Presence of Microbes and the Distribution of Climatic, Environmental, and Geochemical Variables Web Mapping Application

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Frequently anticipated questions:


What does this data set describe?

Title:
Presence of Microbes and the Distribution of Climatic, Environmental, and Geochemical Variables Web Mapping Application
Abstract:
This web application dataset includes data collected by the U.S. Geological Survey (USGS) as well as environmental climatic, geochemical, and mineralogical variables from various sources. NOTE: This web application is no longer being supported, and has been removed from ArcGIS Online as of September 30, 2023. Please see the Process Steps of this metadata record for more information. Layers include: U.S. Boundary Layers (States, Counties, Watersheds, and EPA Regions), Bacillus anthracis PCR results (rpoB, pXO1, pXO2 genetic markers), Outbreak Counties, NOAA U.S. Climate Normals for Precipitation 1981-2010 (inches per year), USDA Census Data and Non-Agricultural Bison Herd Population Data, Soil pH (SSURGO), Soil pH (STATSGO), Slope (SSURGO), Slope (STATSGO), Flood Frequency (SSURGO), Flood Frequency (STATSGO), Drainage Class (SSURGO), Drainage Class (STATSGO), USGS Soil Geochemistry (0-5 cm depth), USGS Soil Geochemistry (A-horizon), USGS Soil Geochemistry (C-horizon), NOAA NCDC - Average Precipitation, NOAA NCDC - Average Temperature, USGS 2012 100m National Elevation Dataset (NED), and the NDFD Real-Time 72 Hour Precipitation Forecast.
Supplemental_Information:
Project Supplemental Information and Problem Definition/Background: In order to protect the environment from current and potential threats posed by uncontrolled, intentional release of hazardous substances, pollutants, and contaminants, the biothreat research community recognizes the need to consider background concentrations to determine whether a detected constituent is part of the naturally occurring environment or a contaminant associated with an accidental or purposeful release. Therefore, background studies for biothreat organisms are necessary to determine the existing risk to the public from endemic microorganisms. The North American Soil Geochemical Landscapes Project (NASGLP) of the USGS Mineral Resources Program collected soil at a density of 1 site per 1600 square km (~13,500 sites across North America) to expand geochemical database information for the U.S., Canada, and Mexico. All samples collected for the NASGLP were uniformly analyzed for more than 40 major and trace elements, and limited microbial characterization (Smith 2005; Smith 2009). Sample collection began in 2007 and was later expanded to include analysis of the samples from the conterminous U.S. (48 states) for the presence of B. anthracis with funding from the USGS and the EPA. A total of 4,786 soil samples were received, cataloged and screened at USGS Coastal and Marine Science Center, St. Petersburg, FL for the presence of Bacillus sp. and B. anthracis. It should be noted that the data represents a snapshot in time and caution should be taken against making direct correlations or causations with this data. Users should be aware that layers in this application represent various units of measure and differing scales and any potential comparisons should be made taking this into consideration. Objectives: The goal of this project was to plot results from soil samples and secondary data (including but not limited to presence/absence of pathogens of interest [B. anthracis, Bacillus species], geochemical composition of the soil, ambient meteorological conditions, soil moisture content, and land use)
  1. How might this data set be cited?
    Douglas, Steven, 2016, Presence of Microbes and the Distribution of Climatic, Environmental, and Geochemical Variables Web Mapping Application: U.S. Geological Survey, St. Petersburg, FL.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -127.52929686992
    East_Bounding_Coordinate: -63.896484372453
    North_Bounding_Coordinate: 51.727028155548
    South_Bounding_Coordinate: 22.91792293528
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 2016
    Ending_Date: 30-Sep-2023
    Currentness_Reference:
    ground condition
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: web application
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      This is a Raster data set.
    2. What coordinate system is used to represent geographic features?
      The map projection used is WGS 1984 Web Mercator Auxiliary Sphere.
      Projection parameters:
      Standard_Parallel: 0.0
      Longitude_of_Central_Meridian: 0.0
      False_Easting: 0.0
      False_Northing: 0.0
      Planar coordinates are encoded using coordinate pair
      Abscissae (x-coordinates) are specified to the nearest 0.001
      Ordinates (y-coordinates) are specified to the nearest 0.001
      Planar coordinates are specified in meter
      The horizontal datum used is WGS84 Web Mercator.
      The ellipsoid used is WGS 84.
      The semi-major axis of the ellipsoid used is 6378137.0.
      The flattening of the ellipsoid used is 1/298.257223563.
  7. How does the data set describe geographic features?
    Entity_and_Attribute_Overview:
    U.S. EPA Region Boundaries GIS layer. The U.S. EPA Region boundaries layer defines the areal extent of EPA regions within the contiguous U.S.
    Entity_and_Attribute_Detail_Citation: Entity_and_Attribute_Overview:
    U.S. State boundaries - The U.S. State Boundaries layer defines the areal extent of states within the contiguous U.S. at a 1:1,000,000 scale.
    Entity_and_Attribute_Detail_Citation: Entity_and_Attribute_Overview:
    U.S. County Boundaries - 2015 County and Equivalent National entities GIS shapefile with a 1:500,000 resolution. The GIS shapefile was downloaded as a zipped file from the U.S. Census Bureau Master Address File/Topologically Integrated Goegraphic Encoding and Referencing system (MAF/TIGER) geographic database.
    Entity_and_Attribute_Detail_Citation: https://www.census.gov/geo/maps-data/data/cbf/cbf_counties.html
    Entity_and_Attribute_Overview:
    HUC-6 Watershed Boundaries - The Watershed Boundary Dataset (WBD) defines the areal extent of surface water drainage to a point except in coastal or lake front areas where there could be multiple outlets as stated by the Federal Standards and Procedures for the National Watershed Boundary Dataset (WBD). This dataset represents the hydrologic unit boundaries to the 6-digit level (1:24,000 scale) for the entire United States. WBD data are delivered as a dataset of polygons that define the boundary of the watershed. The HUC describes where the unit is in the country and the level of the unit.
    Entity_and_Attribute_Detail_Citation: Entity_and_Attribute_Overview:
    Bacillus anthracis PCR detection results (rpoB, pXO1, pXO2 genetic markers). Layers include, "Bacillus sp. PCR Amplicon Strength," "pXO1 pag/lef Genetic Markers," "pXO2 Genetic Marker," "pXO1 and pXO2 Marker Total (pXO1 pag/pXO1 lef/pXO2)," and "rpoB Gene PCR Results." 2007-2013 survey results for the rpoB gene PCR amplicon detection analysis of Bacillus species and B. anthracis presence/absence data were determined in 4,770 soil samples collected across the contiguous United States. Labels for the Bacillus species PCR results and rpoB PCR results of low, medium, high, and none correspond to the associated data release (F7WW7FRJ) scale of l,m,h,n.
    Entity_and_Attribute_Detail_Citation:
    Griffin, D.W., 2016, Experimental PCR Data on Soil DNA Extracts: U.S. Geological Survey data release, https://doi.org/10.5066/F7WW7FRJ.
    Entity_and_Attribute_Overview:
    B. anthracis outbreak counties (2000-2015) - illustrates the counties reporting outbreaks or cases of Bacillus anthracis in agricultural animals and/or wildlife since 2000. State county outbreak and case data were compiled from state animal health organizations and the National Animal Health Reporting System (Griffin et al, 2014; USDA, 2014); U.S. Department of Agriculture, Animal and Plant Health Inspection Service. Available online: http://www.aphis.usda.gov/wps/portal/aphis/home/ (accessed on 8 August 2014). Counties with confirmed outbreaks were assigned a value of "1" and counties with no outbreaks were assigned a value of "O".
    Entity_and_Attribute_Detail_Citation:
    Griffin, D. W., Silvestri, E. E., Bowling, C. Y., Boe, T., Smith, D. B., & Nichols, T. L. (2014). Anthrax and the geochemistry of soils in the contiguous United States. Geosciences, 4(3), 114-127, http://www.mdpi.com/2076-3263/4/3/114/htm.
    Entity_and_Attribute_Overview:
    National Oceanographic and Atmospheric Administration (NOAA) U.S. Climate Normals for Precipitation 1981-2010 (in./yr.) are a three-decade average of monthly precipitation values. This layer has been cached to display between the continental scale and a scale of multiple counties to allow for quick rendering, while keeping the cache size minimal. NOAA 1981-2010 normal data are available for download at ftp://ftp.ncdc.noaa.gov/pub/data/normals/1981-2010/products/
    Entity_and_Attribute_Detail_Citation:
    Arguez, A., I. Durre, S. Applequist, R. S. Vose, M. F. Squires, X. Yin, R. R. Heim, Jr., and T. W. Owen, 2012: NOAA's 1981-2010 U.S. Climate Normals: An Overview. Bulletin of the American Meteorological Society, 93, 1687-1697, https://doi.org/10.1175/BAMS-D-11-00197.1
    Entity_and_Attribute_Overview:
    United States Department of Agriculture (USDA) Census Data - The USDA National Agricultural Statistics Service (NASS) conducted an Agricultural Census in 2012. The density values are calculated as population/square km and displayed in percentile classes of 10%. Bison data (2012), all cattle (2012 - including Beef, Milk, and calves), Equine (2012 - including Donkeys, Mules, Horses and Ponies), farm raised Deer, and farm raised Elk were downloaded at the county level for the contiguous United States. Equine data are available as two separate layers (Donkeys and Mules as one and Horses and Ponies as another). Deer and Elk were also separate datasets. Deer and Elk refer to only farm raised, not wild deer and elk. The Equine layers were combined into one dataset. Deer and Elk were combined into one dataset.
    Entity_and_Attribute_Detail_Citation: https://quickstats.nass.usda.gov/
    Entity_and_Attribute_Overview:
    Estimated Non-Agricultural Bison Population 2006-2014 - Non-agricultural (public lands, Native American land, non-profits, private land) locations of federal, state, local, and non-profit bison herd data was compiled from multiple sources. This data is displayed as the population within each area and divided into 5 percentile groups (quintiles).
    Entity_and_Attribute_Detail_Citation:
    Allen, B., N.D., Bona Fide Bison, The bison herd at Blue Mounds State Park is one of the most genetically authentic in the nation. http://www.dnr.state.mn.us/mcvmagazine/issues/2013/nov-dec/bison.html
    Entity_and_Attribute_Detail_Citation:
    Arizona Game and Fish Dept., N.D., Bison. http://www.azgfd.gov/w_c/conservation/CGMP/CGMP-Bison.pdf
    Entity_and_Attribute_Detail_Citation:
    Boyd, D.P. and Gates, C.C., 2006, A Brief Review of the Status of Plains Bison in North America. Journal of the West, 45 (2), 15; Bureau of Land Management, 2007, Bison Unit Management Plan Unit #15 Henry Mountains. https://wildlife.utah.gov/hunting/biggame/pdf/bison_15.pdf
    Entity_and_Attribute_Detail_Citation:
    Bureau of Land Management, 2007, Bison Herd Unit Management Plan Book Cliffs, Bitter Creek, and Little Creek Herd Unit #10A and #10C. https://wildlife.utah.gov/hunting/biggame/pdf/bison_10.pdf
    Entity_and_Attribute_Detail_Citation:
    Department of the Interior, 2014, DOI bison report: Looking forward. Natural Resource Report NPS/NRSS/BRMD/NRR—2014/821
    Entity_and_Attribute_Detail_Citation:
    National Park Service, Fort Collins, Colorado; Gillins, S., Stone, J., Doely, L., Zaluski, M., Jones, A., Sheppard, S., Sondenaa, A., Wallen, R., Clarke, R., Barndt, S., 2014, 2014 Annual Report of the Interagency Bison Management Plan. http://www.ibmp.info/Library/AnnualReports/2014_IBMP_AnnualReport_final.pdf
    Entity_and_Attribute_Detail_Citation:
    Montana Fish, Wildlife, and Parks, 2011, Plains Bison Ecology, Management, and Conservation. http://fwp.mt.gov/fishAndWildlife/management/bison/plainsEcology.html
    Entity_and_Attribute_Detail_Citation:
    U.S. Fish and Wildlife Service, 2007, Draft Reintroduction Plan for Bison at RMA-NWR. http://www.defenders.org/sites/default/files/publications/draft_bison_reintroduction_plan.pdf
    Entity_and_Attribute_Detail_Citation:
    U.S. Fish and Wildlife Service, 2007, Bison and Elk Management Plan/EIS. http://www.fws.gov/bisonandelkplan/index.html
    Entity_and_Attribute_Detail_Citation: Entity_and_Attribute_Detail_Citation:
    Lewis, C., 2012, 700 Bison Roam Utah's Antelope Island. http://www.utahstories.com/2012/08/700-wild-bison-roam-utahs-antelope-island/
    Entity_and_Attribute_Overview:
    Slope, Soil pH, Flood Frequency Class, and Drainage Class derived from SSURGO (Soil survey geographic database) and STATSGO (State soil geographic database) soil datasets. The SSURGO and STATSGO databases contain information about soil, collected by the National Cooperative Soil Survey over the course of a century. The polygon SSURGO shapefiles and polygon STATSGO shapefiles were joined to the tabular files within each state’s file geodatabase. The first join to be made uses the “mukey” field as the common identifier to join the slope_r, drainagecl, and cokey fields from the “component” table. The second join to be made uses the cokey field as the common identifier to join the ph1to1h2o_r field from the “CHorizon” table. The final join to be made uses the cokey field as the common identifier to join the flodfreqcl field from the “comonth” table. These three joins were repeated for each state. Finally, the SSURGO and STATSGO polygons for each state were merged to create a single Contiguous U.S. shapefile. For the SSURGO data, to create a simpler file that will render more quickly on the web application, the fields were dissolved using the dissolve tool in ArcGIS 10.3.1. Flood frequency maps are the predicted probablility of flooding, areas that are blank do not have a predicted probability of flooding SSURGO (Maps are made at scales ranging from 1:12,000 to 1:31,680) and STATSGO (STATSGO was mapped on the U.S. Geological Survey's 1:250,000-scale topographic quadrangle series). Descriptions for the SSURGO and STATSGO classes are available at the Soil Survey website (http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/ref/?cid=nrcs142p2_054253). (SSURGO metadata is available at: http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/home/?cid=nrcs142p2_053631. STATSGO metadata available at: http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/survey/geo/?cid=nrcs142p2_053631. SSURGO and STATSGO data were downloaded for each state through the USDA Geospatial Data Gateway.
    Entity_and_Attribute_Detail_Citation: https://gdg.sc.egov.usda.gov/
    Entity_and_Attribute_Overview:
    USGS Soil Geochemistry - Inverse Distance Weighted interpolations were made for the elements and minerals in each soil layer from samples taken by the U.S. Geological Survey and presented in Data Series 801. Interpolations for most elements and minerals were made using a resolution of 400m and a fixed search radius of 75 km, based on the methods described in OFR-1082. For more information on interpolations for each soil horizon, see each layer's service description. The final outputs of the interpolations was exported as .tif files. The following elements and minerals, available in Smith et al, 2013, were not included in these maps due to their low precense: Selenium, Silver, Indium, Tellurium, Cesium, Aragonite, Total Zeolites, Heulandite, Analcime, Pyroxene, Gibbsite, Goethite, Gypsum, Hematite, Pyrite, Talc, Serpentine.
    Entity_and_Attribute_Detail_Citation:
    Smith, D.B., Cannon, W.F., Woodruff, L.G., Solano, Federico, Kilburn, J.E., and Fey, D.L., 2013, Geochemical and mineralogical data for soils of the conterminous United States: U.S. Geological Survey Data Series 801, 19 p., http://pubs.usgs.gov/ds/801/.
    Entity_and_Attribute_Detail_Citation:
    Smith, D.B., Cannon, W.F., Woodruff, L.G., Solano, Federico, and Ellefsen, K.J., 2014, Geochemical and mineralogical maps for soils of the conterminous United States: U.S. Geological Survey Open-File Report 2014–1082, 386 p., https://doi.org/10.3133/ofr20141082. ISSN 2331-1258 (online)
    Entity_and_Attribute_Overview:
    NOAA National Climate Data Center (NCDC)- Average Precipitation and NOAA NCDC - Average Temperature - Daily climate data were downloaded for NCDC climate divisions for each state by downloading the CONUS_CLIMATE_DIVISIONS.shp.zip file from ftp://ftp.ncdc.noaa.gov/pub/data/cirs/climdiv. Climate division metadata available at: ftp://ftp.ncdc.noaa.gov/pub/data/cirs/climdiv/divisional-readme.txt
    Entity_and_Attribute_Detail_Citation: http://www7.ncdc.noaa.gov/CDO/CDODivisionalSelect.jsp#
    Entity_and_Attribute_Overview:
    USGS 2012 100m National Elevation Dataset (NED) - 100-meter resolution elevation of the conterminous United States. The elevation data were derived by the USGS from the USGS National Elevation Dataset (NED) data. This dataset was designed by the USGS to provide a seamless national elevation dataset. This layer has been cached to display between the continental scale and a scale of multiple counties to allow for quick rendering while keeping the cache size minimal.
    Entity_and_Attribute_Detail_Citation: Entity_and_Attribute_Overview:
    National Digital Forecast Database (NDFD) Real-Time 72 Hour Precipitation Forecast. This feed displays precipitation forecasts for the 72 hours following time of use. The precipitation data is Quantitative Precipitation Forecast (QPF), which is the amount of expected rainfall (in hundredths of inches), every six hours. This data is recorded by NDFD at 0000, 0600, 1200 and 1800 UTC.
    Entity_and_Attribute_Detail_Citation:

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Steven Douglas
  2. Who also contributed to the data set?
    Acknowledgment of the U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center, as a data source would be appreciated in products developed from these data, and such acknowledgment as is standard for citation and legal practices for data source is expected. Sharing of new data layers developed directly from these data would also be appreciated by the U.S. Geological Survey staff. These data are not legal documents and are not to be used as such.
  3. To whom should users address questions about the data?
    USGS SPCMSC Data Management Group
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    600 4th St S
    St Petersburg, FL
    USA

    727-502-8000 (voice)
    gs-g-spcmsc_data_inquiries@usgs.gov

Why was the data set created?

In cooperation with the U.S. Environmental Protection Agency National Homeland Security Research Center, this dataset was created due to the desire to know the relationship between the presence/absence of Bacillus anthracis and environmental variables. Environmental variables, such as (but not limited to) the geochemical make-up of the soil, ambient meteorological conditions, soil moisture content, land use, and more, are included to help predict persistence and natural occurrence of B. anthracis in the environment. These data will be utilized to provide a graphical representation of areas within the U.S. that may have a high probability of containing these biothreat agents in the soil. Therefore, this web application was developed to help researchers and public health officials prepare for potential contamination events concerning biothreat agents.

How was the data set created?

  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
    Date: 2016 (process 1 of 2)
    Raster and vector shapefiles were processed on a Windows 7 machine running ArcGIS 10.3. Maps and layer symbology were saved to a server geodatabase and published as web mapping Representational State Transfer (REST) services, using local servers at the USGS Coastal and Marine Science Center in St. Petersburg, FL. The web application was created using ArcGIS Online.
    Date: 30-Sep-2023 (process 2 of 2)
    This web application is no longer being supported, and has been removed from ArcGIS Online as of September 30, 2023. Interested users should review this metadata record for more information regarding published sources for data previously accessible through this web application. For questions or concerns, please contact the USGS SPCMSC Data Management Group (g-spcmsc_data_inquiries@usgs.gov).
  3. What similar or related data should the user be aware of?
    Smith, D.B., Cannon, W.F., Woodruff, L.G., Garrett, R.G., Klassen, R., Kilburn, J.E., Horton, J.D., King, H.D., Goldhaber, M.B., and Morrison, J.M., 2005, Major- and Trace-Element Concentrations in Soil from Two Continental-Scale Transects of the United States and Canada: U.S. Geological Survey Open-File Report OFR 2005-1253.

    Smith, D.B., Woodruff, L.G., O'Leary, R.M., Cannon, W.F., Garret, R.G., Kilburn, J.E., and Goldhaber, M.B., 2009, Pilot studies for the North American Soil Geochemical Landscapes Project - Site selection, sampling protocols, analytical methods, and quality control protocols: Applied Geochemistry 24(8), p. 1357-1368.


How reliable are the data; what problems remain in the data set?

  1. How well have the observations been checked?
    No formal attribute accuracy tests were conducted.
  2. How accurate are the geographic locations?
    No formal positional accuracy tests were conducted.
  3. How accurate are the heights or depths?
    No formal positional accuracy tests were conducted.
  4. Where are the gaps in the data? What is missing?
    The datasets included in this web application are considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details. Metadata files were written for layers that were created or changed significantly from the original source. These layers include Non-Agricultural Bison Populations, USDA Census Data, USGS Soil Geochemistry, NOAA NCDC Temperature and Precipitation, and NOAA 1981-2010 Climate Normals.
  5. How consistent are the relationships among the observations, including topology?
    No formal logical accuracy tests were conducted.

How can someone get a copy of the data set?

Are there legal restrictions on access or use of the data?
Access_Constraints None
Use_Constraints Public domain data from the U.S. Government are freely redistributable with proper metadata and source attribution. The U.S. Geological Survey requests to be acknowledged as originator of these data in future products or derivative research.
  1. Who distributes the data set? (Distributor 1 of 1)
    USGS SPCMSC Data Management Group
    U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
    600 4th St S
    St Petersburg, FL
    USA

    727-502-8000 (voice)
    gs-g-spcmsc_data_inquiries@usgs.gov
  2. What's the catalog number I need to order this data set?
  3. What legal disclaimers am I supposed to read?
    Although these data have been processed successfully on a computer system at the U.S. Geological Survey, no warranty expressed or implied is made regarding the display or utility of the data on any other system, or for general or scientific purposes, nor shall the act of distribution constitute any such warranty. The USGS shall not be held liable for improper or incorrect use of the data described or contained herein. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. The U.S. Environmental Protection Agency, through its Office of Research and Development, collaborated on the research described herein under an Interagency Agreement with the U.S. Geological Survey (IA #DW 14957748 and DW 92401101). This document has been subjected to the Agency’s review and has been approved for publication. This report was generated using references (secondary data) that could not be evaluated for accuracy, precision, representativeness, completeness, or comparability and therefore no assurance can be made that the data extracted from these publications meet EPA’s stringent quality assurance requirement. The contents of this document reflect the views of the contributors and do not necessarily reflect the views of the Agency. Mention of trade names or commercial products in this document or in the literature referenced in this document does not constitute endorsement or recommendation for use.
  4. How can I download or order the data?
    • Availability in digital form:
      Data format: REST (Representational State Transfer web mapping service)
      Network links: https://doi.org/10.5066/P93LNS4C
    • Cost to order the data: None


Who wrote the metadata?

Dates:
Last modified: 30-Sep-2023
Metadata author:
USGS SPCMSC Data Management Group
U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center
600 4th St S
St Petersburg, FL
USA

727-502-8000 (voice)
gs-g-spcmsc_data_inquiries@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)

This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/pathogen_web_app_metadata.faq.html>
Generated by mp version 2.9.51 on Thu Sep 21 15:03:56 2023