Cold-water coral microbiomes (Astrangia poculata) from Narragansett Bay: sequence data

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Frequently anticipated questions:

What does this data set describe?

Title:
Cold-water coral microbiomes (Astrangia poculata) from Narragansett Bay: sequence data
Abstract:
The files provided in this data release are the DNA sequence files referenced in Goldsmith and others (2019), which represent a 16S ribosomal ribonucleic acid (rRNA) gene amplicon survey of Astrangia poculata microbiomes completed using Sanger dideoxy sequencing. The coral samples were collected from Narragansett Bay at Fort Wetherill State Park, Jamestown, Rhode Island in 2015 and 2016 (Sharp and others, 2017). Sequences were obtained by first extracting DNA from a fragment of each A. poculata sample comprising mucus, tissue, and skeleton. Bacterial DNA was amplified from all samples by polymerase chain reaction (PCR), using primers 8F (5’–AGA GTT TGA TCC TGG CTC AG) and 1492R (5’–GGT TAC CTT GTT ACG ACT T) to target the 16S rDNA gene in bacteria. Archaeal DNA from two of the samples (FW1B8 and FW1W8) was amplified using primers 21F (5'–TTC CGG TTG ATC CYG CCG GA) and 958R (5'–YCC GGC GTT GAM TCC AAT T) to target the 16S rDNA gene from archaea. All amplicons were visualized on an agarose gel, extracted from the gel, quantitated, cloned into a vector, and used to transform competent cells. Inserts in positive transformants were sequenced by the Clemson University Genomics Computational Laboratory (Clemson, SC). The sequences were processed by trimming vectors and ends, removing sequences less than 50 base pairs (bp), checking for chimeras, classifying taxonomy, and removing unclassified, chloroplast, and mitochondrial sequences. After processing, 806 bacterial operational taxonomic units (OTUs) and 18 archaeal OTUs remained. Sequences representing each OTU have been deposited in the National Center for Biotechnology Information’s (NCBI) GenBank archive, and have been assigned accession numbers MK175495 through MK176300 (bacterial sequences) and MH915525 through MH915542 (archaeal sequences). Minimum information about a marker gene (MIMARKS) compliant metadata files are also included in the data download files. 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?
    Goldsmith, Dawn B., and Kellogg, Christina A., 20190321, Cold-water coral microbiomes (Astrangia poculata) from Narragansett Bay: sequence data: U.S. Geological Survey Data Release doi:10.5066/P9C2XCQQ, U.S. Geological Survey, St. Petersburg, FL.

    Online Links:

    This is part of the following larger work.

    Goldsmith, Dawn B., Pratte, Zoe A., Kellogg, Christina A., Snader, Sara E., and Sharp, Koty H., 20190301, Stability of temperate coral Astrangia poculata microbiome is reflected across different sequencing methodologies: AIMS Microbiology 5(1): 62-76, AIMS Press, Springfield, MO.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -71.359444
    East_Bounding_Coordinate: -71.359443
    North_Bounding_Coordinate: 41.477778
    South_Bounding_Coordinate: 41.477777
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 09-Sep-2015
    Ending_Date: 26-Apr-2016
    Currentness_Reference:
    ground condition
  5. What is the general form of this data set?
    Geospatial_Data_Presentation_Form: FASTA 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_Astrangia.txt, for detailed descriptions of the contents of the data files. Additional information is contained in the Minimum Information about a Marker Gene (MIMARKS) compliant metadata files, entitled “Astrangia_MIMARKS_metadata_bacteria.xlsx”, “Astrangia_MIMARKS_metadata_bacteria.txt”, “Astrangia_MIMARKS_metadata_archaea.xlsx”, and “Astrangia_MIMARKS_metadata_archaea.txt”. Non-proprietary versions of the MIMARKS metadata are also provided in comma separated values (CSV) format and are included in the data download files.
    Entity_and_Attribute_Detail_Citation:
    The entity and attribute information was generated by the individuals 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 A. Kellogg
    U.S. Geological Survey
    600 4th Street South
    St. Petersburg, FL

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

Why was the data set created?

The microbiome of the temperate coral Astrangia poculata was first described in 2017 using next-generation Illumina sequencing to examine the coral’s bacterial and archaeal associates across seasons and among hosts of differing symbiotic status. Microbial communities did not significantly vary according to symbiotic state but did vary by season. The data in this study were obtained via Sanger sequencing in order to assess the impact of sequencing methodology on the detectable diversity of the coral’s microbiome. A second goal of this study was to create a resource for the research community by producing longer sequences that are better suited for the development of probes and primers.

How was the data set created?

  1. From what previous works were the data drawn?
    Sharp (source 1 of 1)
    Sharp, Koty H., Pratte, Zoe A., Kerwin, Allison H., Rotjan, Randi D., and Stewart, Frank J., 20170915, Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata: Microbiome Vol. 5, issue 1, BioMed Central, Springer Nature, London, United Kingdom.

    Online Links:

    Type_of_Source_Media: Digital and/or Hardcopy
    Source_Contribution:
    The samples used to generate the sequences in this dataset were collected as part of the study reported in Sharp and others (2017). In addition, the DNA that was sequenced for this study was extracted from the samples by Sharp and others (2017) as part of their study.
  2. How were the data generated, processed, and modified?
    Date: 15-Sep-2015 (process 1 of 9)
    Paired brown (symbiotic) and white (aposymbiotic) samples of A. poculata were collected as described in Sharp and others (2017). Briefly, samples were collected from Narragansett Bay in September 2015 and April 2016 by SCUBA at depths of 1-5 meters. Paired colonies were selected such that the brown and white members of the pair were no more than 10 centimeters apart. Samples were immediately brought to the surface, frozen in liquid nitrogen, and held at -80ºC until DNA extraction. Data sources used in this process:
    • Sharp
    Date: 2016 (process 2 of 9)
    Eight samples--two sets of paired brown and white colonies collected in the fall (September) and two sets collected in the spring (April) were analyzed by USGS scientists. DNA was extracted from each sample of A. poculata as described in Sharp and others (2017). Briefly, the PowerSoil DNA Isolation Kit (Qiagen, Valencia, CA) was used according to the manufacturer’s protocol to extract DNA from a fragment of each sample comprising mucus, tissue, and skeleton. Data sources used in this process:
    • Sharp
    Date: 2017 (process 3 of 9)
    Bacterial primers: DNA from each sample was amplified by PCR using primers 8F (5’–AGA GTT TGA TCC TGG CTC AG) and 1492R (5’–GGT TAC CTT GTT ACG ACT T) to target the 16S rRNA gene [9,10]. Each 25-microliter (µL) reaction contained 12.5 µL AmpliTaq Gold 360 Master Mix (Applied Biosystems, Foster City, CA), 0.4 µM concentration of each primer, and 10 µL of template DNA. The reaction conditions consisted of 15 minutes (min) of initial denaturation at 95ºC, 30 cycles of (i) 1 min denaturation at 95ºC, (ii) 1 min annealing at 54ºC, and (iii) 2 min extension at 72ºC, and 10 min of final extension at 72ºC. Amplicons were visualized on a 1.5% agarose gel, then extracted from the gel using the QIAquick Gel Extraction Kit (QIAGEN, Germantown, MD) according to the manufacturer’s instructions. Gel-extracted amplicons were quantitated using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) on a Qubit 3.0 fluorometer according to the manufacturer’s instructions.
    Date: 2017 (process 4 of 9)
    Archaeal primers: DNA from two of the samples (FW1B8 and FW1W8) was also amplified using primers 21F (5’–TTC CGG TTG ATC CYG CCG GA) and 958R (5’–YCC GGC GTT GAM TCC AAT T) in order to amplify the 16S rRNA gene from Archaea (DeLong, 1992). Each 25-µL reaction contained 12.5 µL AmpliTaq Gold 360 Master Mix (Applied Biosystems, Foster City, CA), 0.4 µM concentration of each primer, and 10 µL of template DNA. The reaction conditions consisted of 15 min of initial denaturation at 95ºC, 30 cycles of (i) 95ºC for1.5 min, (ii) 55ºC for 1.5 min, and (iii) 72ºC for 1.5 min, and 10 min of final extension at 72ºC (DeLong, 1992). Amplicons were visualized, extracted, and quantitated as described above for the bacterial amplicons.
    Date: 2017 (process 5 of 9)
    Amplicons were cloned into the pDrive vector using the PCR Cloning Plus kit (QIAGEN, Germantown, MD) and used to transform competent cells. After M13 screening, inserts in positive transformants were sequenced by the Clemson University Genomics Computational Laboratory (Clemson, SC). USGS staff received approximately 4,200 raw sequences from the sequencing facility (available, upon request) that were subsequently trimmed and checked for quality assurance/quality control (QA/QC). Those QA/QC procedures resulted in ~1,700 sequences, which are described in Goldsmith and others (2019) and provided in this data release.
    Date: 2018 (process 6 of 9)
    Vector and ends were trimmed from the sequences using Geneious (version 11.1.4; Biomatters Ltd., Auckland, NZ).
    Date: 2018 (process 7 of 9)
    Using QIIME version 1.9.1, all sequences less than 50 bp were removed. Greengenes version 13_8 (http://greengenes.secondgenome.com/) was used through QIIME to perform a chimera check with usearch61 (https://www.drive5.com/usearch/), and to classify taxonomy using an open reference algorithm with a 97% similarity threshold [15]. Singletons were retained, while all other default parameters were used. After chimeric, unclassified, chloroplast, and mitochondrial sequences were removed, 996 bacterial OTUs remained.
    Date: 2018 (process 8 of 9)
    Upon submission of the sequences to NCBI’s GenBank, GenBank’s implementation of version 10 of usearch (64-bit version) using the uchime2_ref command in high confidence mode uncovered 190 additional chimeras. These sequences were removed, resulting in a dataset of 806 bacterial OTUs. Sequences representing each bacterial OTU have been deposited in GenBank under accession numbers MK175495 to MK176300. Sequences representing each archaeal OTU (18 OTUs) have been deposited in GenBank under accession numbers MH915525 to MH915542.
    Date: 13-Oct-2020 (process 9 of 9)
    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?
    Edwards, Ulrike, Rogall, Till, Blöcker, Helmut, Emde, Monica, and Böttger, Erik C., 19891011, Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA: Nucleic Acids Research Vol. 17, issue 19, Oxford University Press (OUP), Oxford, United Kingdom.

    Online Links:

    Other_Citation_Details: Pages 7843-7853
    Stackebrandt, E., and Liesack, W., 1993, Nucleic acids and classification: Academic Press, London, England.

    Other_Citation_Details:
    In Goodfellow M., O'Donnell AG, editors. Handbook of new bacterial systematics, pp 152-189.
    DeLong, E. F., 19920615, Archaea in coastal marine environments.: Proceedings of the National Academy of Sciences Vol. 89, issue 12, Proceedings of the National Academy of Sciences, Washington, D.C., United States.

    Online Links:

    Other_Citation_Details: Pages 5685-5689
    Caporaso, J Gregory, Kuczynski, Justin, Stombaugh, Jesse, Bittinger, Kyle, Bushman, Frederic D, Costello, Elizabeth K, Fierer, Noah, Peña, Antonio Gonzalez, Goodrich, Julia K, Gordon, Jeffrey I, Huttley, Gavin A, Kelley, Scott T, Knights, Dan, Koenig, Jeremy E, Ley, Ruth E, Lozupone, Catherine A, McDonald, Daniel, Muegge, Brian D, Pirrung, Meg, Reeder, Jens, Sevinsky, Joel R, Turnbaugh, Peter J, Walters, William A, Widmann, Jeremy, Yatsunenko, Tanya, Zaneveld, Jesse, and Knight, Rob, 20100411, QIIME allows analysis of high-throughput community sequencing data: Nature Methods Vol. 7, Springer Nature, London, United Kingdom.

    Online Links:

    Other_Citation_Details: Pages 335-336
    Werner, Jeffrey J, Koren, Omry, Hugenholtz, Philip, DeSantis, Todd Z, Walters, William A, Caporaso, J Gregory, Angenent, Largus T, Knight, Rob, and Ley, Ruth E, 20110630, Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys: The ISME Journal Vol. 6, Springer Nature, London, United Kingdom.

    Online Links:

    Other_Citation_Details: Pages 94-103
    McDonald, Daniel, Price, Morgan N, Goodrich, Julia, Nawrocki, Eric P, DeSantis, Todd Z, Probst, Alexander, Andersen, Gary L, Knight, Rob, and Hugenholtz, Philip, 20111201, An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea: The ISME Journal Vol. 6, Springer Nature, London, United Kingdom.

    Online Links:

    Other_Citation_Details: Pages 610-618
    Edgar, Robert C., 20101001, Search and clustering orders of magnitude faster than BLAST: Bioinformatics Vol. 26, issue 19, Oxford University Press (OUP), Oxford, United Kingdom.

    Online Links:

    Other_Citation_Details: Pages 2460-2461
    Edgar, Robert, 20160912, UCHIME2: improved chimera prediction for amplicon sequencing.

    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, 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 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: 13-Oct-2020
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/Astrangia_microbiomes_metadata.faq.html>
Generated by mp version 2.9.50 on Tue Sep 21 18:18:32 2021