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Marine sediment trap metagenomes
This study explores the taxonomic and metabolic diversity of microbes associated with sinking particles in the North Pacific Subtropical Gyre. Marine particles are hotspots of microbial activity, yet the microbial taxa and biochemical processes involved in carbon and energy cycling on sinking particles are poorly understood. Metagenomes generated in this study revealed new insights into the important taxa and metabolisms involved in microbial processing of marine particles.
NCBI BioProject PRJNA270248
# C-MORE sediment trap metagenomes # DeLong Lab - MIT # Ed DeLong # CMORE/HOEDYLAN # date ingested into BCO-DMO: May 22 2015
A HOE-DYLAN 5 sediment trap filled with brine/preservative solution and screened with 335 micron mesh was deployed at station ALOHA in the North Pacific Subtropical Gyre from July 14, 2012 to July 26, 2012. It was filtered onto a 0.2 micron filter, preserved with RNAlater and frozen at -80C. Genomic DNA representing the 0.2-335 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol. The library was dual-indexed according to Illumina's low-plexity pooling guidelines. This library was pooled with 9 others on a 300 bp paired-end sequencing run on a MiSeq instrument using MiSeq reagent kit version 3.
Seawater at station ALOHA in the North Pacific Subtropical Gyre was collected by CTD during the HOE-DYLAN 9 expedition on 08/26/2012. Seawater was prefiltered with a 5 micron filter and microbial communities were collected on a 0.2 micron filter, preserved with RNAlater and frozen at -80C. Genomic DNA representing the 0.2-5 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol. The library was dual-indexed according to Illumina's low-plexity pooling guidelines. This library was pooled with 9 others on a 300 bp paired-end sequencing run on a MiSeq instrument using MiSeq reagent kit version 3.
C-MORE DNA Sampling Protocol
MOBIO Powerwater
Genomic DNA representing the 0.2-335 micron fraction was isolated from frozen filters using a modified MOBIO Powerwater kit protocol and prepared for sequencing using the Illumina Nextera XT DNA sample preparation protocol.
General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
Illumina Nextera XT
Illumina Nextera XT Data Sheet
MiSeq instrument
This library was pooled with 9 others on a 300 bp paired-end sequencing run on a MiSeq instrument using MiSeq reagent kit version 3.
The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics
A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.
A HOE-DYLAN 5 sediment trap filled with brine/preservative solution and screened with 335 micron mesh was deployed at station ALOHA in the North Pacific Subtropical Gyre from July 14, 2012 to July 26, 2012.
filled with brine/preservative solution and screened with 335 micron mesh was deployed at station ALOHA in the North Pacific Subtropical Gyre from July 14, 2012 to July 26, 2012.
Sediment traps are specially designed containers deployed in the water column for periods of time to collect particles from the water column falling toward the sea floor. In general a sediment trap has a jar at the bottom to collect the sample and a broad funnel-shaped opening at the top with baffles to keep out very large objects and help prevent the funnel from clogging. This designation is used when the specific type of sediment trap was not specified by the contributing investigator.
latitude (positive north)
longitude (positive east)
sample ID
depth
date
NCBI BioProject accession number
NCBI SRX accession number
NCBI BioSample accession number
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