Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral Mesocosms – Raw and Processed Data

Metadata also available as - [Outline] - [Parseable text] - [XML]

Frequently anticipated questions:


What does this data set describe?

Title:
Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral Mesocosms – Raw and Processed Data
Abstract:
The files in this data release (Kellogg and others, 2022) are those referenced in the journal article by Evans and others (2022) entitled “Biofilms as Potential Reservoirs of Stony Coral Tissue Loss Disease.” They contain an amplicon sequence variant (ASV) table and the raw 16S ribosomal ribonucleic acid (rRNA) gene amplicon deoxyribonucleic acid (DNA) sequence files from 15 microbial communities (sample names: CnD16B, CnD17B, CnD18B, CnD19B, CnD21B, CnD22B, CnD23B, CnD24B, CnD25B, PsD5B, CnH101B, CnH100B, Pstr4B, Pstr10B, and seawaterB) derived from biofilms on stainless steel plates (316 grade) formed in mesocosms containing diseased corals (stony coral tissue loss disease, n = 10), healthy corals (n = 4), or no coral (n = 1). Also included are the sequence files from a mock community, and two reagent blanks. Corals (Colpophyllia natans and Pseudodiploria strigosa) were collected between January 2019 and March 2021, from various locations throughout the Florida Keys. Plates were added to mesocosm buckets containing ultraviolet (UV)-sterilized, 0.2 micrometer (μm)-filtered seawater and either diseased (n = 10), healthy (n = 4), or no coral (n = 1) at the Smithsonian Marine Station in Fort Pierce, Florida (FL) on March 25, 2021. Plates were removed on March 28, 2021, and placed in individual sterile whirlpaks with RNAlater for future processing. Extraction of DNA from the samples and blanks occurred in April 2021 at the Coral Microbial Ecology Laboratory in St. Petersburg, FL using a QIAGEN DNeasy PowerBiofilm Kit. Library preparation and DNA sequencing were conducted on May 13, 2021, by the Michigan State University RTSF Genomics Core (East Lansing, Michigan) using primers 515F/806R to target the V4 variable region of the 16S rRNA gene. Sequencing was performed on an Illumina MiSeq sequencing system with v2 chemistry to obtain paired-end 250-bp (base pair) reads. The raw 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 PRJNA828575. For more information, please see the README file, README_Biofilm.txt.
Supplemental_Information: N/A
  1. How might this data set be cited?
    Kellogg, Christina A., Evans, James S., and Voelschow, Julie J., 20221021, Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral Mesocosms – Raw and Processed Data:.

    Online Links:

    This is part of the following larger work.

    Kellogg, Christina A., Evans, James S., and Voelschow, Julie J., 20221021, Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral Mesocosms – Raw and Processed Data: U.S. Geological Survey Data Release doi:10.5066/P9T6NW4V.

    Online Links:

  2. What geographic area does the data set cover?
    West_Bounding_Coordinate: -82.63800
    East_Bounding_Coordinate: -80.31060
    North_Bounding_Coordinate: 27.76370
    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: 31-Jan-2019
    Ending_Date: 22-Sep-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_Biofilm.txt, for detailed descriptions of the contents of the raw, processed and ASV data files. Additional information is contained in the minimum information about a marker sequence (MIMARKS) compliant metadata (Biofilm_MIMARKS), as well as the SRA metadata (Biofilm_SRA_metadata). The MIMARKS and SRA metadata files are available for download in the Supplemental Information section of the data release webpage.
    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
    United States

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

Why was the data set created?

The purpose of this experiment was to analyze biofilm microbial communities formed on stainless steel plates in association with 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: 28-Mar-2021 (process 1 of 7)
    Coral collection: Corals used to create these biofilm samples were collected from various locations throughout the Florida Keys between January 2019 and March 2021.
    Date: 23-Mar-2021 (process 2 of 7)
    Sample creation - Preparation of steel plates: Fifteen 316 grade stainless steel plates were cut to approximately 7.5 centimeters (cm) by 5.1 cm on March 23 2021, and cleaned by scrubbing with Liquinox and a Brillo pad on all six sides. The plates were then rinsed with tap water, then deionized (DI) water, and blotted dry with a paper towel. They were then sprayed with 70% ethanol, blotted dry again, wrapped in tinfoil and autoclaved at 121 degrees Celsius (°C) for 30 minutes with a 15-minute drying cycle.
    Date: 28-Mar-2021 (process 3 of 7)
    Sample creation - Biofilm steel plates: On March 25 2021, sterile labeled petri dishes with steel plates were placed in the bottom of each mesocosm containing approximately 18 liters (L) of UV-treated, 0.2 μm-filtered seawater, an air line, and their respective coral samples. The steel plates were positioned in the petri dishes in a way allowing for water from mesocosms to have contact with all sides. A control steel plate was placed in the same manner into a bucket containing 1-2L of filtered seawater and topped off to 18L, and an air line added the following day to match the other coral mesocosm volumes. All plates being added to healthy coral (CnH-101, CnH-100, Pstr-4, and Pstr-10) mesocosms were placed first, and the diseased coral (CnD-16, CnD-17, CnD-18, CnD-19, CnD-21, CnD-22, CnD-23, CnD-24, and CnD-25) mesocosms last, to avoid contamination. Plates were incubated in the buckets until March 28, 2021 (when they were collected), and placed in individual sterile whirlpaks with RNAlater.
    Date: 16-Apr-2021 (process 4 of 7)
    Sample processing: Each plate was scraped, front and back, with a flame-sterilized razor, and rinsed with 1x phosphate buffered saline (PBS), including the razor. The liquid and salt crystals were collected in each sample’s respective sterile petri dish, and transferred into 2 milliliter (mL) sterile tubes.
    Date: 28-Apr-2021 (process 5 of 7)
    The DNA extraction process was performed at the U.S. Geological Survey (USGS) Coral Microbial Ecology Laboratory in St. Petersburg, FL. DNA from CnD-22 and CnD-25 was extracted using a QIAGEN DNeasy PowerBiofilm Kit on April 16, 2021. The remaining 13 samples, along with an extraction kit blank, were extracted on April 22, 2021. A PBS blank was extracted on April 28, 2021. The manufacturer’s protocol (QIAGEN, 2013) was followed with modifications as described: because multiple 2 mL tubes were created for each sample, for step 2, only the first tube was resuspended in 350 microliters (µl) of MBL solution. The entire contents were then transferred into all remaining 2 mL tubes for that sample to resuspend the contents of each consecutively, prior to adding the final combined solution to the bead beat tube. Samples were then bead beat at 2500 revolutions per minute (rpm) for 30 seconds.
    Date: 13-May-2021 (process 6 of 7)
    Sequencing: Library preparation and DNA sequencing were conducted on May 13, 2021, by the Michigan State University RTSF Genomics Core (East Lansing, MI) using primers 515F: GTGCCAGCMGCCGCGGTAA and 806R: GGACTACHVGGGTWTCTAAT to target the V4 variable region of the 16S rRNA gene. Sequencing was performed on an Illumina MiSeq sequencing system with v2 chemistry to obtain paired-end 250-bp reads. Libraries were prepared using the MiSeq Dual Index method developed in the Patrick Schloss lab (Kozich and others, 2013).
    Date: 22-Sep-2021 (process 7 of 7)
    Data analysis - In September 2021 sequences were imported into QIIME2 [version 2021.4] (Bolyen and others, 2019) and trimmed, merged, and sorted into ASVs using DADA2 (Callahan and others, 2016) with the parameters ‘–p-trunc-len-f 200 –p-trunc-len-r 200.’ All sequences assigned as “mitochondria” or “chloroplast” were removed.
  3. What similar or related data should the user be aware of?
    Evans, James S., Paul, Valerie J., and Kellogg, Christina A., 2022, Biofilms as Potential Reservoirs of Stony Coral Tissue Loss Disease: Frontiers in Marine Science Volume 9, Article 1009407.

    Online Links:

    QIAGEN, 20200131, QIAGEN DNeasy PowerBiofilm Kit Handbook.

    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 Volume 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 Volume 13.

    Online Links:

    Other_Citation_Details: Pages 581–583
    Bolyen, Evan, Rideout, Jai Ram, Dillion, Matthew R., and others, and, 20190724, Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2: Nature Biotechnology Volume 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, Florida
    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: 21-Oct-2022
Metadata author:
Christina A. Kellogg
U.S. Geological Survey
Research Microbiologist
600 4th St. South
St. Petersburg, Florida
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/Biofilm_FGDC_metadata.faq.html>
Generated by mp version 2.9.51 on Mon Oct 31 17:37:24 2022