Metadata: 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