Dawn B. Goldsmith
Christina A. Kellogg
20181108
Cold-water coral metagenomes (Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean: raw data
FASTQ and tabular digital data
St. Petersburg, FL
U.S. Geological Survey
https://doi.org/10.5066/P9AA0H3B
In 2009, three unique colonies of the cold-water coral Lophelia pertusa were sampled in the western Atlantic Ocean to examine their microbial metagenomes. Nine additional samples were collected from three sites (Viosca Knoll 826, Viosca Knoll 906, and West Florida Slope) around the Gulf of Mexico in 2009 and 2010. Previous studies have examined the bacterial associates of this coral, but to date, no cold-water coral metagenomes have been published. This analysis characterized and identified microbial associates (bacteria, archaea, eukaryotes, viruses) associated with Lophelia, and also provided a first look at the functional and metabolic capabilities of the Lophelia microbial metagenome. Replicate sampling allowed for supplemental analysis of the variation in metagenomes between individual coral samples and among the four collection sites.
The data were collected in order to examine the microbial associates of the cold-water coral Lophelia pertusa.
20090809
20100930
observed
None planned
-88.380533
-79.615905
29.17027
26.19785
USGS Metadata Identifier
USGS:5c53e0c1-b795-443b-b919-d64cb12f356f
ISO 19115 Topic Category
biota
oceans
USGS Thesaurus
marine biology
marine geology
coelenterates
Geographic Names Information System
Atlantic Ocean
United States of America
Gulf of Mexico
USGS Thesaurus
Holocene
None.
Public domain data from the U.S. Government are freely redistributable with proper metadata and source attribution. The U.S. Geological Survey requests to be acknowledged as originator of these data in future products or derivative research.
Christina Kellogg
St. Petersburg Coastal and Marine Science Center
Mailing and Physical
600 4th Street South
St. Petersburg
FL
33701
(727) 502-8128
U.S. Geological Survey, Coastal and Marine Geology Program, St. Petersburg Coastal and Marine Science Center
Nancy G. Prouty
Christina A. Kellogg
Cheryl L. Morrison
unknown
Multidisciplinary Assessment of Deep-Water Coral Ecosystems: Tools to Detect Impacts of Sub-lethal Stress. Final Technical Report.
publication
Sterling, Virginia
U.S. Department of the Interior, Bureau of Ocean Energy Management, Gulf of Mexico OCS Region
OCS Study BOEM 2018-xxx, 132 p.
Christina A. Kellogg
John T. Lisle
Julia P. Galkiewicz
20090220
Culture-Independent Characterization of Bacterial Communities Associated with the Cold-Water Coral Lophelia pertusa in the Northeastern Gulf of Mexico
publication
Washington, D.C.
Applied and Environmental Microbiology
No formal attribute accuracy tests were conducted.
No formal logical consistency tests were conducted.
Dataset is considered complete for the information presented, as described in the abstract, except as follows. The information for every sample except sample CK8 is accompanied (in a .csv file) by information about the sequencing run: the flow cell ID, the lane of the plate on which the sample was sequenced, the index used for demultiplexing the samples, and the name of the operator at the sequencing facility who performed the sequencing. The sequencing facility did not produce this information for sample CK8. Users are advised to read the rest of the metadata record carefully for additional details.
Branches of L. pertusa coral samples were collected from four study sites between August 2009 and September 2010. Samples acquired during cruises in August and September 2009 with names prefixed by 3705 or 3731 were collected by the Johnson-Sea-Link submersible (Harbor Branch Oceanographic Institution), using the Kellogg sampler (Kellogg et al., 2009). The sampler’s individual compartments were cleaned at the surface using ethanol, filled with sterile deionized water and sealed. Coral branches were collected and placed into the containers after ambient seawater evacuated the freshwater, and the containers were re-sealed at depth. Samples with names beginning with ROV were collected using the remotely-operated vehicle (ROV) Kraken II (University of Connecticut) during a research cruise in September 2010. The ROV carried several individual polyvinylchloride quivers that were cleaned with ethanol, filled with sterile deionized water and sealed at the surface with rubber stoppers. Immediately prior to collection, a quiver was opened, the sample placed inside, and the quiver sealed before the ROV continued its deployment. Upon return to the surface, all L. pertusa samples were transferred to sterile tubes, covered in Thermo Fisher Scientific's RNAlater Stabilization Solution and incubated overnight at 4 degrees Celsius (ºC) to allow the preservative to permeate the coral tissues before transfer to -20ºC. Subsequent processing occurred at the Environmental Microbiology Laboratory in St. Petersburg, FL.
20100930
Microbial deoxyribonucleic acid (DNA) was extracted following the specialized protocol developed for this coral (https://coastal.er.usgs.gov/coral-microbes/discovre/lophelia-extraction.html). In short, the coral's calcium carbonate skeleton was cracked open using a sterile mortar and pestle. The mucus and tissue were airbrushed away from the skeleton using a sterile buffer. The slurry was sheared by repeated passage through a syringe, then centrifuged to remove larger clumps of tissue. A Percoll cushion was used to separate the coral cells from the microbial cells. The microbial fraction was filtered onto a 0.22 μm Sterivex cartridge and the microbial assemblage DNA was extracted from that filter using a Qiagen DNeasy Blood and Tissue kit following the manufacturer's protocol for Gram-positive bacteria but with reagent volumes doubled in the initial steps.
20120130
The shotgun metagenome (untargeted sequencing of all genomes present in a sample) dataset was produced by random shearing of the DNA, construction of a TruSeq library, and sequencing on an Illumina HiSeq 2000 sequencing system by Argonne National Laboratory. Raw sequence data from all metagenome samples are available from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) under Bioproject number PRJNA471489.
20130331
Added keywords section with USGS persistent identifier as theme keyword.
20201013
U.S. Geological Survey
VeeAnn A. Cross
Marine Geologist
Mailing and Physical
384 Woods Hole Road
Woods Hole
MA
02543-1598
508-548-8700 x2251
508-457-2310
vatnipp@usgs.gov
Please refer to the "README" file, README_Lophelia_metagenomes.txt, for detailed descriptions of the contents of the raw data file. Additional information is contained in the Minimum Information about a Metagenome Sequence (MIMS) compliant metadata, Lophelia_metagenomes_MIMS_compliant_metadata, which is included in each data download file.
The entity and attribute information was 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.
Christina A. Kellogg
U.S. Geological Survey
mailing and physical
600 4th Street S
St. Petersburg
FL
33701
USA
727-502-8128
ckellogg@usgs.gov
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.
FASTQ, CSV
https://coastal.er.usgs.gov/data-release/doi-P9AA0H3B/data/Lophelia_metagenomes_raw_data_1.zip
https://coastal.er.usgs.gov/data-release/doi-P9AA0H3B/data/Lophelia_metagenomes_raw_data_2.zip
None
20211109
Christina Kellogg
St. Petersburg Coastal and Marine Science Center
Mailing and Physical
600 4th Street South
St. Petersburg
FL
33701
(727) 502-8128
ckellogg@usgs.gov
Content Standard for Digital Geospatial Metadata
FGDC-STD-001-1998