These findings support the link between the consumption of Alewife and Rainbow Smelt and thiamine deficiency. Conclusions Our findings support a link between strain-specific dietary preferences and susceptibility to TDC in Lake Trout. Preferential stocking of strains less prone to TDC, such as the strain derived from a humper morph from Lake Superior, could enhance restoration success in Lake Ontario. This strategy may be especially effective given the continued dominance of Alewife in the lake's prey base and the current management priorities supporting fisheries for Pacific salmon Oncorhynchus spp.

North American Journal of Fisheries Management↗
USGS2025

Manipulation of the Symbiodiniaceae microbiome confers multigenerational impacts on symbioses and reproductive ecology of its Exaiptasia diaphana host

Symbiodiniaceae-associated microbiota strongly influence cnidarian symbioses. We systematically reduced the bacterial and fungal communities associated with Symbiodiniaceae to study potential effects on the cnidarian holobiont Exaiptasia diaphana (Aiptasia). Clonal anemones were inoculated with xenic Breviolum minutum (SSB01) and microbiome-manipulated cultures after antibacterial or antifungal treatment. The asexual reproduction of pedal laceration allowed for three generations of clonal aposymbiotic Aiptasia to be utilised in this study, from the initial adult generation (G0), to the first (G1), and second (G2) generation. We inoculated small and large G1 Aiptasia with SSB01 algae and monitored onset of symbiosis, rate of algal proliferation, and holobiont characteristics. Sequencing the 16S and 18S rRNA gene regions identified significant differences in the bacterial and fungal communities of the G0 and G1 generations, alongside differences between the size classes of small and large G1 anemones. The microbiome of larger G1 individuals was distinct to the smaller G1 anemones, suggesting a microbiome maturation process. Control Breviolum minutum cultures exhibited a significantly greater proliferation rate in large G1 anemones when compared to antibacterial or antifungal treated cultures, whereas the opposite trend was documented in the small G1 anemones. Although no differences were observed between algal photochemical parameters, or the growth and polyp activity of G1 juveniles, we observed a significant influence in the production of G2 clones between treatments. Overall, we provide strong ecological implications of manipulating Symbiodiniaceae microbiome, not for the algae themselves, but for the maturation of the host Aiptasia, as well as for the cnidarian holobiont over multiple generations.

The ISME Journal↗
USGS2025

Laboratory assessment for recovery of porcine circovirus 2 and porcine reproductive and respiratory syndrome virus using two types of commercially available hollow-fiber ultrafilters

Groundwater near swine farms is an uninvestigated reservoir for porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circoviruses (PCVs). Enteric microorganisms are often collected from groundwater via dead-end ultrafiltration, but recovery of PRRSV and PCV with this method has not been assessed. We recovered PRRSV2 and PCV2 by dead-end ultrafiltration followed by polyethylene glycol (PEG) precipitation, nucleic acid extraction, and reverse-transcription quantitative real-time PCR. We also compared 2 commercial hemodialysis ultrafilters (Asahi Kasei Rexeed-25A, Nipro Elisio-25H) and compared PRRSV2 recovery in these filters to other waterborne microorganisms. On average, 8 ± 1% of PRRSV2 was recovered by dead-end ultrafiltration and PEG precipitation, compared to 25 ± 6% for adenovirus 41. Full-process recovery of bacteria in the same filters was 5–15%; Cryptosporidium parvum recovery was 42 ± 12%. PCV2 was detected in 4 of 12 replicate filters, but low stock concentrations precluded quantitative recovery estimates. Elisio-25H ultrafilters performed similarly to Rexeed-25A filters for all organisms tested and is an effective replacement for the Rexeed-25A, which is no longer available in the United States. Our recovery of PRRSV2 and PCV2 by dead-end ultrafiltration in the laboratory suggests that PRRSV2 detection limits are as low as 3–50 genomic copies/L in sample volumes of 100–1,500 L. Based on quantitative microbial risk assessment, these concentrations are relevant to PRRSV2 infection rates in the U.S. swine herd.

Journal of Veterinary Diagnostic Investigation↗
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

Transcriptional changes in wild Yukon River Chinook Salmon associated with Ichthyophonus infections

Objective We compared differentially expressed genes in Chinook Salmon Oncorhynchus tshawytscha with three divergent Ichthyophonus statuses (undetected, subclinical infections, or clinical disease; n = 100) to investigate associated transcriptomic responses. Disease associated with the fish parasite Ichthyophonus sp. was first diagnosed in adult Chinook Salmon from the Yukon River in the late 1980s and has subsequently been implicated in premature host mortality. Methods Chinook Salmon tissue sample collections and Ichthyophonus infection data were leveraged from a multi-agency collaboration during summer 2022 at three locations along the main-stem Yukon River that spanned nearly 2,000 km of freshwater migration (lower, middle, and upper river). We sequenced the transcriptome and compared this to infection status based on routine diagnostic procedures. Results Among the 17,569 genes for which messenger RNA was detected, we identified a transcription signature in the skeletal muscle that was associated with Ichthyophonus infections and included 53 differentially expressed genes. The differentially expressed genes and their pathways included those known for involvement in immune functions, energy synthesis, cellular breakdown, and reproduction—all processes that are known to be influenced by senescence during spawning migrations. Conclusions Results demonstrate a clear transcriptional difference between diseased fish (clinical disease group) and those in which Ichthyophonus was undetected, including identifying candidate markers for infection in this population. These results provide a foundation for development of nonlethal biomarkers to evaluate potential Ichthyophonus infections in Chinook Salmon based on gene transcription, protein products, or gene variants (e.g., polymorphisms).

Journal of Aquatic Animal Health↗