Raw sequencing and amplicon sequence variant data from bacterial communities shed by Montastraea cavernosa coral fragments into filtered seawater mesocosms

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Frequently anticipated questions:

What does this data set describe?

Title:
Raw sequencing and amplicon sequence variant data from bacterial communities shed by Montastraea cavernosa coral fragments into filtered seawater mesocosms
Abstract:
The files provided in this U.S. Geological Survey (USGS) data release (Kellogg and others, 2021) include an amplicon sequence variant (ASV) table and the raw 16S rRNA gene amplicon files from six microbial communities (Mcav17, Mcav18, McH-101, McH-103, McD-57, and McD-58) derived from mesocosms consisting of filtered seawater in which either healthy or diseased (stony coral tissue loss disease) fragments of Montastraea cavernosa had been incubated, as well as sequence files of a mock community and extraction kit blank. Mesocosms were inoculated at the Smithsonian Marine Station located in Fort Pierce, Florida, during two separate trips: one in October 2019 and the other in November 2020. The coral fragments were collected between April 2018 and November 2020, from various locations throughout the Florida Keys. Mesocosms were set up by placing the coral fragments into filtered seawater for 4-5 days and then the fragments were removed so the water could be processed. The mock community was sequenced to assess any biases in the sequencing technology, while extraction blanks were sequenced to identify any contaminants in the DNA extraction kit.
  1. How might this data set be cited?
    Kellogg, Christina A., Evans, James S., and Voelschow, Julie J., 20211122, Raw sequencing and amplicon sequence variant data from bacterial communities shed by Montastraea cavernosa coral fragments into filtered seawater mesocosms:.

    This is part of the following larger work.

    Kellogg, Christina A., Evans, James S., and Voelschow, Julie J., 20210528, Bacterial Communities Shed by Montastraea cavernosa Coral Fragments into Filtered Seawater Mesocosms—Raw Data: U.S. Geological Survey data release doi:10.5066/P9B13K8N, U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center, St. Petersburg, Florida.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -80.3106
    East_Bounding_Coordinate: -80.3106
    North_Bounding_Coordinate: 27.45957
    South_Bounding_Coordinate: 27.45956
    Description_of_Geographic_Extent: Florida
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
    Beginning_Date: 25-Oct-2019
    Ending_Date: 24-Aug-2021
    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_BacteriaFilters.txt, for detailed descriptions of the contents of the raw and ASV data files. Additional information is contained in the minimum information about a marker sequence (MIMARKS) compliant metadata, MIMARKS_BacteriaFilters.xlsx as well as SRA_metadata_BacteriaFilters.xlsx, which is also 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
    • James S. Evans
    • 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
    Research Microbiologist
    600 4th St. South
    St. Petersburg, Florida

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

Why was the data set created?

The purpose of this experiment was to identify and compare microbial communities shed by corals into the mesocosms. 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 16 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 PRJNA731170.

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: 23-Oct-2019 (process 1 of 8)
    Coral collection - The coral fragment for mesocosm McH-101 was collected in April 2018 from the Florida Keys while the fragment for mesocosm McH-103 was acquired on January 31, 2019, from the Florida Keys National Marine Sanctuary in Key West. Both healthy coral fragments were maintained in a holding tank at the Smithsonian Marine Station located in Ft. Pierce, FL, until the first mesocosm experiment began in October 2019. Coral samples for mesocosms Mcav17 and Mcav18 were collected from a patch reef near Summerland Key (24.54767, -81.45697) on October 23, 2019. Coral samples for mesocosms McD-57 and McD-58 were obtained from a patch reef near Marathon (24.68982, -81.02978) on November 1, 2020. The second mesocosms were inoculated at the Smithsonian Marine Station in November 2020.
    Date: 29-Oct-2019 (process 2 of 8)
    Sample creation - first mesocosm inoculations: The mesocosms were initially set up and processed at the Smithsonian Marine Station (27.45956, -80.31060). Mesocosm seawater came from a storage tank that recirculated it through an ultraviolet (UV) sterilizer, 20-micrometer (µm) filter, and an activated carbon filter. The seawater was 0.22-µm filtered prior to use in 18-liter (L) mesocosms and is referred to as ‘filtered seawater.’ For samples McH-101, McH-103, Mcav17, and Mcav18, coral fragments were placed in filtered seawater mesocosms and allowed to naturally shed microbes from October 25 to October 29, 2019.
    Date: 07-Nov-2020 (process 3 of 8)
    Sample creation - second mesocosm inoculations: The second mesocosms were also instituted and processed at the Smithsonian Marine Station in Ft. Pierce, Florida, using the same configurations described in the previous step. For sample McD-57, the coral fragment was placed in filtered seawater mesocosm and allowed to naturally shed microbes from November 3-6, 2020. For sample McD-58, the coral fragment was placed in filtered seawater mesocosm and allowed to naturally shed microbes from November 3 to November 7, 2020.
    Date: 29-Oct-2019 (process 4 of 8)
    Sample creation - first filtration: Samples McH-101 and McH-103 were processed on October 28, 2019, and samples Mcav17 and Mcav18 were processed October 29, 2019. For samples McH-101, McH-103, Mcav17, and Mcav18, the coral fragments were removed from the 18L mesocosms and the water was pre-filtered through a sterile 200-micron mesh to remove loose debris. A Pall tangential flow filtration (TFF) system employing five 100 kDa T-series Centramate filter cassettes was used to concentrate the microbial community in each sample from the 18L original volume down to 210-250 milliliter (ml) concentrate. The microbial concentrate was filtered through a sterile Corning 430756 unit containing a 0.22-µm cellulose nitrate filter and then the filter was cut out of the unit with a sterile razor blade, transferred to a sterile whirlpak bag and frozen at -20°C until extracted for DNA.
    Date: 07-Nov-2020 (process 5 of 8)
    Sample creation - second filtration: Sample McD-57 was processed November 6, 2020. Sample McD-58 was processed November 7, 2020. For samples McD-57 and McD-58, the coral fragments were removed from the 18L mesocosms and the water was pre-filtered through a sterile 106-micron mesh to remove loose debris. A Pall tangential flow filtration system employing five 100 kDa T-Series Centramate filter cassettes was used to concentrate the microbial community in each sample from the 18L original volume down to 190-230 ml concentrate. The microbial concentrate was first filtered through a sterile ThermoScientific 126-0080 unit containing a 0.8-µm cellulose nitrate filter to remove any eukaryotes. The filtrate was then filtered through a sterile Corning 430756 unit containing a 0.22-µm cellulose nitrate filter and then the filter was cut out of the unit with a sterile razor blade, transferred to a sterile whirlpak bag and frozen at -20°C, until extracted for DNA.
    Date: 01-Mar-2021 (process 6 of 8)
    DNA extraction - The DNA extraction process was performed in March 2021, at the USGS Coral Microbial Ecology Laboratory located in St. Petersburg, FL. DNA was extracted from the 0.22-µm cellulose nitrate filters using Qiagen’s DNeasy PowerBiofilm Kit (QIAGEN, 2020), following manufacturer’s instructions in the Quick Start Protocol dated November 2016.
    Date: 26-Mar-2021 (process 7 of 8)
    Sequencing - Sequencing was done by the Michigan State University RTSF Genomics Core (East Lansing, MI). USGS submitted eight samples (n=6, plus one mock community and one extraction kit blank) of microbial metagenomic DNA for amplicon library preparation of the bacterial 16S-V4 hypervariable region and Illumina sequencing. Libraries were prepared using the MiSeq Dual Index method developed in the Patrick Schloss lab (Kozich and others, 2013). Primers 515f/806r were used to amplify the V4 region. All reactions were batch normalized using Invitrogen SequalPrep DNA Normalization plates. Product recovered from the plates was pooled and concentrated using an Amicon spin column. This pool was cleaned up using AMPure XP magnetic SPRI 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. The pool was loaded onto an Illumina MiSeq v2 Nano flow cell and sequencing was performed in a 2x250bp paired end format using a v2 500 cycle reagent cartridge. Custom sequencing and index primers complementary to the 515f/806r oligomers 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 v2.20.0.
    Date: 24-Aug-2021 (process 8 of 8)
    Data analysis - Data files (BacteriaFilters_ASV_Table.zip) containing tabulations of ASVs, their DNA sequences, their taxonomic identification, and the abundance (number of sequence reads) for each of the samples and controls were added in the version 2.0 update of this data release (Kellogg and others, 2021). Sequences were imported into QIIME2 [version 2021.4] (Bolyen and others, 2019) and trimmed, merged, and sorted into amplicon sequence variants (ASVs) using DADA2 (Callahan and others, 2016) and the parameters ‘–p-trim-left-f 13 –p-trim-left-r 13 –p-trunc-len- f 200 –p-trunc-len-r 200.’ Taxonomy was assigned using the pre-trained Silva classifier silva-138-99-515-806-nb-classifier (Bokulich and others, 2018). All ASVs assigned as “mitochondria” or “chloroplast” were removed.
  3. What similar or related data should the user be aware of?
    QIAGEN, 20200131, Qiagen DNeasy PowerBiofilm Kit.

    Online Links:

    Kozich, James J., Westcott, Sarah L., Baxter, Nielson T., Highlander, Sarah K., and Schloss, Patrick D., 2013, 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 79(17).

    Online Links:

    Other_Citation_Details: pages 5112–5120
    Callahan, Benjamin J., McMurdie, Paul J., Rosen, Michael J., Han, Andrew W., Amy Jo A. Johnson, and Holmes, Susan P., 20160523, DADA2: High-resolution sample inference from Illumina amplicon data: Nature Methods 13.

    Online Links:

    Other_Citation_Details: pages 581-583
    Bokulich, Nicholas A., Kaehler, Benjamin D., Rideout, Jai Ram, Dillion, Matthew, Bolyen, Evan, Knight, Rob, Huttley, Gavin A., and Caporaso, J. Gregory, 20180517, Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin: Microbiome 6(90).

    Online Links:

    Other_Citation_Details: pages 1-17
    Bolyen, Evan, Rideout, Jai Ram, Dillion, Matthew R., Bokulich, Nicholas A., Abnet, Christian C., Al-Ghalith, Gabriel A., Alxander, Harriet, Alm, Eric J., Arumugam, Manimozhiyan, and Asnicar, Francesco, 20190724, Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2: Nature Biotechnology 37.

    Online Links:

    Other_Citation_Details: pages 852-857

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:
None. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations.
  1. Who distributes the data set? (Distributor 1 of 1)
    Christina A. Kellogg
    U.S. Geological Survey
    Research Microbiologist
    600 4th St. 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: 22-Nov-2021
Metadata author:
Christina A. Kellogg
U.S. Geological Survey
Research Microbiologist
600 4th St. South
St. Petersburg, FL
United States

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/BacteriaFilters_FGDC_metadata.faq.html>
Generated by mp version 2.9.50 on Mon Nov 22 11:44:35 2021