Metadata: Identification_Information: Citation: Citation_Information: Originator: Christina A. Kellogg Originator: Dawn B. Goldsmith Publication_Date: 20180820 Title: Cold-water coral microbiomes (Primnoa spp.) from Gulf of Alaska, Baltimore Canyon, and Norfolk Canyon: raw data Geospatial_Data_Presentation_Form: SFF files, QUAL files, and FNA files (FASTA files) Publication_Information: Publication_Place: St. Petersburg, FL Publisher: U.S. Geological Survey Online_Linkage: https://doi.org/10.5066/F7P55KMJ Description: Abstract: The files in this data release are the raw DNA sequence files referenced in the journal article by Goldsmith and others (2018) entitled "Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype". They represent a 16S ribosomal ribonucleic acid (rRNA) gene amplicon survey of the corals’ microbiomes (Primnoa spp.) completed using Roche 454 pyrosequencing with Titanium series reagents. The 16S rRNA gene was amplified using primers for the V4-V5 region (fwd: 5? AYTGGGYDTAAAGNG, rev: 5? CCGTCAATTYYTTTRAGTTT). The data also include two 23S rRNA gene Sanger sequences from Rhabdochlamydia bacteria from the microbiomes of Alaskan Primnoa corals. The 23S rRNA gene was amplified using forward primer 5? GATGCCTTGGCATTGATAGGCGATGAAGGA and reverse primer 5? TGGCTCATCATGCAAAAGGCA. Samples from Baltimore Canyon (in the Atlantic Ocean) were collected in 2012. Samples from Norfolk Canyon (in the Atlantic Ocean) were collected in 2012-2013. Samples from the Gulf of Alaska (Tracy Arm Fjord) were collected in 2011-2012. The raw data files associated with this study have also been submitted to the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under Bioproject number PRJNA348705. The 23S sequences have been submitted to NCBI (GenBank) under accession numbers KY010287 and KY010288. Minimum information about a marker gene (MIMARKS) compliant metadata is provided in "Primnoa_metadata.txt", which is included in the data download file. For more information, please contact Christina Kellogg at the U.S. Geological Survey (USGS) St. Petersburg Coastal and Marine Science Center, 600 4th Street South, St. Petersburg, Florida, USA, 33701; Telephone: (727) 502-8128; Email: ckellogg@usgs.gov. Purpose: 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. Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 2011 Ending_Date: 2013 Currentness_Reference: ground condition Status: Progress: Complete Maintenance_and_Update_Frequency: Not planned Spatial_Domain: Bounding_Coordinates: West_Bounding_Coordinate: -133.3165 East_Bounding_Coordinate: -73.8334 North_Bounding_Coordinate: 57.8890 South_Bounding_Coordinate: 37.0523 Keywords: Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:ef241c52-0356-4a95-b63e-a40164314000 Theme: Theme_Keyword_Thesaurus: ISO 19115 Topic Category Theme_Keyword: biota Theme_Keyword: oceans Theme: Theme_Keyword_Thesaurus: Global Change Master Science Directory Theme_Keyword: Biological Classification < Bacteria Theme_Keyword: Biological Classification < Animals < Cnidarians Theme: Theme_Keyword_Thesaurus: USGS Thesaurus Theme_Keyword: marine biology Theme_Keyword: marine geology Theme_Keyword: coelenterates Place: Place_Keyword_Thesaurus: Geographic Names Information Systems (GNIS) Place_Keyword: Atlantic Ocean Place_Keyword: Gulf of Alaska Temporal: Temporal_Keyword_Thesaurus: USGS Thesaurus Temporal_Keyword: Modern 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. Point_of_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: Christina A. Kellogg Contact_Organization: U.S. Geological Survey Contact_Address: Address_Type: mailing and physical Address: 600 4th Street S City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Country: USA Contact_Voice_Telephone: 727-502-8000 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Cross_Reference: Citation_Information: Originator: Dawn B. Goldsmith Originator: Christina A. Kellogg Originator: Cheryl L. Morrison Originator: Michael A. Gray Originator: Robert P. Stone Originator: Rhian G. Waller Originator: Sandra D. Brooke Originator: Steve W. Ross Publication_Date: 20180817 Title: Comparison of microbiomes of cold-water corals Primnoa pacifica and Primnoa resedaeformis, with possible link between microbiome composition and host genotype Geospatial_Data_Presentation_Form: publication Publication_Information: Publication_Place: New York, NY Publisher: Springer Nature, Scientific Reports Cross_Reference: Citation_Information: Originator: Christina A. Kellogg Publication_Date: 20190610 Title: Microbiomes of stony and soft deep-sea corals share rare core bacteria Geospatial_Data_Presentation_Form: publication Series_Information: Series_Name: Microbiome Issue_Identification: Volume 7, Issue 1 Publication_Information: Publication_Place: London, United Kingdom Publisher: Springer Nature, BMC Online_Linkage: https://doi.org/10.1186/s40168-019-0697-3 Cross_Reference: Citation_Information: Originator: Karin D. E. Everett Originator: Linda J. Hornung Originator: Arthur A. Andersen Publication_Date: 199903 Title: Rapid Detection of the Chlamydiaceae and Other Families in the Order Chlamydiales: Three PCR Tests Geospatial_Data_Presentation_Form: publication Publication_Information: Publication_Place: Washington, D.C. Publisher: Journal of Clinical Microbiology Cross_Reference: Citation_Information: Originator: J. Gregory Caporaso and others Publication_Date: 20100501 Title: QIIME allows analysis of high-throughput community sequencing data Geospatial_Data_Presentation_Form: publication Publication_Information: Publication_Place: New York, NY Publisher: Nature Methods Cross_Reference: Citation_Information: Originator: Shinichi Sunagawa Originator: Cheryl M. Woodley Originator: Monica Medina Publication_Date: 201003 Title: Threatened Corals Provide Underexplored Microbial Habitats Geospatial_Data_Presentation_Form: publication Publication_Information: Publication_Place: San Francisco, CA Publisher: PLOS One 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. Users are advised to read the rest of the metadata record carefully for additional details. Positional_Accuracy: Horizontal_Positional_Accuracy: Horizontal_Positional_Accuracy_Report: No formal positional accuracy tests were conducted Vertical_Positional_Accuracy: Vertical_Positional_Accuracy_Report: No formal positional accuracy tests were conducted Lineage: Process_Step: Process_Description: 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. Process_Date: 20120131 Process_Step: Process_Description: 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. Process_Date: 20120831 Process_Step: Process_Description: 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. Process_Date: 20130531 Process_Step: Process_Description: 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. Process_Date: 20130630 Process_Step: Process_Description: 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. Process_Date: 20130809 Process_Step: Process_Description: 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. Process_Date: 20151031 Process_Step: Process_Description: 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." Process_Date: 20160511 Process_Step: Process_Description: Added keywords section with USGS persistent identifier as theme keyword. Process_Date: 20201013 Process_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: U.S. Geological Survey Contact_Person: VeeAnn A. Cross Contact_Position: Marine Geologist Contact_Address: Address_Type: Mailing and Physical Address: 384 Woods Hole Road City: Woods Hole State_or_Province: MA Postal_Code: 02543-1598 Contact_Voice_Telephone: 508-548-8700 x2251 Contact_Facsimile_Telephone: 508-457-2310 Contact_Electronic_Mail_Address: vatnipp@usgs.gov Entity_and_Attribute_Information: Detailed_Description: Entity_Type: Entity_Type_Label: Primnoa_metadata.txt Entity_Type_Definition: Please refer to the "README" file, README_Primnoa.txt, for a description of the contents of the MIMARKS compliant Primnoa metadata file. Entity_Type_Definition_Source: USGS Detailed_Description: Entity_Type: Entity_Type_Label: Primnoa3008_map.txt and Primnoaprim1_map.txt Entity_Type_Definition: 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. Entity_Type_Definition_Source: USGS Attribute: Attribute_Label: SampleID Attribute_Definition: Identifier for sample Attribute_Definition_Source: USGS Attribute_Domain_Values: Unrepresentable_Domain: Internal feature number (short version) unique to each sample Attribute: Attribute_Label: BarcodeSequence Attribute_Definition: DNA sequence used as a bar code to identify individual samples in a multiplexed sequencing run. Attribute_Definition_Source: USGS Attribute_Domain_Values: Unrepresentable_Domain: 10-base DNA sequence, unique to each sample on a sequencing plate, used to identify individual samples in a multiplexed sequencing run. Attribute: Attribute_Label: LinkerPrimerSequence Attribute_Definition: Forward primer used to amplify a section of bacterial 16S ribosomal DNA Attribute_Definition_Source: USGS Attribute_Domain_Values: Unrepresentable_Domain: DNA sequence at one end of the conserved bacterial 16S ribosomal DNA Attribute: Attribute_Label: ReversePrimer Attribute_Definition: Reverse primer used to amplify a section of bacterial 16S ribosomal DNA Attribute_Definition_Source: USGS Attribute_Domain_Values: Unrepresentable_Domain: DNA sequence at other end of the conserved bacterial 16S ribosomal DNA Attribute: Attribute_Label: Plate Attribute_Definition: Identifier for plate Attribute_Definition_Source: USGS Attribute_Domain_Values: Unrepresentable_Domain: Identifier for plate on which the sample was sequenced Attribute: Attribute_Label: Name Attribute_Definition: Identifier for sample Attribute_Definition_Source: USGS Attribute_Domain_Values: Unrepresentable_Domain: Internal feature number (long version) unique to each sample Attribute: Attribute_Label: Species Attribute_Definition: Species of coral from which bacterial DNA was extracted Attribute_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: P_resedaeformis Enumerated_Domain_Value_Definition: Primnoa resedaeformis Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: P_pacifica Enumerated_Domain_Value_Definition: Primnoa pacifica Enumerated_Domain_Value_Definition_Source: USGS Attribute: Attribute_Label: OceanBasin Attribute_Definition: Ocean in which sample was collected Attribute_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Atlantic Enumerated_Domain_Value_Definition: Atlantic Ocean Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Pacific Enumerated_Domain_Value_Definition: Pacific Ocean Enumerated_Domain_Value_Definition_Source: USGS Attribute: Attribute_Label: Location Attribute_Definition: Location in which sample was collected Attribute_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Norfolk_Canyon Enumerated_Domain_Value_Definition: Norfolk Canyon in the Atlantic Ocean Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Baltimore_Canyon Enumerated_Domain_Value_Definition: Baltimore Canyon in the Atlantic Ocean Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Tracy_Arm_Fjord Enumerated_Domain_Value_Definition: Tracy Arm Fjord in the Gulf of Alaska, Pacific Ocean Enumerated_Domain_Value_Definition_Source: USGS Attribute: Attribute_Label: Temperature Attribute_Definition: Temperature of water from which sample was collected Attribute_Definition_Source: USGS Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 4.6 Range_Domain_Maximum: 10.79 Attribute_Units_of_Measure: degrees Celsius Attribute: Attribute_Label: Depth Attribute_Definition: Depth of water from which sample was collected Attribute_Definition_Source: USGS Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 10 Range_Domain_Maximum: 576 Attribute_Units_of_Measure: meters Attribute: Attribute_Label: Salinity Attribute_Definition: Salinity of water from which sample was collected Attribute_Definition_Source: USGS Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 26.9 Range_Domain_Maximum: 35.47 Attribute_Units_of_Measure: practical salinity units Attribute: Attribute_Label: Latitude Attribute_Definition: Latitude of location from which sample was collected Attribute_Definition_Source: USGS Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 37.052256 Range_Domain_Maximum: 57.888983 Attribute: Attribute_Label: Longitude Attribute_Definition: Longitude of location from which sample was collected Attribute_Definition_Source: USGS Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: -73.833355 Range_Domain_Maximum: -133.31645 Attribute: Attribute_Label: Month Attribute_Definition: Month in which sample was collected Attribute_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Jan Enumerated_Domain_Value_Definition: January Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: May Enumerated_Domain_Value_Definition: May Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Aug Enumerated_Domain_Value_Definition: August Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Sept Enumerated_Domain_Value_Definition: September Enumerated_Domain_Value_Definition_Source: USGS Attribute: Attribute_Label: Year Attribute_Definition: Year in which sample was collected Attribute_Definition_Source: USGS Attribute_Domain_Values: Range_Domain: Range_Domain_Minimum: 2011 Range_Domain_Maximum: 2013 Attribute: Attribute_Label: Description Attribute_Definition: Notes particular to the sample Attribute_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: NA Enumerated_Domain_Value_Definition: Not applicable Enumerated_Domain_Value_Definition_Source: USGS Attribute_Domain_Values: Enumerated_Domain: Enumerated_Domain_Value: Contaminated Enumerated_Domain_Value_Definition: Sample should be treated as contaminated Enumerated_Domain_Value_Definition_Source: USGS Detailed_Description: Entity_Type: Entity_Type_Label: Chlamydiales_23S.txt Entity_Type_Definition: Please refer to the "README" file for descriptions of the contents of the Chlamydiales_23S file Entity_Type_Definition_Source: USGS Distribution_Information: Distributor: Contact_Information: Contact_Person_Primary: Contact_Person: Christina A. Kellogg Contact_Organization: U.S. Geological Survey Contact_Address: Address_Type: mailing and physical Address: 600 4th Street S City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Country: USA Contact_Voice_Telephone: 727-502-8000 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Distribution_Liability: 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. Standard_Order_Process: Digital_Form: Digital_Transfer_Information: Format_Name: ASCII Format_Version_Number: None Format_Specification: Text file Format_Information_Content: 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. Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-F7P55KMJ/data/Primnoa_raw_data.zip Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-F7P55KMJ/data/Chlamydiales_23S.txt Fees: None Technical_Prerequisites: 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. Metadata_Reference_Information: Metadata_Date: 20201013 Metadata_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: Christina A. Kellogg Contact_Organization: U.S. Geological Survey Contact_Address: Address_Type: mailing and physical Address: 600 4th Street S City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Country: USA Contact_Voice_Telephone: 727-502-8000 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata Metadata_Standard_Version: FGDC-STD-001-1998