Cold-water coral microbiomes (Acanthogorgia spp. Desmophyllum dianthus, and Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean off the southeast coast of the United States: raw sequencing data

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Frequently anticipated questions:

What does this data set describe?

Title:
Cold-water coral microbiomes (Acanthogorgia spp. Desmophyllum dianthus, and Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean off the southeast coast of the United States: raw sequencing data
Abstract:
The files provided in this U.S. Geological Survey (USGS) data release (Kellogg and Voelschow, 2021) are the raw DNA sequence files referenced in the associated journal article (Kellogg and Pratte, 2021) entitled, “Unexpected diversity of Endozoicomonas in deep-sea corals.”. This dataset, PRJNA699458_16S-V3V4_raw_data_1.zip, represents the 16S rRNA gene amplicon surveys of 28 samples of deep-sea corals, including Acanthogorgia aspera (n=5), Acanthogorgia spissa (n=4), Desmophyllum dianthus (n=7), and Lophelia pertusa [Desmophyllum pertusum] (n=12), plus a kit extraction control blank. The sequencing targeted the V3-V4 variable region (primers 341F/806R) and was completed using an Illumina MiSeq sequencing system with version 2 chemistry to obtain paired-end reads.
  1. How might this data set be cited?
    Kellogg, Christina A., and Voelschow, Julie J., 20210830, Cold-water coral microbiomes (Acanthogorgia spp. Desmophyllum dianthus, and Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean off the southeast coast of the United States: raw sequencing data:.

    This is part of the following larger work.

    Kellogg, Christina A., and Voelschow, Julie J., 20210830, Cold-water Coral Microbiomes (Acanthogorgia spp., Desmophyllum dianthus, and Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean off the Southeast Coast of the United States—Raw Data: U.S. Geological Survey Data Release doi:10.5066/P9Z1HPKR, U.S. Geological Survey, St. Petersburg, FL.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -84.72679
    East_Bounding_Coordinate: -74.51234
    North_Bounding_Coordinate: 37.05002
    South_Bounding_Coordinate: 26.20576
    Description_of_Geographic_Extent: Gulf of Mexico and Atlantic Ocean
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 11-May-2013
    Ending_Date: 25-Apr-2019
    Currentness_Reference:
    ground condition
  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_PRJNA699458.txt, for detailed descriptions of the contents of the raw data files. Additional information is contained in the minimum information about a marker sequence (MIMARKS) compliant metadata, PRJNA699458_MIMARKS.xlsx, which is included in the data download files.
    Entity_and_Attribute_Detail_Citation:
    The entity and attribute information were 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
    • Julie J. Voelschow
  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 South
    St. Petersburg, FL

    (727)-502-8128 (voice)

Why was the data set created?

During four research cruises conducted from 2013 to 2019, deep-sea coral samples were collected from various locations (nine sample sites, in total) in the Gulf of Mexico and Atlantic Ocean off the east coast of the United States for microbial analysis. Sample DNA extraction occurred at the USGS Coral Microbial Ecology Laboratory in St. Petersburg, Florida while polymerase chain reaction (PCR) amplification and sequencing were performed by RTSF Genomics Core at Michigan State University in East Lansing, Michigan. The 56 raw metagenomic data files associated with this data release have also been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under BioProject number PRJNA699458.

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: 25-Apr-2019 (process 1 of 3)
    Sample collection and preservation: Samples from Norfolk Canyon were collected in 2013 on the National Oceanic and Atmospheric Administration (NOAA) ship Ronald H. Brown using the remotely operated vehicle (ROV) Jason II (research cruise RB-13-03-HBH Deepwater Canyons). The samples acquired from west Florida sites Many Mounds and Okeanos Ridge were collected in 2017 on the NOAA ship Nancy Foster using the ROV Odysseus (NF1708 Southeast Florida Deep Coral Initiative). The 2018 and 2019 collections were part of NOAA's DeepSEARCH program and were conducted on the R/V Atlantis using the human occupied vehicle (HOV) Alvin (AT41) and the NOAA ship Ronald H. Brown using the ROV Jason II (RB1903), respectively. Subsamples of coral colonies were collected using the respective vehicle’s manipulator arm to remove a branch (or in the case of D. dianthus, the entire cup coral). Samples were placed into individual, thermally-insulated containers that had been precleaned (washed with freshwater, interiors wiped with 100% ethanol to remove any biofilms or particulates from prior collections), filled with freshwater, and sent down sealed. When opened to receive a coral collection, the freshwater was replaced by seawater local to the collection site due to density differences. The containers were then sealed at depth to prevent microbial contamination from other sample collections or passing through different water masses during vehicle recovery. At the conclusion of the dive, containers were brought aboard their respective vessel and into a cold room or laboratory and samples were removed using ethanol-sterilized forceps. All corals were lightly rinsed with sterile 1xPBS (phosphate-buffered saline) to remove any loosely associated surface microbes. For octocorals (A. aspera, A. spissa), branches that had not been in contact with the manipulator claw were cut off using ethanol-sterilized shears and transferred to sterile tubes. For the stony corals (D. dianthus, L. pertusa), samples were placed into sterile aluminum weigh boats and a flame-sterilized hammer was used to break open the calyces to expose polyp tissue, which was transferred to sterile tubes. All samples were preserved with RNAlater, stored for 24 hours at 4°C to allow the preservative to infiltrate the tissues, and then moved to -20 °C until processing. Subsamples of the corals collected for microbial analyses were shared with researchers conducting population genetics/taxonomy studies, allowing for accurate host identification of octocorals and the possibility of interpreting microbiome trends against coral genotypes.
    Date: 31-Jul-2019 (process 2 of 3)
    DNA extraction: The DNA extraction process was performed on July 30th and July 312st, 2019, at the USGS Coral Microbial Ecology Laboratory. Just prior to extraction, coral samples were rinsed with 0.2 µm-filtered and autoclaved 1xPBS to remove RNAlater. Coral pieces were placed into sterile microcentrifuge tubes using flame-sterilized forceps, 2 ml of the sterile 1xPBS was added to the tube, which was then inverted 3 times and then centrifuged at 4 000 xg for 30 sec. The coral samples were then weighed using sterile technique and approximately 0.1–0.2 g per sample were used for extraction. Extractions were done in duplicate for each coral using Qiagen’s DNeasy PowerBiofilm kits (QIAGEN, 2020; catalog number 24000-50) and replicates were combined at the end. The manufacturer’s protocol was followed with the exception that a FastPrep was used on setting 5 (~3100 rpm) for homogenization in place of a PowerLyzer. Kit blank (extractions with no sample added) were processed at the same time as the samples. DNA was quantified using a Qubit, extractions diluted to approximately 30 ng/µl, and submitted for sequencing.
    Date: 09-Nov-2020 (process 3 of 3)
    Sequencing: PCR amplification and sequencing were performed by Michigan State University Genomics Core. The V3-V4 regions of the 16S rRNA gene were amplified with the primers 341F (CCTACGGGAGGCAGCAG) and 806R (GGACTACHVGGGTWTCTAAT). One µl of genomic DNA was added to 7.5 µl of 2x Dream Taq Master Mix and 6.4 µl of a 0.5 µM primer mix. Amplification conditions were an initial melting period of 2 minutes at 95°C, followed by 30 cycles of 95°C for 40 seconds, 50°C for 30 seconds, and 72°C for 60 seconds, and a final anneal step at 72°C for 7 minutes. After PCR the output of all reactions was batch normalized using an Invitrogen SequalPrep DNA Normalization Plate, and all material recovered from the plate was pooled. The pooled material was cleaned up and concentrated using AmpureXP magnetic beads. The pool was quality controlled and quantified using a combination of Qubit dsDNA HS, Agilent 4200 TapeStation HS DNA1000 and Kapa Illumina Library Quantification qPCR assays. This pool was loaded onto an Illumina MiSeq v2 Standard flow cell and sequencing was carried out in a 2x250bp paired end format using a MiSeq v2 500 cycle reagent cartridge. Custom sequencing and index primers complementary to the 341F/806R sequences used for preparing the libraries were added to appropriate wells of the reagent cartridge. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.54 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.19.1.
  3. What similar or related data should the user be aware of?
    QIAGEN, 20200131, DNEasy PowerBiofilm Kit Handbook.

    Online Links:

    Kellogg, Christina A., and Pratt, Zoe A., 20210902, Unexpected diversity of Endozoicomonas in deep-sea corals.

    Online Links:

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.
  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. Please see 'Distribution Info' for details.
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
    St. Petersburg Coastal and Marine Science Center
    600 4th Street South
    St. Petersburg, FL
    United States

    (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 A. Kellogg
St. Petersburg Coastal and Marine Science Center
600 4th Street South
St. Petersburg, FL

(727) 502-8128 (voice)
ckellogg@usgs.gov
Metadata standard:
FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata (FGDC-STD-001.1-1999)
This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/PRJNA699458_FGDC_metadata.faq.html>
Generated by mp version 2.9.50 on Tue Nov 9 16:47:42 2021