Metadata: Identification_Information: Citation: Citation_Information: Originator: Dawn B. Goldsmith Originator: Christina A. Kellogg Publication_Date: 20190321 Title: Cold-water coral microbiomes (Astrangia poculata) from Narragansett Bay: sequence data Geospatial_Data_Presentation_Form: FASTA and tabular digital data Series_Information: Series_Name: U.S. Geological Survey Data Release Issue_Identification: doi:10.5066/P9C2XCQQ Publication_Information: Publication_Place: St. Petersburg, FL Publisher: U.S. Geological Survey Online_Linkage: https://doi.org/10.5066/P9C2XCQQ Larger_Work_Citation: Citation_Information: Originator: Dawn B. Goldsmith Originator: Zoe A. Pratte Originator: Christina A. Kellogg Originator: Sara E. Snader Originator: Koty H. Sharp Publication_Date: 20190301 Title: Stability of temperate coral Astrangia poculata microbiome is reflected across different sequencing methodologies Geospatial_Data_Presentation_Form: Publication (Journal) Series_Information: Series_Name: AIMS Microbiology Issue_Identification: 5(1): 62-76 Publication_Information: Publication_Place: Springfield, MO Publisher: AIMS Press Online_Linkage: https://doi.org/10.3934/microbiol.2019.1.62 Description: Abstract: The files provided in this data release are the DNA sequence files referenced in Goldsmith and others (2019), which represent a 16S ribosomal ribonucleic acid (rRNA) gene amplicon survey of Astrangia poculata microbiomes completed using Sanger dideoxy sequencing. The coral samples were collected from Narragansett Bay at Fort Wetherill State Park, Jamestown, Rhode Island in 2015 and 2016 (Sharp and others, 2017). Sequences were obtained by first extracting DNA from a fragment of each A. poculata sample comprising mucus, tissue, and skeleton. Bacterial DNA was amplified from all samples by polymerase chain reaction (PCR), using primers 8F (5’–AGA GTT TGA TCC TGG CTC AG) and 1492R (5’–GGT TAC CTT GTT ACG ACT T) to target the 16S rDNA gene in bacteria. Archaeal DNA from two of the samples (FW1B8 and FW1W8) was amplified using primers 21F (5'–TTC CGG TTG ATC CYG CCG GA) and 958R (5'–YCC GGC GTT GAM TCC AAT T) to target the 16S rDNA gene from archaea. All amplicons were visualized on an agarose gel, extracted from the gel, quantitated, cloned into a vector, and used to transform competent cells. Inserts in positive transformants were sequenced by the Clemson University Genomics Computational Laboratory (Clemson, SC). The sequences were processed by trimming vectors and ends, removing sequences less than 50 base pairs (bp), checking for chimeras, classifying taxonomy, and removing unclassified, chloroplast, and mitochondrial sequences. After processing, 806 bacterial operational taxonomic units (OTUs) and 18 archaeal OTUs remained. Sequences representing each OTU have been deposited in the National Center for Biotechnology Information’s (NCBI) GenBank archive, and have been assigned accession numbers MK175495 through MK176300 (bacterial sequences) and MH915525 through MH915542 (archaeal sequences). Minimum information about a marker gene (MIMARKS) compliant metadata files are also included in the data download files. 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: The microbiome of the temperate coral Astrangia poculata was first described in 2017 using next-generation Illumina sequencing to examine the coral’s bacterial and archaeal associates across seasons and among hosts of differing symbiotic status. Microbial communities did not significantly vary according to symbiotic state but did vary by season. The data in this study were obtained via Sanger sequencing in order to assess the impact of sequencing methodology on the detectable diversity of the coral’s microbiome. A second goal of this study was to create a resource for the research community by producing longer sequences that are better suited for the development of probes and primers. Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 20150909 Ending_Date: 20160426 Currentness_Reference: ground condition Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Bounding_Coordinates: West_Bounding_Coordinate: -71.359444 East_Bounding_Coordinate: -71.359443 North_Bounding_Coordinate: 41.477778 South_Bounding_Coordinate: 41.477777 Keywords: 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 Theme: Theme_Keyword_Thesaurus: Global Change Master Science Directory Theme_Keyword: Biological Classification < Bacteria Theme_Keyword: Biological Classification < Animals < Cnidarians Place: Place_Keyword_Thesaurus: Geographic Names Information Systems (GNIS) Place_Keyword: Narragansett Bay Place_Keyword: Fort Wetherill State Park Place_Keyword: Jamestown Place_Keyword: Rhode Island 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 South City: St. Petersburg State_or_Province: FL Postal_Code: 33701 Contact_Voice_Telephone: (727) 502-8128 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Data_Set_Credit: U.S. Geological Survey, Coastal and Marine Geology Program, St. Petersburg Coastal and Marine Science Center Cross_Reference: Citation_Information: Originator: Ulrike Edwards Originator: Till Rogall Originator: Helmut Blöcker Originator: Monica Emde Originator: Erik C. Böttger Publication_Date: 19891011 Title: Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA Geospatial_Data_Presentation_Form: Publication Series_Information: Series_Name: Nucleic Acids Research Issue_Identification: Vol. 17, issue 19 Publication_Information: Publication_Place: Oxford, United Kingdom Publisher: Oxford University Press (OUP) Other_Citation_Details: Pages 7843-7853 Online_Linkage: https://doi.org/10.1093/nar/17.19.7843 Cross_Reference: Citation_Information: Originator: E. Stackebrandt Originator: W. Liesack Publication_Date: 1993 Title: Nucleic acids and classification Geospatial_Data_Presentation_Form: Publication Publication_Information: Publication_Place: London, England Publisher: Academic Press Other_Citation_Details: In Goodfellow M., O'Donnell AG, editors. Handbook of new bacterial systematics, pp 152-189. Cross_Reference: Citation_Information: Originator: E. F. DeLong Publication_Date: 19920615 Title: Archaea in coastal marine environments. Geospatial_Data_Presentation_Form: Publication Series_Information: Series_Name: Proceedings of the National Academy of Sciences Issue_Identification: Vol. 89, issue 12 Publication_Information: Publication_Place: Washington, D.C., United States Publisher: Proceedings of the National Academy of Sciences Other_Citation_Details: Pages 5685-5689 Online_Linkage: https://doi.org/10.1073/pnas.89.12.5685 Cross_Reference: Citation_Information: Originator: J Gregory Caporaso Originator: Justin Kuczynski Originator: Jesse Stombaugh Originator: Kyle Bittinger Originator: Frederic D Bushman Originator: Elizabeth K Costello Originator: Noah Fierer Originator: Antonio Gonzalez Peña Originator: Julia 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 Pirrung Originator: Jens Reeder Originator: Joel R Sevinsky Originator: Peter J Turnbaugh Originator: William A Walters Originator: Jeremy Widmann Originator: Tanya Yatsunenko Originator: Jesse Zaneveld Originator: Rob Knight Publication_Date: 20100411 Title: QIIME allows analysis of high-throughput community sequencing data Geospatial_Data_Presentation_Form: Publication Series_Information: Series_Name: Nature Methods Issue_Identification: Vol. 7 Publication_Information: Publication_Place: London, United Kingdom Publisher: Springer Nature Other_Citation_Details: Pages 335-336 Online_Linkage: https://doi.org/10.1038/nmeth.f.303 Cross_Reference: Citation_Information: Originator: Jeffrey J Werner Originator: Omry Koren Originator: Philip Hugenholtz Originator: Todd Z DeSantis Originator: William A Walters Originator: J Gregory Caporaso Originator: Largus T Angenent Originator: Rob Knight Originator: Ruth E Ley Publication_Date: 20110630 Title: Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys Geospatial_Data_Presentation_Form: Publication Series_Information: Series_Name: The ISME Journal Issue_Identification: Vol. 6 Publication_Information: Publication_Place: London, United Kingdom Publisher: Springer Nature Other_Citation_Details: Pages 94-103 Online_Linkage: https://doi.org/10.1038/ismej.2011.82 Cross_Reference: Citation_Information: Originator: Daniel McDonald Originator: Morgan N Price Originator: Julia Goodrich Originator: Eric P Nawrocki Originator: Todd Z DeSantis Originator: Alexander Probst Originator: Gary L Andersen Originator: Rob Knight Originator: Philip Hugenholtz Publication_Date: 20111201 Title: An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea Geospatial_Data_Presentation_Form: Publication Series_Information: Series_Name: The ISME Journal Issue_Identification: Vol. 6 Publication_Information: Publication_Place: London, United Kingdom Publisher: Springer Nature Other_Citation_Details: Pages 610-618 Online_Linkage: https://doi.org/10.1038/ismej.2011.139 Cross_Reference: Citation_Information: Originator: Robert C. Edgar Publication_Date: 20101001 Title: Search and clustering orders of magnitude faster than BLAST Geospatial_Data_Presentation_Form: Publication Series_Information: Series_Name: Bioinformatics Issue_Identification: Vol. 26, issue 19 Publication_Information: Publication_Place: Oxford, United Kingdom Publisher: Oxford University Press (OUP) Other_Citation_Details: Pages 2460-2461 Online_Linkage: https://doi.org/10.1093/bioinformatics/btq461 Cross_Reference: Citation_Information: Originator: Robert Edgar Publication_Date: 20160912 Title: UCHIME2: improved chimera prediction for amplicon sequencing Geospatial_Data_Presentation_Form: Publication Online_Linkage: https://doi.org/10.1101/074252 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: Source_Information: Source_Citation: Citation_Information: Originator: Koty H. Sharp Originator: Zoe A. Pratte Originator: Allison H. Kerwin Originator: Randi D. Rotjan Originator: Frank J. Stewart Publication_Date: 20170915 Title: Season, but not symbiont state, drives microbiome structure in the temperate coral Astrangia poculata Geospatial_Data_Presentation_Form: Publication Series_Information: Series_Name: Microbiome Issue_Identification: Vol. 5, issue 1 Publication_Information: Publication_Place: London, United Kingdom Publisher: BioMed Central, Springer Nature Online_Linkage: https://doi.org/10.1186/s40168-017-0329-8 Type_of_Source_Media: Digital and/or Hardcopy Source_Time_Period_of_Content: Time_Period_Information: Multiple_Dates/Times: Single_Date/Time: Calendar_Date: 20150909 Single_Date/Time: Calendar_Date: 20160429 Source_Currentness_Reference: publication date Source_Citation_Abbreviation: Sharp Source_Contribution: The samples used to generate the sequences in this dataset were collected as part of the study reported in Sharp and others (2017). In addition, the DNA that was sequenced for this study was extracted from the samples by Sharp and others (2017) as part of their study. Process_Step: Process_Description: Paired brown (symbiotic) and white (aposymbiotic) samples of A. poculata were collected as described in Sharp and others (2017). Briefly, samples were collected from Narragansett Bay in September 2015 and April 2016 by SCUBA at depths of 1-5 meters. Paired colonies were selected such that the brown and white members of the pair were no more than 10 centimeters apart. Samples were immediately brought to the surface, frozen in liquid nitrogen, and held at -80ºC until DNA extraction. Source_Used_Citation_Abbreviation: Sharp Process_Date: 20150915 Process_Step: Process_Description: Eight samples--two sets of paired brown and white colonies collected in the fall (September) and two sets collected in the spring (April) were analyzed by USGS scientists. DNA was extracted from each sample of A. poculata as described in Sharp and others (2017). Briefly, the PowerSoil DNA Isolation Kit (Qiagen, Valencia, CA) was used according to the manufacturer’s protocol to extract DNA from a fragment of each sample comprising mucus, tissue, and skeleton. Source_Used_Citation_Abbreviation: Sharp Process_Date: 2016 Process_Step: Process_Description: Bacterial primers: DNA from each sample was amplified by PCR using primers 8F (5’–AGA GTT TGA TCC TGG CTC AG) and 1492R (5’–GGT TAC CTT GTT ACG ACT T) to target the 16S rRNA gene [9,10]. Each 25-microliter (µL) reaction contained 12.5 µL AmpliTaq Gold 360 Master Mix (Applied Biosystems, Foster City, CA), 0.4 µM concentration of each primer, and 10 µL of template DNA. The reaction conditions consisted of 15 minutes (min) of initial denaturation at 95ºC, 30 cycles of (i) 1 min denaturation at 95ºC, (ii) 1 min annealing at 54ºC, and (iii) 2 min extension at 72ºC, and 10 min of final extension at 72ºC. Amplicons were visualized on a 1.5% agarose gel, then extracted from the gel using the QIAquick Gel Extraction Kit (QIAGEN, Germantown, MD) according to the manufacturer’s instructions. Gel-extracted amplicons were quantitated using a Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) on a Qubit 3.0 fluorometer according to the manufacturer’s instructions. Process_Date: 2017 Process_Step: Process_Description: Archaeal primers: DNA from two of the samples (FW1B8 and FW1W8) was also amplified using primers 21F (5’–TTC CGG TTG ATC CYG CCG GA) and 958R (5’–YCC GGC GTT GAM TCC AAT T) in order to amplify the 16S rRNA gene from Archaea (DeLong, 1992). Each 25-µL reaction contained 12.5 µL AmpliTaq Gold 360 Master Mix (Applied Biosystems, Foster City, CA), 0.4 µM concentration of each primer, and 10 µL of template DNA. The reaction conditions consisted of 15 min of initial denaturation at 95ºC, 30 cycles of (i) 95ºC for1.5 min, (ii) 55ºC for 1.5 min, and (iii) 72ºC for 1.5 min, and 10 min of final extension at 72ºC (DeLong, 1992). Amplicons were visualized, extracted, and quantitated as described above for the bacterial amplicons. Process_Date: 2017 Process_Step: Process_Description: Amplicons were cloned into the pDrive vector using the PCR Cloning Plus kit (QIAGEN, Germantown, MD) and used to transform competent cells. After M13 screening, inserts in positive transformants were sequenced by the Clemson University Genomics Computational Laboratory (Clemson, SC). USGS staff received approximately 4,200 raw sequences from the sequencing facility (available, upon request) that were subsequently trimmed and checked for quality assurance/quality control (QA/QC). Those QA/QC procedures resulted in ~1,700 sequences, which are described in Goldsmith and others (2019) and provided in this data release. Process_Date: 2017 Process_Step: Process_Description: Vector and ends were trimmed from the sequences using Geneious (version 11.1.4; Biomatters Ltd., Auckland, NZ). Process_Date: 2018 Process_Step: Process_Description: Using QIIME version 1.9.1, all sequences less than 50 bp were removed. Greengenes version 13_8 (http://greengenes.secondgenome.com/) was used through QIIME to perform a chimera check with usearch61 (https://www.drive5.com/usearch/), and to classify taxonomy using an open reference algorithm with a 97% similarity threshold [15]. Singletons were retained, while all other default parameters were used. After chimeric, unclassified, chloroplast, and mitochondrial sequences were removed, 996 bacterial OTUs remained. Process_Date: 2018 Process_Step: Process_Description: Upon submission of the sequences to NCBI’s GenBank, GenBank’s implementation of version 10 of usearch (64-bit version) using the uchime2_ref command in high confidence mode uncovered 190 additional chimeras. These sequences were removed, resulting in a dataset of 806 bacterial OTUs. Sequences representing each bacterial OTU have been deposited in GenBank under accession numbers MK175495 to MK176300. Sequences representing each archaeal OTU (18 OTUs) have been deposited in GenBank under accession numbers MH915525 to MH915542. Process_Date: 2018 Entity_and_Attribute_Information: Overview_Description: Entity_and_Attribute_Overview: Please refer to the "README" file, README_Astrangia.txt, for detailed descriptions of the contents of the data files. Additional information is contained in the Minimum Information about a Marker Gene (MIMARKS) compliant metadata files, entitled “Astrangia_MIMARKS_metadata_bacteria.xlsx”, “Astrangia_MIMARKS_metadata_bacteria.txt”, “Astrangia_MIMARKS_metadata_archaea.xlsx”, and “Astrangia_MIMARKS_metadata_archaea.txt”. Non-proprietary versions of the MIMARKS metadata are also provided in comma separated values (CSV) format and are included in the data download files. Entity_and_Attribute_Detail_Citation: The entity and attribute information was generated by the individuals 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 and Physical 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: FASTA, CSV, XLSX Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9C2XCQQ/data/Astrangia_archaeal_seqs_data.zip Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9C2XCQQ/data/Astrangia_bacterial_seqs_data.zip Fees: None Metadata_Reference_Information: Metadata_Date: 20190820 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