In this work, we utilize a transect of core top, mid- to late Holocene, sediments from the Eastern Siberian Sea to the central Arctic Ocean, spanning gradients in upper-ocean water column properties, to examine regional planktic foraminiferal species abundances and geochemistry. We present species- and morphotype-specific foraminiferal assemblages at these sites and stable isotope analyses of neogloboquadrinids. We find little variation in planktic species populations, and only small variations in N. pachyderma morphotype distributions, between sites. Spatial averages of N. pachyderma morphotype and N. incompta δ18O values show no significant differences, suggesting a similar calcification depth for all morphotypes of N. pachyderma and N. incompta across our sites, which we estimate to be between ∼ 50–150 m. Values of δ18O of a group of unencrusted specimens delineate a shallower calcification habitat. Neogloboquadrina pachyderma-2 Mg/Ca values yield temperatures outside the range of observations using available calibration equations, pointing toward the need for more Arctic-specific Mg/Ca-temperature calibrations.
Global changes in climate and land use are threatening natural ecosystems, biodiversity, and the ecosystem services people rely on. This is why it is necessary to track and monitor spatiotemporal change at a level of detail that can inform science, management, and policy development. The current constellation of multiple Landsat and Sentinel-2 satellites collecting imagery at predominantly
The Great Basin is an arid province located in the interior western United States. The region encompasses millions of hectares and quaking aspen (Populus tremuloides Michx.) forests comprise a minor portion of the total area. However, montane aspen forests play a disproportionately large role in providing ecosystem services in the region, including water retention, biodiversity, wildlife habitat, livestock forage, and recreational uses. With warming temperatures, increasing evaporative demand, and heightened precipitation variability, the future of aspen has become a critical concern. Using dendroecological approaches, we assessed growth patterns of 20 aspen stands across three geographically isolated “sky island” mountain ranges spanning portions of the north-central Great Basin. We anticipated that the growth of Great Basin aspen would be strongly influenced by regional climatic patterns and largely in synchrony. Results revealed a more complex growth dynamic that varied among mountain ranges and across environmental gradients. In particular, aspen climate-growth relationships in the slightly dryer Ruby Mountains were strongly and positively correlated (r > 0.5) with previous fall to winter moisture availability. The Jarbidge Mountains had a positive but modest relationship with previous fall to winter moisture availability (r > 0.3). Climate-growth response in the Santa Rosa Mountains, the wettest range, showed no significant response to moisture availability during any time period examined but had greater tree-ring growth with warmer May temperatures. Although tree-ring centennial (1910 – 2010) growth trends were positive for all three mountain ranges, only the Santa Rosa Mountains maintained a positive recent growth trend (1970 – 2010). Moreover, distinct temporal shifts in tree growth-climate relationships in each mountain range suggest potentially unique aspen population adaptations to climate variability. For instance, in two of the mountain ranges, there was a shift from positive/neutral to negative growth relationships with temperature starting around the 1963 – 1987 time period, while tree growth also began simultaneously responding more positively to moisture availability. These growth shifts and observed enhanced sensitivities to monthly and seasonal climate variables over time may reflect dynamic tree growth responses caused by ongoing global climate change, but that may be tempered by local or regional factors, such as the relative availability and timing of soil moisture provided by spring snowmelt. A better understanding of biogeographic variation and causality in aspen growth could provide multiple management pathways governed by resilience characteristics in the face of future anthropogenic and climatic threats.
Hybrid Knowledge-Guided Machine Learning (KGML) models, which are deep learning models that utilize scientific theory and process-based model simulations, have shown improved performance over their process-based counterparts for the simulation of water temperature and hydrodynamics. We highlight the modular compositional learning (MCL) methodology as a novel design choice for the development of hybrid KGML models in which the model is decomposed into modular sub-components that can be process-based models and/or deep learning models. We develop a hybrid MCL model that integrates a deep learning model into a modularized, process-based model. To achieve this, we first train individual deep learning models with the output of the process-based models. In a second step, we fine-tune one deep learning model with observed field data. In this study, we replaced process-based calculations of vertical diffusive transport with deep learning. Finally, this fine-tuned deep learning model is integrated into the process-based model, creating the hybrid MCL model with improved overall projections for water temperature dynamics compared to the original process-based model. We further compare the performance of the hybrid MCL model with the process-based model and two alternative deep learning models and highlight how the hybrid MCL model has the best performance for projecting water temperature, Schmidt stability, buoyancy frequency, and depths of different isotherms. Modular compositional learning can be applied to existing modularized, process-based model structures to make the projections more robust and improve model performance by letting deep learning estimate uncertain process calculations.
Deep-water coral reefs are found worldwide and harbor biodiversity levels that are comparable to their shallow-water counterparts. However, the genetic diversity and population structure of deep-water species remain poorly explored, and historical taxonomical issues still need to be resolved. Here we used microsatellite markers as well as ultraconserved elements (UCE) and exons to shed light on the population structure, genetic diversity, and phylogenetic position of the genus Madrepora, which contains M. oculata, one of the most widespread scleractinian species. Population structure of 107 samples from three Southwestern Atlantic sedimentary basins revealed the occurrence of a cryptic species, herein named M. piresae sp. nov. (authored by Kitahara, Capel and Zilberberg), which can be found in sympatry with M. oculata. Phylogeny reconstructions based on 134 UCEs and exon regions corroborated the population genetic data, with the recovery of two well-supported groups, and reinforced the polyphyly of the family Oculinidae. In order to better accommodate the genus Madrepora, while reducing taxonomical confusion associated with the name Madreporidae, we propose the monogeneric family Bathyporidae fam. nov. (authored by Kitahara, Capel, Zilberberg and Cairns). Our findings advance the knowledge on the widespread deep-water genus Madrepora, resolve a long-standing question regarding the phylogenetic position of the genus, and highlight the need of a worldwide review of the genus.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.ympev.2023.107994","usgsCitation":"Capel, K.C., Zilberberg, C., Carpes, R.M., Morrison, C., Vaga, C.F., Quattrini, A., Quek, R.Z., Huang, D., Cairns, S.D., and Kitahara, M.V., 2024, How long have we been mistaken? Multi-tools shedding light into the systematics of the widespread deep-water genus Madrepora Linnaeus, 1758 (Scleractinia): Molecular Phylogenetics and Evolution, v. 191, 107994, 10 p., https://doi.org/10.1016/j.ympev.2023.107994.","productDescription":"107994, 10 p.","ipdsId":"IP-154239","costCenters":[{"id":50464,"text":"Eastern Ecological Science Center","active":true,"usgs":true}],"links":[{"id":425471,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"191","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Capel, Katia C. C.","contributorId":333882,"corporation":false,"usgs":false,"family":"Capel","given":"Katia","email":"","middleInitial":"C. C.","affiliations":[{"id":79999,"text":"Center for Marine Biology, São Paulo University, São Sebastião, São Paulo, Brazil","active":true,"usgs":false}],"preferred":false,"id":894214,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Zilberberg, Carla","contributorId":333883,"corporation":false,"usgs":false,"family":"Zilberberg","given":"Carla","email":"","affiliations":[{"id":80000,"text":"Department of Zoology, Institute of Biodiversity and Sustainability – Nupem, Federal University of Rio de Janeiro, Macaé, Rio de Janeiro, Brazil","active":true,"usgs":false}],"preferred":false,"id":894215,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Carpes, Raphael M.","contributorId":333884,"corporation":false,"usgs":false,"family":"Carpes","given":"Raphael","email":"","middleInitial":"M.","affiliations":[{"id":80000,"text":"Department of Zoology, Institute of Biodiversity and Sustainability – Nupem, Federal University of Rio de Janeiro, Macaé, Rio de Janeiro, Brazil","active":true,"usgs":false}],"preferred":false,"id":894216,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Morrison, Cheryl 0000-0001-9425-691X cmorrison@usgs.gov","orcid":"https://orcid.org/0000-0001-9425-691X","contributorId":202644,"corporation":false,"usgs":true,"family":"Morrison","given":"Cheryl","email":"cmorrison@usgs.gov","affiliations":[{"id":365,"text":"Leetown Science Center","active":true,"usgs":true}],"preferred":true,"id":894217,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Vaga, Claudia F.","contributorId":333885,"corporation":false,"usgs":false,"family":"Vaga","given":"Claudia","email":"","middleInitial":"F.","affiliations":[{"id":80002,"text":"Center for Marine Biology, São Paulo University, São Sebastião, São Paulo, Brazil; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo, São Paulo, Brazil","active":true,"usgs":false}],"preferred":false,"id":894218,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Quattrini, Andrea M.","contributorId":333886,"corporation":false,"usgs":false,"family":"Quattrini","given":"Andrea M.","affiliations":[{"id":80003,"text":"Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States of America","active":true,"usgs":false}],"preferred":false,"id":894219,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Quek, Randolph Z. B.","contributorId":333887,"corporation":false,"usgs":false,"family":"Quek","given":"Randolph","email":"","middleInitial":"Z. B.","affiliations":[{"id":80004,"text":"Department of Biological Sciences, National University of Singapore, Singapore","active":true,"usgs":false}],"preferred":false,"id":894220,"contributorType":{"id":1,"text":"Authors"},"rank":7},{"text":"Huang, Danwei","contributorId":333888,"corporation":false,"usgs":false,"family":"Huang","given":"Danwei","email":"","affiliations":[{"id":80005,"text":"Department of Biological Sciences, National University of Singapore, Singapore; Lee Kong Chian Natural History Museum, National University of Singapore, Singapore","active":true,"usgs":false}],"preferred":false,"id":894221,"contributorType":{"id":1,"text":"Authors"},"rank":8},{"text":"Cairns, Stephen D.","contributorId":333889,"corporation":false,"usgs":false,"family":"Cairns","given":"Stephen","email":"","middleInitial":"D.","affiliations":[{"id":80003,"text":"Department of Invertebrate Zoology, Smithsonian Institution, Washington DC, United States of America","active":true,"usgs":false}],"preferred":false,"id":894222,"contributorType":{"id":1,"text":"Authors"},"rank":9},{"text":"Kitahara, Marcelo V.","contributorId":333890,"corporation":false,"usgs":false,"family":"Kitahara","given":"Marcelo","email":"","middleInitial":"V.","affiliations":[{"id":80006,"text":"Center for Marine Biology, São Paulo University; Graduate Program in Zoology, Department of Zoology, Institute of Biosciences, University of São Paulo; Department of Invertebrate Zoology, Smithsonian Institution","active":true,"usgs":false}],"preferred":false,"id":894223,"contributorType":{"id":1,"text":"Authors"},"rank":10}]}} ,{"id":70250781,"text":"70250781 - 2024 - Divergent physiological responses of hydric and mesic riparian plant species to a Colorado River experimental flow","interactions":[],"lastModifiedDate":"2024-03-26T14:29:38.056229","indexId":"70250781","displayToPublicDate":"2023-12-22T07:10:18","publicationYear":"2024","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3086,"text":"Plant Ecology","active":true,"publicationSubtype":{"id":10}},"title":"Divergent physiological responses of hydric and mesic riparian plant species to a Colorado River experimental flow","docAbstract":"Riparian plant species can differ in their responses to streamflow variation in ways that strongly influence the composition and functioning of riparian plant communities. Quantifying these differences and the potential asymmetry of responses to low- versus high-flow phases of stream fluctuations is important for predicting and managing vegetation responses to variation in flow regimes. We measured the physiological response of two riparian plant species with different habitat preferences to an experimental flow that progressed from a low-flow to high-flow phase. Schedonorous arundinaceus, a hydric grass growing in near-channel habitat, exhibited significant and biologically substantial declines in stem water potential (SWP) during the low-flow phase of the experiment and a saturating increase in leaf relative water content (LRWC) during the high-flow phase. These patterns are consistent with cavitation risk in response to low-flow anomalies and saturating responses to high-flow anomalies in this hydric species. Pluchea sericea, a mesic shrub growing at intermediate elevations above the channel, exhibited a decrease in LRWC during the low-flow phase and an increase in SWP during the high-flow phase. These patterns are consistent with protection from stem cavitation risk during drought through leaf dehydration and opportunistic increases in water status in response to high-flow anomalies in this mesic species. The asymmetrical responses of both species to low- versus high-flow phases demonstrate unique physiological responses to flow anomalies of contrasting directions attributable to species habitat preferences and functional strategies that can be used by managers to predict non-linear vegetation responses to flow variation.
We paired mercury (Hg) concentrations in dragonfly larvae with water chemistry in 29 U.S. national parks to highlight how ecological and biogeochemical context (habitat, dissolved organic carbon [DOC]) influence drivers of Hg bioaccumulation. Although prior studies have defined influences of biogeochemical variables on Hg production and bioaccumulation, it has been challenging to determine their influence across diverse habitats, regions, or biogeochemical conditions within a single study. We compared global (i.e., all sites), habitat-specific, and DOC-class models to illuminate how these controls on biotic Hg vary. Although the suite of important biogeochemical factors across all sites (e.g., aqueous Hg, DOC, sulfate [SO42−], and pH) was consistent with general findings in the literature, contrasting the restricted models revealed more nuanced controls on biosentinel Hg. Comparing habitats, aqueous (filtered) total mercury (THg) and SO42− were important in lentic systems whereas aqueous (filtered) methylmercury (MeHg), DOC, pH, and SO42− were important in lotic and wetland systems. The ability to identify important variables varied among habitats, with less certainty in lentic (model weight (W) = 0.05) than lotic (W = 0.11) or wetland habitats (W = 0.23), suggesting that biogeochemical drivers of bioaccumulation are more variable, or obscured by other aspects of Hg cycling, in these habitats. Results revealed a contrast in the importance of aqueous MeHg versus aqueous THg between DOC-classes: in low-DOC sites (<8.5 mg/L), availability of upstream inputs of MeHg appeared more important for bioaccumulation; in high-DOC sites (>8.5 mg/L) THg was more important, suggesting a link to in-situ controls on bioavailability of Hg for MeHg production. Mercury bioaccumulation (indicated by bioaccumulation factor) was more efficient in low DOC-class sites, likely due to reduced partitioning of aqueous MeHg to DOC. Together, findings highlight substantial variation in the drivers of Hg bioaccumulation and suggest consideration of these factors in natural resource management and decision-making.
","language":"English","publisher":"Elsevier","doi":"10.1016/j.scitotenv.2023.169396","usgsCitation":"Nelson, S.J., Willacker, J., Eagles-Smith, C., Flanagan Pritz, C.M., Chen, C.Y., Klemmer, A.J., and Krabbenhoft, D.P., 2024, Habitat and dissolved organic carbon modulate variation in the biogeochemical drivers of mercury bioaccumulation in dragonfly larvae at the national scale: Science of the Total Environment, v. 912, 169396, https://doi.org/10.1016/j.scitotenv.2023.169396.","productDescription":"169396","ipdsId":"IP-159769","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":425714,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"912","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Nelson, Sarah J.","contributorId":167269,"corporation":false,"usgs":false,"family":"Nelson","given":"Sarah","email":"","middleInitial":"J.","affiliations":[{"id":7063,"text":"University of Maine","active":true,"usgs":false}],"preferred":false,"id":894958,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Willacker, James 0000-0002-6286-5224","orcid":"https://orcid.org/0000-0002-6286-5224","contributorId":207883,"corporation":false,"usgs":true,"family":"Willacker","given":"James","email":"","affiliations":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":894959,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Eagles-Smith, Collin A. 0000-0003-1329-5285","orcid":"https://orcid.org/0000-0003-1329-5285","contributorId":221745,"corporation":false,"usgs":true,"family":"Eagles-Smith","given":"Collin A.","affiliations":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":894960,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Flanagan Pritz, Colleen M 0000-0002-0466-2103","orcid":"https://orcid.org/0000-0002-0466-2103","contributorId":299600,"corporation":false,"usgs":false,"family":"Flanagan Pritz","given":"Colleen","email":"","middleInitial":"M","affiliations":[{"id":36189,"text":"National Park Service","active":true,"usgs":false}],"preferred":false,"id":894961,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Chen, Celia Y.","contributorId":145630,"corporation":false,"usgs":false,"family":"Chen","given":"Celia","email":"","middleInitial":"Y.","affiliations":[{"id":16179,"text":"Dartmouth College, Hanover NH","active":true,"usgs":false}],"preferred":false,"id":894962,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Klemmer, Amanda J","contributorId":219891,"corporation":false,"usgs":false,"family":"Klemmer","given":"Amanda","email":"","middleInitial":"J","affiliations":[],"preferred":false,"id":894963,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Krabbenhoft, David P. 0000-0003-1964-5020 dpkrabbe@usgs.gov","orcid":"https://orcid.org/0000-0003-1964-5020","contributorId":1658,"corporation":false,"usgs":true,"family":"Krabbenhoft","given":"David","email":"dpkrabbe@usgs.gov","middleInitial":"P.","affiliations":[{"id":5044,"text":"National Research Program - Central Branch","active":true,"usgs":true},{"id":37464,"text":"WMA - Laboratory & Analytical Services Division","active":true,"usgs":true},{"id":37947,"text":"Upper Midwest Water Science Center","active":true,"usgs":true},{"id":677,"text":"Wisconsin Water Science Center","active":true,"usgs":true}],"preferred":true,"id":894964,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70250846,"text":"70250846 - 2024 - Using an open-source tool to develop a three-dimensional hydrogeologic framework of the Kobo Valley, Ethiopia","interactions":[],"lastModifiedDate":"2024-01-09T16:47:27.725312","indexId":"70250846","displayToPublicDate":"2023-12-20T10:36:40","publicationYear":"2024","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1816,"text":"Geosciences","active":true,"publicationSubtype":{"id":10}},"title":"Using an open-source tool to develop a three-dimensional hydrogeologic framework of the Kobo Valley, Ethiopia","docAbstract":"Groundwater resource management requires understanding the groundwater basin’s hydrogeology and would be improved with the development of a three-dimensional hydrogeologic framework model (HFM). A wide range of methods and software exist to quantify the extent, structure, and properties of geologic systems. However, most geologic software is proprietary and cost-prohibitive for use in developing countries. GemPy is a Python-based, open-source (no-cost) tool for generating three-dimensional geological models. This study uses available data and GemPy to develop the Kobo Valley Hydrogeologic Framework Model (KV-HFM), a three-dimensional HFM for Kobo Valley in northern Ethiopia, which is part of the East African Rift System. The KV-HFM is a conceptual model that comprises the hydrostratigraphy, structural features, and hydraulic properties of the Kobo Valley groundwater system. The limited data described the extent and altitude of the hydrostratigraphic units using the GemPy implicit potential–field interpolation. The KV-HFM showed the existence of an east-to-west, structural-based groundwater divide composed of volcanic rock and clay. This divide splits the catchment into two groundwater systems with limited interconnected flow. This study illustrates the use of open-source software for developing an HFM using sparse, existing geologic data.
","language":"English","publisher":"MDPI","doi":"10.3390/geosciences14010003","usgsCitation":"Mekonen, S.S., Boyce, S.E., Mohammed, A.K., and Disse, M., 2024, Using an open-source tool to develop a three-dimensional hydrogeologic framework of the Kobo Valley, Ethiopia: Geosciences, v. 14, no. 1, 3, 27 p., https://doi.org/10.3390/geosciences14010003.","productDescription":"3, 27 p.","ipdsId":"IP-133573","costCenters":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"links":[{"id":440882,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.3390/geosciences14010003","text":"Publisher Index Page"},{"id":424222,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"Ethiopia","otherGeospatial":"Afar Depression, Kobo Valley catchment","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n 39.3,\n 12.4\n ],\n [\n 39.3,\n 11.9\n ],\n [\n 39.8333,\n 11.9\n ],\n [\n 39.8333,\n 12.4\n ],\n [\n 39.3,\n 12.4\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"14","issue":"1","noUsgsAuthors":false,"publicationDate":"2023-12-20","publicationStatus":"PW","contributors":{"authors":[{"text":"Mekonen, Sisay Simachew","contributorId":333048,"corporation":false,"usgs":false,"family":"Mekonen","given":"Sisay","email":"","middleInitial":"Simachew","affiliations":[{"id":79717,"text":"Hydrology and River Basin Management Department, Technical University of Munich","active":true,"usgs":false}],"preferred":false,"id":891768,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Boyce, Scott E. 0000-0003-0626-9492 seboyce@usgs.gov","orcid":"https://orcid.org/0000-0003-0626-9492","contributorId":4766,"corporation":false,"usgs":true,"family":"Boyce","given":"Scott","email":"seboyce@usgs.gov","middleInitial":"E.","affiliations":[{"id":154,"text":"California Water Science Center","active":true,"usgs":true}],"preferred":true,"id":891769,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Mohammed, Abdella K.","contributorId":333049,"corporation":false,"usgs":false,"family":"Mohammed","given":"Abdella","email":"","middleInitial":"K.","affiliations":[{"id":79718,"text":"Hydraulic and Water Resources Engineering, Arba Minch University","active":true,"usgs":false}],"preferred":false,"id":891770,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Disse, Markus","contributorId":333050,"corporation":false,"usgs":false,"family":"Disse","given":"Markus","email":"","affiliations":[{"id":79717,"text":"Hydrology and River Basin Management Department, Technical University of Munich","active":true,"usgs":false}],"preferred":false,"id":891771,"contributorType":{"id":1,"text":"Authors"},"rank":4}]}} ,{"id":70250683,"text":"70250683 - 2024 - Effects of temperature on viral load, inclusion body formation, and host response in Pacific Herring with viral erythrocytic necrosis (VEN)","interactions":[],"lastModifiedDate":"2024-03-11T14:27:56.161748","indexId":"70250683","displayToPublicDate":"2023-12-20T08:47:37","publicationYear":"2024","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2177,"text":"Journal of Aquatic Animal Health","active":true,"publicationSubtype":{"id":10}},"title":"Effects of temperature on viral load, inclusion body formation, and host response in Pacific Herring with viral erythrocytic necrosis (VEN)","docAbstract":"The primary objective of this study was to determine the effects of temperature on viral erythrocytic necrosis (VEN) progression under controlled conditions. Secondarily, this study was intended to evaluate the combined effects of temperature and VEN on the Pacific Herring Clupea palasii transcriptome.
The effects of temperature on VEN progression were assessed by waterborne exposure of laboratory-reared, specific-pathogen-free Pacific Herring to tissues homogenates containing erythrocytic necrosis virus (ENV) at 6.9, 9.0, or 13.5°C.
Exposure of Pacific Herring to ENV resulted in the establishment of infections characterized by high infection prevalence (89%; 40/45) and mean viral loads (5.5 log10[gene copies/μg genomic DNA]) in kidney tissues at 44 days postexposure. Mean viral loads were significantly higher in fish from the ambient (mean = 9.0°C) and warm (mean = 13.5°C) treatments (6.1–6.2 log10[gene copies/total genomic DNA]) than in fish from the cool (mean = 6.9°C) treatment (4.3 log10[gene copies/μg genomic DNA]). Similarly, the peak proportion of diseased fish was directly related to temperature, with cytoplasmic inclusion bodies detected in 21% of fish from the cool treatment, 52% of fish from the ambient treatment, and 60% of fish from the warm treatment. The mean VEN load in each fish (enumerated as the percentage of erythrocytes with cytoplasmic inclusions) at 44 days postexposure increased with temperature from 15% in the cool treatment to 36% in the ambient treatment and 32% in the warm treatment. Transcriptional analysis indicated that the number of differentially expressed genes among ENV-exposed Pacific Herring increased with temperature, time postexposure, and viral load. Correlation network analysis of transcriptomic data showed robust activation of interferon and viral immune responses in the hepatic tissue of infected individuals independent of other experimental variables.
Results from this controlled laboratory study, combined with previous observations of natural epizootics in wild populations, support the conclusion that temperature is an important disease cofactor for VEN in Pacific Herring.
","language":"English","publisher":"American Fisheries Society","doi":"10.1002/aah.10202","usgsCitation":"Salzer, J.E., Greer, J.B., Groner, M., MacKenzie, A., Gregg, J.L., and Hershberger, P., 2024, Effects of temperature on viral load, inclusion body formation, and host response in Pacific Herring with viral erythrocytic necrosis (VEN): Journal of Aquatic Animal Health, v. 36, no. 1, p. 45-56, https://doi.org/10.1002/aah.10202.","productDescription":"12 p.","startPage":"45","endPage":"56","ipdsId":"IP-152500","costCenters":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"links":[{"id":423886,"rank":1,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"36","issue":"1","noUsgsAuthors":false,"publicationDate":"2023-12-20","publicationStatus":"PW","contributors":{"authors":[{"text":"Salzer, Joanne Elizabeth 0000-0002-6235-2779","orcid":"https://orcid.org/0000-0002-6235-2779","contributorId":296752,"corporation":false,"usgs":true,"family":"Salzer","given":"Joanne","email":"","middleInitial":"Elizabeth","affiliations":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"preferred":true,"id":890952,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Greer, Justin Blaine 0000-0001-6660-9976","orcid":"https://orcid.org/0000-0001-6660-9976","contributorId":265183,"corporation":false,"usgs":true,"family":"Greer","given":"Justin","email":"","middleInitial":"Blaine","affiliations":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"preferred":true,"id":890953,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Groner, Maya L. 0000-0002-3381-6415","orcid":"https://orcid.org/0000-0002-3381-6415","contributorId":292708,"corporation":false,"usgs":false,"family":"Groner","given":"Maya","middleInitial":"L.","affiliations":[{"id":62985,"text":"Senior Research Scientist, Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME 04544","active":true,"usgs":false}],"preferred":false,"id":890954,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"MacKenzie, Ashley 0000-0002-7402-7877 amackenzie@usgs.gov","orcid":"https://orcid.org/0000-0002-7402-7877","contributorId":150817,"corporation":false,"usgs":true,"family":"MacKenzie","given":"Ashley","email":"amackenzie@usgs.gov","affiliations":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"preferred":true,"id":890955,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Gregg, Jacob L. 0000-0001-5328-5482 jgregg@usgs.gov","orcid":"https://orcid.org/0000-0001-5328-5482","contributorId":203912,"corporation":false,"usgs":true,"family":"Gregg","given":"Jacob","email":"jgregg@usgs.gov","middleInitial":"L.","affiliations":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"preferred":true,"id":890956,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Hershberger, Paul 0000-0002-2261-7760","orcid":"https://orcid.org/0000-0002-2261-7760","contributorId":203322,"corporation":false,"usgs":true,"family":"Hershberger","given":"Paul","affiliations":[{"id":654,"text":"Western Fisheries Research Center","active":true,"usgs":true}],"preferred":true,"id":890957,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70250627,"text":"70250627 - 2024 - Legacy sediment as a potential source of orthophosphate: Preliminary conceptual and geochemical models for the Susquehanna River, Chesapeake Bay watershed, USA","interactions":[],"lastModifiedDate":"2023-12-21T12:59:23.83208","indexId":"70250627","displayToPublicDate":"2023-12-20T06:56:07","publicationYear":"2024","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3352,"text":"Science of the Total Environment","active":true,"publicationSubtype":{"id":10}},"title":"Legacy sediment as a potential source of orthophosphate: Preliminary conceptual and geochemical models for the Susquehanna River, Chesapeake Bay watershed, USA","docAbstract":"Nutrient pollution from agriculture and urban areas plus acid mine drainage (AMD) from legacy coal mines are primary causes of water-quality impairment in the Susquehanna River, which is the predominant source of freshwater and nutrients entering the Chesapeake Bay. Recent increases in the delivery of dissolved orthophosphate (PO4) from the river to the bay may be linked to long-term increases in pH, decreased acidity of precipitation, and decreased acidity, iron, and aluminum loading from widespread AMD. Since the 1950s, baseline pH increased from ~6.5 to ~8 in the West Branch and “North Branch” of the Susquehanna River, which drain bituminous and anthracite coalfields of Pennsylvania. A current baseline pH of ~8 and daily maxima exceeding 9 have been documented along the lower Susquehanna River. In response to improved river quality, bioavailable PO4 now may be released into solution from legacy sediment that has filled major impoundments in lower reaches of the river. At typical pH (5–8) of natural water, aqueous PO4 species tend to be adsorbed by hydrous iron, aluminum, and manganese oxides that coat soil and sediment particles; however, PO4 may be substantially desorbed at pH >8. We created a geochemical model that simulates equilibrium aqueous/solid distributions of PO4 as pH and other solution characteristics change. Considering current conditions in the lower Susquehanna River, the model demonstrates potential for extensive release of adsorbed PO4 at pH >8. Empirical data from laboratory experiments corroborate model results. The transfer of PO4 into the water column may increase algae growth, which removes CO2 and drives pH to higher values, facilitating additional PO4 release and exacerbating the potential for harmful algal blooms. Thus, legacy sediment is a currently unquantified source of PO4 that warrants consideration by resource managers and programs collaborating to reduce phosphorus loads to the bay and similar settings worldwide.
Coastal mangrove forests provide a suite of environmental services, including sequestration of anthropogenic contamination. Yet, research lags on the environmental fate and potential human health risks of mangrove-sequestered contaminants in the context of mangrove removal for development and range shifts due to climate change. To address this, we conducted a study on Moloka'i, Hawai'i, comparing microplastic and pesticide contamination in coastal compartments both at areas modified by non-native red mangroves (Rhizophora mangle) and unmodified, open coastline. Sediment, porewater, and mangrove plant tissues were collected to quantify microplastic and pesticide concentrations across ecosystem type. Average microplastics were similar between mangrove (8.89 items/kg) and non-mangrove areas (9.01 items/kg) in sediment and porewater, but mangrove roots were a substantial reservoir of microplastics (2004 items/kg). Additionally, there was a strong relationship between proximity to urban development and microplastics detected. Six pesticides were detected, most commonly the insecticide bifenthrin, found in most sediment samples (11.3 ng/g), all root samples (243.3 ng/g), and one propagule sample (8.60 ng/g). Other pesticides detected with appreciable concentrations include the neonicotinoid insecticide imidacloprid and the legacy insecticide transformation product, p,p’-DDE. The other detections, all at concentrations < 1 ng/g, were p,p’-DDT, trifluralin, and permethrin. The high concentrations of bifenthrin in roots compared to lower concentrations detected in sediment suggest that mangrove roots strongly accumulate some pesticides, indicating mangrove roots as a sink for organic contaminants. Study methods could be applied to other Hawaiian Islands and other locations where mangroves have been introduced to further examine the observed trends. Additional information is needed to investigate the fate and cycling of pesticides and microplastics adhered to mangrove roots, to better inform non-native mangrove removal efforts on Moloka'i and elsewhere.
Water level is an important guide for water resource management and wetland ecosystems, defining one of the most basic processes in hydrology. This research seeks to investigate the possibility of complementing numerical modeling with a Machine Learning (ML) model to forecast daily water levels in the southern Everglades in Florida, USA. An exact analytical solution to water level may not be possible, but using the computational methods afforded by ML, the traditional numerical techniques may be enhanced to generate more robust, scalable predictions. Five locations were chosen for application of the Time-Delayed Neural Network (TDNN) and Long-Short Term Memory Recurrent Neural Network (LSTM-RNN) ML models, which were built to estimate water level with 1, 2, 3, 7 and 10 day forecasts using a simulation step of 1 day. The results showed that rainfall forecasts from weather models could improve water-level forecasts if the accuracy and performance of the weather models can be improved. The ML models presented here improve water-level predictions from a historical hydrologic model for a 24 hour forecast horizon.
","largerWorkType":{"id":4,"text":"Book"},"largerWorkTitle":"Advanced hydroinformatics: Machine learning and optimization for water resources","largerWorkSubtype":{"id":15,"text":"Monograph"},"language":"English","publisher":"American Geophysical Union","doi":"10.1002/9781119639268.ch7","usgsCitation":"Forde, C.S., Bhattacharya, B., Solomatine, D., Swain, E., and Aumen, N., 2024, Forecasting water levels using machine (deep) learning to complement numerical modelling in the southern Everglades, USA, chap. 7 of Advanced hydroinformatics: Machine learning and optimization for water resources, p. 177-211, https://doi.org/10.1002/9781119639268.ch7.","productDescription":"35 p.","startPage":"177","endPage":"211","ipdsId":"IP-140554","costCenters":[{"id":27821,"text":"Caribbean-Florida Water Science Center","active":true,"usgs":true}],"links":[{"id":440912,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"http://dx.doi.org/10.1002/9781119639268.ch7","text":"Publisher Index Page"},{"id":423841,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Florida","otherGeospatial":"Everglades","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -80.1037093889116,\n 26.92620905192487\n ],\n [\n -81.32930131865726,\n 26.92620905192487\n ],\n [\n -81.32930131865726,\n 25.096697437852114\n ],\n [\n -80.1037093889116,\n 25.096697437852114\n ],\n [\n -80.1037093889116,\n 26.92620905192487\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","noUsgsAuthors":false,"publicationDate":"2023-12-15","publicationStatus":"PW","contributors":{"editors":[{"text":"Corzo Perez, Gerald A.","contributorId":332614,"corporation":false,"usgs":false,"family":"Corzo Perez","given":"Gerald","email":"","middleInitial":"A.","affiliations":[],"preferred":false,"id":890674,"contributorType":{"id":2,"text":"Editors"},"rank":1},{"text":"Solomatine, Dimitri 0000-0003-2031-9871","orcid":"https://orcid.org/0000-0003-2031-9871","contributorId":298962,"corporation":false,"usgs":false,"family":"Solomatine","given":"Dimitri","email":"","affiliations":[{"id":49677,"text":"IHE Delft Institute for Water Education","active":true,"usgs":false}],"preferred":false,"id":890675,"contributorType":{"id":2,"text":"Editors"},"rank":2}],"authors":[{"text":"Forde, Courtney S 0000-0003-2084-6698","orcid":"https://orcid.org/0000-0003-2084-6698","contributorId":298960,"corporation":false,"usgs":false,"family":"Forde","given":"Courtney","email":"","middleInitial":"S","affiliations":[{"id":64740,"text":"Caribbean Institute for Meteorology and Hydrology","active":true,"usgs":false}],"preferred":false,"id":856773,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Bhattacharya, Biswa 0000-0002-8046-589X","orcid":"https://orcid.org/0000-0002-8046-589X","contributorId":298961,"corporation":false,"usgs":false,"family":"Bhattacharya","given":"Biswa","email":"","affiliations":[{"id":49677,"text":"IHE Delft Institute for Water Education","active":true,"usgs":false}],"preferred":false,"id":856774,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Solomatine, Dimitri 0000-0003-2031-9871","orcid":"https://orcid.org/0000-0003-2031-9871","contributorId":298962,"corporation":false,"usgs":false,"family":"Solomatine","given":"Dimitri","email":"","affiliations":[{"id":49677,"text":"IHE Delft Institute for Water Education","active":true,"usgs":false}],"preferred":false,"id":856775,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Swain, Eric 0000-0001-7168-708X","orcid":"https://orcid.org/0000-0001-7168-708X","contributorId":223705,"corporation":false,"usgs":true,"family":"Swain","given":"Eric","affiliations":[{"id":269,"text":"FLWSC-Ft. Lauderdale","active":true,"usgs":true}],"preferred":true,"id":856776,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Aumen, Nicholas 0000-0002-5277-2630","orcid":"https://orcid.org/0000-0002-5277-2630","contributorId":223550,"corporation":false,"usgs":true,"family":"Aumen","given":"Nicholas","affiliations":[{"id":269,"text":"FLWSC-Ft. Lauderdale","active":true,"usgs":true}],"preferred":true,"id":856777,"contributorType":{"id":1,"text":"Authors"},"rank":5}]}} ,{"id":70251815,"text":"70251815 - 2024 - Numbers of wildlife fatalities at renewable energy facilities in a targeted development region","interactions":[],"lastModifiedDate":"2024-02-29T15:01:41.057961","indexId":"70251815","displayToPublicDate":"2023-12-15T08:30:47","publicationYear":"2024","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":2980,"text":"PLoS ONE","active":true,"publicationSubtype":{"id":10}},"title":"Numbers of wildlife fatalities at renewable energy facilities in a targeted development region","docAbstract":"Increased interest in renewable energy has fostered development of wind and solar energy facilities globally. However, energy development sometimes has negative environmental impacts, such as wildlife fatalities. Efforts by regional land managers to balance energy potential while minimizing fatality risk currently rely on datasets that are aggregated at continental, but not regional scales, that focus on single species, or that implement meta-analyses that inappropriately use inferential statistics. We compiled and summarized fatality data from 87 reports for solar and wind facilities in the Mojave and Sonoran Deserts region of southern California within the Desert Renewable Energy Conservation Plan area. Our goal was to evaluate potential temporal and guild-specific patterns in fatalities, especially for priority species of conservation concern. We also aimed to provide a perspective on approaches interpreting these types of data, given inherent limitations in how they were collected. Mourning doves (Zenaida macroura), Chukar (Alectoris chukar) and California Quail (Callipepla californica), and passerines (Passeriformes), accounted for the most commonly reported fatalities. However, our aggregated count data were derived from raw, uncorrected totals, and thus reflect an absolute minimum number of fatalities for the monitored period. Additionally, patterns in the raw data suggested that many species commonly documented as fatalities (e.g., waterbirds and other nocturnal migrants, bats) are rarely counted during typical pre-construction use surveys. This may explain the more commonly observed mismatch between pre-construction risk assessment and actual fatalities. Our work may serve to guide design of future scientific research to address temporal and spatial patterns in fatalities and to apply rigorous guild-specific survey methodologies to estimate populations at risk from renewable energy development.
","language":"English","publisher":"PLoS","doi":"10.1371/journal.pone.0295552","usgsCitation":"Conkling, T., Fesnock, A.L., and Katzner, T., 2024, Numbers of wildlife fatalities at renewable energy facilities in a targeted development region: PLoS ONE, v. 18, no. 12, e0295552, 15 p., https://doi.org/10.1371/journal.pone.0295552.","productDescription":"e0295552, 15 p.","ipdsId":"IP-142188","costCenters":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"links":[{"id":440915,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1371/journal.pone.0295552","text":"Publisher Index Page"},{"id":426127,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"California","geographicExtents":"{\n \"type\": \"FeatureCollection\",\n \"features\": [\n {\n \"type\": \"Feature\",\n \"properties\": {},\n \"geometry\": {\n \"coordinates\": [\n [\n [\n -116.41388196440452,\n 32.63301172668308\n ],\n [\n -114.71231156077859,\n 32.71521061573718\n ],\n [\n -114.41844327520268,\n 34.121883375452825\n ],\n [\n -115.258371375603,\n 35.51347324917859\n ],\n [\n -116.44620706269673,\n 36.348306541123236\n ],\n [\n -120.9361068529251,\n 35.49816148699837\n ],\n [\n -117.83770190615772,\n 34.11965094145391\n ],\n [\n -116.41388196440452,\n 32.63301172668308\n ]\n ]\n ],\n \"type\": \"Polygon\"\n }\n }\n ]\n}","volume":"18","issue":"12","noUsgsAuthors":false,"publicationDate":"2023-12-15","publicationStatus":"PW","contributors":{"authors":[{"text":"Conkling, Tara 0000-0003-1926-8106","orcid":"https://orcid.org/0000-0003-1926-8106","contributorId":217915,"corporation":false,"usgs":true,"family":"Conkling","given":"Tara","email":"","affiliations":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":895658,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Fesnock, Amy L.","contributorId":334447,"corporation":false,"usgs":false,"family":"Fesnock","given":"Amy","email":"","middleInitial":"L.","affiliations":[{"id":80149,"text":"Desert District Office, U.S. Bureau of Land Management","active":true,"usgs":false}],"preferred":false,"id":895659,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Katzner, Todd E. 0000-0003-4503-8435 tkatzner@usgs.gov","orcid":"https://orcid.org/0000-0003-4503-8435","contributorId":191353,"corporation":false,"usgs":true,"family":"Katzner","given":"Todd E.","email":"tkatzner@usgs.gov","affiliations":[{"id":290,"text":"Forest and Rangeland Ecosystem Science Center","active":false,"usgs":true}],"preferred":true,"id":895660,"contributorType":{"id":1,"text":"Authors"},"rank":3}]}} ,{"id":70250646,"text":"70250646 - 2024 - PCB concentrations in riparian spiders (Tetragnathidae) consistently reflect concentrations in water and aquatic macroinvertebrates, but not sediment: Analysis of a seven-year field study","interactions":[],"lastModifiedDate":"2023-12-22T13:11:32.000134","indexId":"70250646","displayToPublicDate":"2023-12-14T07:09:38","publicationYear":"2024","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3352,"text":"Science of the Total Environment","active":true,"publicationSubtype":{"id":10}},"title":"PCB concentrations in riparian spiders (Tetragnathidae) consistently reflect concentrations in water and aquatic macroinvertebrates, but not sediment: Analysis of a seven-year field study","docAbstract":"Tetragnathid spiders have been used as sentinels to study the biotransport of contaminants between aquatic and terrestrial environments because a significant proportion of their diet consists of adult aquatic insects. A key knowledge gap in assessing tetragnathid spiders as sentinels is understanding the consistency of the year-to-year relationship between contaminant concentrations in spiders and sediment, water, and macroinvertebrates. We collected five years of data over a seven-year investigation at a PCB contaminated-sediment site to investigate if concentrations in spiders were consistently correlated with concentrations in sediment, water, and aquatic macroinvertebrates. Despite significant year-to-year variability in spider PCB concentrations, they were not correlated with sediment concentrations (p = 0.186). However, spider PCB concentrations were significantly, positively correlated with PCB concentrations in water (p < 0.0001, annual r2 = 0.35–0.84) and macroinvertebrates (p < 0.0001; annual r2 = 0.59–0.71). Analysis of covariance (ANCOVA) showed that spider PCB concentrations varied consistently with water (β = 0.63) and macroinvertebrate PCB concentrations (β = 1.023) among years. Overall, this study filled a critical knowledge gap in the utilization of tetragnathid spiders as sentinels of aquatic pollution by showing that despite year-to-year changes in PCB concentrations across environmental compartments, consistent relationships existed between spiders and water and aquatic macroinvertebrates.
The southern tip of North America coalesces into one of the world’s largest freshwater wetlands, the Everglades, Florida, USA. Though this region is much like an island, home to high biodiversity and endemism, it is also the site of a century of development and associated landscape-scale species invasions. Melaleuca quinquenervia (hereafter melaleuca), a tree native to tropical Australia, was planted extensively throughout south Florida as street trees, levee stabilizers, and later to reduce standing water in marshy areas. Through extensive cooperation with the United States Department of Agriculture’s Australian Biological Control Laboratory, several biological control agents were released, three of which later successfully established. Herein we examine evidence that plant community shifts determined from vegetation surveys and remotely sensed images reflect changes from melaleuca-dominated wetlands (before management) to native communities (after management). Melaleuca-dominated community types decreased from 1990 to 2020 by more than 99%. Vegetation surveys also reflect an increase in cypress wetlands, pinelands, and open water wetlands, all of which were dominated by melaleuca in previous decades. We also found the normalized difference vegetation index (NDVI) increased in melaleuca-invaded wetlands during peak infestations but decreased again after communities recovered to sawgrass-dominated wetlands. These responses are concomitant with the development of integrative management techniques for melaleuca that include mechanical, chemical, and biological control. Our results confirm previous findings that biological control likely augments conventional management methods by limiting recovery of invasive species.
Bobcats (Lynx rufus) are terrestrial mammals that also inhabit tree islands (i.e., topographically elevated patches of forested land) embedded in the subtropical Everglades wetlands, which serve as a dry refuge habitat during the wet season in this region of Florida, USA. The Comprehensive Everglades Restoration Plan seeks to restore Everglades water flow to pre-drainage conditions, but little is known about how water levels or other landscape-level factors may influence mammalian occurrence, such as bobcats, on the tree islands in this ecosystem. We used game camera records and occupancy modeling to test for effects of static habitat variables and dynamic hydrologic variables. We hypothesized that deep water levels would limit the accessibility of tree islands to bobcats; therefore, we predicted that bobcat occupancy would decline with higher water levels. We also tested for the effect of an expanding invasive snake (i.e., Burmese python [Python molarus bivittatus]) using output from a model constructed to predict density and spread of Burmese pythons across southern Florida. We hypothesized that increases in Burmese pythons on the landscape would influence the food resources of bobcats, resulting in reduced bobcat occupancy at higher predicted densities of pythons. We built detection histories using 1,855 bobcat images from game cameras set on 87 tree islands in an Everglades conservation area from 2005–2019. Bobcat occupancy was significantly diminished when predicted Burmese python densities exceeded approximately 3 Burmese pythons/km2. Bobcat occupancy probability also increased with tree-island density around the focal tree island. Although water depth and hydroperiod surrounding tree islands appeared in our top 3 candidate models, the hydrologic variables had weak effects on bobcat occupancy. Our results suggest that while hydrologic dynamics may play a role, the invasive Burmese python has stronger influences on bobcat occupancy of tree islands in this Everglades conservation area.
The economic feasibility of gas production from hydrate deposits is critical for hydrate to become an energy resource. Permeability in hydrate-bearing sediments dictates gas and water flow rates and needs to be accurately evaluated. Published permeability studies of hydrate-bearing sediments mostly quantify vertical permeability; however, the flow is mainly horizontal during gas production in layered reservoirs. Additionally, ASTM standards require a hydraulic gradient of 10–30 to be used during laboratory permeability measurements, but the gradient is much higher in the field, particularly near a production well. To address these issues, this study focuses on the hydraulic properties of a sandy silt subsample of the hydrate reservoir and a clayey silt subsample of the fine-grained, hydrate-free interbed recovered from a GC955 deep-water Gulf of Mexico gas hydrate reservoir. We characterize the sediment pore space with water retention curves for both hydrate-free and hydrate-bearing samples (hydrate saturation, Sh =80 %). Vertical deformation with increasing stress is also quantified while consolidating the samples to the 4 MPa in situ vertical effective stress. The customized permeameter measures both the horizontal and vertical permeability with increasing stress. Results show that high hydraulic gradients lower permeability in the flow direction, possibly due to increased flow tortuosity and local sediment compaction from the high seepage force. Assuming a single permeability value, even though hydraulic gradients decrease with distance from the well, is not realistic for field estimations. The results highlight that permeability anisotropy, hydrate saturation, stress conditions, and hydraulic gradient all substantially impact reservoir permeability during production.
Wildfires are increasing in size and severity across much of the western United States, exposing vulnerable wildland-urban interfaces to post-fire hazards. The Mediterranean chaparral region of Northern California contains many high sloping watersheds prone to hazardous post-fire flood events and identifying watersheds at high risk of soil loss and debris flows is a priority for post-fire response and management. Uncrewed Aerial Systems (UAS; aka drones) offer post-fire management teams the ability to quickly mobilize and survey burned areas with very high-resolution imagery (∼1 cm), facilitating emergency management and post-fire hazard assessment. However, adoption of this technology by hazard response teams may be hindered by complicated workflows for UAS data acquisition, image processing and analysis. We present an open-source workflow using mature Geographic Information Systems (GIS) software and Python packages in a Jupyter Notebook environment that guides users through classification of true-color UAS imagery to generate high resolution burn severity maps which can then be scaled across larger watersheds using Sentinel-2 normalized burn ratio (NBR) images. Soil burn severity classifications using a weighted brightness (WB) image and Char Index (CI) generated from UAS imagery were validated with in-situ data and random stratified points, resulting in the CI having the highest overall accuracy of 87.5%. CI also displayed a marginally stronger relationship over the WB with the post-fire Sentinel-2 NBR, R2 = 0.79 and R2 = 0.78 respectively. Our methods offer the unique opportunity to standardize GIS workflows, promoting replication through transparency, while improving the user's understanding of scientific GIS functionality.
VNIR-SWIR (400–2500 nm) reflectance measurements were made on the surfaces of various cores, cuttings and sample splits of sedimentary rocks from the Tertiary Jackson Group, and Catahoula, Oakville and Goliad Formations. These rocks vary in composition and texture from mudstone and claystone to sandstone and are known host rocks for roll front uranium occurrences in Karnes and Live Oak Counties, Texas. Spectral reflectance profiles, 569 in total, were reduced to 125 representative spectral signatures, which were analyzed using the U.S. Geological Survey's (USGS) Material Identification and Characterization Algorithm (MICA). MICA uses an automated continuum-removal procedure together with a least-squares linear regression to determine the fit of observed sample spectral absorption features to those of reference mineral standards in a spectral library. The reference minerals include various clay, mica, carbonate, ferric and ferrous iron minerals and their mixtures. In addition, absorption feature band-depth analysis was done to identify rock surfaces exhibiting absorption features related to uranium and zeolite minerals, which were not included in the command files used to execute MICA.
Rocks from each of the four geologic units produced broadly similar spectral signatures as a result of comparable mineral compositions, but there were some notable differences. For example, Ca- and Na-montmorillonite was matched most frequently to the spectral absorption features in 2-μm (∼2000–2500 nm) wavelengths, while goethite occurred often at 1-μm (∼400–1000 nm) wavelengths. The latter is related to limonitic iron-staining in and around oxidized zones of the uranium roll front as described in previous papers. Rocks of the Jackson Group differed from those of the Catahoula, Oakville and Goliad units in that the former exhibited spectral features we interpret as being due to the presence of lignite-bearing mudstone layers. Goliad rocks exhibit spectral features related to dolomite, gypsum, anhydrite, and an unidentified green clay mineral that is possibly glauconite. Jackson Group rocks also exhibit weak but well-resolved absorption features at 964 and 1157 nm related to either or both zeolite minerals clinoptilolite and heulandite. These zeolite minerals and a few spectra exhibiting hydrous silica absorption features are indicative of alteration of volcanic glass in tuffaceous mudstone and claystone layers. A few sample spectra exhibited strong absorption features at around 1135 nm related to the uranium mineral coffinite. Both the 1135 nm coffinite and 1157 nm zeolite absorption features overlap somewhat, potentially making them difficult to distinguish without additional hyperspectral field, laboratory or remote sensing data.
The results of this study were compared to mixtures of minerals described for ore, gangue and alteration minerals in deposit models for sandstone-hosted uranium, sedimentary bentonite and sedimentary zeolite. Use of these spectra can help facilitate mapping of both waste materials from the legacy mining of the above commodities, as well as future exploration and resource assessment activities.
","language":"English","publisher":"Elsever","doi":"10.1016/j.gexplo.2023.107370","usgsCitation":"Hubbard, B.E., Gallegos, T., Stengel, V.G., Hoefen, T.M., Kokaly, R.F., and Elliott, B., 2024, Hyperspectral (VNIR-SWIR) analysis of roll front uranium host rocks and industrial minerals from Karnes and Live Oak Counties, Texas Coastal Plain: Journal of Geochemical Exploration, v. 257, 107370, 20 p., https://doi.org/10.1016/j.gexplo.2023.107370.","productDescription":"107370, 20 p.","ipdsId":"IP-136836","costCenters":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true},{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true},{"id":245,"text":"Eastern Mineral and Environmental Resources Science Center","active":true,"usgs":true},{"id":583,"text":"Texas Water Science Center","active":true,"usgs":true},{"id":49175,"text":"Geology, Energy & Minerals Science Center","active":true,"usgs":true}],"links":[{"id":440969,"rank":0,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1016/j.gexplo.2023.107370","text":"Publisher Index Page"},{"id":423384,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"country":"United States","state":"Texas","county":"Karnes County, Live Oak County","geographicExtents":"{\"type\":\"FeatureCollection\",\"features\":[{\"type\":\"Feature\",\"geometry\":{\"type\":\"Polygon\",\"coordinates\":[[[-97.6145,29.1096],[-97.755,29.0056],[-97.5693,28.8157],[-97.7706,28.6717],[-97.7743,28.669],[-97.7812,28.6646],[-97.7847,28.6688],[-97.7882,28.6716],[-97.7929,28.6721],[-97.8267,28.6715],[-97.8276,28.6742],[-97.8291,28.6761],[-97.8353,28.679],[-97.8461,28.6824],[-97.8538,28.6839],[-97.859,28.6845],[-97.8637,28.6841],[-97.8641,28.6874],[-97.8682,28.6902],[-97.8795,28.6932],[-97.8913,28.6998],[-97.8954,28.7013],[-97.8975,28.7032],[-97.8995,28.7055],[-97.8989,28.7073],[-97.8999,28.7092],[-97.9035,28.7116],[-97.9127,28.7168],[-97.9189,28.7187],[-98.0037,28.6896],[-98.0894,28.6599],[-98.0167,28.5323],[-97.8084,28.1788],[-97.8136,28.1757],[-97.8896,28.1253],[-97.8991,28.1185],[-97.9007,28.1167],[-97.9018,28.1135],[-97.9008,28.1108],[-97.9009,28.1071],[-97.902,28.1048],[-97.9047,28.0998],[-97.9059,28.0934],[-97.9041,28.0846],[-97.9021,28.079],[-97.9013,28.0726],[-97.8988,28.0684],[-97.8963,28.0646],[-97.8943,28.0609],[-97.8923,28.0595],[-98.2338,28.0607],[-98.3343,28.06],[-98.3358,28.4775],[-98.336,28.4982],[-98.3363,28.6117],[-98.099,28.7882],[-98.1879,28.8807],[-97.7292,29.224],[-97.6145,29.1096]]]},\"properties\":{\"name\":\"Karnes\",\"state\":\"TX\"}}]}","volume":"257","noUsgsAuthors":false,"publicationStatus":"PW","contributors":{"authors":[{"text":"Hubbard, Bernard E. 0000-0002-9315-2032","orcid":"https://orcid.org/0000-0002-9315-2032","contributorId":213146,"corporation":false,"usgs":true,"family":"Hubbard","given":"Bernard","email":"","middleInitial":"E.","affiliations":[{"id":245,"text":"Eastern Mineral and Environmental Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":889919,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Gallegos, Tanya J. 0000-0003-3350-6473","orcid":"https://orcid.org/0000-0003-3350-6473","contributorId":206859,"corporation":false,"usgs":true,"family":"Gallegos","given":"Tanya J.","affiliations":[{"id":241,"text":"Eastern Energy Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":889920,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Stengel, Victoria G. 0000-0003-0481-3159 vstengel@usgs.gov","orcid":"https://orcid.org/0000-0003-0481-3159","contributorId":5932,"corporation":false,"usgs":true,"family":"Stengel","given":"Victoria","email":"vstengel@usgs.gov","middleInitial":"G.","affiliations":[{"id":583,"text":"Texas Water Science Center","active":true,"usgs":true}],"preferred":true,"id":889921,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Hoefen, Todd M. 0000-0002-3083-5987 thoefen@usgs.gov","orcid":"https://orcid.org/0000-0002-3083-5987","contributorId":403,"corporation":false,"usgs":true,"family":"Hoefen","given":"Todd","email":"thoefen@usgs.gov","middleInitial":"M.","affiliations":[{"id":171,"text":"Central Mineral and Environmental Resources Science Center","active":true,"usgs":true},{"id":211,"text":"Crustal Geophysics and Geochemistry Science Center","active":true,"usgs":true}],"preferred":true,"id":889922,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Kokaly, Raymond F. 0000-0003-0276-7101","orcid":"https://orcid.org/0000-0003-0276-7101","contributorId":205165,"corporation":false,"usgs":true,"family":"Kokaly","given":"Raymond","email":"","middleInitial":"F.","affiliations":[{"id":35995,"text":"Geology, Geophysics, and Geochemistry Science Center","active":true,"usgs":true},{"id":5078,"text":"Southwest Regional Director's Office","active":true,"usgs":true}],"preferred":true,"id":889923,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Elliott, Brent","contributorId":148952,"corporation":false,"usgs":false,"family":"Elliott","given":"Brent","email":"","affiliations":[{"id":17599,"text":"Texas Bureau of Economic Geology","active":true,"usgs":false}],"preferred":false,"id":889924,"contributorType":{"id":1,"text":"Authors"},"rank":6}]}} ,{"id":70250282,"text":"70250282 - 2024 - Comparison of δ13C analyses of individual foraminifer (Orbulina universa) shells by secondary ion mass spectrometry and gas source mass spectrometry","interactions":[],"lastModifiedDate":"2023-12-01T12:49:36.531165","indexId":"70250282","displayToPublicDate":"2023-12-01T06:42:23","publicationYear":"2024","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":3233,"text":"Rapid Communications in Mass Spectrometry","active":true,"publicationSubtype":{"id":10}},"displayTitle":"Comparison of δ13C analyses of individual foraminifer (Orbulina universa) shells by secondary ion mass spectrometry and gas source mass spectrometry","title":"Comparison of δ13C analyses of individual foraminifer (Orbulina universa) shells by secondary ion mass spectrometry and gas source mass spectrometry","docAbstract":"Rationale: The use of secondary ion mass spectrometry (SIMS) to perform micrometer-scale in situ carbon isotope (δ13C) analyses of shells of marine microfossils called planktic foraminifers holds promise to explore calcification and ecological processes. The potential of this technique, however, cannot be realized without comparison to traditional whole-shell δ13C values measured by gas source mass spectrometry (GSMS).
Methods: Paired SIMS and GSMS δ13C values measured from final chamber fragments of the same shell of the planktic foraminifer Orbulina universa are compared. The SIMS–GSMS δ13C differences (Δ13CSIMS-GSMS) were determined via paired analysis of hydrogen peroxide-cleaned fragments of modern cultured specimens and of fossil specimens from deep-sea sediments that were either untreated, sonicated, and cleaned with hydrogen peroxide or vacuum roasted. After treatment, fragments were analyzed by a CAMECA IMS 1280 SIMS instrument and either a ThermoScientific MAT-253 or a Fisons Optima isotope ratio mass spectrometer (GSMS).
Results: Paired analyses of cleaned fragments of cultured specimens (n = 7) yield no SIMS–GSMS δ13C difference. However, paired analyses of untreated (n = 18) and cleaned (n = 12) fragments of fossil shells yield average Δ13CSIMS-GSMS values of 0.8‰ and 0.6‰ (±0.2‰, 2 SE), respectively, while vacuum roasting of fossil shell fragments (n = 11) removes the SIMS–GSMS δ13C difference.
Conclusions: The noted Δ13CSIMS-GSMS values are most likely due to matrix effects causing sample–standard mismatch for SIMS analyses but may also be a combination of other factors such as SIMS measurement of chemically bound water. The volume of material analyzed via SIMS is ~105 times smaller than that analyzed by GSMS; hence, the extent to which these Δ13CSIMS-GSMS values represent differences in analyte or instrument factors remains unclear.
","language":"English","publisher":"Wiley","doi":"10.1002/rcm.9658","usgsCitation":"Wycech, J.B., Kelly, D.C., Kozdon, R., Ishida, A., Kitajima, K., Spero, H.J., and Valley, J.W., 2024, Comparison of δ13C analyses of individual foraminifer (Orbulina universa) shells by secondary ion mass spectrometry and gas source mass spectrometry: Rapid Communications in Mass Spectrometry, v. 38, no. 2, e9658, 13 p., https://doi.org/10.1002/rcm.9658.","productDescription":"e9658, 13 p.","ipdsId":"IP-154888","costCenters":[{"id":164,"text":"Central Energy Resources Science Center","active":true,"usgs":true}],"links":[{"id":440980,"rank":1,"type":{"id":40,"text":"Open Access Publisher Index Page"},"url":"https://doi.org/10.1002/rcm.9658","text":"Publisher Index Page"},{"id":435083,"rank":0,"type":{"id":30,"text":"Data Release"},"url":"https://doi.org/10.5066/P9524ENX","text":"USGS data release","linkHelpText":"The Stable Carbon Isotope Dataset of Individual Foraminifer (Orbulina universa) Shells Measured by Secondary Ion Mass Spectrometry and Gas-Source Mass Spectrometry"},{"id":423136,"type":{"id":24,"text":"Thumbnail"},"url":"https://pubs.usgs.gov/thumbnails/outside_thumb.jpg"}],"volume":"38","issue":"2","noUsgsAuthors":false,"publicationDate":"2023-11-21","publicationStatus":"PW","contributors":{"authors":[{"text":"Wycech, Jody Brae 0000-0002-7073-3037","orcid":"https://orcid.org/0000-0002-7073-3037","contributorId":303104,"corporation":false,"usgs":true,"family":"Wycech","given":"Jody","email":"","middleInitial":"Brae","affiliations":[{"id":164,"text":"Central Energy Resources Science Center","active":true,"usgs":true}],"preferred":true,"id":889271,"contributorType":{"id":1,"text":"Authors"},"rank":1},{"text":"Kelly, Daniel Clay 0000-0002-3241-1635","orcid":"https://orcid.org/0000-0002-3241-1635","contributorId":332025,"corporation":false,"usgs":false,"family":"Kelly","given":"Daniel","email":"","middleInitial":"Clay","affiliations":[{"id":79362,"text":"University of Wisconsin-Madison Department of Geoscience","active":true,"usgs":false}],"preferred":false,"id":889272,"contributorType":{"id":1,"text":"Authors"},"rank":2},{"text":"Kozdon, Reinhard 0000-0001-6347-456X","orcid":"https://orcid.org/0000-0001-6347-456X","contributorId":261206,"corporation":false,"usgs":false,"family":"Kozdon","given":"Reinhard","email":"","affiliations":[{"id":28041,"text":"Lamont-Doherty Earth Observatory, Columbia University","active":true,"usgs":false}],"preferred":false,"id":889275,"contributorType":{"id":1,"text":"Authors"},"rank":3},{"text":"Ishida, Akizumi 0000-0002-1580-8534","orcid":"https://orcid.org/0000-0002-1580-8534","contributorId":332027,"corporation":false,"usgs":false,"family":"Ishida","given":"Akizumi","email":"","affiliations":[{"id":79363,"text":"Tohoku University Department of Earth Science","active":true,"usgs":false}],"preferred":false,"id":889273,"contributorType":{"id":1,"text":"Authors"},"rank":4},{"text":"Kitajima, Kouki 0000-0001-7634-4924","orcid":"https://orcid.org/0000-0001-7634-4924","contributorId":332026,"corporation":false,"usgs":false,"family":"Kitajima","given":"Kouki","email":"","affiliations":[{"id":79362,"text":"University of Wisconsin-Madison Department of Geoscience","active":true,"usgs":false}],"preferred":false,"id":889274,"contributorType":{"id":1,"text":"Authors"},"rank":5},{"text":"Spero, Howard J. 0000-0001-5465-8607","orcid":"https://orcid.org/0000-0001-5465-8607","contributorId":294388,"corporation":false,"usgs":false,"family":"Spero","given":"Howard","email":"","middleInitial":"J.","affiliations":[{"id":63564,"text":"University of California Davis, Department of Earth and Planetary Sciences","active":true,"usgs":false}],"preferred":false,"id":889276,"contributorType":{"id":1,"text":"Authors"},"rank":6},{"text":"Valley, John W.","contributorId":52895,"corporation":false,"usgs":false,"family":"Valley","given":"John","email":"","middleInitial":"W.","affiliations":[{"id":16925,"text":"University of Wisconsin-Madison","active":true,"usgs":false}],"preferred":false,"id":889277,"contributorType":{"id":1,"text":"Authors"},"rank":7}]}} ,{"id":70250498,"text":"70250498 - 2024 - Etiology of a fish kill, Including the endangered Tidewater Goby (Eucyclogobius newberryi), in a northeastern pacific coastal lagoon","interactions":[],"lastModifiedDate":"2024-04-10T15:48:58.718851","indexId":"70250498","displayToPublicDate":"2023-11-30T06:55:28","publicationYear":"2024","noYear":false,"publicationType":{"id":2,"text":"Article"},"publicationSubtype":{"id":10,"text":"Journal Article"},"seriesTitle":{"id":1584,"text":"Estuaries and Coasts","active":true,"publicationSubtype":{"id":10}},"displayTitle":"Etiology of a fish kill, Including the endangered Tidewater Goby (Eucyclogobius newberryi), in a northeastern pacific coastal lagoon","title":"Etiology of a fish kill, Including the endangered Tidewater Goby (Eucyclogobius newberryi), in a northeastern pacific coastal lagoon","docAbstract":"Ecological disturbances such as fish kills can negatively impact ecosystem processes in coastal lagoons. To gain an understanding of factors causing fish kills, we examined conditions associated with a summertime fish kill in a northeastern Pacific coastal lagoon (Rodeo Lagoon, CA, USA). Examination of available data indicated the fish kill was likely caused by hypoxia involving the following etiology: (1) strong onshore winds (up to 12 m/s) mixed a stratified water column, (2) water column mixing transported nutrients from near the bed into the photic zone, (3) increased nutrient concentrations in the photic zone (> 200%) together with high solar irradiance fueled a phytoplankton bloom, (4) death and decomposition of phytoplankton (72% decrease in abundance) contributed to biological oxygen demand that led to (5) hypoxic conditions (as low as 0.6 mg/L) that caused the fish kill. The event resulted in the death of an estimated 3677 Tidewater Goby (Eucyclogobius newberryi), a species listed as endangered under the US Endangered Species Act, and numerous (but not enumerated) Threespine Stickleback (Gasterosteus aculeatus), unidentified sculpins (Cottidae), and macroinvertebrates (primarily Amphipoda). The processes contributing to the event are likely re-occurring phenomena responsible for observed periodic fish kills. Coastal lagoons with limited freshwater inflows and connection to the Pacific Ocean may retain nutrients and be susceptible to similar events.