Coral microbiome preservation and extraction method comparison of samples collected in March and August 2018-raw data

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Frequently anticipated questions:

What does this data set describe?

Title:
Coral microbiome preservation and extraction method comparison of samples collected in March and August 2018-raw data
Abstract:
The files in this this U.S. Geological Survey (USGS) data release (Kellogg and others, 2021) are the raw 16S ribosomal ribonucleic acid (rRNA) gene amplicon deoxyribonucleic acid (DNA) sequence files from 90 samples of tropical and cold-water corals, as well as sequence files from a mock community and extraction blanks for the kits used for DNA extraction. The mock community was sequenced in order to assess any biases in the sequencing technology, while extraction blanks were sequenced in order to identify any contaminants in the DNA extraction kits. The tropical coral samples (three species) were collected by permit (#FKNMS-2017-064) in March 2018 from a nursery in the Florida Keys National Marine Sanctuary. The cold-water coral samples (two species) were collected in August 2018 from two locations in the Atlantic Ocean.
Supplemental_Information:
Sequencing data were extracted from samples via the PowerBiofilm DNA Isolation Kit owned by MO BIO Laboratories, Inc. MO BIO Laboratories was purchased by the molecular diagnostics company, Qiagen, which resulted in the sequencing kit being renamed to the Qiagen DNEasy PowerBiofilm DNA Isolation Kit. Data files included in Methods_comparison_Qiagen_raw_data.zip reflect this name change, however, the metadata processing steps refer to the original kit name because it was still applicable during data processing. The 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 PRJNA544686. For additional details and interpretations, please see Pratte and Kellogg (2021).
  1. How might this data set be cited?
    Kellogg, Christina A., Goldsmith, Dawn B., and Voelschow, Julie J., 20210629, Coral microbiome preservation and extraction method comparison of samples collected in March and August 2018-raw data:.

    This is part of the following larger work.

    Kellogg, Christina A., Goldsmith, Dawn B., and Voelschow, Julie J., 20210629, Coral microbiome preservation and extraction method comparison of samples collected in March and August 2018-raw data: U.S. Geological Survey Data Release doi:10.5066/P96GBWDM, U.S. Geological Survey, St. Petersburg, FL.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -81.45441
    East_Bounding_Coordinate: -75.16639
    North_Bounding_Coordinate: 34.9410185
    South_Bounding_Coordinate: 24.661751
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 27-Mar-2018
    Ending_Date: 30-Aug-2018
    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_Methods_Comp.txt, for detailed descriptions of the contents of the raw data files. Additional information is contained in the minimum information about a marker gene sequence (MIMARKS) compliant metadata, Methods_Comp_MIMARKS_compliant_metadata.csv, which is included in each data download folder.
    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
    • Dawn B. Goldsmith
    • 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?

The purpose of this experiment was to compare preservation and DNA extraction methods across tropical and cold-water corals.

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: 27-Mar-2018 (process 1 of 4)
    All tropical coral samples (Montastraea cavernosa, Porites astreoides, and Stephanocoenia intersepta) were collected manually by permit in March 2018 from a nursery in the Florida Keys National Marine Sanctuary, temporarily housed at the facility of Mote Marine Laboratory & Aquarium’s Elizabeth Moore International Center for Coral Reef Research & Restoration in Summerland Key, Florida. Samples beginning with MCR, PAR, and SIR were transferred to sterile tubes, covered in RNAlater, and incubated overnight at 4°C to allow the preservative to permeate the coral tissues before transfer to -20°C for long-term storage. Samples beginning with MCS, PAS, and SIS were transferred to sterile tubes, covered in DNA/RNA Shield, and incubated overnight at 4°C to allow the preservative to permeate the coral tissues before transfer to -20°C for long-term storage. Samples beginning with MCN, PAN, and SIN were double-bagged in sterile Whirl-Pak bags (Nasco, Fort Atkinson, WI, USA) and then stored in liquid nitrogen until transfer to -80°C for long-term storage. Person who carried out this activity:
    Christina A Kellogg
    U.S. Geological Survey, Southeast Region
    Research Microbiologist
    600 4Th Street South
    St. Petersburg, FL
    United States

    727-502-8128 (voice)
    727-502-8181 (FAX)
    ckellogg@usgs.gov
    Date: 24-Aug-2018 (process 2 of 4)
    All cold-water coral samples (Lophelia pertusa and Paragorgia johnsoni) were collected by the sampling arm of a crewed submersible. 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 LP and PJ were collected in August 2018 on cruise AT-41 on the R/V Atlantis using the Alvin submersible (Woods Hole Oceanographic Institution). Samples with names beginning with LP were collected from Richardson Hills on dive A4963, while samples with names beginning with PJ were collected from Pamlico Canyon on dive A4969. Upon return to the surface, samples beginning with LPR, PJR, LPS, and PJS were transferred to sterile tubes, covered in preservative, and incubated overnight at 4°C to allow the preservative to permeate the coral tissues before transfer to -20°C for long-term storage. The preservative used for samples LPR and PJR was RNAlater (Life Technologies, Grand Island, NY, USA), while the preservative used for samples LPS and PJS was DNA/RNA Shield (Zymo Research, Irvine, CA, USA). Samples beginning with LPN and PJN were transferred to sterile tubes and then stored in liquid nitrogen until transfer to -80°C for long-term storage. Person who carried out this activity:
    Christina A Kellogg
    U.S. Geological Survey, Southeast Region
    Research Microbiologist
    600 4Th Street South
    St. Petersburg, FL
    United States

    727-502-8128 (voice)
    727-502-8181 (FAX)
    ckellogg@usgs.gov
    Date: 28-Nov-2018 (process 3 of 4)
    Homogenization of cells and extraction of DNA from the samples occurred at the Coral Microbial Ecology Laboratory in St. Petersburg, FL. All samples were wrapped in sterile aluminum foil and crushed with a hammer. For samples ending in numbers 1, 2, and 3, cells were disrupted by adding the crushed samples and 300 microliters of molecular grade water to Lysing Matrix A and homogenizing them for 20 seconds in a FastPrep bead mill homogenizer at setting 6.5 (MP Biomedicals, Santa Ana, CA). DNA was extracted from those samples using the Maxwell RSC Blood DNA Kit with a Maxwell RSC Instrument (model AS4500) (Promega, Fitchburg, WI). DNA Lysis Buffer (300 microliters) and Proteinase K (25 microliters) from the kit were added to each sample. Samples were mixed by inversion three times, incubated for one hour in a 56°C, mixed again by inversion three times, and centrifuged at 2500 rpm for 30 seconds. The supernatant of each sample was transferred to a front well of the cartridge in the Maxwell RSC Instrument. Sections 3B and 5 of the manufacturer’s protocol (Promega, 2018) were then followed to complete the DNA extraction. DNA was extracted from samples ending in numbers 4, 5, and 6 using the Qiagen PowerBiofilm DNA Isolation Kit according to the manufacturer’s instructions (Qiagen, 2015) with two modifications to adapt the protocol to the samples. Bead beating (Step 5 of the homogenization section of the protocol) was accomplished using a FastPrep homogenizer for 30 seconds at setting 5. Step 3 of the vacuum section of the protocol was conducted by centrifuging the samples for 1 minute at 13000xg. Two extraction blanks for each method were also prepared: one substituted phosphate-buffered saline solution for the sample and the other substituted nuclease-free water for the sample. Person who carried out this activity:
    Christina A Kellogg
    U.S. Geological Survey, Southeast Region
    Research Microbiologist
    600 4th Street South
    St. Petersburg, FL
    United States

    727-502-8128 (voice)
    727-502-8181 (FAX)
    ckellogg@usgs.gov
    Date: 18-Mar-2019 (process 4 of 4)
    Library preparation and sequencing were conducted by Glomics, Inc. (Norman, OK). To target the V4 region of the 16S rRNA gene, a fusion primer set was constructed using primers 515F (5′ GTGCCAGCMGCCGCGGTAA) and 806RB (5′ GGACTACNVGGGTWTCTAAT) (Apprill and others, 2015) along with adapters, indices, linkers, and pads in accordance with the dual-index sequencing strategy of Kozich and others (2013). Amplicons were purified, quantified, and pooled in equal concentrations for sequencing on a MiSeq sequencing system with v2 chemistry to obtain paired-end 250-bp reads. A mock community was also sequenced in order to assess any biases in the sequencing technology. The raw data files associated with this data release have also been submitted to the NCBI Sequence Read Archive (SRA) under Bioproject number PRJNA544686.
  3. What similar or related data should the user be aware of?
    Pratte, Zoe A., and Kellogg, Christina A., 2021, Comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes: Frontiers in Marine Science 8:684161.

    Online Links:

    Kozich, James J., Westcott, Sarah L., Baxter, Nielson T., Highlander, Sarah K., and Schloss, Patrick D., 20130807, Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform: Applied and Environmental Microbiology vol. 79, issue 17, American Society for Microbiology, Washington, D.C..

    Online Links:

    Other_Citation_Details: ppg. 5112-5120
    Apprill, Amy, McNally, Sean, Parsons, Rachel, and Weber, Laura, 20150604, Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton: Aquatic Microbial Ecology vol. 75, issue 2, Inter-Research Science Center, n/a.

    Online Links:

    Other_Citation_Details: ppg. 129-137
    Promega, 20180401, Maxwell RSC Blood DNA Kit.

    Online Links:

    Qiagen, 20151117, DNEasy PowerBiofilm Kit Handbook.

    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?
    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. 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. 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
    U.S. Geological Survey
    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: 23-Sep-2021
Metadata author:
Christina A. Kellogg
U.S. Geological Survey
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/coral_microbiome_methods_comp_FGDC_metadata.faq.html>
Generated by mp version 2.9.50 on Thu Sep 23 11:18:09 2021