Cold-water coral metagenomes (Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean: raw data

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Frequently anticipated questions:

What does this data set describe?

Title:
Cold-water coral metagenomes (Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean: raw data
Abstract:
In 2009, three unique colonies of the cold-water coral Lophelia pertusa were sampled in the western Atlantic Ocean to examine their microbial metagenomes. Nine additional samples were collected from three sites (Viosca Knoll 826, Viosca Knoll 906, and West Florida Slope) around the Gulf of Mexico in 2009 and 2010. Previous studies have examined the bacterial associates of this coral, but to date, no cold-water coral metagenomes have been published. This analysis characterized and identified microbial associates (bacteria, archaea, eukaryotes, viruses) associated with Lophelia, and also provided a first look at the functional and metabolic capabilities of the Lophelia microbial metagenome. Replicate sampling allowed for supplemental analysis of the variation in metagenomes between individual coral samples and among the four collection sites.
  1. How might this data set be cited?
    Goldsmith, Dawn B., and Kellogg, Christina A., 20181108, Cold-water coral metagenomes (Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean: raw data: U.S. Geological Survey, St. Petersburg, FL.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -88.380533
    East_Bounding_Coordinate: -79.615905
    North_Bounding_Coordinate: 29.17027
    South_Bounding_Coordinate: 26.19785
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 09-Aug-2009
    Ending_Date: 30-Sep-2010
    Currentness_Reference:
    observed
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: FASTQ and tabular digital data
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
    2. What coordinate system is used to represent geographic features?
  7. How does the data set describe geographic features?
    Entity_and_Attribute_Overview:
    Please refer to the "README" file, README_Lophelia_metagenomes.txt, for detailed descriptions of the contents of the raw data file. Additional information is contained in the Minimum Information about a Metagenome Sequence (MIMS) compliant metadata, Lophelia_metagenomes_MIMS_compliant_metadata, which is included in each data download file.
    Entity_and_Attribute_Detail_Citation:
    The entity and attribute information was generated by the individual and/or agency identified as the originator of the dataset. Please review the rest of the metadata record for additional details and information.

Who produced the data set?

  1. Who are the originators of the data set? (may include formal authors, digital compilers, and editors)
    • Dawn B. Goldsmith
    • Christina A. Kellogg
  2. Who also contributed to the data set?
    U.S. Geological Survey, Coastal and Marine Geology Program, St. Petersburg Coastal and Marine Science Center
  3. To whom should users address questions about the data?
    Christina Kellogg
    St. Petersburg Coastal and Marine Science Center
    600 4th Street South
    St. Petersburg, FL

    (727) 502-8128 (voice)

Why was the data set created?

The data were collected in order to examine the microbial associates of the cold-water coral Lophelia pertusa.

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: 30-Sep-2010 (process 1 of 4)
    Branches of L. pertusa coral samples were collected from four study sites between August 2009 and September 2010. Samples acquired during cruises in August and September 2009 with names prefixed by 3705 or 3731 were collected by the Johnson-Sea-Link submersible (Harbor Branch Oceanographic Institution), using the Kellogg sampler (Kellogg et al., 2009). The sampler’s individual compartments were cleaned at the surface using ethanol, filled with sterile deionized water and sealed. Coral branches were collected and placed into the containers after ambient seawater evacuated the freshwater, and the containers were re-sealed at depth. Samples with names beginning with ROV were collected using the remotely-operated vehicle (ROV) Kraken II (University of Connecticut) during a research cruise in September 2010. The ROV carried several individual polyvinylchloride quivers that were cleaned with ethanol, filled with sterile deionized water and sealed at the surface with rubber stoppers. Immediately prior to collection, a quiver was opened, the sample placed inside, and the quiver sealed before the ROV continued its deployment. Upon return to the surface, all L. pertusa samples were transferred to sterile tubes, covered in Thermo Fisher Scientific's RNAlater Stabilization Solution and incubated overnight at 4 degrees Celsius (ºC) to allow the preservative to permeate the coral tissues before transfer to -20ºC. Subsequent processing occurred at the Environmental Microbiology Laboratory in St. Petersburg, FL.
    Date: 30-Jan-2012 (process 2 of 4)
    Microbial deoxyribonucleic acid (DNA) was extracted following the specialized protocol developed for this coral (https://coastal.er.usgs.gov/coral-microbes/discovre/lophelia-extraction.html). In short, the coral's calcium carbonate skeleton was cracked open using a sterile mortar and pestle. The mucus and tissue were airbrushed away from the skeleton using a sterile buffer. The slurry was sheared by repeated passage through a syringe, then centrifuged to remove larger clumps of tissue. A Percoll cushion was used to separate the coral cells from the microbial cells. The microbial fraction was filtered onto a 0.22 μm Sterivex cartridge and the microbial assemblage DNA was extracted from that filter using a Qiagen DNeasy Blood and Tissue kit following the manufacturer's protocol for Gram-positive bacteria but with reagent volumes doubled in the initial steps.
    Date: 31-Mar-2013 (process 3 of 4)
    The shotgun metagenome (untargeted sequencing of all genomes present in a sample) dataset was produced by random shearing of the DNA, construction of a TruSeq library, and sequencing on an Illumina HiSeq 2000 sequencing system by Argonne National Laboratory. Raw sequence data from all metagenome samples are available from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under Bioproject number PRJNA471489.
    Date: 13-Oct-2020 (process 4 of 4)
    Added keywords section with USGS persistent identifier as theme keyword. Person who carried out this activity:
    U.S. Geological Survey
    Attn: VeeAnn A. Cross
    Marine Geologist
    384 Woods Hole Road
    Woods Hole, MA

    508-548-8700 x2251 (voice)
    508-457-2310 (FAX)
    vatnipp@usgs.gov
  3. What similar or related data should the user be aware of?
    Prouty, Nancy G., Kellogg, Christina A., and Morrison, Cheryl L., unknown, Multidisciplinary Assessment of Deep-Water Coral Ecosystems: Tools to Detect Impacts of Sub-lethal Stress. Final Technical Report.: U.S. Department of the Interior, Bureau of Ocean Energy Management, Gulf of Mexico OCS Region, Sterling, Virginia.

    Other_Citation_Details: OCS Study BOEM 2018-xxx, 132 p.
    Kellogg, Christina A., Lisle, John T., and Galkiewicz, Julia P., 20090220, Culture-Independent Characterization of Bacterial Communities Associated with the Cold-Water Coral Lophelia pertusa in the Northeastern Gulf of Mexico: Applied and Environmental Microbiology, Washington, D.C..

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?
  3. How accurate are the heights or depths?
  4. Where are the gaps in the data? What is missing?
    Dataset is considered complete for the information presented, as described in the abstract, except as follows. The information for every sample except sample CK8 is accompanied (in a .csv file) by information about the sequencing run: the flow cell ID, the lane of the plate on which the sample was sequenced, the index used for demultiplexing the samples, and the name of the operator at the sequencing facility who performed the sequencing. The sequencing facility did not produce this information for sample CK8. Users are advised to read the rest of the metadata record carefully for additional details.
  5. How consistent are the relationships among the observations, including topology?
    No formal logical consistency 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)
    Christina A. Kellogg
    U.S. Geological Survey
    600 4th Street S
    St. Petersburg, FL
    USA

    727-502-8128 (voice)
    ckellogg@usgs.gov
  2. What's the catalog number I need to order this data set?
  3. What legal disclaimers am I supposed to read?
    Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), 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.
  4. How can I download or order the data?

Who wrote the metadata?

Dates:
Last modified: 09-Nov-2021
Metadata author:
Christina Kellogg
St. Petersburg Coastal and Marine Science Center
600 4th Street South
St. Petersburg, FL

(727) 502-8128 (voice)
ckellogg@usgs.gov
Metadata standard:
Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)
This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Lophelia_metagenome_metadata.faq.html>
Generated by mp version 2.9.50 on Tue Nov 9 16:47:42 2021