Created April 22, 2020
Modified June 30, 2020
State Final no updates expected

Acquisition Description

Location: North Atlantic, western flank of the mid-Atlantic Ridge 22.75589 N 46.08125 W

DNA was extracted using the method described in (Mills et al. 2012) as modified by B. K. Reese for nucleic acids in low biomass open ocean sediments. The interior of the whole-round core for sample U1382B 7H-5 was subsampled using sterile techniques and was divided into 25 splits, each weighing ~0.5 g. Initial cell lysis was achieved using five cycles of freeze (liquid nitrogen), thaw (55oC water bath) and vortex steps while stabilizing nucleic acids in a Tris–EDTA–glucose buffer. This step was followed by the addition of lysozyme to the buffer and incubation at 30oC for 10 minutes. Samples were then treated twice with buffered phenol, chloroform and isoamyl alcohol (25:24:1; pH 8.0), and sodium dodecyl sulfate to dissolve the cell membrane and solubilize both high and low molecular weight proteins. Nucleic acids within the aqueous layer above the phenol–chloroform layer were then precipitated in an ethanol and sodium acetate solution. The ethanol solution was decanted following centrifugation of samples at 4°C. Lastly, DNA pellets were resuspended in sterile water, combined into one sample. We quantified the DNA content using a Quibit fluorometer (Thermo Scientific, Waltham, MA, USA) and assessed its quality on a NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA) prior to sequencing at the Marine Biological Laboratory Keck facility (Woods Hole, MA, USA). Extraction blanks were included with each sample extraction and yielded no measurable DNA.

Processing Description

Raw reads were quality controlled using cutadapt (v1.7.1) and Trimmomatic (v0.33). The QCed sequences were searched for SSU rRNA fragments using Meta-RNA (v.H3). SSU rRNA fragments were assembled using EMIRGE (v.1.3) utilizing SILVA SSU as the reference database using the SINA web portal aligner (Ludwig et al. 2004; Capella-Gutiérrez et al. 2009; Pruesse et al. 2012).


Quibit fluorometer (Thermo Scientific, Waltham, MA, USA) [Fluorometer]

A fluorometer or fluorimeter is a device used to measure parameters of fluorescence: its intensity and wavelength distribution of emission spectrum after excitation by a certain spectrum of light. The instrument is designed to measure the amount of stimulated electromagnetic radiation produced by pulses of electromagnetic radiation emitted into a water sample or in situ.

NanoDrop 1000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA) [Spectrophotometer]

An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples.

Dataset Maintainers

Adina PaytanUniversity of California-Santa Cruz (UC Santa Cruz)
Delphine DefforeyUniversity of California-Santa Cruz (UC Santa Cruz)
Amber YorkUniversity of California-Santa Cruz (UC Santa Cruz)
Amber YorkUniversity of California-Santa Cruz (UC Santa Cruz)
Amber YorkWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title Potential phosphorus uptake mechanisms of the deep sedimentary biosphere
Acronym Deep sea sediments
Created November 7, 2016
Modified November 7, 2016
Project Description

The goal of this project is to explore potential microbial P uptake mechanisms in marine sediments beneath the North Atlantic Gyre and their effects on the relative distribution of organic P compounds as a function of burial depth and changing redox conditions. We use a combination of metagenomic analyses and solution 31P nuclear magnetic resonance spectroscopy (31P NMR) to investigate (1) the presence of microbial functional genes pertaining to P uptake and metabolism and (2) the possible P substrates for the deep biosphere in these oligotrophic sediments.

NSF C-DEBI Award #156246 to Dr. Adina Paytan

NSF C-DEBI Award #157598 to Dr. Delphine Defforey 

Data Project Maintainers
Adina PaytanUniversity of California-Santa Cruz (UC Santa Cruz)Principal Investigator
Benjamin J. TullyTexas A&M University (TAMU)Co-Principal Investigator
Jason B. SylvanUniversity of Southern California (USC)Co-Principal Investigator
Delphine DefforeyUniversity of California-Santa Cruz (UC Santa Cruz)Co-Principal Investigator
Barbara J. Cade-MenunAgriculture and Agri-Food Canada (AGR GC)Co-Principal Investigator
Brandi Kiel ReeseTexas A&M, Corpus Christi (TAMU-CC)Co-Principal Investigator
Laura A. ZinkeUniversity of Southern California (USC)Co-Principal Investigator