Cold-water coral microbiomes (Anthothela spp.) from Baltimore and Norfolk Canyons: raw and processed data

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Metadata:

Identification_Information
Data_Quality_Information
Entity_and_Attribute_Information
Distribution_Information
Metadata_Reference_Information

Identification_Information:

Citation:

Citation_Information:

Originator: Christina A. Kellogg
Originator: Julie J. Voelschow
Publication_Date: 20220418
Title:

Cold-water coral microbiomes (Anthothela spp.) from Baltimore and Norfolk Canyons: raw and processed data

Geospatial_Data_Presentation_Form:

SFF files, QUAL files, FNA files (FASTA files), and tabular digital data

Larger_Work_Citation:

Citation_Information:

Originator: Christina A. Kellogg
Originator: Stephanie N. Lawler
Publication_Date: 20151211
Title:

Cold-water coral microbiomes (Anthothela spp.) from Baltimore and Norfolk Canyons: raw and processed data

Geospatial_Data_Presentation_Form:

SFF files, QUAL files, FNA files (FASTA files), and tabular digital data

Series_Information:

Series_Name: U.S. Geological Survey data release
Issue_Identification: doi:10.5066/F7CZ356K

Publication_Information:

Publication_Place: St. Petersburg, Florida
Publisher:

U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center

Online_Linkage: https://doi.org/10.5066/F7CZ356K

Description:

Abstract:

The files included in this data release are the raw and processed deoxyribonucleic acid (DNA) sequence files referenced in the journal article by Lawler and others (2016) entitled “Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species”. They represent a 16S rRNA gene amplicon survey of cold-water corals (Anthothela spp.) microbiomes completed using Roche 454 pyrosequencing with titanium reagents. The samples used in this study were collected from cold-water corals between 2012-2013, at Baltimore and Norfolk Canyons in the Atlantic Ocean. The raw data files associated with this study were also submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), under Bioproject number PRJNA296835.

Purpose:

This experiment was conducted to explore the diversity and abundance of microbial associates in Anthothela species.

Supplemental_Information:

Coral samples were collected under Field Activity Number (FAN) 12DCM02 and 13DCM01. FANs are unique identifiers assigned by the U.S. Geological Survey (USGS) to provide more information about the activities conducted in the field for a study. Please visit the Coastal and Marine Geoscience Data System (CMGDS) field activity webpage for more information about each FAN related to this dataset, https://cmgds.marine.usgs.gov/fan_info.php?fan=12DCM02 and https://cmgds.marine.usgs.gov/fan_info.php?fan=13DCM01.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 20120910
Ending_Date: 20130520

Currentness_Reference: ground condition

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Bounding_Coordinates:

West_Bounding_Coordinate: -74.605852
East_Bounding_Coordinate: -73.834483
North_Bounding_Coordinate: 38.181985
South_Bounding_Coordinate: 37.023429

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:02451394-0747-4b0c-a7f5-99ccfdfb44e1

Theme:

Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: oceans
Theme_Keyword: biota

Theme:

Theme_Keyword_Thesaurus: MECS
Theme_Keyword: Microbial Communities

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: reef ecosystems
Theme_Keyword: microbiology
Theme_Keyword: laboratory methods
Theme_Keyword: DNA sequencing
Theme_Keyword: genetics
Theme_Keyword: coelenterates

Place:

Place_Keyword_Thesaurus: Marine Realms Information Bank (MRIB)
Place_Keyword: continental shelf
Place_Keyword: cnidarians [coelenterates]

Place:

Place_Keyword_Thesaurus: CommonGeographicAreas
Place_Keyword: Mid Atlantic

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.

Point_of_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Christina A. Kellogg
Contact_Organization: U.S. Geological Survey

Contact_Position: Research Microbiologist
Contact_Address:

Address_Type: mailing
Address: 600 4th St. South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States

Contact_Voice_Telephone: 727-502-8128
Contact_Electronic_Mail_Address: ckellogg@usgs.gov

Cross_Reference:

Citation_Information:

Originator: Mo BIO Laboratories, Inc.
Publication_Date: 20130816
Title: MO BIO's PowerPlant DNA Isolation Kit Handbook
Edition: 08162013
Geospatial_Data_Presentation_Form: Instructional manual
Online_Linkage:

https://www.qiagen.com/us/resources/resourcedetail?id=ceb406b8-0d48-4675-a376-e76709099c74&lang=en

Cross_Reference:

Citation_Information:

Originator: Shinichi Sunagawa
Originator: Cheryl M. Woodley
Originator: Monica Medina
Publication_Date: 20100305
Title: Threatened Corals Provide Underexplored Microbial Habitats
Geospatial_Data_Presentation_Form: publication
Series_Information:

Series_Name: PLOS One
Issue_Identification: Volume 5, Number 3

Online_Linkage: https://doi.org/10.1371/journal.pone.0009554

Cross_Reference:

Citation_Information:

Originator: Stephanie N. Lawler
Originator: Christina A. Kellogg
Originator: Scott C. France
Originator: Rachel W. Clostio
Originator: Sandra D. Brooke
Originator: Steve W. Ross
Publication_Date: 20160405
Title:

Coral-Associated Bacterial Diversity is Conserved Across Two Deep-Sea Anthothela Species

Geospatial_Data_Presentation_Form: publication
Series_Information:

Series_Name: Frontiers in Microbiology
Issue_Identification: Volume 7

Online_Linkage: https://doi.org/10.3389/fmicb.2016.00458

Cross_Reference:

Citation_Information:

Originator: Gregory J. Caporaso
Originator: Justin Kuczynski
Originator: Jesse Stombaugh
Originator: Kyle Bittinger
Originator: Frederic D. Bushman
Originator: Elizabeth K. Costello
Originator: Noah Fierer
Originator: Antonio Gonzalez Pena
Originator: Julie K. Goodrich
Originator: Jeffrey I. Gordon
Originator: Gavin A. Huttley
Originator: Scott T. Kelley
Originator: Dan Knights
Originator: Jeremy E. Koenig
Originator: Ruth E. Ley
Originator: Catherine A. Lozupone
Originator: Daniel McDonald
Originator: Brian D. Muegge
Originator: Meg Oirrung
Originator: Jens Reeder
Originator: Joel R. Sevinsky
Originator: Peter J. Tumbaugh
Originator: William A. Walters
Originator: Jeremy Widmann
Originator: Tanya Yatzunenko
Originator: Jesse Zaneveld
Originator: Rob Knight
Publication_Date: 20100501
Title:

QIIME allows analysis of high-throughput community sequencing data

Geospatial_Data_Presentation_Form: publication
Series_Information:

Series_Name: Nature Methods
Issue_Identification: 7(5): 335–336

Online_Linkage: doi:10.1038/nmeth.f.303
Online_Linkage:

https://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3156573&blobtype=pdf

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report: No formal attribute accuracy tests were conducted.

Logical_Consistency_Report: No formal logical accuracy tests were conducted.
Completeness_Report:

Dataset is considered complete for the information presented, as described in the abstract.

Lineage:

Process_Step:

Process_Description:

Coral collection: Twenty-three Anthothelidae colonies were sampled using remotely-operated vehicles during two separate cruises (August 2012 and May 2013) from Baltimore Canyon and Norfolk Canyon, in the Mid-Atlantic ocean. Coral samples were preserved in sterile 50 milliliter (mL) tubes and stored overnight in RNAlater at 4 degrees Celsius (˚C) before extended storage at -20˚C.

Process_Date: 20130520

Process_Step:

Process_Description:

DNA extraction: DNA was extracted in July 2013, using MOBIO PowerPlant DNA Isolation Kit (now Qiagen), with modifications per the Sunagawa lab protocol (2010), including the addition of lysozyme and extended incubation periods at room temperature (~21˚C), 24˚C, and 65˚C.

Process_Date: 20130724

Process_Step:

Process_Description:

DNA sequencing: In August 2013, a 16S rRNA gene amplicon survey of the corals microbiomes was completed by Selah Genomics (Greenville, SC), using Roche 454 pyrosequencing with titanium reagents, using primers targeting the V4-V5 hypervariable region of the16S rRNA gene (563F/926R); V4-forward: 5’-AYTGGGYDTAAAGNG and V5-reverse: 5’ CGTATCGCCTCCCTCGCGCCATCAG.

Process_Date: 20130813

Process_Step:

Process_Description:

Data analysis: Sequence data were analyzed using the bioinformatic packages Quantitative Insights Into Microbial Ecology (QIIME) version 1.5.0 and QIIME 1.9.1 packages (Caporaso and others, 2010). Please refer to the file entitled “Anthothela_workflow.txt," which is included as a supplemental file in the processed_data.zip package 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.

Process_Date: 20150901

Entity_and_Attribute_Information:

Overview_Description:

Entity_and_Attribute_Overview:

Please refer to the "README" file, README.txt, for detailed descriptions of the contents of the Anthothela raw data files and the processed data files. Additional information is contained in the metadata file, anthothela_metadata.txt, which is also included in the raw_data.zip downloadable file of this data release (Kellogg and Lawler, 2015).

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.

Distribution_Information:

Distributor:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Christina A. Kellogg
Contact_Organization: U.S. Geological Survey

Contact_Position: Research Microbiologist
Contact_Address:

Address_Type: mailing
Address: 600 4th St. South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States

Contact_Voice_Telephone: 727-502-8128
Contact_Electronic_Mail_Address: ckellogg@usgs.gov

Distribution_Liability:

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.

Standard_Order_Process:

Digital_Form:

Digital_Transfer_Information:

Format_Name: data download

Digital_Transfer_Option:

Online_Option:

Computer_Contact_Information:

Network_Address:

Network_Resource_Name:

https://coastal.er.usgs.gov/data-release/doi-F7CZ356K/data/raw_data.zip

Network_Resource_Name:

https://coastal.er.usgs.gov/data-release/doi-F7CZ356K/data/processed_data.zip

Fees: None

Metadata_Reference_Information:

Metadata_Date: 20230515
Metadata_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Christina A. Kellogg
Contact_Organization: U.S. Geological Survey

Contact_Position: Research Microbiologist
Contact_Address:

Address_Type: mailing
Address: 600 4th St. South
City: St. Petersburg
State_or_Province: Florida
Postal_Code: 33701
Country: United States

Contact_Voice_Telephone: 727-502-8128
Contact_Electronic_Mail_Address: ckellogg@usgs.gov

Metadata_Standard_Name:

FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata

Metadata_Standard_Version: FGDC-STD-001.1-1999

This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Anthothela_BaltimoreNorfolk_FGDC_metadata.html>