Metadata: Identification_Information: Citation: Citation_Information: Originator: Christina A. Kellogg Originator: James S. Evans Originator: Julie J. Voelschow Publication_Date: 20230801 Title: Prokaryotic Communities Shed by Diseased and Healthy Corals (Diploria labyrinthiformis, Pseudodiploria strigosa, Montastraea cavernosa, Colpophyllia natans, and Orbicella faveolata) into Filtered Seawater Mesocosms – Raw and Processed Data 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: 20230801 Title: Prokaryotic Communities Shed by Diseased and Healthy Coral (Diploria labyrinthiformis, Pseudodiploria strigosa, Montastraea cavernosa, Colpophyllia natans, and Orbicella faveolata) into Filtered Seawater Mesocosms - Raw and Processed Data Geospatial_Data_Presentation_Form: FASTQ and tabular digital data Series_Information: Series_Name: U.S. Geological Survey data release Issue_Identification: doi:10.5066/P9LRIX9E 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/P9LRIX9E Description: Abstract: The files in this data release (Kellogg and others, 2023) are those referenced in the journal article by Evans and others (2023) entitled “Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD).” They contain an amplicon sequence variant (ASV) table and the raw 16S rRNA gene amplicon files from fifty-six 0.22-micrometer (µm) pore size filters, as well as six reagent blanks, three mock communities, and a 0.22-µm-filtered ultraviolet (UV)-treated seawater (FSW) control. The 0.22 µm pore size filters contained tangential flow filtration (TFF) concentrated microbial communities derived from bucket mesocosms consisting of approximately 18 liters (L) of UV-treated FSW in which either healthy or diseased corals (Diploria labyrinthiformis, Pseudodiploria strigosa, Montastraea cavernosa, Colpophyllia natans, and Orbicella faveolata) had been incubated, and a FSW control. Colonies and fragments of apparently healthy corals were collected from Florida reefs or nurseries between April 2018 and September 2020 and transported to the Smithsonian Marine Station (SMS) in Fort Pierce, Florida. These samples were transferred to indoor, temperature-controlled water tables containing FSW and maintained along with other corals as part of the SMS long-term healthy coral stock. Corals exhibiting signs consistent with stony coral tissue loss disease (SCTLD) were collected from the reef immediately prior to each experimental run (Run 1 – October 2019, Run 2 – November 2020, and Run 3 – March 2021), and transported to SMS to be placed in individual mesocosms with weighted air lines. Apparently healthy corals of the same or similar species (i.e., same genus or family) were simultaneously transferred from the SMS healthy stock tanks into identical individual mesocosms. All mesocosms were housed within outdoor water tables containing recirculating freshwater maintained at approximately 28 degrees Celsius (°C) and located under a mesh canopy to allow some sunlight attenuation. Separate “healthy” and “diseased” water tables were maintained to prevent cross-contamination between the different mesocosm types. All corals were incubated within the mesocosms for 2-5 days to enrich the water with microbes. Following the incubation period, the corals were removed from their mesocosms, and the seawater was poured through a sterilized mesh screen (200 µm for Run 1, and 106 µm for Runs 2 and 3). The water was TFF-concentrated, then sequentially passed through a sterile 0.8 µm pore size nitrocellulose filter unit (Runs 2 and 3) and a sterile 0.22 µm pore size nitrocellulose filter unit (all three runs). The 0.22 µm pore size filters were then cut from the units using ethanol-sterilized blades, with portions frozen at -20°C for later processing. Extraction of deoxyribonucleic acid (DNA) from the samples and blanks occurred between February and May 2021 at the U.S. Geological Survey St. Petersburg Coastal and Marine Science Center (USGS SPCMSC) Coral Microbial Ecology Laboratory in St. Petersburg, FL, USA using Qiagen DNeasy PowerBiofilm kits. Library preparation and DNA sequencing were conducted on July 28th, 2021 by the Michigan State University RTSF Genomics Core (East Lansing, MI) using primers 515F: GTGCCAGCMGCCGCGGTAA and 806R: GGACTACHVGGGTWTCTAAT to target the V4 variable region of the 16S ribosomal ribonucleic acid (rRNA) gene on a MiSeq sequencing system with v2 chemistry to obtain paired-end 250-base pair (bp) reads. Purpose: The purpose of this experiment was to investigate the size class of microorganism(s) associated with SCTLD transmission. This dataset represents the prokaryotic community shed by SCTLD-diseased and apparently healthy coral (Diploria labyrinthiformis, Pseudodiploria strigosa, Montastraea cavernosa, Colpophyllia natans, and Orbicella faveolata) into mesocosms as part of this study. Supplemental_Information: The raw 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 PRJNA918331. Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 201804 Ending_Date: 20220506 Currentness_Reference: ground condition Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Description_of_Geographic_Extent: Florida, Michigan Bounding_Coordinates: West_Bounding_Coordinate: -84.474 East_Bounding_Coordinate: -80.3106 North_Bounding_Coordinate: 42.7228 South_Bounding_Coordinate: 27.45956 Keywords: Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:d5d9052f-c4f9-4962-bd20-a255e52c3a77 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: laboratory methods Theme_Keyword: microbiology Theme_Keyword: coelenterates Theme_Keyword: bacteria Theme_Keyword: DNA sequencing Place: Place_Keyword_Thesaurus: Geographic Names Information System (GNIS) Place_Keyword: Florida Keys Place_Keyword: Atlantic Ocean Place_Keyword: Gulf of Mexico 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 Native_Data_Set_Environment: Environment as of Metadata Creation: Microsoft Windows 10 Version 6.2 (Build 9200); Real Time Analysis (v1.18.54); Illumina Bcl2fastq (v2.20.0); QIIME2 (v. 2022.2); MAFFT (v. 7.0); FastTree 2. Cross_Reference: Citation_Information: Originator: James S. Evans Originator: Valerie J. Paul Originator: Blake Ushijima Originator: Kelly A. Pitts Originator: Christina A. Kellogg Publication_Date: 202308 Title: Investigating microbial size classes associated with the transmission of stony coral tissue loss disease (SCTLD) Geospatial_Data_Presentation_Form: Journal Series_Information: Series_Name: PeerJ Issue_Identification: Volume 11, Article 15836 Online_Linkage: https://doi.org/10.7717/peerj15836 Cross_Reference: Citation_Information: Originator: Qiagen Publication_Date: 20200131 Title: Qiagen DNeasy PowerBiofilm kit handbook Geospatial_Data_Presentation_Form: Instructional Manual Online_Linkage: https://www.qiagen.com/us/resources/download.aspx?id=c5363245-cd9c-4314-b8fb-c4f8b4d669c4&lang=en Cross_Reference: Citation_Information: Originator: James S. Evans Originator: Valerie J. Paul Originator: Blake Ushijima Originator: Christina A. Kellogg Publication_Date: 20220208 Title: Combining tangential flow filtration and size fractionation of mesocosm water as a method for the investigation of waterborne coral diseases Geospatial_Data_Presentation_Form: Journal Series_Information: Series_Name: Biology Methods and Protocols Issue_Identification: Volume 7(1) Other_Citation_Details: Pages 1-8 Online_Linkage: https://doi.org/10.1093/biomethods/bpac007 Cross_Reference: Citation_Information: Originator: John H. Paul Originator: Sunny C. Jiang Originator: Joan B. Rose Publication_Date: 19910801 Title: Concentration of viruses and dissolved DNA from aquatic environments by vortex flow filtration Geospatial_Data_Presentation_Form: Journal Series_Information: Series_Name: Applied and Environmental Microbiology Issue_Identification: Volume 57(8) Other_Citation_Details: Pages 2197-2204 Online_Linkage: https://doi.org/10.1128/aem.57.8.2197-2204.1991 Cross_Reference: Citation_Information: Originator: Nicholas A. Bokulich Originator: Benjamin D. Kaehler Originator: Jai Ram Rideout Originator: Matthew Dillon 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: Journal Series_Information: Series_Name: Microbiome Issue_Identification: Volume 6(90) Online_Linkage: https://doi.org/10.1186/s40168-018-0470-z Cross_Reference: Citation_Information: Originator: Michael S. Robeson II Originator: Devon R. O'Rourke Originator: Benjamin D. Kaehler Originator: Michal Ziemski Originator: Matthew R. Dillion Originator: Jeffrey T. Foster Originator: Nicholas A. Bokulich Publication_Date: 20211108 Title: RESCRIPt: Reproducible sequence taxonomy reference database management Geospatial_Data_Presentation_Form: Journal Series_Information: Series_Name: PLOS Computational Biology Issue_Identification: Volume 17(11) Online_Linkage: https://doi.org/10.1371/journal.pcbi.1009581 Cross_Reference: Citation_Information: Originator: Siddhartha Mandal Originator: Will Van Treuren Originator: Richard A. White Originator: Merete Eggesbo Originator: Rob Knight Originator: Shyamal D. Peddada Publication_Date: 20150529 Title: Analysis of composition of microbiomes: a novel method for studying microbial composition Geospatial_Data_Presentation_Form: Journal Series_Information: Series_Name: Microbial Ecology in Health and Disease Issue_Identification: Article: 27663 Online_Linkage: https://doi.org/10.3402/mehd.v26.27663 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: Source_Information: Source_Citation: Citation_Information: Originator: Cynthia C. Becker Originator: Marilyn Brandt Originator: Carolyn A. Miller Originator: Amy Apprill Publication_Date: 20210825 Title: Microbial bioindicators of Stony Coral Tissue Loss Disease identified in corals and overlying waters using a rapid field-based sequencing approach Geospatial_Data_Presentation_Form: tabular digital data Series_Information: Series_Name: Environmental Microbiology Issue_Identification: Volume 24(3) Online_Linkage: https://doi.org/10.1111/1462-2920.15718 Type_of_Source_Media: SCTLD bioindicator ASVs Source_Time_Period_of_Content: Time_Period_Information: Single_Date/Time: Calendar_Date: 20210825 Source_Currentness_Reference: publication date Source_Citation_Abbreviation: (Becker and others, 2021) Source_Contribution: Compare SCTLD bioindicator ASVs to identify 100% sequence identity matches between Becker and others (2021) and this data release. Process_Step: Process_Description: Healthy coral collection: Healthy corals used to create these samples were collected from various reefs and nurseries throughout Florida between April 2018 and September 2020 and were maintained in indoor temperature-controlled water tables containing UV-treated and 0.22 µm-filtered seawater at the SMS. Process_Date: 20200901 Process_Step: Process_Description: SCTLD coral collection: Immediately prior to each of the three experimental runs (Run 1 was conducted in October 2019, Run 2 was conducted in November 2020, and Run 3 was conducted in March 2021), fragments of SCTLD-symptomatic corals were collected by divers from Florida reefs, transported to SMS, and transferred directly into individual mesocosm buckets containing ~18 L of the UV-treated FSW and a weighted air line for water circulation and oxygenation. Process_Date: 20210322 Process_Step: Process_Description: Initial sample preparation: For all three experimental runs, as the diseased corals were transferred into their mesocosms, healthy corals of the same or similar species were transferred from their indoor water tables, into identical individual mesocosms. All mesocosms were housed within outdoor water tables containing recirculating freshwater maintained at ~28°C and located under a mesh canopy to allow some sunlight attenuation. Separate “healthy” and “diseased” water tables were maintained to prevent cross-contamination between the different mesocosm types. All corals were incubated within these mesocosms for 2-5 days to enrich the water with microbes. Process_Date: 20210326 Process_Step: Process_Description: Sample preparation: Following the 2-5 day incubation period, each coral colony was removed from its mesocosm, and the remaining seawater was filtered through an ethanol-sterilized 200 µm (Run 1) or 106 µm (Runs 2 & 3) mesh screen to remove particulates. Using a peristaltic pump, the water from each mesocosm was then pumped through a TFF manifold containing five Centramate 100 kiloDalton (kDa) filter cassettes, as described by Evans and others (2022). Anything larger than 100 kDa (including microorganisms) was retained within the sample, while anything smaller than 100 kDa was filtered out (Paul and others, 1991). For all three runs, healthy corals were processed first, then the TFF system was flushed with bleach solution for one hour and held overnight permeated with bleach solution. Once the TFF system was disinfected, the diseased corals were processed in the same manner as the healthy. Process_Date: 20210328 Process_Step: Process_Description: Size fractionation: TFF-concentrated water, along with the FSW control, was sequentially passed through a sterile filter unit containing a 50 millimeter (mm) 0.8 µm pore size cellulose nitrate membrane filter (Runs 2 & 3) and a sterile filter unit containing a ~47 mm 0.22 µm pore size nitrocellulose membrane filter (Runs 1, 2, & 3). The 0.22 µm filters were cut from the filter units using an ethanol-sterilized razor blade, with a portion of each filter frozen at -20°C for later processing. Process_Date: 20210328 Process_Step: Process_Description: DNA extraction: Between February and May 2021, at the Coral Microbial Ecology Laboratory in St. Petersburg, FL, USA, DNA was extracted from the frozen portions of all 0.22 µm pore size filters using Qiagen DNeasy Power Biofilm kits (Qiagen, 2020). The Quickstart protocol (v. November 2016) was followed, except bead beating was performed on a BioSpec Products Mini Beadbeater at 2500 revolutions per minute (rpm) instead of on a PowerLyzer 24 Homogenizer at 3200 rpm. Blanks using kit reagents were also extracted, and positive controls (MSA-3001 ABRF-MGRG 10 Strain Even Mix Genomic Material, ATCC) were incorporated for downstream processing. Process_Date: 20210506 Process_Step: Process_Description: Sequencing: Library preparation and DNA sequencing were conducted in July, 2021 by the Michigan State University RTSF Genomics Core (East Lansing, MI) for amplicon library preparation and sequencing. The universal 16S (V4 region) primers 515F: GTGCCAGCMGCCGCGGTAA and 806R: GGACTACHVGGGTWTCTAAT were used to target the V4 variable region of the 16S rRNA gene on a MiSeq sequencing system with v2 chemistry to obtain paired-end 250-bp reads. Bases were called via Illumina Real Time Analysis (v1.18.54), with all output demultiplexed and converted to fastq files via Illumina Bcl2fastq (v2.20.0). Process_Date: 20210728 Source_Produced_Citation_Abbreviation: SCTLD_FullFilterSet_raw_data.zip Process_Contact: Contact_Information: Contact_Organization_Primary: Contact_Organization: Michigan State University RTSF Genomics Core Contact_Address: Address_Type: mailing and physical Address: 612 Wilson Road, S-18B City: East Lansing State_or_Province: MI Postal_Code: 48824 Country: United States Contact_Voice_Telephone: N/A Contact_Electronic_Mail_Address: gtsf@msu.edu Process_Step: Process_Description: Data analysis: Demultiplexed sequences were imported into QIIME2 (v. 2022.2) and denoised with DADA2 under default parameters, with truncation set to position 200. Taxonomy was assigned using a pre-trained naïve Bayes classifier SILVA-138-99-515-806 (Bokulich and others, 2018; Robeson and others, 2021) and sequences matching chloroplasts or mitochondria were removed from the final table. A phylogenetic tree was generated using MAFFT (v. 7.0) and FastTree 2. An unrarefied amplicon sequence variant (ASV) table was generated. Process_Date: 20220506 Source_Produced_Citation_Abbreviation: SCTLD_FullFilterSet_ASV_Table.zip Source_Produced_Citation_Abbreviation: SCTLD_FullFilterSet_ASV_Table_Eukaryota.zip Process_Step: Process_Description: Data analysis: BLASTn comparisons were run through the NCBI website to identify ASVs detected in this study that represent 100% sequence identity matches for the overlapping region of SCTLD bioindicator ASVs (Becker and others, 2021) from the U.S. Virgin Islands and disease-associated ASVs from Florida SCTLD studies. Source_Used_Citation_Abbreviation: (Becker and others, 2021) Process_Date: 20230407 Source_Produced_Citation_Abbreviation: SCTLD_FullFilterSet_SCTLD_bioindicators.zip Process_Step: Process_Description: Data analysis: Differential abundance analyses were performed using the analysis of composition of microbiomes, or 'ANCOM' (Mandal and others, 2015) analysis plugin (QIIME2 version 2022.2) of the ASV table "SCTLD_FullFilterSet_ASV_Table" was used to produce differential abundance analysis. Sequence IDs, W values, and whether the null hypothesis is rejected are indicated, along with percent abundance of each sequence ID for each percentile (0%, 25%, 50%, 75%, and 100%) for diseased and healthy mesocosms. Process_Date: 20230407 Source_Produced_Citation_Abbreviation: SCTLD_FullFilterSet_ANCOM_results.zip Entity_and_Attribute_Information: Overview_Description: Entity_and_Attribute_Overview: Please refer to the "README" file, README_SCTLD_FullFilterSet.txt, for detailed descriptions of the contents of the raw, processed and ASV data files. Additional information is contained in the minimum information about a marker sequence (MIMARKS) compliant metadata (SCTLD_FullFilterSet_MIMARKS), as well as the SRA metadata (SCTLD_FullFilterSet_SRA_metadata). The MIMARKS and SRA metadata files are available for download in the Supplemental Information section of the data release webpage (doi:10.5066/P9LRIX9E). 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: 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, text, comma-delimited text, Microsoft Excel format Digital_Transfer_Option: Online_Option: Computer_Contact_Information: Network_Address: Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9LRIX9E/data/SCTLD_FullFilterSet_raw_data.zip Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9LRIX9E/data/SCTLD_FullFilterSet_ASV_Table.zip Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9LRIX9E/data/SCTLD_FullFilterSet_ASV_Table_Eukaryota.zip Fees: None Metadata_Reference_Information: Metadata_Date: 20230801 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