Metadata: Identification_Information: Citation: Citation_Information: Originator: Christina A. Kellogg Originator: Dawn B. Goldsmith Originator: Julie J. Voelschow Publication_Date: 20210629 Title: Coral microbiome preservation and extraction method comparison of samples collected in March and August 2018-raw data Geospatial_Data_Presentation_Form: FASTQ and tabular digital data Larger_Work_Citation: Citation_Information: Originator: Christina A. Kellogg Originator: Dawn B. Goldsmith Originator: Julie J. Voelschow Publication_Date: 20210629 Title: Coral microbiome preservation and extraction method comparison of samples collected in March and August 2018-raw data Series_Information: Series_Name: U.S. Geological Survey Data Release Issue_Identification: doi:10.5066/P96GBWDM Publication_Information: Publication_Place: St. Petersburg, FL Publisher: U.S. Geological Survey Online_Linkage: https://doi.org/10.5066/P96GBWDM Description: Abstract: The files in this this U.S. Geological Survey (USGS) data release (Kellogg and others, 2021) are the raw 16S ribosomal ribonucleic acid (rRNA) gene amplicon deoxyribonucleic acid (DNA) sequence files from 90 samples of tropical and cold-water corals, as well as sequence files from a mock community and extraction blanks for the kits used for DNA extraction. The mock community was sequenced in order to assess any biases in the sequencing technology, while extraction blanks were sequenced in order to identify any contaminants in the DNA extraction kits. The tropical coral samples (three species) were collected by permit (#FKNMS-2017-064) in March 2018 from a nursery in the Florida Keys National Marine Sanctuary. The cold-water coral samples (two species) were collected in August 2018 from two locations in the Atlantic Ocean. Purpose: The purpose of this experiment was to compare preservation and DNA extraction methods across tropical and cold-water corals. Supplemental_Information: Sequencing data were extracted from samples via the PowerBiofilm DNA Isolation Kit owned by MO BIO Laboratories, Inc. MO BIO Laboratories was purchased by the molecular diagnostics company, Qiagen, which resulted in the sequencing kit being renamed to the Qiagen DNEasy PowerBiofilm DNA Isolation Kit. Data files included in Methods_comparison_Qiagen_raw_data.zip reflect this name change, however, the metadata processing steps refer to the original kit name because it was still applicable during data processing. The raw metagenomic 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 PRJNA544686. For additional details and interpretations, please see Pratte and Kellogg (2021). Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 20180327 Ending_Date: 20180830 Currentness_Reference: ground condition Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Bounding_Coordinates: West_Bounding_Coordinate: -81.45441 East_Bounding_Coordinate: -75.16639 North_Bounding_Coordinate: 34.9410185 South_Bounding_Coordinate: 24.661751 Keywords: Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:ba147df0-0de1-4f37-92f6-2712c0e21547 Theme: Theme_Keyword_Thesaurus: ISO 19115 Topic Category Theme_Keyword: biota Theme_Keyword: oceans Theme: Theme_Keyword_Thesaurus: USGS Thesaurus Theme_Keyword: marine biology Theme_Keyword: marine geology Theme_Keyword: coelenterates Theme_Keyword: Holocene Place: Place_Keyword_Thesaurus: Geographic Names Information System Place_Keyword: Summerland Key Place_Keyword: Atlantic Ocean Place_Keyword: Pamlico Canyon Place_Keyword: Florida Keys Place: Place_Keyword_Thesaurus: None Place_Keyword: Richardson Hills Access_Constraints: None. Please see 'Distribution Info' for details. 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 South City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Contact_Voice_Telephone: (727) 502-8128 Cross_Reference: Citation_Information: Originator: Zoe A. Pratte Originator: Christina A. Kellogg Publication_Date: 2021 Title: Comparison of preservation and extraction methods on five taxonomically disparate coral microbiomes Geospatial_Data_Presentation_Form: publication Series_Information: Series_Name: Frontiers in Marine Science Issue_Identification: 8:684161 Online_Linkage: https://doi.org/10.3389/fmars.2021.684161 Cross_Reference: Citation_Information: Originator: James J. Kozich Originator: Sarah L. Westcott Originator: Nielson T. Baxter Originator: Sarah K. Highlander Originator: Patrick D. Schloss Publication_Date: 20130807 Title: Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform Geospatial_Data_Presentation_Form: publication Series_Information: Series_Name: Applied and Environmental Microbiology Issue_Identification: vol. 79, issue 17 Publication_Information: Publication_Place: Washington, D.C. Publisher: American Society for Microbiology Other_Citation_Details: ppg. 5112-5120 Online_Linkage: https://doi.org/10.1128/AEM.01043-13 Cross_Reference: Citation_Information: Originator: Amy Apprill Originator: Sean McNally Originator: Rachel Parsons Originator: Laura Weber Publication_Date: 20150604 Title: Minor revision to V4 region SSU rRNA 806R gene primer greatly increases detection of SAR11 bacterioplankton Geospatial_Data_Presentation_Form: publication Series_Information: Series_Name: Aquatic Microbial Ecology Issue_Identification: vol. 75, issue 2 Publication_Information: Publication_Place: n/a Publisher: Inter-Research Science Center Other_Citation_Details: ppg. 129-137 Online_Linkage: https://doi.org/10.3354/ame01753 Cross_Reference: Citation_Information: Originator: Promega Publication_Date: 20180401 Title: Maxwell RSC Blood DNA Kit Geospatial_Data_Presentation_Form: publication Online_Linkage: https://www.promega.com/-/media/files/resources/protocols/technical-manuals/101/maxwell-rsc-blood-dna-kit-protocol.pdf?la=en Cross_Reference: Citation_Information: Originator: Qiagen Publication_Date: 20151117 Title: DNEasy PowerBiofilm Kit Handbook Geospatial_Data_Presentation_Form: publication Online_Linkage: https://www.qiagen.com/us/resources/download.aspx?id=c5363245-cd9c-4314-b8fb-c4f8b4d669c4&lang=en Data_Quality_Information: Attribute_Accuracy: Attribute_Accuracy_Report: No formal attribute accuracy tests were conducted. Logical_Consistency_Report: No formal logical consistency tests were conducted. Completeness_Report: Dataset is considered complete for the information presented. 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: All tropical coral samples (Montastraea cavernosa, Porites astreoides, and Stephanocoenia intersepta) were collected manually by permit in March 2018 from a nursery in the Florida Keys National Marine Sanctuary, temporarily housed at the facility of Mote Marine Laboratory & Aquarium’s Elizabeth Moore International Center for Coral Reef Research & Restoration in Summerland Key, Florida. Samples beginning with MCR, PAR, and SIR were transferred to sterile tubes, covered in RNAlater, and incubated overnight at 4°C to allow the preservative to permeate the coral tissues before transfer to -20°C for long-term storage. Samples beginning with MCS, PAS, and SIS were transferred to sterile tubes, covered in DNA/RNA Shield, and incubated overnight at 4°C to allow the preservative to permeate the coral tissues before transfer to -20°C for long-term storage. Samples beginning with MCN, PAN, and SIN were double-bagged in sterile Whirl-Pak bags (Nasco, Fort Atkinson, WI, USA) and then stored in liquid nitrogen until transfer to -80°C for long-term storage. Process_Date: 20180327 Process_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: Christina A Kellogg Contact_Organization: U.S. Geological Survey, Southeast Region Contact_Position: Research Microbiologist Contact_Address: Address_Type: mailing address Address: 600 4Th Street South City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Country: United States Contact_Voice_Telephone: 727-502-8128 Contact_Facsimile_Telephone: 727-502-8181 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Process_Step: Process_Description: All cold-water coral samples (Lophelia pertusa and Paragorgia johnsoni) were collected by the sampling arm of a crewed submersible. The sampler’s individual compartments were cleaned at the surface using ethanol, filled with sterile deionized water, and sealed. Coral branches were collected and placed into the containers after ambient seawater evacuated the freshwater, and the containers were re-sealed at depth. Samples with names beginning with LP and PJ were collected in August 2018 on cruise AT-41 on the R/V Atlantis using the Alvin submersible (Woods Hole Oceanographic Institution). Samples with names beginning with LP were collected from Richardson Hills on dive A4963, while samples with names beginning with PJ were collected from Pamlico Canyon on dive A4969. Upon return to the surface, samples beginning with LPR, PJR, LPS, and PJS were transferred to sterile tubes, covered in preservative, and incubated overnight at 4°C to allow the preservative to permeate the coral tissues before transfer to -20°C for long-term storage. The preservative used for samples LPR and PJR was RNAlater (Life Technologies, Grand Island, NY, USA), while the preservative used for samples LPS and PJS was DNA/RNA Shield (Zymo Research, Irvine, CA, USA). Samples beginning with LPN and PJN were transferred to sterile tubes and then stored in liquid nitrogen until transfer to -80°C for long-term storage. Process_Date: 20180824 Process_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: Christina A Kellogg Contact_Organization: U.S. Geological Survey, Southeast Region Contact_Position: Research Microbiologist Contact_Address: Address_Type: mailing address Address: 600 4Th Street South City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Country: United States Contact_Voice_Telephone: 727-502-8128 Contact_Facsimile_Telephone: 727-502-8181 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Process_Step: Process_Description: Homogenization of cells and extraction of DNA from the samples occurred at the Coral Microbial Ecology Laboratory in St. Petersburg, FL. All samples were wrapped in sterile aluminum foil and crushed with a hammer. For samples ending in numbers 1, 2, and 3, cells were disrupted by adding the crushed samples and 300 microliters of molecular grade water to Lysing Matrix A and homogenizing them for 20 seconds in a FastPrep bead mill homogenizer at setting 6.5 (MP Biomedicals, Santa Ana, CA). DNA was extracted from those samples using the Maxwell RSC Blood DNA Kit with a Maxwell RSC Instrument (model AS4500) (Promega, Fitchburg, WI). DNA Lysis Buffer (300 microliters) and Proteinase K (25 microliters) from the kit were added to each sample. Samples were mixed by inversion three times, incubated for one hour in a 56°C, mixed again by inversion three times, and centrifuged at 2500 rpm for 30 seconds. The supernatant of each sample was transferred to a front well of the cartridge in the Maxwell RSC Instrument. Sections 3B and 5 of the manufacturer’s protocol (Promega, 2018) were then followed to complete the DNA extraction. DNA was extracted from samples ending in numbers 4, 5, and 6 using the Qiagen PowerBiofilm DNA Isolation Kit according to the manufacturer’s instructions (Qiagen, 2015) with two modifications to adapt the protocol to the samples. Bead beating (Step 5 of the homogenization section of the protocol) was accomplished using a FastPrep homogenizer for 30 seconds at setting 5. Step 3 of the vacuum section of the protocol was conducted by centrifuging the samples for 1 minute at 13000xg. Two extraction blanks for each method were also prepared: one substituted phosphate-buffered saline solution for the sample and the other substituted nuclease-free water for the sample. Process_Date: 20181128 Process_Contact: Contact_Information: Contact_Person_Primary: Contact_Person: Christina A Kellogg Contact_Organization: U.S. Geological Survey, Southeast Region Contact_Position: Research Microbiologist Contact_Address: Address_Type: mailing address Address: 600 4th Street South City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Country: United States Contact_Voice_Telephone: 727-502-8128 Contact_Facsimile_Telephone: 727-502-8181 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Process_Step: Process_Description: Library preparation and sequencing were conducted by Glomics, Inc. (Norman, OK). To target the V4 region of the 16S rRNA gene, a fusion primer set was constructed using primers 515F (5′ GTGCCAGCMGCCGCGGTAA) and 806RB (5′ GGACTACNVGGGTWTCTAAT) (Apprill and others, 2015) along with adapters, indices, linkers, and pads in accordance with the dual-index sequencing strategy of Kozich and others (2013). Amplicons were purified, quantified, and pooled in equal concentrations for sequencing on a MiSeq sequencing system with v2 chemistry to obtain paired-end 250-bp reads. A mock community was also sequenced in order to assess any biases in the sequencing technology. The raw data files associated with this data release have also been submitted to the NCBI Sequence Read Archive (SRA) under Bioproject number PRJNA544686. Process_Date: 20190318 Entity_and_Attribute_Information: Overview_Description: Entity_and_Attribute_Overview: Please refer to the "README" file, README_Methods_Comp.txt, for detailed descriptions of the contents of the raw data files. Additional information is contained in the minimum information about a marker gene sequence (MIMARKS) compliant metadata, Methods_Comp_MIMARKS_compliant_metadata.csv, which is included in each data download folder. 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_Address: Address_Type: mailing address Address: 600 4th Street South City: St. Petersburg State_or_Province: FL 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: Digital Data Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P96GBWDM/data/Methods_comparison_Promega_raw_data.zip Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P96GBWDM/data/Methods_comparison_Qiagen_raw_data.zip Fees: None Metadata_Reference_Information: Metadata_Date: 20210923 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 South City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Contact_Voice_Telephone: (727) 502-8128 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata Metadata_Standard_Version: FGDC-STD-001-1998