AndreaBozzo/ceres-open-data-index huggingface dataset:
Geodatabase of the datasets that represent the three subareas of the Silurian-Devonian aquifer, Illinois, Indiana, Iowa, Kentucky, Michigan, Missouri, Ohio, Tennessee, and Wisconsin

This geodatabase includes spatial datasets that represent the Silurian-Devonian 
aquifers in the States of Illinois, Indiana, Iowa, Kentucky, Michigan, Missouri, Ohio, 
Tennessee, and Wisconsin. Included are: 
(1) polygon extents; datasets that 
represent the aquifer system extent, and the entire extent subdivided into subareas, 
(2) raster datasets for the altitude of the top and bottom surfaces of the entire aquifer 
(where data are available), and 
(3) altitude contours used to generate the surface rasters. The digitized contours are 
supplied for reference.
		
The extent of the Silurian-Devonian aquifers is from the linework of the Silurian-Devonian 
aquifer extent maps in U.S. Geological Survey U.S. Geological Survey Hydrologic Atlas 730, 
Chapters J and K, (USGS HA 730-J, -K) and a digital version of the aquifer extent presented 
in the National Aquifer Code Reference List, available at 
http://water.usgs.gov/ogw/NatlAqCode-reflist.html , "silurian.zip". The extent was then 
modified for each subarea:
		
Subarea 1 (sa1): Primarily in Ohio and Indiana, subject of U.S. Geological Survey 
Professional Paper 1423 B (USGS PP 1423B).
		
Subarea 2 (sa2): In Iowa. Digital data were available from the Iowa Geologic Survey.
		
Subarea 3 (sa3): Remaining area in Illinois, Wisconsin, Michigan, and Kentucky. 
Extent is that part of the National Aquifer Code Reference List polygon that 
remained when the areas of sa1 and sa2 were removed.
		
The altitude and thickness contours that were available for each subarea were 
compiled or generated from georeferenced figures of altitude contours in 
USGS PP 1423B for sa1, digital data from IAGS for sa2. There were no 
vertical data for sa3. 
		
The resultant top and bottom altitude values were interpolated into surface rasters 
within a GIS using tools that create hydrologically correct surfaces from contour data, 
derive the altitude from the thickness (depth from the land surface), and merge the 
subareas into a single surface. The primary tool was an enhanced version of "Topo to Raster" 
used in ArcGIS, ArcMap, Esri 2014.  The raster surfaces were corrected in the areas where 
the altitude of an underlying layer of the aquifer exceeded the altitude of an overlying layer.

Tags: aquifer, aquifer-system, devonian, extent, groundwater, illinois, indiana, inlandwaters, iowa, kentucky, michigan, missouri, ohio, silurian, silurian-devonian, tennessee, united-states, usgs-617a906e-a558-4e0d-92b9-1463f648f19f, wisconsin
Organization: Department of the Interior
Elevation Data from Fountain Creek between Colorado Springs and the Confluence of Fountain Creek at the Arkansas River, Colorado, 2021

The U.S. Geological Survey, in cooperation with Colorado Springs Utilities, has been collecting topographic data annually since 2012 at 10 study areas along Fountain Creek, Colorado. The 10 study areas are located along Fountain Creek between Colorado Springs and the confluence of Fountain Creek and the Arkansas River in Pueblo. This data release presents topographic survey data, Light Detection and Ranging (lidar) survey data, elevation rasters, and elevation-change rasters collected or generated in 2021 as part of that monitoring effort. Topographic survey points were collected using real-time kinematic Global Navigation Satellite Systems (RTK-GNSS). These point data, along with lidar point clouds, were used to generate 2021 elevation rasters and 2015-21 elevation-change rasters. These survey data and maps provide an annual assessment of the geomorphic changes at each study area.

Tags: channel-change, colorado, colorado-springs, el-paso-county, flood, fountain, fountain-creek, geomorphology, inlandwaters, lidar, point-cloud, pueblo, pueblo-county, sediment-transport, topographic-survey, uas, usgs-617c7727d34ea58c3c700606
Organization: Department of the Interior
Central South Dakota Airborne Lidar Validation - Field Survey Data

U.S. Geological Survey (USGS) scientists conducted field data collection efforts during the time periods of April 25 - 26, 2017, October 24 - 28, 2017, and July 25 - 26, 2018, using a combination of surveying technologies to map and validate topography, structures, and other features at five sites in central South Dakota.  The five sites included the Chamberlain Explorers Athletic Complex and the Chamberlain High School in Chamberlain, SD, Hanson Lake State Public Shooting Area near Corsica, SD, the State Capital Grounds in Pierre, SD, and Platte Creek State Recreation Area near Platte, SD.  The work was initiated as an effort to evaluate airborne Geiger-Mode and Single Photon light detection and ranging (lidar) data that were collected over parts of central South Dakota.  Both Single Photon and Geiger-Mode lidar offer the promise of being able to map areas at high altitudes, thus requiring less time than traditional airborne lidar collections, while acquiring higher point densities.  Real Time Kinematic Global Navigational Satellite System (RTK-GNSS), total station, and ground-based lidar (GBL) data were collected to evaluate data collected by the Geiger-Mode and Single Photon systems.

Tags: 3d-elevation-program, 3dep, biota, chamberlain, chamberlain-explorers-athletic-complex, chamberlain-high-school, corsica, earth-resources-observation-and-science-center, elevation, eros, gbl, geoscientificinformation, global-navigational-satellite-system, gnss, ground-based-lidar, hanson-lake-state-public-shooting-area, lidar, light-detection-and-ranging, location, national-geospatial-program, ngp-elevation-applied-research-calibration-validation, pierre, platte, platte-creek-state-recreation-area, south-dakota-state-capitol-grounds, state-of-south-dakota, terrestrial-laser-scanner, tls, total-station, u-s-geological-survey, usgs, usgs-617997d7d34ea58c3c6fa1ff
Organization: Department of the Interior
Microbial community analyses of groundwater collected during an enhanced bioremediation experiment of trichlorethylene in a fractured rock aquifer, West Trenton, NJ (2008-2015).

These datasets contain microbial community data from groundwater samples collected at an in situ bioremediation site located at the former Naval Air Warfare Center (NAWC), West Trenton, NJ.  DNA was extracted from groundwater samples collected from monitoring wells at the NAWC study site from July 2008 through July 2015 and analyzed for microbial community structure.  Sample collection coincided with a groundwater bioremediation experiment investigating the microbial degradation of the contaminant trichloroethylene (TCE) prevalent in the targeted region of the aquifer. Nutrient addition and a microbial consortium, commercially developed to stimulate the degradation of TCE and TCE byproducts, was introduced to the contaminated groundwater on October 15, 2008.  This data release contains microbial community data including taxonomy, alpha, and beta diversity from next-generation sequencing of the V4 region of 16S rRNA from groundwater samples collected during the 7-year observation period.  A further discussion and interpretation of the data is presented by Jennifer C Underwood, Denise M Akob, Michelle Mi Lorah, Thomas E Imbrigiotta, Ronald W Harvey, Claire R Tiedeman, Microbial community response to a bioaugmentation test to degrade trichloroethylene in a fractured rock aquifer, Trenton, N.J, FEMS Microbiology Ecology, Volume 98, Issue 7, July 2022, fiac077, https://doi.org/10.1093/femsec/fiac077.

Tags: 16s-rrna-sequencing, aquifer, bioaugmentation, bioremediation, contamination-and-pollution, groundwater, microbial-analysis, naval-air-warfare-center, taxonomy, trichlorethylene, usgs-61786ac4d34ea58c3c6f9c1f, west-trenton-nj
Organization: Department of the Interior
Rangewide occupancy and post-fire recovery of California Gnatcatchers in southern California, 2020

Data presented are results of surveys for California Gnatcatchers and vegetation sampling conducted in 2020 to address two inter-related questions:
(1) How have gnatcatchers and their habitat recovered in areas burned by wildfires in 2003, 2007, and 2014?, and
(2) What is the current regional occupancy of gnatcatchers throughout their southern California range?
In 2020 a fifth fire category was added (2015-2019) which changed the sample sizes for the other fire categories: 2003-2006 (102 points), 2007-2010 (106 points), 2011-2014 (95 points), 2015-2019 (25 points), unburned (96 points). All post-fire study points were in San Diego County. The regional occupancy surveys included 327 points in 2020 throughout southern California. The post-fire and regional datasets are not mutually exclusive, with some points serving in both analyses. Vegetation data were collected at each point to facilitate analyses identifying habitat correlates of California gnatcatcher occurrence.

Tags: biogeography, biota, coastal-sage-scrub, endangered-species, los-angeles-county, occupancy, plant-and-animal-tagging, post-fire-recovery, san-bernardino-county, san-diego-county, southern-california, survey, usgs-617841f4d34e4c6b7fe2a4e6, ventura-county, western-riverside-county
Organization: Department of the Interior
A Novel Gonadotropic Microsporidian Parasite (Microsporidium clinchi n. sp.) Infecting a Declining Population of Pheasantshell Mussels (Actinonaias pectorosa) (Unioinidae) from the Clinch River, USA

Freshwater mussels of the order Unionida are among the most endangered animal groups globally, but the causes of population declines are often enigmatic with little known about the role of disease. In 2018, we collected wild adult pheasantshell (Actinonaias pectorosa) and mucket (Actinonaias ligamentina) during an epidemiologic survey investigating an ongoing mussel mass mortality event in the Clinch River, USA. Histopathology and transmission electron microscopy showed a novel microsporidian parasite primarily infecting the ovary of pheasantshell. Sequencing of the small subunit rRNA gene produced a 1333 bp sequence with greatest similarity to Pseudonosema cristatellae (AF484694.1; 86.36%; e-value = 0), a microsporidium infecting the freshwater bryozoan (Cristatella mucedo). Microsporidia were observed in 65% (17/26) of the examined female pheasantshell (A. pectorosa) and in no (0/2) female mucket (A. ligamentina), and occurred at mortality and non-mortality sites. Our findings indicate that a novel parasite, Microsporidium clinchi n. sp., is present in pheasantshell in the Clinch River, USA, and while likely not a cause of mass mortality, could reduce fecundity and recruitment in this declining population and threaten the success of reintroductions. Surveillance for M. clinchi n. sp. and evaluation of brood stock and their progeny for microsporidia would therefore be prudent.

Tags: actinonaias-pectorosa, biota, bivalves, freshwater-mussel, histopathology, microsporidia, microsporidium-clinchi-n-sp, pcr, tem, unionid, usgs-61781c32d34e4c6b7fe2a42a
Organization: Department of the Interior
Sagebrush recovery analyzed with a dynamic reference approach in southwestern Wyoming, USA 1985-2018

Identifying ecologically relevant reference sites is important for evaluating ecosystem recovery, but the relevance of references that are temporally static is unclear in the context of vast landscapes with disturbance and environmental contexts varying over space and time. This question is pertinent for landscapes dominated by sagebrush (Artemisia spp.) which face a suite of threats from disturbance and development but also have lengthy recovery times. Here, we applied a dynamic reference approach to studying and projecting recovery of sagebrush on former oil and gas well pads in southwestern Wyoming, USA, using over 3 decades of remote sensing data (1985–2018). We also used quantile regression to evaluate factors that may affect recovery including soils, weather, elevation, and well pad characteristics. We then created projections for percent recovery and years to recovery (relative to references and thresholds for greater sage-grouse [Centrocercus urophasianus] habitat) across the study area. This approach substantially increased our sample, and therefore inferential base, and illustrated benefits of using dynamic references and quantile regression to evaluate and project recovery of vegetation such as sagebrush. In this data release, we provide datasets used to fit models and projection maps for percent recovery and years to recovery across the study area and in areas identified as greater sage-grouse habitat.

Tags: atmospheric-and-climatic-processes, biota, habitat-alteration-and-disturbance, habitats, natural-resource-management, remediation, soil-moisture, southwestern-wyoming, united-states-of-america, upper-colorado-river-basin, usgs-61772e7dd34e4c6b7fe2a096, usgs-ema-low-pl-sagebrush-steppe, usgs-ema-low-sb-smc-greater-sage-grouse, usgs-ema-low-sb-smc-native-species-restoration, usgs-ema-low-ss-oil-and-gas, wyoming, wyoming-landscape-conservation-initiative
Organization: Department of the Interior
Soil, plant, and elevation characteristics of tidal and managed impounded wetlands in Suisun Marsh, California, USA (2018-2019)

These datasets provide information on soil properties, plant species cover, and soil surface elevation in a tidal wetland and a managed impounded wetland in northern Suisun Marsh, California, USA.

Tags: antioch-dunes, biota, california, coastal-ecosystems, ecology, fire, nitrogen-cycling, usgs-61e9dd8fd34e8b818ad984e0, water-management
Organization: Department of the Interior
Okanogan Basin Pacific lamprey eDNA detections and translocations for 2012-2020 (ver. 1.1, April 2022)

Prior to the initiation of translocation efforts in 2017, Pacific lamprey (Entosphenus tridentatus) were last documented in the Okanogan river subbasin in 2010. It appears as if lamprey were extirpated in the Okanogan subbasin some time shortly after that. However, until 2017, monitoring and management actions for lamprey were minimal in the Okanogan subbasin. This lack of monitoring has resulted in a large gap in understanding of the recent historical status of Pacific lamprey distribution throughout the Okanogan subbasin. Recent (beginning in 2017) translocation efforts have helped to rebound or reestablish lamprey in the Okanogan subbasin. Analysis of archived eDNA samples from the Okanogan river and its tributaries provides insight into the recent history of Pacific lamprey distribution and habitat preferences within the subbasin.

Tags: biota, british-columbia, columbia-basin, edna, entosphenus-tridentatus, environment, environmental-dna, inlandwaters, lamprey, migratory-species, okanogan-river, translocation, usgs-61e9e215d34e8b818ad984f3, washington
Organization: Department of the Interior
Phytoplankton identification and biovolume data for field samples from Detroit Lake, Oregon, collected in August 2019 and August 2020

This dataset contains taxonomic and biovolume data for phytoplankton sampled from Detroit Lake, OR, in August, 2019, and August, 2020. Taxonomy is reported to the lowest possible taxonomic level along with total and percent biovolume.
Surface grab samples for phytoplankton enumeration were collected with a van Dorn type sampler and then transferred into a clearn polycarbonate churn. Whole water samples were dispensed for total nutrients and phytoplankton identification and enumeration, the latter preserved with 1 percent Lugol's iodine solution.  
Samples were analyzed at BSA Environmental Services in Beachwood, Ohio. Cell numbers of all identified phytoplankton taxa were quantified on a per milliliter basis using the Utermohl method (Lund et al. 1958). Samples were thoroughly mixed prior to settling an aliquot to ensure that the organisms were evenly distributed. Various aliquots were measured and delivered into custom Utermohl chambers and the organisms allowed to settle in darkness undisturbed for at least 20 hours within an enclosure protected from vibration and temperature alteration (Burkholder and Wetzel 1989). Counts were performed on a LEICA DMiL at 800X or 1260X. Scans at multiple magnifications were conducted and the abundance of common taxa estimated by random field counts. At least 300 natural units (colonies, filaments, unicells) or 50 random fields were enumerated to the lowest possible taxonomic level from each sample. Cell biovolumes were estimated using formulae for solid geometric shapes that most closely match the cell shape (Hillebrand et al., 1999), based on measurements of 10 organisms per taxon for each sample where possible.
These monitoring data were collected as part of the City of Salem's source water protection program that includes several sites within Detroit Lake and sites downstream in the North Santiam River down to Salem's Geren Island Drinking Water Treatment Plant. These data can be used to understand which phytoplankton taxa are dominant and a measure of their biomass (biovolume). These data also may be used to trigger sampling for cyanotoxins.
REFERENCES:
Burkholder, J.M. and R.G. Wetzel. 1989. Epiphytic microalgae on natural substrata in REFERENCES a hardwater lake: seasonal dynamics of community structure, biomass and ATP content. Arch. Hydrobiol., Suppl. 83:1-56.
Hillebrand, H., C.D. Dürselen, D. Kirschtel, U. Pollingher, and T. Zohary. 1999. Biovolume calculation for pelagic and benthic microalgae. Journal of Phycology. 35: 403-424.
Lund, J.W.G., C. Kipling and E.D. LeCren. 1958. The inverted microscope method of estimating algal numbers and the statistical basis of estimates by counting. Hydrobiologia 11:143-170.

Tags: algae, biovolume, detroit-lake, farming, habs, lakes, oregon, phytoplankton, taxonomy, united-states, usgs-618051bfd34e9f2789e0a7f7
Organization: Department of the Interior
Water quality, habitat, sampling methods and characteristics for grass carp in Truman Reservoir Missouri, 2017-2019

Diploid and triploid Grass Carp (Ctenopharyngodon Idella) tagged with acoustic transmitters were observed in Truman Reservoir, Missouri from February 2017 to March 2019 to determine habitat usage in winter. Habitat parameters were measured at used and available sites to model habitat preference. In addition, tagged fish were targeted during removal attempts to determine the efficacy of using tagged Judas Grass Carp in removing wild conspecifics. This dataset includes information on tagged Grass Carp and habitats they selected as well as capture events and characteristics of the wild fish caught during these attempts.

Tags: benton-county, biota, fish, grass-carp, habitat-selection, harry-s-truman-reservoir, henry-county, hickory-county, invasive-species, missouri, removal, sampling, st-clair-county, usgs-6176e881d34ef46ec173d072
Organization: Department of the Interior
Wetland elevation and soil characteristics across Bayou Sauvage National Wildlife Refuge (2020-2021)

The recent completion of the US Army Corps of Engineers (USACE) Hurricane and Storm Damage Risk Reduction System (HSDRRS) for New Orleans has effectively blocked surface water exchange between Bayou Sauvage National Wildlife Refuge (BSNWR) and the surrounding Lake(s) Pontchartrain and Borgne and the Gulf of Mexico to which it was once connected. Monitoring changes in hydrology, water quality, bird habitat variability, and resident waterbird and nekton communities within BSNWR is important to the long-term sustainability of these aquatic resources for use by visitors and aquatic life in these habitats. In particular, landscape and hydrologic modifications from management and restoration projects in southeastern Louisiana have led to areas of impounded and unimpounded marshland which can greatly affect soil characteristics. Understanding the differences in soil characteristics among impounded and unimpounded areas can provide information on habitat health, structure, and function, making it crucial to assess soil responses to hydrologic management practices. Triplicate 40x10cm cores were collected at six marsh sites, three impounded and three unimpounded, in BSNWR in 2020 and 2021 to assess the variation of soil bulk density and soil organic matter between three impounded and unimpounded areas. Cores were collected at least five meters from any edge in a section of the marsh with representative local vegetation. Excessive debris on the soil surface was removed prior to coring. Elevation of sites were also determined using Real-Time Kinematics (RTK) to determine the extent of flooding and water depth of each site.

Tags: bayou-sauvage-national-wildlife-refuge, bulk-density, core-analysis, elevation, new-orleans, soil-organic-matter, usgs-6176d51fd34ef46ec173cf89, wetland-ecosystems
Organization: Department of the Interior
Nearshore bathymetry data from the Elwha River delta, Washington, July 2018, collected from kayak

This part of the data release presents bathymetry data from the Elwha River delta collected in July 2018 (USGS Field Activity Number 2018-648-FA) using a kayak. The kayak was equipped with a single-beam echosounder and a survey-grade global navigation satellite system (GNSS) receiver.

Tags: bathymetry, bathymetry-and-elevation, clallam-county, cmhrp, coastal-and-marine-hazards-and-resources-program, elevation, elwha-river, global-positioning-system-gps-observations, gps-measurement, marine-geophysics, olympic-peninsula, pacific-coastal-and-marine-science-center, pcmsc, sea-floor-characteristics, single-beam-echo-sounder, strait-of-juan-de-fuca, u-s-geological-survey, usgs, usgs-6172f789d34ea36449a882a3
Organization: Department of the Interior
Summary Descriptive Characteristics by Catchment Concerning Lidar-derived Ditches in Eastern North Carolina, 2014-2015

Artificial drainage has major ecosystem impacts through the development of extensive ditch networks that reduce storage and induce large-scale vegetation changes. This has been a widespread practice of water table management for agriculture in Eastern North Carolina. However, these features are challenging to identify, and because of their structure, have been determined by non-natural factors. A dataset of open ditches was processed by calculating terrain openness (also called positive openness): a value based a line-of-sight approach to measure the surrounding eight zenith angles as viewed above the landscape surface. The result from calculating openness with high resolution digital elevation models (DEMs, or Lidar) was then refined by masking natural water ways (stream valleys) and channels that are associated with transportation and urban areas. This shapefile is a depiction of National Hydrography Dataset (NHD) Plus V2 catchments, defined by a COMID, with summary statistics about the ditches identified in the course of this project.

Tags: agriculture, artificial-drainage, beaufort, bertie, bladen, boundaries, brunswick, camden, canals, carteret, chowan, columbus, craven, cumberland, currituck, dare, ditches, duplin, edgecombe, farming, franklin, gates, geomorphology, geoscientificinformation, geospatial-analysis, greene, halifax, harnett, hertford, hoke, hyde, hydrology, inlandwaters, johnston, jones, lenoir, lidar, martin, montgomery, moore, nash, new-hanover, north-carolina, northampton, onslow, pamlico, pasquotank, pender, perquimans, pitt, richmond, robeson, sampson, scotland, transportation, tyrrell, usgs-6172b916d34ea36449a8818a, wake, washington, water-cycle, wayne, wilson
Organization: Department of the Interior