Dataset is considered complete for the information presented, as described in the abstract. Users are advised to read the rest of the metadata record carefully for additional details.
Horizontal_Positional_Accuracy:
Horizontal_Positional_Accuracy_Report: No formal positional accuracy tests were conducted
Vertical_Positional_Accuracy:
Vertical_Positional_Accuracy_Report: No formal positional accuracy tests were conducted
Process_Step:
Process_Description:
Primnoa pacifica coral samples were collected from the Aleutian Islands, Alaska, using self-contained underwater breathing apparatus (SCUBA) equipment. Divers wearing clean nitrile gloves donned at the surface sampled the first Primnoa colony encountered on the dive (i.e. no other corals were touched before collecting the samples for this study). Small pieces of coral were broken from the colony by hand and placed into sterile 50 milliliter (mL) tubes. Upon return to the surface, the ambient seawater in the tubes was decanted and replaced with Thermo Fisher Scientific's RNAlater Stabilization Solution (RNAlater). The tubes were kept at 4 degrees Celsius (ºC) overnight and then moved to –20ºC for long term storage. Samples collected in Alaska were shipped overnight, surrounded by ice packs, to the USGS St. Petersburg, Florida environmental microbiology lab for further processing.
Process_Date: 20120131
Process_Step:
Process_Description:
Primnoa resedaeformis coral samples were collected from Baltimore Canyon during the 2012 Deepwater Canyons cruise on the National Oceanic and Atmospheric Administration (NOAA) Research Vessel (R/V) Nancy Foster using the remotely-operated vehicle (ROV) Kraken 2. Small pieces of the coral were collected using the ROV’s manipulator arm and placed into containers that had been washed, sterilized with ethanol, and filled with freshwater while the ROV was on deck. Upon recovery of the ROV, the samples were removed from the containers using ethanol-sterilized forceps, trimmed (if necessary) with ethanol-sterilized shears, and placed into 50 mL tubes. The tubes were filled with RNAlater and placed at 4ºC overnight, then transferred to –20ºC for long term storage.
Process_Date: 20120831
Process_Step:
Process_Description:
Primnoa resedaeformis coral samples were collected from Norfolk Canyon during the 2013 Deepwater Canyons cruise on the NOAA R/V Ronald Brown using the ROV Jason II. Small pieces of the coral were collected using the ROV’s manipulator arm and placed into containers that had been washed, sterilized with ethanol, and filled with freshwater while the ROV was on deck. Upon recovery of the ROV, the samples were removed from the quivers using ethanol-sterilized forceps, trimmed (if necessary) with ethanol-sterilized shears, and placed into 50 mL tubes. The tubes were filled with RNAlater and placed at 4ºC overnight, then transferred to –20ºC for long term storage.
Process_Date: 20130531
Process_Step:
Process_Description:
DNA was extracted from the samples using the MOBIO PowerPlant DNA Isolation Kit following the suggested modifications in Sunagawa and others (2010). Briefly, approximately 50 mg aliquots of tissue slurry from each sample were processed with the addition of a lysozyme step and additional smaller beads to expedite physical lysis. Three extractions were done per coral sample and then recombined by sample after elution of the DNA from the spin column. The DNA samples were quantified with a Thermo Fisher Scientific Quant-iT PicoGreen dsDNA Assay Kit, per the manufacturer’s protocol.
Process_Date: 20130630
Process_Step:
Process_Description:
DNA samples were amplified with primers targeting the V4-V5 hypervariable region (563F/926R) of the 16S rRNA gene: forward primer (5? AYTGGGYDTAAAGNG) and reverse primer (5? CCGTCAATTYYTTTRAGTTT). The forward primer was tagged with multiplex identifier (MID) tags so the samples could be combined for sequencing on two plates. Amplification, pooling and 454 sequencing using GS FLX Titanium chemistry were performed by Selah Genomics, Inc. Sequence data from all samples were deposited in the NCBI SRA under Bioproject number PRJNA348705.
Process_Date: 20130809
Process_Step:
Process_Description:
Sequence data were analyzed using the bioinformatic package Quantitative Insights Into Microbial Ecology (QIIME), version 1.9.1 (Caporaso and others, 2010, Nature Methods 7:335-336, doi:10.1038/nmeth.f.303). Please refer to the file entitled "Primnoa_workflow.txt," which is included as a supplemental file and details the scripts run in QIIME. The workflow file contains the default or chosen settings used for each script, as well as the names of the input/output files associated with each script.
Process_Date: 20151031
Process_Step:
Process_Description:
Primers designed to amplify the 23S rRNA gene in members of the Chlamydiales order (Everett and others, 1999) were used to amplify DNA extracted from the Primnoa pacifica samples. One sample of Primnoa pacifica, AKPP1, produced a 600-bp polymerase chain reaction (PCR) product that was visible on an agarose gel. The product was cloned into a vector and used to transform competent cells. After screening, the inserts in positive transformants were sequenced by Eurofins (
http://www.eurofinsus.com/) using Sanger sequencing. Two unique sequences resulted, and are contained in the file entitled "Chlamydiales_23S.txt."
Process_Step:
Process_Description:
Added keywords section with USGS persistent identifier as theme keyword.
Process_Date: 20201013
Process_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey
Contact_Person: VeeAnn A. Cross
Contact_Position: Marine Geologist
Contact_Address:
Address_Type: Mailing and Physical
Address: 384 Woods Hole Road
City: Woods Hole
State_or_Province: MA
Postal_Code: 02543-1598
Contact_Voice_Telephone: 508-548-8700 x2251
Contact_Facsimile_Telephone: 508-457-2310
Contact_Electronic_Mail_Address: vatnipp@usgs.gov
