Screening Coral Tissue Samples (Colpophyllia natans) Collected From the Florida Keys Using a Quantitative Polymerase Chain Reaction (qPCR) Antibiotic Resistance Gene Microarray – Raw Data

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Metadata:

Identification_Information
Data_Quality_Information
Entity_and_Attribute_Information
Distribution_Information
Metadata_Reference_Information

Identification_Information:

Citation:

Citation_Information:

Originator: Christina A. Kellogg
Originator: Julie J. Voelschow
Publication_Date: 20260217
Title:

Screening Coral Tissue Samples (Colpophyllia natans) Collected From the Florida Keys Using a Quantitative Polymerase Chain Reaction (qPCR) Antibiotic Resistance Gene Microarray – Raw Data

Geospatial_Data_Presentation_Form: tabular digital data
Larger_Work_Citation:

Citation_Information:

Originator: Christina A. Kellogg
Originator: Julie J. Voelschow
Publication_Date: 20260217
Title:

Screening Coral Tissue Samples (Colpophyllia natans) Collected From the Florida Keys Using a Quantitative Polymerase Chain Reaction (qPCR) Antibiotic Resistance Gene Microarray – Raw Data

Geospatial_Data_Presentation_Form: tabular digital data
Series_Information:

Series_Name: U.S. Geological Survey data release
Issue_Identification: doi:10.5066/P9AST28V

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/P9AST28V

Description:

Abstract:

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.

Purpose:

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.

Supplemental_Information:

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

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 20221117
Ending_Date: 20230217

Currentness_Reference: ground condition

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent: Florida Keys
Bounding_Coordinates:

West_Bounding_Coordinate: -80.625280
East_Bounding_Coordinate: -80.616667
North_Bounding_Coordinate: 24.911667
South_Bounding_Coordinate: 24.902778

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:e0e10791-cd17-4bc1-921b-e1ebbe276674

Theme:

Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: biota
Theme_Keyword: oceans

Theme:

Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: bacteria
Theme_Keyword: polymerase chain reaction
Theme_Keyword: microbiology
Theme_Keyword: coelenterates

Theme:

Theme_Keyword_Thesaurus: None
Theme_Keyword: antibiotic resistance genes
Theme_Keyword: quantitative polymerase chain reaction

Place:

Place_Keyword_Thesaurus: Geographic Names Information System (GNIS)
Place_Keyword: Florida Keys
Place_Keyword: State of Florida

Access_Constraints:

No access constraints. Please see 'Distribution Information' for details.

Use_Constraints:

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.

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: MacOS Ventura 13.6.6, Applied Biosystems StepOnePlus™ Real-Time PCR System Software (version 2.2.2).

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: Qiagen GeneGlobe
Publication_Date: 20220731
Title:

Microbial DNA qPCR Instructions for Use: For real-time PCR-based profiling/detection of microbial species, antibiotic resistance genes or virulence factor genes

Geospatial_Data_Presentation_Form: Instructional Manual
Online_Linkage:

https://www.qiagen.com/us/resources/resourcedetail?id=e4e55f41-52c3-424e-83d2-0d20fa577435&lang=en

Cross_Reference:

Citation_Information:

Originator: Karen L. Neely
Originator: Christina A. Kellogg
Originator: Julie J. Voelschow
Originator: Allison R. Cauvin
Originator: Sydney A. M. Reed
Originator: Ewelina Rubin
Originator: Julie L. Meyer
Publication_Date: 20260216
Title:

Assessment of antibiotic resistance genes in Caribbean corals, including those treated with amoxicillin

Geospatial_Data_Presentation_Form: publication
Series_Information:

Series_Name: Coral Reefs
Issue_Identification: Unknown

Online_Linkage: https://doi.org/10.1007/s00338-026-02832-z

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report:

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.

Logical_Consistency_Report:

Each array contains positive controls (PPC 1, PPC 2, and PPC 3) to detect inhibition.

Completeness_Report:

Dataset is considered complete for the information presented, as described in the abstract.

Lineage:

Process_Step:

Process_Description:

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.

Process_Date: 20221117
Source_Produced_Citation_Abbreviation: Cnat2022_ARG_SampleInventory.csv
Source_Produced_Citation_Abbreviation: Cnat2022_ARG_SampleInventory.xlsx

Process_Step:

Process_Description:

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).

Process_Date: 20221215

Process_Step:

Process_Description:

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).

Process_Date: 20230217
Source_Produced_Citation_Abbreviation: Cnat2022_ARG_Ct.zip
Source_Produced_Citation_Abbreviation: Cnat2022_ARG_RawFluorescence.zip

Entity_and_Attribute_Information:

Detailed_Description:

Entity_Type:

Entity_Type_Label: Cnat2022_ARG_SampleInventory
Entity_Type_Definition:

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.

Entity_Type_Definition_Source: USGS

Attribute:

Attribute_Label: Date
Attribute_Definition: The date the coral sample was collected.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: 11/17/2022
Enumerated_Domain_Value_Definition:

The date the coral sample was collected in the format of MM/DD/YYYY

Enumerated_Domain_Value_Definition_Source: USGS

Attribute:

Attribute_Label: Site
Attribute_Definition: The location the coral sample was collected.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Cheeca Rocks, Florida Keys
Enumerated_Domain_Value_Definition: The coral samples were collected at Cheeca Rocks, Florida Keys.
Enumerated_Domain_Value_Definition_Source: USGS

Attribute:

Attribute_Label: Bag #
Attribute_Definition: A unique identifier used to organize the sample.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 2
Range_Domain_Maximum: 24

Attribute:

Attribute_Label: Species
Attribute_Definition: Species of coral.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: CNAT
Enumerated_Domain_Value_Definition:

CNAT was used as an abbreviation for the coral species Colpophyllia natans.

Enumerated_Domain_Value_Definition_Source: USGS

Attribute:

Attribute_Label: Status
Attribute_Definition:

Determination of whether the coral had previously been treated with the antibiotic amoxicillin base2B. The samples were untreated, treated once, or treated several times.

Attribute_Definition_Source: USGS
Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Never treated
Enumerated_Domain_Value_Definition: The sample was never treated with amoxicillin base2B.
Enumerated_Domain_Value_Definition_Source: USGS

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Treated once
Enumerated_Domain_Value_Definition: The sample had been treated once with amoxicillin base2B.
Enumerated_Domain_Value_Definition_Source: USGS

Attribute_Domain_Values:

Enumerated_Domain:

Enumerated_Domain_Value: Treated many
Enumerated_Domain_Value_Definition:

The sample had been treated more than once with amoxicillin base2B.

Enumerated_Domain_Value_Definition_Source: USGS

Attribute:

Attribute_Label: Depth (ft)
Attribute_Definition: The depth at which the coral samples were collected in feet.
Attribute_Definition_Source: USGS
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 9
Range_Domain_Maximum: 13
Attribute_Units_of_Measure: feet

Attribute:

Attribute_Label: DNA concentration applied to array (ng)
Attribute_Definition:

The amount of extracted DNA used to create the master mix for the sample's qPCR run, in nanograms.

Attribute_Definition_Source: USGS
Attribute_Domain_Values:

Range_Domain:

Range_Domain_Minimum: 1100
Range_Domain_Maximum: 10246
Attribute_Units_of_Measure: nanograms

Overview_Description:

Entity_and_Attribute_Overview:

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.

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: USGS SPCMSC Data Management
Contact_Organization:

U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center

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: 727-502-8000
Contact_Electronic_Mail_Address: gs-g-spcmsc_data_inquiries@usgs.gov

Resource_Description:

Cnat#_RawFluor.csv, Cnat#_Ct.csv, Cnat2022_ARG_SampleInventory.csv, Cnat2022_ARG_SampleInventory.xlsx, Cnat2022_ARG_DataDictionary.docx

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 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.

Standard_Order_Process:

Digital_Form:

Digital_Transfer_Information:

Format_Name:

comma-delimited text, Microsoft Excel format, Microsoft Word format

Digital_Transfer_Option:

Online_Option:

Computer_Contact_Information:

Network_Address:

Network_Resource_Name:

https://coastal.er.usgs.gov/data-release/doi-P9AST28V/data/Cnat2022_ARG_Ct.zip

Network_Resource_Name:

https://coastal.er.usgs.gov/data-release/doi-P9AST28V/data/Cnat2022_ARG_RawFluorescence.zip

Fees: None

Metadata_Reference_Information:

Metadata_Date: 20260217
Metadata_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: USGS SPCMSC Data Management
Contact_Organization:

U.S. Geological Survey, St. Petersburg Coastal and Marine Science Center

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: 727-502-8000
Contact_Electronic_Mail_Address: gs-g-spcmsc_data_inquiries@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

This page is <https://cmgds.marine.usgs.gov/catalog/spcmsc/Cnat2022_ARG_FGDC_metadata.html>