Functional gene microarray data from cold-water corals (Acanthogorgia spp., Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) from the Atlantic Ocean off the Southeast Coast of the United States–Raw Data and Sample Site Information

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Identification_Information:

Citation:

Citation_Information:

Originator: Christina A. Kellogg
Originator: Julie J. Voelschow
Publication_Date: 20230814
Title:

Functional gene microarray data from cold-water corals (Acanthogorgia spp., Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) from the Atlantic Ocean off the Southeast Coast of the United States–Raw Data and Sample Site Information

Geospatial_Data_Presentation_Form: tabular digital data
Larger_Work_Citation:

Citation_Information:

Originator: Christina A. Kellogg
Originator: Julie J. Voelschow
Publication_Date: 20230814
Title:

Functional Gene Microarray Data From Cold-water Corals (Acanthogorgia spp., Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) From the Atlantic Ocean off the Southeast Coast of the United States–Raw Data

Geospatial_Data_Presentation_Form: tabular digital data
Series_Information:

Series_Name: US Geological Survey data release
Issue_Identification: doi:10.5066/P9RPE8YX

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/P9RPE8YX

Description:

Abstract:

The files in this data release (Kellogg and Voelschow, 2023) contain normalized microarray probe intensity values from GeoChip 5.0S microarrays referenced in the journal article entitled “Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities” by Pratte and others (2023). The GeoChip 5.0S microarrays, provided by Glomics Inc., contain 57,498 oligonucleotide probes that target 383 microbial (archaeal, bacterial, and fungal) genes and cover 151,797 coding sequences within the following metabolic categories: carbon, sulfur, and nitrogen cycling, as well as metal homeostasis, antibiotic resistance, and contaminant degradation. One microarray was run per coral (number of samples [n] = 11), using 400 nanograms (ng) of DNA extracted from the sample, plus a microarray run as a reagent blank (n = 1). The coral samples included one Acanthogorgia aspera, one Acanthogorgia spissa, three Desmophyllum dianthus, three Desmophyllum pertusum (formerly Lophelia pertusa) and three Enallopsammia profounda species. Corals were collected during two research cruises: the first in August 2018 and the second in April 2019, from six sites offshore of the southeastern coast of the United States in water depths ranging from 296–1567 meters (m). Coral samples were flash frozen in liquid nitrogen on the ship and stored at -80 degrees Celsius (°C) until processed. Extraction of deoxyribose nucleic acid (DNA) from the coral samples and kit blank occurred on August 5, 2019, at the Coral Microbial Ecology Laboratory in St. Petersburg, Florida (FL) using a QIAGEN DNeasy PowerBiofilm kit. Then, DNA samples were sent to Glomics Inc. on August 6, 2019, for application of GeoChip 5.0S microarrays. For more information, please see the README file and metadata files.

Purpose:

The purpose of this experiment was to identify microbial functional genes associated with deep-sea, cold-water corals in the Atlantic.

Supplemental_Information:

Coral samples were collected under Field Activity Number (FAN) 2018-042-FA and 2019-314-FA. 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/fan_info.php?fan=2018-042-FA and https://cmgds.marine.usgs.gov/fan_info.php?fan=2019-314-FA.

Time_Period_of_Content:

Time_Period_Information:

Range_of_Dates/Times:

Beginning_Date: 20180824
Ending_Date: 20190429

Currentness_Reference: ground condition

Status:

Progress: Complete
Maintenance_and_Update_Frequency: None planned

Spatial_Domain:

Description_of_Geographic_Extent: Atlantic Ocean
Bounding_Coordinates:

West_Bounding_Coordinate: -79.19408
East_Bounding_Coordinate: -75.15013
North_Bounding_Coordinate: 34.93145
South_Bounding_Coordinate: 31.2876

Keywords:

Theme:

Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:bde2bcd6-a8c3-4397-8d66-99698e57a4c4

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: microbiology
Theme_Keyword: coelenterates
Theme_Keyword: DNA sequencing

Place:

Place_Keyword_Thesaurus: Geographic Names Information System (GNIS)
Place_Keyword: Atlantic Ocean

Place:

Place_Keyword_Thesaurus: None
Place_Keyword: United States
Place_Keyword: Pamlico Canyon
Place_Keyword: Pea Island Seep
Place_Keyword: Cape Lookout
Place_Keyword: Richardson Ridge
Place_Keyword: Blake Deep
Place_Keyword: Savannah Bank

Access_Constraints: None
Use_Constraints: None
Point_of_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Christina A. Kellogg
Contact_Organization:

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

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: Zoe A. Pratte
Originator: Frank J. Stewart
Originator: Christina A. Kellogg
Publication_Date: 20230809
Title:

Functional gene composition and metabolic potential of deep-sea coral-associated microbial communities

Geospatial_Data_Presentation_Form: publication
Series_Information:

Series_Name: Coral Reefs
Issue_Identification: 2023

Online_Linkage: https://doi.org/10.1007/s00338-023-02409-0

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: Zhenmei Lu
Originator: Ye Deng
Originator: Joy D. Van Nostrand
Originator: Zhili He
Originator: James Voordeckers
Originator: Aifen Zhou
Originator: Yong-Jin Lee
Originator: Olivia U. Mason
Originator: Eric A. Dubinsky
Originator: Krystle L. Chavarria
Originator: Lauren M. Tom
Originator: Julian L. Fortney
Originator: Regina Lamendella
Originator: Janet K. Jansson
Originator: Patrik D'haeseleer
Originator: Terry C. Hazen
Originator: Jizhong Zhou
Publication_Date: 20110804
Title:

Microbial gene functions enriched in the Deepwater Horizon deep-sea oil plume

Geospatial_Data_Presentation_Form: publication
Series_Information:

Series_Name: The ISME Journal
Issue_Identification: Volume 6

Other_Citation_Details: Pages 451-460
Online_Linkage: https://doi.org/10.1038/ismej.2011.91

Cross_Reference:

Citation_Information:

Originator: Zhili He
Originator: Terry J. Gentry
Originator: Christopher W. Schadt
Originator: Liyou Wu
Originator: Jost Liebich
Originator: Song C. Chong
Originator: Zhijian Huang
Originator: Weimin Wu
Originator: Baohua Gu
Originator: Phil Jardine
Originator: Craig Criddle
Originator: Jizhong Zhou
Publication_Date: 20070501
Title:

GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes

Geospatial_Data_Presentation_Form: publication
Series_Information:

Series_Name: The ISME Jounal
Issue_Identification: Volume 1

Other_Citation_Details: Pages 67-77
Online_Linkage: https://doi.org/10.1038/ismej.2007.2

Cross_Reference:

Citation_Information:

Originator: Liyou Wu
Originator: Xueduan Liu
Originator: Christopher W. Schadt
Originator: Jizhong Shou
Publication_Date: 20060701
Title:

Microarray-based analysis of subnanogram quantities of microbial community DNAs by using whole-community genome amplification

Geospatial_Data_Presentation_Form: publication
Series_Information:

Series_Name: Applied and Environmental Microbiology
Issue_Identification: Volume 72, No. 7

Online_Linkage: https://doi.org/10.1128/AEM.02738-05

Data_Quality_Information:

Attribute_Accuracy:

Attribute_Accuracy_Report: No formal attribute accuracy tests were conducted.

Logical_Consistency_Report: No formal logical accuracy tests were conducted.
Completeness_Report:

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

Positional_Accuracy:

Horizontal_Positional_Accuracy:

Horizontal_Positional_Accuracy_Report: No formal horizontal positional accuracy tests were conducted.

Vertical_Positional_Accuracy:

Vertical_Positional_Accuracy_Report: No formal vertical positional accuracy tests were conducted.

Lineage:

Process_Step:

Process_Description:

Sample collection: Coral samples were collected during two research cruises, one in 2018 and the other in 2019, from sites off the southeastern coast of the United States (Cape Lookout, Pamlico Canyon, Blake Escarpment, Richardson Ridge, Pea Island Seep, and Savannah Bank) supporting the DeepSEARCH project. Samples from 2018 were collected using the submersible 'Alvin' and support vessel research vessel (RV) 'Atlantis', and the samples from 2019 were collected using the remotely-operated vehicle (ROV) 'Jason II' from the National Oceanic and Atmospheric Administration's (NOAA) ship 'Ronald H. Brown'.

Process_Date: 20190425
Process_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Christina A. Kellogg
Contact_Organization:

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

Contact_Position: Research Microbiologist
Contact_Address:

Address_Type: mailing and physical
Address: 600 4th Street 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

Process_Step:

Process_Description:

Sample preparation: On the ship after collection, the coral samples were gently rinsed with 1x phosphate-buffered saline (PBS) to remove surface microbes. Stony coral samples (Desmophyllum dianthus, Desmophyllum pertusum, and Enallopsammia profunda) were placed in a sterile aluminum weigh boats and broken open with a flame sterilized hammer to expose the polyp tissue for processing. Branches of the octocoral samples (Acanthogorgia aspera and Acanthogorgia spissa) were removed for processing using sterile shears. All subsamples were individually wrapped in pre-sterilized aluminum foil, placed into a Whirlpak back and flash frozen in liquid nitrogen, and then transferred to a -80°C freezer when the cruises were over.

Process_Date: 20190425
Process_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Christina A. Kellogg
Contact_Organization:

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

Contact_Position: Research Microbiologist
Contact_Address:

Address_Type: mailing and physical
Address: 600 4th Street 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

Process_Step:

Process_Description:

DNA extraction: Extraction of DNA occurred at the Coral Microbiology Laboratory in St. Petersburg, Florida in August 2019, using QIAGEN’s DNeasy PowerBiofilm kit. Samples were extracted in duplicate, and then combined at the end for a total of 200 microliters (µL) of DNA solution per coral. QIAGEN’s protocol was followed (edition March 2018) using a vacuum manifold, with few alterations. To compensate for the weight of the skeleton, stony coral samples used 0.2 grams (g) to 0.65 g per extraction tube.

Process_Date: 20190805
Process_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Christina A. Kellogg
Contact_Organization:

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

Contact_Position: Research Microbioloigst
Contact_Address:

Address_Type: mailing and physical
Address: 600 4th Street 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

Process_Step:

Process_Description:

Processing data: Approximately 180 µL per sample was shipped on dry ice to Glomics Inc. (Norman, Oklahoma) for application to GeoChip 5.0S microarrays. 400 nanograms (ng) of DNA was used directly for labeling, for each sample. The kit blank had an undetectable concentration of DNA, but was labeled using the same process as the samples. Fluorescence-labeling, hybridization of the microarrays, and scanning were carried out as described by Lu and others (2011). Glomics Inc. conducted a data normalization to the samples, and only probed spots that were above a designated limit (a signal-to-noise ratio of greater than or equal to 2 in at least one sample) were retained (Wu, and others 2006; He, and others 2007)

Process_Date: 20190925
Process_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Glomics Inc.

Contact_Address:

Address_Type: mailing and physical
Address: 3750 West Main Street, STE AA
City: Norman
State_or_Province: OK
Postal_Code: 73072
Country: United States

Contact_Voice_Telephone: 405-312-2900
Contact_Electronic_Mail_Address: geochip@glomics.com

Spatial_Data_Organization_Information:

Direct_Spatial_Reference_Method: Point
Point_and_Vector_Object_Information:

SDTS_Terms_Description:

SDTS_Point_and_Vector_Object_Type: Point
Point_and_Vector_Object_Count: 11

Spatial_Reference_Information:

Horizontal_Coordinate_System_Definition:

Geographic:

Latitude_Resolution: 0.0197864699
Longitude_Resolution: 0.0228595953
Geographic_Coordinate_Units: Decimal degrees

Geodetic_Model:

Horizontal_Datum_Name: World Geodetic System of 1984
Ellipsoid_Name: WGS_1984
Semi-major_Axis: 6378137.0
Denominator_of_Flattening_Ratio: 298.257223563

Vertical_Coordinate_System_Definition:

Altitude_System_Definition:

Altitude_Datum_Name: North American Vertical Datum 1988
Altitude_Resolution: 0.01
Altitude_Distance_Units: meters
Altitude_Encoding_Method: Attribute values

Entity_and_Attribute_Information:

Overview_Description:

Entity_and_Attribute_Overview:

Please refer to the "README" file, README_GeoChip.txt, for detailed descriptions of the contents of the GeoChip raw and processed data files. Additional information is contained in the metadata 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: 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-P9RPE8YX/data/GeoChip_raw_data.zip

Fees: None

Metadata_Reference_Information:

Metadata_Date: 20230911
Metadata_Contact:

Contact_Information:

Contact_Person_Primary:

Contact_Person: Christina A. Kellogg
Contact_Organization:

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

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

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