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.
URL | https://www.bco-dmo.org/dataset/809862 |
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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).
Instruments
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
Name | Affiliation | Contact |
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Adina Paytan | University of California-Santa Cruz (UC Santa Cruz) | ✓ |
Delphine Defforey | University of California-Santa Cruz (UC Santa Cruz) | ✓ |
Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
Amber York | University of California-Santa Cruz (UC Santa Cruz) | |
Amber York | Woods Hole Oceanographic Institution (WHOI BCO-DMO) |
BCO-DMO Project Info
Project Title | Potential phosphorus uptake mechanisms of the deep sedimentary biosphere |
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Acronym | Deep sea sediments |
URL | https://www.bco-dmo.org/project/664073 |
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
Name | Affiliation | Role |
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Adina Paytan | University of California-Santa Cruz (UC Santa Cruz) | Principal Investigator |
Benjamin J. Tully | Texas A&M University (TAMU) | Co-Principal Investigator |
Jason B. Sylvan | University of Southern California (USC) | Co-Principal Investigator |
Delphine Defforey | University of California-Santa Cruz (UC Santa Cruz) | Co-Principal Investigator |
Barbara J. Cade-Menun | Agriculture and Agri-Food Canada (AGR GC) | Co-Principal Investigator |
Brandi Kiel Reese | Texas A&M, Corpus Christi (TAMU-CC) | Co-Principal Investigator |
Laura A. Zinke | University of Southern California (USC) | Co-Principal Investigator |