Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

This dataset includes links to 515F-926R 16S rRNA gene sequencing accessions archived at NCBI and associated collection data from seawater and sediment samples from the Mariana and Kermadec trenches from April and November 2014.

For those accessions with a status of 'not yet available' at NCBI, they will be made available once the paper has been published, likely by mid-2018. Please check back for them then or contact the PI.

This data set is associated with PI Douglas Bartlett (NSF OCE-1536776) and R/V Thomas G. Thompson from Apr. 10 - May 20 to the Kermadec Trench adjacent to New Zealand and Schmidt Ocean Institute R/V Falkor cruise FK141109 from Nov. 9 - Dec. 9, 2014, to the Mariana Trench. During the cruises, sediment and water samples were collected. Additional details can be found at: https://schmidtocean.org/cruise/expanding-mariana-trench-perspectives/ and https://scripps.ucsd.edu/labs/dbartlett/contact/challenger-deep-cruise-2014/

Seawater (40-120 L per sample) was serially filtered through 3.0 (47 mm diameter), 0.2 (47 mm or Sterivex), and 0.1 µm (142 mm) polycarbonate filters using a peristaltic pump. Filters were then placed into a sucrose buffer (Rusch et al., 2007) and frozen at -80°C. DNA was extracted from whole filters using a protocol previously described (Fuhrman et al., 1988; Tarn et al., 2016). Negative controls using blank filters were extracted in concomitance with every extraction performed.

DNA from sediment (5 g wet-weight) samples was extracted using a modified version of Lysis Protocol II described by Lever et al. (2015). 2.5 V of lysis solution (30 mM EDTA, 30 mM Tris-HCl, 800 mM guanidine hydrochloride, 0.5% Triton X-100, final pH 10) and 500 µmol pyrophosphate was added to each sample and the mixture briefly vortexed. Samples were then subjected to two 15 minute freeze-thaw cycles at -80°C, followed by incubation at 50°C with shaking at 150 rpm  for one hour. Samples were centrifuged and the supernatant was treated twice with 1 V chloroform isoamyl alcohol. DNA was precipitated using 5 M NaCl and ethanol for two hours at room temperature and resuspended in nuclease-free water. Extracted DNA was cleaned again using a Quick-gDNA MiniPrep kit (Zymo Research, Irvine, CA). Negative control blanks, consisting of all reagents but no sediment material, were performed in concomitance with every extraction.

The V4-V5 16S rRNA gene region between 515f-926R was amplified (Parada et al., 2015) and tagged with Illumina barcodes using a secondary PCR procedure. Samples were pooled at equimolar concentrations and sent for sequencing on an Illumina Miseq at the Institute for Genomic Medicine Genomics Center (University of California, San Diego, La Jolla, CA).

BCO-DMO Processing:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- split lat and lon into separate columns and rounded to 4 decimal places
- removed blank spaces in 3 sample names.

Award Abstract from NSF:
The deepest portion of the ocean is present in ocean trenches, whose steep walls descend from approximately 4 miles down to depths that in some cases are close to 7 miles below the seawater surface. At these locations Earth's crust is recycled. Perhaps not surprisingly given their remoteness, deep ocean trenches are the least understood habitats in the ocean. The researchers participating in this project are working to characterize the microbes present in two of the deepest trenches present on Earth, both in the Pacific Ocean, the Kermadec Trench located north of New Zealand, and the Mariana Trench, located east and south of the island of Guam. Most of the Mariana Trench is located within the United States Mariana Trench Marine National Monument. Relatively little is known about the diversity and adaptations of the microorganisms in deep ocean trenches. An unknown fraction of the microbes present have descended from shallow waters above and are unlikely to participate in any nutrient cycles in the deep sea. Others are adapted to near freezing temperatures and up to pressures greater than 10e7 kilograms per square meter (16,000 pounds per square inch). These latter microbes perform important roles recycling organic matter. But who are they? This project is contributing to the training of diverse undergraduate and graduate students participating in research, additional undergraduate students learning about microbes inhabiting extreme environments in a web-based class, and additional graduate students and postdoctoral scientists participating in an advanced training course being offered in Antarctica.

Experiments being performed include direct counts of prokaryotes and viruses in seawater and sediments, analyses of the abundance and phylogenetic breadth of culturable heterotrophic bacteria at a range of pressures, measurements of bacterial community species diversity and richness both within and across seawater and sediment samples, as well as within and across the two trench systems, measurements of microbial activity as a function of pressure and the identification of high pressure-active cells. The data generated from these analyses are being integrated into the results of additional chemical, geological and biological measurements performed by others as a part of the National Science Foundation funded Hadal Ecosystems Studies Project. Two of the working hypotheses are that prokaryote numbers and diversity are generally positively correlated with surface productivity and proximity to the trench axis and that bacterial taxa exist which are endemic to specific trenches, present in multiple trenches and more widely distributed in deep-sea environments.