Metadata: Identification_Information: Citation: Citation_Information: Originator: Christina A. Kellogg Originator: James S. Evans Originator: Julie J. Voelschow Publication_Date: 20211122 Title: Raw sequencing and amplicon sequence variant data from bacterial communities shed by Montastraea cavernosa coral fragments into filtered seawater mesocosms Edition: 2.0 Geospatial_Data_Presentation_Form: FASTQ and tabular digital data Larger_Work_Citation: Citation_Information: Originator: Christina A. Kellogg Originator: James S. Evans Originator: Julie J. Voelschow Publication_Date: 20210528 Title: Bacterial Communities Shed by Montastraea cavernosa Coral Fragments into Filtered Seawater Mesocosms—Raw Data Geospatial_Data_Presentation_Form: publication Series_Information: Series_Name: U.S. Geological Survey data release Issue_Identification: doi:10.5066/P9B13K8N 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/P9B13K8N Description: Abstract: The files provided in this U.S. Geological Survey (USGS) data release (Kellogg and others, 2021) include an amplicon sequence variant (ASV) table and the raw 16S rRNA gene amplicon files from six microbial communities (Mcav17, Mcav18, McH-101, McH-103, McD-57, and McD-58) derived from mesocosms consisting of filtered seawater in which either healthy or diseased (stony coral tissue loss disease) fragments of Montastraea cavernosa had been incubated, as well as sequence files of a mock community and extraction kit blank. Mesocosms were inoculated at the Smithsonian Marine Station located in Fort Pierce, Florida, during two separate trips: one in October 2019 and the other in November 2020. The coral fragments were collected between April 2018 and November 2020, from various locations throughout the Florida Keys. Mesocosms were set up by placing the coral fragments into filtered seawater for 4-5 days and then the fragments were removed so the water could be processed. The mock community was sequenced to assess any biases in the sequencing technology, while extraction blanks were sequenced to identify any contaminants in the DNA extraction kit. Purpose: The purpose of this experiment was to identify and compare microbial communities shed by corals into the mesocosms. Sample DNA extraction occurred at the USGS Coral Microbial Ecology Laboratory in St. Petersburg, Florida, while polymerase chain reaction (PCR) amplification and sequencing were performed by RTSF Genomics Core at Michigan State University in East Lansing, Michigan. The 16 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 PRJNA731170. Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 20191025 Ending_Date: 20210824 Currentness_Reference: ground condition Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Bounding_Coordinates: West_Bounding_Coordinate: -80.3106 East_Bounding_Coordinate: -80.3106 North_Bounding_Coordinate: 27.45957 South_Bounding_Coordinate: 27.45956 Description_of_Geographic_Extent: Florida Keywords: Theme: Theme_Keyword_Thesaurus: ISO 19115 Topic Category Theme_Keyword: biota Theme_Keyword: oceans Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:83f95ddf-34dc-4dd1-a5c1-3db973a46f7d Theme: Theme_Keyword_Thesaurus: USGS Thesaurus Theme_Keyword: marine biology Theme_Keyword: laboratory methods Theme_Keyword: bacteria Theme_Keyword: microbiology Theme_Keyword: coelenterates Place: Place_Keyword_Thesaurus: Geographic Names Information System Place_Keyword: Florida Keys Place_Keyword: Atlantic Ocean 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 Address: 600 4th St. South City: St. Petersburg State_or_Province: Florida Postal_Code: 33701 Contact_Voice_Telephone: 727-502-8128 Contact_Electronic_Mail_Address: ckellogg@usgs.gov Cross_Reference: Citation_Information: Originator: QIAGEN Publication_Date: 20200131 Title: Qiagen DNeasy PowerBiofilm Kit Geospatial_Data_Presentation_Form: publication Online_Linkage: https://www.qiagen.com/us/products/discovery-and-translational-research/dna-rna-purification/dna-purification/microbial-dna/dneasy-powerbiofilm-kit/ 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: 2013 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: 79(17) Other_Citation_Details: pages 5112–5120 Online_Linkage: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753973/ Cross_Reference: Citation_Information: Originator: Benjamin J. Callahan Originator: Paul J. McMurdie Originator: Michael J. Rosen Originator: Andrew W. Han Originator: Amy Jo A. Johnson Originator: Susan P. Holmes Publication_Date: 20160523 Title: DADA2: High-resolution sample inference from Illumina amplicon data Geospatial_Data_Presentation_Form: publication Series_Information: Series_Name: Nature Methods Issue_Identification: 13 Other_Citation_Details: pages 581-583 Online_Linkage: https://doi.org/10.1038/nmeth.3869 Cross_Reference: Citation_Information: Originator: Nicholas A. Bokulich Originator: Benjamin D. Kaehler Originator: Jai Ram Rideout Originator: Matthew Dillion Originator: Evan Bolyen Originator: Rob Knight Originator: Gavin A. Huttley Originator: J. Gregory Caporaso Publication_Date: 20180517 Title: Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin Geospatial_Data_Presentation_Form: publication Series_Information: Series_Name: Microbiome Issue_Identification: 6(90) Other_Citation_Details: pages 1-17 Online_Linkage: https://doi.org/10.1186/s40168-018-0470-z Cross_Reference: Citation_Information: Originator: Evan Bolyen Originator: Jai Ram Rideout Originator: Matthew R. Dillion Originator: Nicholas A. Bokulich Originator: Christian C. Abnet Originator: Gabriel A. Al-Ghalith Originator: Harriet Alxander Originator: Eric J. Alm Originator: Manimozhiyan Arumugam Originator: Francesco Asnicar Publication_Date: 20190724 Title: Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2 Geospatial_Data_Presentation_Form: publication Series_Information: Series_Name: Nature Biotechnology Issue_Identification: 37 Other_Citation_Details: pages 852-857 Online_Linkage: https://doi.org/10.1038/s41587-019-0209-9 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, as described in the abstract. Lineage: Process_Step: Process_Description: Coral collection - The coral fragment for mesocosm McH-101 was collected in April 2018 from the Florida Keys while the fragment for mesocosm McH-103 was acquired on January 31, 2019, from the Florida Keys National Marine Sanctuary in Key West. Both healthy coral fragments were maintained in a holding tank at the Smithsonian Marine Station located in Ft. Pierce, FL, until the first mesocosm experiment began in October 2019. Coral samples for mesocosms Mcav17 and Mcav18 were collected from a patch reef near Summerland Key (24.54767, -81.45697) on October 23, 2019. Coral samples for mesocosms McD-57 and McD-58 were obtained from a patch reef near Marathon (24.68982, -81.02978) on November 1, 2020. The second mesocosms were inoculated at the Smithsonian Marine Station in November 2020. Process_Date: 20191023 Process_Step: Process_Description: Sample creation - first mesocosm inoculations: The mesocosms were initially set up and processed at the Smithsonian Marine Station (27.45956, -80.31060). Mesocosm seawater came from a storage tank that recirculated it through an ultraviolet (UV) sterilizer, 20-micrometer (µm) filter, and an activated carbon filter. The seawater was 0.22-µm filtered prior to use in 18-liter (L) mesocosms and is referred to as ‘filtered seawater.’ For samples McH-101, McH-103, Mcav17, and Mcav18, coral fragments were placed in filtered seawater mesocosms and allowed to naturally shed microbes from October 25 to October 29, 2019. Process_Date: 20191029 Process_Step: Process_Description: Sample creation - second mesocosm inoculations: The second mesocosms were also instituted and processed at the Smithsonian Marine Station in Ft. Pierce, Florida, using the same configurations described in the previous step. For sample McD-57, the coral fragment was placed in filtered seawater mesocosm and allowed to naturally shed microbes from November 3-6, 2020. For sample McD-58, the coral fragment was placed in filtered seawater mesocosm and allowed to naturally shed microbes from November 3 to November 7, 2020. Process_Date: 20201107 Process_Step: Process_Description: Sample creation - first filtration: Samples McH-101 and McH-103 were processed on October 28, 2019, and samples Mcav17 and Mcav18 were processed October 29, 2019. For samples McH-101, McH-103, Mcav17, and Mcav18, the coral fragments were removed from the 18L mesocosms and the water was pre-filtered through a sterile 200-micron mesh to remove loose debris. A Pall tangential flow filtration (TFF) system employing five 100 kDa T-series Centramate filter cassettes was used to concentrate the microbial community in each sample from the 18L original volume down to 210-250 milliliter (ml) concentrate. The microbial concentrate was filtered through a sterile Corning 430756 unit containing a 0.22-µm cellulose nitrate filter and then the filter was cut out of the unit with a sterile razor blade, transferred to a sterile whirlpak bag and frozen at -20°C until extracted for DNA. Process_Date: 20191029 Process_Step: Process_Description: Sample creation - second filtration: Sample McD-57 was processed November 6, 2020. Sample McD-58 was processed November 7, 2020. For samples McD-57 and McD-58, the coral fragments were removed from the 18L mesocosms and the water was pre-filtered through a sterile 106-micron mesh to remove loose debris. A Pall tangential flow filtration system employing five 100 kDa T-Series Centramate filter cassettes was used to concentrate the microbial community in each sample from the 18L original volume down to 190-230 ml concentrate. The microbial concentrate was first filtered through a sterile ThermoScientific 126-0080 unit containing a 0.8-µm cellulose nitrate filter to remove any eukaryotes. The filtrate was then filtered through a sterile Corning 430756 unit containing a 0.22-µm cellulose nitrate filter and then the filter was cut out of the unit with a sterile razor blade, transferred to a sterile whirlpak bag and frozen at -20°C, until extracted for DNA. Process_Date: 20201107 Process_Step: Process_Description: DNA extraction - The DNA extraction process was performed in March 2021, at the USGS Coral Microbial Ecology Laboratory located in St. Petersburg, FL. DNA was extracted from the 0.22-µm cellulose nitrate filters using Qiagen’s DNeasy PowerBiofilm Kit (QIAGEN, 2020), following manufacturer’s instructions in the Quick Start Protocol dated November 2016. Process_Date: 20210301 Process_Step: Process_Description: Sequencing - Sequencing was done by the Michigan State University RTSF Genomics Core (East Lansing, MI). USGS submitted eight samples (n=6, plus one mock community and one extraction kit blank) of microbial metagenomic DNA for amplicon library preparation of the bacterial 16S-V4 hypervariable region and Illumina sequencing. Libraries were prepared using the MiSeq Dual Index method developed in the Patrick Schloss lab (Kozich and others, 2013). Primers 515f/806r were used to amplify the V4 region. All reactions were batch normalized using Invitrogen SequalPrep DNA Normalization plates. Product recovered from the plates was pooled and concentrated using an Amicon spin column. This pool was cleaned up using AMPure XP magnetic SPRI beads. The pool was quality controlled and quantified using a combination of Qubit dsDNA HS, Agilent 4200 TapeStation HS DNA1000 and Kapa Illumina Library Quantification qPCR assays. The pool was loaded onto an Illumina MiSeq v2 Nano flow cell and sequencing was performed in a 2x250bp paired end format using a v2 500 cycle reagent cartridge. Custom sequencing and index primers complementary to the 515f/806r oligomers were added to appropriate wells of the reagent cartridge. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.54 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v2.20.0. Process_Date: 20210326 Process_Step: Process_Description: Data analysis - Data files (BacteriaFilters_ASV_Table.zip) containing tabulations of ASVs, their DNA sequences, their taxonomic identification, and the abundance (number of sequence reads) for each of the samples and controls were added in the version 2.0 update of this data release (Kellogg and others, 2021). Sequences were imported into QIIME2 [version 2021.4] (Bolyen and others, 2019) and trimmed, merged, and sorted into amplicon sequence variants (ASVs) using DADA2 (Callahan and others, 2016) and the parameters ‘–p-trim-left-f 13 –p-trim-left-r 13 –p-trunc-len- f 200 –p-trunc-len-r 200.’ Taxonomy was assigned using the pre-trained Silva classifier silva-138-99-515-806-nb-classifier (Bokulich and others, 2018). All ASVs assigned as “mitochondria” or “chloroplast” were removed. Process_Date: 20210824 Entity_and_Attribute_Information: Overview_Description: Entity_and_Attribute_Overview: Please refer to the "README" file, README_BacteriaFilters.txt, for detailed descriptions of the contents of the raw and ASV data files. Additional information is contained in the minimum information about a marker sequence (MIMARKS) compliant metadata, MIMARKS_BacteriaFilters.xlsx as well as SRA_metadata_BacteriaFilters.xlsx, which is also included in the data download files. 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 Address: 600 4th St. 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: text, comma-delimited text, Microsoft Excel format File_Decompression_Technique: Winzip or 7zip Transfer_Size: 880.8 Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9B13K8N/data/BacteriaFilters_Raw_data.zip Fees: None Metadata_Reference_Information: Metadata_Date: 20211122 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: FL 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