Cold-water coral metagenomes (Lophelia pertusa) from the Gulf of Mexico and Atlantic Ocean: raw data

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.

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.

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.

Added keywords section with USGS persistent identifier as theme keyword.