• Metagenomics analysis of groundwater, surface water, and sand samples at Jeorse Park in East Chicago, Indiana, 2017

    Metadata Updated: March 22, 2021

    This dataset provides results of a targeted bacterial community metagenomic analysis of surface water, groundwater, and sand samples at Jeorse Park on Lake Michigan in East Chicago, Indiana. Seventy-two samples were collected from 6 sites in 2017. Samples were analyzed for the 16S ribosomal RNA (16S rRNA) gene (the S in 16S refers to the rate of sedimentation, in Svedberg units, of the RNA molecule in a centrifugal field), and one sample was excluded because it produced too few reads. The 16S rRNA gene is the most conserved of three rRNA genes (16S, 23S, and 5S) and is considered the most reliable for identification and taxonomic classification of bacterial species (Bouchet and others, 2008). Taxonomic analysis was performed using Illumina paired-end sequencing by MiSeq to sequence V3-V4 of the gene. Determination of the relative abundance of bacterial species found in water can be used to track sources of fecal contamination by detecting host-specific markers in the sample. The U.S. Geological Survey (USGS), in cooperation with the Great Lakes Restoration Initiative, collected data to study the sources and occurrences of continual high E. coli detections at urban beaches along the Lake Michigan shoreline in Northwest Indiana and northeastern Illinois. High E. coli detections cause the beaches to be closed for recreational use until results from additional samples verify that E. coli levels have fallen below the threshold of 235 cells per 100 ml. The project used microbial source tracking (MST) and metagenomics analyses to identify the sources of E. coli. Additionally, continuous water quality parameters and surface-water samples were collected to look at biological and environmental indicators. Synoptic surveys of water quality, circulation/transport, and bathymetry were done to help study surface-water flow patterns. Groundwater samples were taken to compare with surface-water E. coli results. Groundwater wells were installed at Jeorse Park Beach in 2017 and additional wells were installed at Whihala West beach in late 2017 and early 2018. This data release contains three files. One file, entitled "metagenomics_sample_identification.txt,” contains a list of each sample, along with the site identifier (site ID), station name, replicate number, date of sampling, and substrate from which the sample was taken. The next file, entitled “metagenomics_taxonomy.txt,” contains a taxonomic classification of the 16S rRNA sequences obtained from every sample. The third file, contains metadata regarding the collection and analysis of the samples. Reference: Bouchet, Valerie, Huot, Heather, and Goldstein, Richard, 2008, Molecular genetic basis of ribotyping: Clinical Microbiology Reviews, 21(2), 262-273, https://doi.org/10.1128/cmr.00026-07.

    Access & Use Information

    License: No license information was provided.

    Downloads & Resources


    Metadata Date August 27, 2020
    Metadata Created Date March 22, 2021
    Metadata Updated Date March 22, 2021
    Reference Date(s) January 1, 2019 (publication)
    Frequency Of Update notPlanned

    Metadata Source

    Harvested from USGS-Harvest

    Additional Metadata

    Resource Type Dataset
    Metadata Date August 27, 2020
    Metadata Created Date March 22, 2021
    Metadata Updated Date March 22, 2021
    Reference Date(s) January 1, 2019 (publication)
    Responsible Party U.S. Geological Survey, Ohio-Kentucky-Indiana Water Science Center (Point of Contact)
    Contact Email
    Access Constraints Use Constraints: Although there are no restrictions or legal prerequisites for using the data, users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations., Access Constraints: None, however, acknowledgement of the U.S. Geological Survey would be appreciated in products derived from these data.
    Bbox East Long -87.390189170837
    Bbox North Lat 41.821069149796
    Bbox South Lat 41.625297877782
    Bbox West Long -87.605109214783
    Coupled Resource
    Frequency Of Update notPlanned
    Licence Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this information product, for the most part, is in the public domain, it may also contain copyrighted materials as noted in the text. Permission to reproduce copyrighted items must be secured from the copyright owner whenever applicable. The data have been approved for release and publication by the U.S. Geological Survey (USGS). Although the data have been subjected to rigorous review and are substantially complete, the USGS reserves the right to revise the data pursuant to further analysis and review. Furthermore, the data are released on the condition that neither the USGS nor the U.S. Government may be held liable for any damages resulting from authorized or unauthorized use. Although the 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 or the U.S. Government shall not be held liable for improper or incorrect use of the data described and/or contained herein. Users of this data are advised to read all metadata and associated documentation thoroughly to understand appropriate use and data limitations.
    Metadata Language eng; USA
    Metadata Type geospatial
    Progress completed
    Spatial Data Service Type
    Spatial Reference System
    Spatial Harvester True
    Temporal Extent Begin 2017-08-21
    Temporal Extent End 2017-09-25

    Didn't find what you're looking for? Suggest a dataset here.