Cold-water coral microbiomes (Primnoa spp.) from Gulf of Alaska, Baltimore Canyon, and Norfolk Canyon: raw data

Frequently anticipated questions:

• What does this data set describe?
  1. How might this data set be cited?
  2. What geographic area does the data set cover?
  3. What does it look like?
  4. Does the data set describe conditions during a particular time period?
  5. What is the general form of this data set?
  6. How does the data set represent geographic features?
  7. How does the data set describe geographic features?
• Who produced the data set?
  1. Who are the originators of the data set?
  2. Who also contributed to the data set?
  3. To whom should users address questions about the data?
• Why was the data set created?
• How was the data set created?
  1. From what previous works were the data drawn?
  2. How were the data generated, processed, and modified?
  3. What similar or related data should the user be aware of?
• How reliable are the data; what problems remain in the data set?
  1. How well have the observations been checked?
  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?
  5. How consistent are the relationships among the data, including topology?
• How can someone get a copy of the data set?
  1. Are there legal restrictions on access or use of the data?
  2. Who distributes the data?
  3. What's the catalog number I need to order this data set?
  4. What legal disclaimers am I supposed to read?
  5. How can I download or order the data?
• Who wrote the metadata?

What does this data set describe?

1. How might this data set be cited?
   Kellogg, Christina A., and Goldsmith, Dawn B., 20180820, Cold-water coral microbiomes (Primnoa spp.) from Gulf of Alaska, Baltimore Canyon, and Norfolk Canyon: raw data: U.S. Geological Survey, St. Petersburg, FL.

   Online Links:

   • https://doi.org/10.5066/F7P55KMJ

2. What geographic area does the data set cover?

   West_Bounding_Coordinate: -133.3165
   East_Bounding_Coordinate: -73.8334
   North_Bounding_Coordinate: 57.8890
   South_Bounding_Coordinate: 37.0523
   

3. What does it look like?
4. Does the data set describe conditions during a particular time period?

   Beginning_Date: 2011

   Ending_Date: 2013

   Currentness_Reference:

   ground condition

5. What is the general form of this data set?

   Geospatial_Data_Presentation_Form: SFF files, QUAL files, and FNA files (FASTA files)
   

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?

   Primnoa_metadata.txt

   Please refer to the "README" file, README_Primnoa.txt, for a description of the contents of the MIMARKS compliant Primnoa metadata file. (Source: USGS)

   Primnoa3008_map.txt and Primnoaprim1_map.txt

   The file titled “Primnoa3008_map.txt” is the mapping file that accompanies the sequencing files ID2UZ7K01.sff and ID2UZ7K02.sff, which were created during the first sequencing run. This file corresponds to sequences from samples collected in Norfolk Canyon. “Primnoaprim1_map.txt” is the mapping file associated with sequencing files H8MF54001.sff and H8MF54002.sff, products of the second sequencing run. This file corresponds to sequences from samples collected in Baltimore Canyon and Tracy Arm Fjord. (Source: USGS)

   SampleID

   Identifier for sample (Source: USGS) Internal feature number (short version) unique to each sample

   BarcodeSequence

   DNA sequence used as a bar code to identify individual samples in a multiplexed sequencing run. (Source: USGS) 10-base DNA sequence, unique to each sample on a sequencing plate, used to identify individual samples in a multiplexed sequencing run.

   LinkerPrimerSequence

   Forward primer used to amplify a section of bacterial 16S ribosomal DNA (Source: USGS) DNA sequence at one end of the conserved bacterial 16S ribosomal DNA

   ReversePrimer

   Reverse primer used to amplify a section of bacterial 16S ribosomal DNA (Source: USGS) DNA sequence at other end of the conserved bacterial 16S ribosomal DNA

   Plate

   Identifier for plate (Source: USGS) Identifier for plate on which the sample was sequenced

   Name

   Identifier for sample (Source: USGS) Internal feature number (long version) unique to each sample

   Species

   Species of coral from which bacterial DNA was extracted (Source: USGS)

   Value	Definition
   P_resedaeformis	Primnoa resedaeformis
   P_pacifica	Primnoa pacifica

   OceanBasin

   Ocean in which sample was collected (Source: USGS)

   Value	Definition
   Atlantic	Atlantic Ocean
   Pacific	Pacific Ocean

   Location

   Location in which sample was collected (Source: USGS)

   Value	Definition
   Norfolk_Canyon	Norfolk Canyon in the Atlantic Ocean
   Baltimore_Canyon	Baltimore Canyon in the Atlantic Ocean
   Tracy_Arm_Fjord	Tracy Arm Fjord in the Gulf of Alaska, Pacific Ocean

   Temperature

   Temperature of water from which sample was collected (Source: USGS)

   Range of values
   Minimum:	4.6
   Maximum:	10.79
   Units:	degrees Celsius

   Depth

   Depth of water from which sample was collected (Source: USGS)

   Range of values
   Minimum:	10
   Maximum:	576
   Units:	meters

   Salinity

   Salinity of water from which sample was collected (Source: USGS)

   Range of values
   Minimum:	26.9
   Maximum:	35.47
   Units:	practical salinity units

   Latitude

   Latitude of location from which sample was collected (Source: USGS)

   Range of values
   Minimum:	37.052256
   Maximum:	57.888983

   Longitude

   Longitude of location from which sample was collected (Source: USGS)

   Range of values
   Minimum:	-73.833355
   Maximum:	-133.31645

   Month

   Month in which sample was collected (Source: USGS)

   Value	Definition
   Jan	January
   May	May
   Aug	August
   Sept	September

   Year

   Year in which sample was collected (Source: USGS)

   Range of values
   Minimum:	2011
   Maximum:	2013

   Description

   Notes particular to the sample (Source: USGS)

   Value	Definition
   NA	Not applicable
   Contaminated	Sample should be treated as contaminated

   Chlamydiales_23S.txt

   Please refer to the "README" file for descriptions of the contents of the Chlamydiales_23S file (Source: USGS)

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
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 S

   St. Petersburg, FL
   

   USA

   727-502-8000 (voice)

   ckellogg@usgs.gov

Why was the data set created?

These data were obtained in order to assess the microbiomes of two species of cold-water corals, Primnoa pacifica and Primnoa resedaeformis. The study objectives were to identify any conserved bacterial core community and to identify differences between the microbiomes of these two species of the same genus.

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: 31-Jan-2012 (process 1 of 8)

   Primnoa pacifica coral samples were collected from the Aleutian Islands, Alaska, using self-contained underwater breathing apparatus (SCUBA) equipment. Divers wearing clean nitrile gloves donned at the surface sampled the first Primnoa colony encountered on the dive (i.e. no other corals were touched before collecting the samples for this study). Small pieces of coral were broken from the colony by hand and placed into sterile 50 milliliter (mL) tubes. Upon return to the surface, the ambient seawater in the tubes was decanted and replaced with Thermo Fisher Scientific's RNAlater Stabilization Solution (RNAlater). The tubes were kept at 4 degrees Celsius (ºC) overnight and then moved to –20ºC for long term storage. Samples collected in Alaska were shipped overnight, surrounded by ice packs, to the USGS St. Petersburg, Florida environmental microbiology lab for further processing.

   Date: 31-Aug-2012 (process 2 of 8)

   Primnoa resedaeformis coral samples were collected from Baltimore Canyon during the 2012 Deepwater Canyons cruise on the National Oceanic and Atmospheric Administration (NOAA) Research Vessel (R/V) Nancy Foster using the remotely-operated vehicle (ROV) Kraken 2. Small pieces of the coral were collected using the ROV’s manipulator arm and placed into containers that had been washed, sterilized with ethanol, and filled with freshwater while the ROV was on deck. Upon recovery of the ROV, the samples were removed from the containers using ethanol-sterilized forceps, trimmed (if necessary) with ethanol-sterilized shears, and placed into 50 mL tubes. The tubes were filled with RNAlater and placed at 4ºC overnight, then transferred to –20ºC for long term storage.

   Date: 31-May-2013 (process 3 of 8)

   Primnoa resedaeformis coral samples were collected from Norfolk Canyon during the 2013 Deepwater Canyons cruise on the NOAA R/V Ronald Brown using the ROV Jason II. Small pieces of the coral were collected using the ROV’s manipulator arm and placed into containers that had been washed, sterilized with ethanol, and filled with freshwater while the ROV was on deck. Upon recovery of the ROV, the samples were removed from the quivers using ethanol-sterilized forceps, trimmed (if necessary) with ethanol-sterilized shears, and placed into 50 mL tubes. The tubes were filled with RNAlater and placed at 4ºC overnight, then transferred to –20ºC for long term storage.

   Date: 30-Jun-2013 (process 4 of 8)

   DNA was extracted from the samples using the MOBIO PowerPlant DNA Isolation Kit following the suggested modifications in Sunagawa and others (2010). Briefly, approximately 50 mg aliquots of tissue slurry from each sample were processed with the addition of a lysozyme step and additional smaller beads to expedite physical lysis. Three extractions were done per coral sample and then recombined by sample after elution of the DNA from the spin column. The DNA samples were quantified with a Thermo Fisher Scientific Quant-iT PicoGreen dsDNA Assay Kit, per the manufacturer’s protocol.

   Date: 09-Aug-2013 (process 5 of 8)

   DNA samples were amplified with primers targeting the V4-V5 hypervariable region (563F/926R) of the 16S rRNA gene: forward primer (5? AYTGGGYDTAAAGNG) and reverse primer (5? CCGTCAATTYYTTTRAGTTT). The forward primer was tagged with multiplex identifier (MID) tags so the samples could be combined for sequencing on two plates. Amplification, pooling and 454 sequencing using GS FLX Titanium chemistry were performed by Selah Genomics, Inc. Sequence data from all samples were deposited in the NCBI SRA under Bioproject number PRJNA348705.

   Date: 31-Oct-2015 (process 6 of 8)

   Sequence data were analyzed using the bioinformatic package Quantitative Insights Into Microbial Ecology (QIIME), version 1.9.1 (Caporaso and others, 2010, Nature Methods 7:335-336, doi:10.1038/nmeth.f.303). Please refer to the file entitled "Primnoa_workflow.txt," which is included as a supplemental file and details the scripts run in QIIME. The workflow file contains the default or chosen settings used for each script, as well as the names of the input/output files associated with each script.

   Date: 11-May-2016 (process 7 of 8)

   Primers designed to amplify the 23S rRNA gene in members of the Chlamydiales order (Everett and others, 1999) were used to amplify DNA extracted from the Primnoa pacifica samples. One sample of Primnoa pacifica, AKPP1, produced a 600-bp polymerase chain reaction (PCR) product that was visible on an agarose gel. The product was cloned into a vector and used to transform competent cells. After screening, the inserts in positive transformants were sequenced by Eurofins (http://www.eurofinsus.com/) using Sanger sequencing. Two unique sequences resulted, and are contained in the file entitled "Chlamydiales_23S.txt."

   Date: 13-Oct-2020 (process 8 of 8)

   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?
   Goldsmith, Dawn B., Kellogg, Christina A., Morrison, Cheryl L., Gray, Michael A., Stone, Robert P., Waller, Rhian G., Brooke, Sandra D., and Ross, Steve W., 20180817, Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype: Springer Nature, Scientific Reports, New York, NY.

   Kellogg, Christina A., 20190610, Microbiomes of stony and soft deep-sea corals share rare core bacteria: Microbiome Volume 7, Issue 1, Springer Nature, BMC, London, United Kingdom.

   Online Links:

   • https://doi.org/10.1186/s40168-019-0697-3

   Karin D. E. Everett, Hornung, Linda J., and Andersen, Arthur A., 199903, Rapid Detection of the Chlamydiaceae and Other Families in the Order Chlamydiales: Three PCR Tests: Journal of Clinical Microbiology, Washington, D.C..

   J. Gregory Caporaso and others, 20100501, QIIME allows analysis of high-throughput community sequencing data: Nature Methods, New York, NY.

   Sunagawa, Shinichi, Woodley, Cheryl M., and Medina, Monica, 201003, Threatened Corals Provide Underexplored Microbial Habitats: PLOS One, San Francisco, CA.

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 S

   St. Petersburg, FL
   

   USA

   727-502-8000 (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?

   Although these data have been processed successfully on a computer system at 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. The USGS shall not be held liable for improper or incorrect use of the data described or contained herein. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.

4. How can I download or order the data?
   • Availability in digital form:

     Data format:	Text file containing workflow for bioinformatic analysis. The workflow file details the scripts run in the bioinformatic package QIIME (Caporaso and others, 2010, Nature Methods 7:335-336, doi:10.1038/nmeth.f.303), default or chosen settings used for each script, and the names of the input/output files associated with each script. in format ASCII (version None) Text file
     Network links:	https://coastal.er.usgs.gov/data-release/doi-F7P55KMJ/data/Primnoa_raw_data.zip https://coastal.er.usgs.gov/data-release/doi-F7P55KMJ/data/Chlamydiales_23S.txt

   • Cost to order the data: None

5. What hardware or software do I need in order to use the data set?

   SFF files, QUAL files, and FNA files (FASTA files) can be read by QIIME and mothur (https://www.mothur.org/), both of which are free software. FASTA files can also be read by text editors.

Who wrote the metadata?

Dates:

Last modified: 13-Oct-2020

Metadata author:

Christina A. Kellogg

U.S. Geological Survey

600 4th Street S

St. Petersburg, FL

USA

727-502-8000 (voice)

ckellogg@usgs.gov

Metadata standard:

Content Standard for Digital Geospatial Metadata (FGDC-STD-001-1998)