Cold-water coral microbiomes (Lophelia pertusa) from 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 microbiomes (Lophelia pertusa) from Gulf of Mexico and Atlantic Ocean: raw data
Abstract:
The files in this data release are the raw deoxyribonucleic acid (DNA) sequence files referenced in the submitted journal article by Christina A. Kellogg, Dawn B. Goldsmith and Michael A. Gray entitled "Biogeographic comparison of Lophelia-associated bacterial communities in the western Atlantic reveals conserved core microbiome". They represent a 16S ribosomal ribonucleic acid (rRNA) gene amplicon survey of the coral’s microbiomes completed using Roche 454 pyrosequencing with Titanium series reagents. Samples from the Gulf of Mexico were collected in 2009 and 2010. Samples from the Atlantic Ocean were collected in 2009. The raw data files associated with this study have also been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under Bioproject number PRJNA305617. Minimum information about a marker gene (MIMARKS) compliant metadata is provided in "Lophelia metadata", which is included in the data download file. For more information, please contact Christina Kellogg at the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center, 600 4th Street South, St. Petersburg, Florida, USA, 33701; Telephone: (727) 502-8128; email: ckellogg@usgs.gov.
  1. How might this data set be cited?
    Kellogg, Christina A., and Goldsmith, Dawn B., 20170321, Cold-water coral microbiomes (Lophelia pertusa) from 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: 88.379637
    East_Bounding_Coordinate: 79.61613
    North_Bounding_Coordinate: 29.17027
    South_Bounding_Coordinate: 26.197992
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 2009
    Ending_Date: 2010
    Currentness_Reference:
    ground condition
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: SFF files, QUAL files, and FNA files (FASTA files)
  6. How does the data set represent geographic features?
    1. How are geographic features stored in the data set?
      This is a Point 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.txt, for detailed descriptions of the contents of the Lophelia raw data file. Additional information is contained in the MIMARKS metadata file, Lophelia_metadata.txt, which is included in the Lophelia_raw_data.zip 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)
    • Christina A. Kellogg
    • Dawn B. Goldsmith
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
    Christina A. Kellogg
    U.S. Geological Survey
    600 4th Street S
    St. Petersburg, FL
    USA

    727-502-8128 (voice)
    ckellogg@usgs.gov

Why was the data set created?

Over the last decade, publications on deep-sea corals have tripled. Most attention has been paid to Lophelia pertusa, a globally distributed scleractinian coral that creates critical three-dimensional habitat in the deep ocean. The bacterial community associated with L. pertusa has been previously described by a number of studies at sites in the Mediterranean Sea, Norwegian fjords, off the shore of Great Britain, and in the Gulf of Mexico (GOM); however, use of different methodologies prevents direct comparisons in most cases. The study objectives were to address intra-regional variation and to identify any conserved bacterial core community.

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 6)
    Three biological replicates (individual colonies of L. pertusa) were sampled at four sites: Viosca Knoll 906 (VK906), Viosca Knoll 826 (VK826), West Florida Slope 1 (WFS1), and Atlantic 1 (ATL1). 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, placed into the containers after ambient seawater evacuated the freshwater, and the containers were re-sealed at depth. Samples with names beginning with ROV00 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 -20º C for long-term storage.
    Date: 30-Jan-2012 (process 2 of 6)
    Two polyps from each coral sample (taken from the middle or tip of the branch to avoid any potential contamination at the base where the sampling claw was in contact with the coral) were combined to homogenize the variability of the bacterial community that may exist between polyps. The calyces containing polyps of L. pertusa were broken from the main branch with sterile pliers and placed into sterile aluminum dishes. The calyces were cracked open with a sterile hammer and the tissue was removed from the skeleton using an airbrush with sterile phosphate buffered saline (PBS) and sterile forceps, taking care to minimize dilution of the sample with the PBS. While mainly tissue, the samples may have entrained some coral mucus, since no specific effort was made to exclude it. DNA was extracted from the samples using the MOBIO PowerPlant DNA Isolation Kit following the suggested modifications in Sunagawa et al. (2010). Briefly, approximately 50 mg aliquots of the tissue slurry from each sample were processed with the addition of a lysozyme step and additional, smaller beads to expedite physical lysis. Three extractions were done per coral sample (for a total of 36 extractions) and then recombined by sample after elution of the DNA from the spin column (resulting in 12 DNA samples, one per coral). The DNA samples were quantified with a Thermo Fisher Scientific Quanti-iT PicoGreen dsDNA Assay Kit, per the manufacturer’s protocol.
    Date: 28-Feb-2012 (process 3 of 6)
    DNA samples were amplified with primers targeting the V4-V5 hypervariable region (563F/926R) of the 16S rRNA gene: forward primer (5′ AYTGGGYDTAAAGNG) and reverse primer (5′ CCGTCAATTYYTTTRAGTTT). The forward primer was tagged with one of four multiplex (MID) tags so the samples could be combined for sequencing on three plates. Amplification, pooling and 454 sequencing using GS FLX Titanium chemistry were performed by EnGenCore LLC. Sequence data from all samples were deposited in the NCBI SRA under Bioproject number PRJNA305617.
    Date: 15-Aug-2015 (process 4 of 6)
    Sequence data were analyzed using the bioinformatic package Quantitative Insights Into Microbial Ecology (QIIME) version 1.8 (Caporaso et al., 2010, Nature Methods 7:335-336, doi:10.1038/nmeth.f.303). Please refer to the file entitled "Lophelia_workflow_2016_10_19.txt," which is included as a supplemental file and details the scripts run in QIIME. The workflow file contains the default or chosen settings used for each script, as well as the names of the input/output files associated with each script.
    Date: 28-Mar-2018 (process 5 of 6)
    Keywords section of metadata optimized by correcting variations of theme keyword thesauri and updating/adding keywords. Person who carried out this activity:
    U.S. Geological Survey
    Attn: Arnell S. Forde
    Geologist
    600 4th Street South
    St. Petersburg, FL

    727-502-8000 (voice)
    aforde@usgs.gov
    Date: 13-Oct-2020 (process 6 of 6)
    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?
    Kellogg, Christina A., Goldsmith, Dawn B., and Gray, Michael A., 20170504, Biogeographic Comparison of Lophelia-Associated Bacterial Communities in the Western Atlantic Reveals Conserved Core Microbiome: Frontiers in Microbiology, Lausanne, Switzerland.

    Kellogg, Christina A., 20190610, Microbiomes of stony and soft deep-sea corals share rare core bacteria: Microbiome Volume 7, Issue 1, BMC, Springer Nature, London, United Kingdom.

    Online Links:

    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..

    Sunagawa, Shinichi, Woodley, Cheryl M., and Medina, Monica, 201003, Threatened Corals Provide Underexplored Microbial Habitats: PLoS One, San Francisco, CA.

    J. Gregory Caporaso et al., 20100501, QIIME allows analysis of high-throughput community sequencing data: Nature Methods, New York, NY.

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?
    Dataset is 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.
  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)
    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?
    Although these data have been processed successfully on a computer system at 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. 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.
  4. How can I download or order the data?
    • Availability in digital form:
      Data format: The text files included in this release contain additional data details and information associated with the bioinformatic analysis. The workflow file details the scripts run in the bioinformatic package QIIME (Caporaso et al., 2010, Nature Methods 7:335-336, doi:10.1038/nmeth.f.303), default or chosen settings used for each script, and the names of the input/output files associated with each script. in format ASCII (version None) Text file
      Network links: https://coastal.er.usgs.gov/data-release/doi-F7M32SXM/data/Lophelia_raw_data.zip
    • Cost to order the data: None

  5. What hardware or software do I need in order to use the data set?
    SFF files, QUAL files, and FNA files (FASTA files) can be read by QIIME and mothur (https://www.mothur.org/), both of which are free software. FASTA files can also be read by text editors.

Who wrote the metadata?

Dates:
Last modified: 13-Oct-2020
Metadata author:
Christina A. Kellogg
U.S. Geological Survey
Environmental Microbiologist
600 4th Street S
St. Petersburg, FL
USA

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/Cold_water_coral_microbiomes_Lophelia_pertusa_from_Gulf_of_Mexico_and_Atlantic_Ocean_raw_data.faq.html>
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