Christina A. Kellogg Julie J. Voelschow 20260217 tabular digital data Christina A. Kellogg Julie J. Voelschow 20260217 tabular digital data U.S. Geological Survey data release doi:10.5066/P9AST28V St. Petersburg, Florida U.S. Geological Survey - St. Petersburg Coastal and Marine Science Center https://doi.org/10.5066/P9AST28V The files in this data release are those referenced in the journal article by Neely and others (2026) entitled "Assessment of antibiotic resistance genes in Caribbean corals, including those treated with amoxicillin." They represent the raw fluorescence data and threshold cycle (Ct) data generated from quantitative polymerase chain reaction (qPCR) microarray runs using deoxyribonucleic acid (DNA) extractions from 12 coral (Colpophyllia natans) samples as templates. These files were produced by the Applied Biosystems StepOnePlus™ Real-Time PCR System Software (version 2.2.2). The coral tissue samples were collected on November 17th, 2022, from Cheeca Rocks in the Florida Keys from depths ranging from 9 to 13 feet (2.7 to 4.0 meters). The samples were collected purpose of determining whether there is a higher incidence or diversity of microbial antibiotic resistance genes (ARG) in corals that have previously been treated for stony coral tissue loss disease (SCTLD) with amoxicillin base2B as compared to untreated coral. Tissue samples were preserved in RNAlater, and frozen until shipped for processing. The frozen coral samples were sent from Nova Southeastern University (Fort Lauderdale, Florida) and received on November 23rd 2022, by the U.S. Geological Survey St. Petersburg Coastal and Marine Science Center (USGS SPCMSC) Coral Microbial Ecology Laboratory in St. Petersburg, Florida (FL), USA, and immediately frozen at minus twenty degrees Celsius (-20°C) until processing. Microbial DNA extractions from the coral samples were performed on December 13th 2022, using a Qiagen Dneasy PowerBiofilm kit. All qPCR runs were performed between January and February 2023 on an Applied Biosystems StepOnePlus™ Real-Time PCR System, using Qiagen Microbial DNA qPCR Arrays ARG (BAID-1901ZRC-24), and data files were exported as Microsoft Excel files (.xls) and converted into comma-separated values (.csv) files. The data files were then edited to remove columns that contained no values, or that did not apply to this dataset. The purpose of this experiment was to examine whether there is a higher incidence or diversity of microbial antibiotic resistance genes in corals that have been previously treated for SCTLD with amoxicillin base 2B as compared to untreated corals. Coral samples were collected under Field Activity Number (FAN) 2022-343-DD. FANs are unique identifiers assigned by the U.S. Geological Survey (USGS) to provide more information about the activities conducted in the field for a study. Please visit the Coastal and Marine Geoscience Data System (CMGDS) field activity webpage for more information about each FAN related to this dataset, https://cmgds.marine.usgs.gov/services/activity.php?fan=2022-343-DD. Block Type: 96well Chemistry: TAQMAN Experiment Run timeframe: January and February 2023 Instrument Type: steponeplus Passive Reference: ROX Analysis Type: Singleplex Endogenous Control: Pan Bacteria 1.1, Pan Bacteria 1.2, Pan Bacteria 1.3, Pan Bacteria 3.1, Pan Bacteria 3.2, Pan Bacteria 3.3 RQ Min/Max Confidence Level 95.0 20221117 20230217 ground condition Complete None planned Florida Keys -80.625280 -80.616667 24.911667 24.902778 USGS Metadata Identifier USGS:e0e10791-cd17-4bc1-921b-e1ebbe276674 ISO 19115 Topic Category biota oceans USGS Thesaurus bacteria polymerase chain reaction microbiology coelenterates None antibiotic resistance genes quantitative polymerase chain reaction Geographic Names Information System (GNIS) Florida Keys State of Florida No access constraints. Please see 'Distribution Information' for details. These data are marked with a Creative Commons CC0 1.0 Universal License. These data are in the public domain and do not have any use constraints. Users are advised to read the dataset's metadata thoroughly to understand appropriate use and data limitations. Christina A. Kellogg U.S. Geological Survey Research Microbiologist mailing

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St. Petersburg Florida 33701 United States 727-502-8128 ckellogg@usgs.gov Environment as of Metadata Creation: MacOS Ventura 13.6.6, Applied Biosystems StepOnePlus™ Real-Time PCR System Software (version 2.2.2). Qiagen 20200131 Instructional Manual https://www.qiagen.com/us/resources/download.aspx?id=c5363245-cd9c-4314-b8fb-c4f8b4d669c4&lang=en Qiagen GeneGlobe 20220731 Instructional Manual https://www.qiagen.com/us/resources/resourcedetail?id=e4e55f41-52c3-424e-83d2-0d20fa577435&lang=en Karen L. Neely Christina A. Kellogg Julie J. Voelschow Allison R. Cauvin Sydney A. M. Reed Ewelina Rubin Julie L. Meyer 20260216 publication Coral Reefs Unknown https://doi.org/10.1007/s00338-026-02832-z Each array contains endogenous controls (Pan Bacteria 1.1, Pan Bacteria 1.2, Pan Bacteria 1.3, Pan Bacteria 3.1, Pan Bacteria 3.2, and Pan Bacteria 3.3) meant to standardize data processing for each run. Each array contains positive controls (PPC 1, PPC 2, and PPC 3) to detect inhibition. Dataset is considered complete for the information presented, as described in the abstract. Coral collection and preservation: The coral samples were collected on November 17th, 2022 from Cheeca Rocks in the Florida Keys from depths ranging from 9 to 13 feet (2.7 to 4.0 meters). Four of the samples collected had never been treated with the antibiotic (amoxicillin base2B) used to treat for SCTLD, four had been treated once, and four had been treated several times. Coral samples were preserved in RNAlater, and frozen until processed. A sample inventory data file (Cnat2022_ARG_SampleInventory) is also included in this release to provide collection details about the coral samples used in this study. 20221117 Cnat2022_ARG_SampleInventory.csv Cnat2022_ARG_SampleInventory.xlsx DNA extraction: The frozen coral samples were sent from Nova Southeastern University in Fort Lauderdale, FL and received on November 23rd, 2022, by the USGS SPCMSC Coral Microbial Ecology Laboratory in St. Petersburg, FL and immediately frozen at -20°C until processing. Microbial DNA extractions from the coral samples were performed on December 13th 2022, using a Qiagen DNeasy PowerBiofilm kit (Qiagen, 2020). 20221215 qPCR runs: DNA quantification was performed for the extractions (Qubit 3 Fluorometer, Invitrogen) to determine what volume of the template DNA would be used for each reaction master mix. Between 1100 to 10246 nanograms (ng) from each extraction was used to create the master mix for each plate. All qPCR runs were performed on an Applied Biosystems StepOnePlus™ Real-Time PCR System, using Qiagen Microbial DNA qPCR Arrays ARG (Qiagen, 2022). Each run produced raw fluorescence data and threshold cycle data files, that were exported as Microsoft Excel files (.xls) and were then converted to comma-separated values (.csv) files, for inclusion in this data release. The raw fluorescence (Cnat#_RawFluor) and threshold cycle data (Cnat#_Ct) files were organized into individual .csv files with 12 data files per data type. Please see the accompanying data dictionary (.docx) for more information about these data files. These files are referenced in the journal article (Neely and others, 2026). 20230217 Cnat2022_ARG_Ct.zip Cnat2022_ARG_RawFluorescence.zip Cnat2022_ARG_SampleInventory Comma-separated values (.csv) and Microsoft Excel Worksheet (.xlsx) files containing collection and sample information about the coral samples collected from Cheeca Rocks on November 17th 2022 used in the qPCR analysis. USGS Date The date the coral sample was collected. USGS 11/17/2022 The date the coral sample was collected in the format of MM/DD/YYYY USGS Site The location the coral sample was collected. USGS Cheeca Rocks, Florida Keys The coral samples were collected at Cheeca Rocks, Florida Keys. USGS Bag # A unique identifier used to organize the sample. USGS 2 24 Species Species of coral. USGS CNAT CNAT was used as an abbreviation for the coral species Colpophyllia natans. USGS Status Determination of whether the coral had previously been treated with the antibiotic amoxicillin base2B. The samples were untreated, treated once, or treated several times. USGS Never treated The sample was never treated with amoxicillin base2B. USGS Treated once The sample had been treated once with amoxicillin base2B. USGS Treated many The sample had been treated more than once with amoxicillin base2B. USGS Depth (ft) The depth at which the coral samples were collected in feet. USGS 9 13 feet DNA concentration applied to array (ng) The amount of extracted DNA used to create the master mix for the sample's qPCR run, in nanograms. USGS 1100 10246 nanograms The detailed attribute descriptions for the 12 raw fluorescence (Cnat2022_ARG_RawFluorescence.zip) and threshold cycle data files (Cnat2022_ARG_Ct.zip) are provided in the included data dictionary (Cnat2022_ARG_DataDictionary.docx). These metadata are not complete without this file, and users should refer to the data dictionary when viewing the data file. 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. USGS SPCMSC Data Management U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center mailing

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St. Petersburg Florida 33701 United States 727-502-8000 gs-g-spcmsc_data_inquiries@usgs.gov Cnat#_RawFluor.csv, Cnat#_Ct.csv, Cnat2022_ARG_SampleInventory.csv, Cnat2022_ARG_SampleInventory.xlsx, Cnat2022_ARG_DataDictionary.docx 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 for other purposes, nor on all computer systems, nor shall the act of distribution constitute any such warranty. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government. comma-delimited text, Microsoft Excel format, Microsoft Word format https://coastal.er.usgs.gov/data-release/doi-P9AST28V/data/Cnat2022_ARG_Ct.zip https://coastal.er.usgs.gov/data-release/doi-P9AST28V/data/Cnat2022_ARG_RawFluorescence.zip None 20260217 USGS SPCMSC Data Management U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center mailing

600 4th St. South

St. Petersburg Florida 33701 United States 727-502-8000 gs-g-spcmsc_data_inquiries@usgs.gov FGDC Biological Data Profile of the Content Standard for Digital Geospatial Metadata FGDC-STD-001.1-1999