Metadata: Identification_Information: Citation: Citation_Information: Originator: Christina A. Kellogg Originator: James S. Evans Originator: Julie J. Voelschow Publication_Date: 20221021 Title: Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral Mesocosms – Raw and Processed Data Geospatial_Data_Presentation_Form: FASTQ and tabular digital data Online_Linkage: https://doi.org/10.5066/P9T6NW4V Larger_Work_Citation: Citation_Information: Originator: Christina A. Kellogg Originator: James S. Evans Originator: Julie J. Voelschow Publication_Date: 20221021 Title: Prokaryotic Communities From Marine Biofilms Formed on Stainless Steel Plates in Coral 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/P9T6NW4V Online_Linkage: https://doi.org/10.5066/P9T6NW4V Description: Abstract: The files in this data release (Kellogg and others, 2022) are those referenced in the journal article by Evans and others (2022) entitled “Biofilms as Potential Reservoirs of Stony Coral Tissue Loss Disease.” They contain an amplicon sequence variant (ASV) table and the raw 16S ribosomal ribonucleic acid (rRNA) gene amplicon deoxyribonucleic acid (DNA) sequence files from 15 microbial communities (sample names: CnD16B, CnD17B, CnD18B, CnD19B, CnD21B, CnD22B, CnD23B, CnD24B, CnD25B, PsD5B, CnH101B, CnH100B, Pstr4B, Pstr10B, and seawaterB) derived from biofilms on stainless steel plates (316 grade) formed in mesocosms containing diseased corals (stony coral tissue loss disease, n = 10), healthy corals (n = 4), or no coral (n = 1). Also included are the sequence files from a mock community, and two reagent blanks. Corals (Colpophyllia natans and Pseudodiploria strigosa) were collected between January 2019 and March 2021, from various locations throughout the Florida Keys. Plates were added to mesocosm buckets containing ultraviolet (UV)-sterilized, 0.2 micrometer (μm)-filtered seawater and either diseased (n = 10), healthy (n = 4), or no coral (n = 1) at the Smithsonian Marine Station in Fort Pierce, Florida (FL) on March 25, 2021. Plates were removed on March 28, 2021, and placed in individual sterile whirlpaks with RNAlater for future processing. Extraction of DNA from the samples and blanks occurred in April 2021 at the Coral Microbial Ecology Laboratory in St. Petersburg, FL using a QIAGEN DNeasy PowerBiofilm Kit. Library preparation and DNA sequencing were conducted on May 13, 2021, by the Michigan State University RTSF Genomics Core (East Lansing, Michigan) using primers 515F/806R to target the V4 variable region of the 16S rRNA gene. Sequencing was performed on an Illumina MiSeq sequencing system with v2 chemistry to obtain paired-end 250-bp (base pair) reads. 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 PRJNA828575. For more information, please see the README file, README_Biofilm.txt. Purpose: The purpose of this experiment was to analyze biofilm microbial communities formed on stainless steel plates in association with corals. Supplemental_Information: N/A Time_Period_of_Content: Time_Period_Information: Range_of_Dates/Times: Beginning_Date: 20190131 Ending_Date: 20210922 Currentness_Reference: ground condition Status: Progress: Complete Maintenance_and_Update_Frequency: None planned Spatial_Domain: Description_of_Geographic_Extent: Florida Bounding_Coordinates: West_Bounding_Coordinate: -82.63800 East_Bounding_Coordinate: -80.31060 North_Bounding_Coordinate: 27.76370 South_Bounding_Coordinate: 27.45956 Keywords: Theme: Theme_Keyword_Thesaurus: USGS Metadata Identifier Theme_Keyword: USGS:fc2f69c7-5de6-47d7-94e7-f2290dadcad6 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 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 Cross_Reference: Citation_Information: Originator: James S. Evans Originator: Valerie J. Paul Originator: Christina A. Kellogg Publication_Date: 2022 Title: Biofilms as Potential Reservoirs of Stony Coral Tissue Loss Disease Geospatial_Data_Presentation_Form: Journal Series_Information: Series_Name: Frontiers in Marine Science Issue_Identification: Volume 9, Article 1009407 Online_Linkage: https://doi.org/10.3389/fmars.2022.1009407 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 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: Journal Series_Information: Series_Name: Applied and Environmental Microbiology Issue_Identification: Volume 79(17) Other_Citation_Details: Pages 5112–5120 Online_Linkage: https://doi.org/10.1128%2FAEM.01043-13 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: Journal Series_Information: Series_Name: Nature Methods Issue_Identification: Volume 13 Other_Citation_Details: Pages 581–583 Online_Linkage: https://doi.org/10.1038/nmeth.3869 Cross_Reference: Citation_Information: Originator: Evan Bolyen Originator: Jai Ram Rideout Originator: Matthew R. Dillion Originator: and others Publication_Date: 20190724 Title: Reproducible, Interactive, Scalable and Extensible Microbiome Data Science Using QIIME 2 Geospatial_Data_Presentation_Form: Journal Series_Information: Series_Name: Nature Biotechnology Issue_Identification: Volume 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: Corals used to create these biofilm samples were collected from various locations throughout the Florida Keys between January 2019 and March 2021. Process_Date: 20210328 Process_Step: Process_Description: Sample creation - Preparation of steel plates: Fifteen 316 grade stainless steel plates were cut to approximately 7.5 centimeters (cm) by 5.1 cm on March 23 2021, and cleaned by scrubbing with Liquinox and a Brillo pad on all six sides. The plates were then rinsed with tap water, then deionized (DI) water, and blotted dry with a paper towel. They were then sprayed with 70% ethanol, blotted dry again, wrapped in tinfoil and autoclaved at 121 degrees Celsius (°C) for 30 minutes with a 15-minute drying cycle. Process_Date: 20210323 Process_Step: Process_Description: Sample creation - Biofilm steel plates: On March 25 2021, sterile labeled petri dishes with steel plates were placed in the bottom of each mesocosm containing approximately 18 liters (L) of UV-treated, 0.2 μm-filtered seawater, an air line, and their respective coral samples. The steel plates were positioned in the petri dishes in a way allowing for water from mesocosms to have contact with all sides. A control steel plate was placed in the same manner into a bucket containing 1-2L of filtered seawater and topped off to 18L, and an air line added the following day to match the other coral mesocosm volumes. All plates being added to healthy coral (CnH-101, CnH-100, Pstr-4, and Pstr-10) mesocosms were placed first, and the diseased coral (CnD-16, CnD-17, CnD-18, CnD-19, CnD-21, CnD-22, CnD-23, CnD-24, and CnD-25) mesocosms last, to avoid contamination. Plates were incubated in the buckets until March 28, 2021 (when they were collected), and placed in individual sterile whirlpaks with RNAlater. Process_Date: 20210328 Process_Step: Process_Description: Sample processing: Each plate was scraped, front and back, with a flame-sterilized razor, and rinsed with 1x phosphate buffered saline (PBS), including the razor. The liquid and salt crystals were collected in each sample’s respective sterile petri dish, and transferred into 2 milliliter (mL) sterile tubes. Process_Date: 20210416 Process_Step: Process_Description: The DNA extraction process was performed at the U.S. Geological Survey (USGS) Coral Microbial Ecology Laboratory in St. Petersburg, FL. DNA from CnD-22 and CnD-25 was extracted using a QIAGEN DNeasy PowerBiofilm Kit on April 16, 2021. The remaining 13 samples, along with an extraction kit blank, were extracted on April 22, 2021. A PBS blank was extracted on April 28, 2021. The manufacturer’s protocol (QIAGEN, 2013) was followed with modifications as described: because multiple 2 mL tubes were created for each sample, for step 2, only the first tube was resuspended in 350 microliters (µl) of MBL solution. The entire contents were then transferred into all remaining 2 mL tubes for that sample to resuspend the contents of each consecutively, prior to adding the final combined solution to the bead beat tube. Samples were then bead beat at 2500 revolutions per minute (rpm) for 30 seconds. Process_Date: 20210428 Process_Step: Process_Description: Sequencing: Library preparation and DNA sequencing were conducted on May 13, 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 rRNA gene. Sequencing was performed on an Illumina MiSeq sequencing system with v2 chemistry to obtain paired-end 250-bp reads. Libraries were prepared using the MiSeq Dual Index method developed in the Patrick Schloss lab (Kozich and others, 2013). Process_Date: 20210513 Process_Step: Process_Description: Data analysis - In September 2021 sequences were imported into QIIME2 [version 2021.4] (Bolyen and others, 2019) and trimmed, merged, and sorted into ASVs using DADA2 (Callahan and others, 2016) with the parameters ‘–p-trunc-len-f 200 –p-trunc-len-r 200.’ All sequences assigned as “mitochondria” or “chloroplast” were removed. Process_Date: 20210922 Entity_and_Attribute_Information: Overview_Description: Entity_and_Attribute_Overview: Please refer to the "README" file, README_Biofilm.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 (Biofilm_MIMARKS), as well as the SRA metadata (Biofilm_SRA_metadata). The MIMARKS and SRA metadata files are available for download in the Supplemental Information section of the data release webpage. 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: 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-P9T6NW4V/data/Biofilm_Raw_Data.zip Network_Resource_Name: https://coastal.er.usgs.gov/data-release/doi-P9T6NW4V/data/Biofilm_ASV_Table.zip Fees: None Metadata_Reference_Information: Metadata_Date: 20221021 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