Dataset: Sedtrap Metagenomes
Deployment: KM1219

Marine sediment trap metagenomes

Principal Investigator:

Edward DeLong (Massachusetts Institute of Technology, MIT-Dept CEE)

Data Manager:

Jasmine Nahorniak (Oregon State University, OSU-CEOAS)

BCO-DMO Data Manager:

Stephen R. Gegg (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Center for Microbial Oceanography: Research and Education (C-MORE)

Current State:

Final no updates expected

Version:

22 May 2015

Deployment Synonyms:

HOE-DYLAN IX

Version Date:

2015-05-22

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/559257/data

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Description

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

Methods & Sampling

Dataset acquisition description

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

Data Processing Description

Dataset Processing Description

More information about this dataset deployment

Funding

Award Number	Funding Source
AI-MO9.12.1	Agouron Institute
DBI-0424599	NSF Division of Biological Infrastructure
DBI-1202684	NSF Division of Biological Infrastructure
GBMF3777	Gordon and Betty Moore Foundation
unknown C-MORE DOE	US Department of Energy
unknown C-MORE Moore	Gordon and Betty Moore Foundation

Instruments

Automated DNA Sequencer

Supplied Name: MOBIO Powerwater

Supplied Description:

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.

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.

Automated DNA Sequencer

Supplied Name: Illumina Nextera XT

Supplied Description:

Illumina Nextera XT

Illumina Nextera XT Data Sheet

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.

Automated DNA Sequencer

Supplied Name: MiSeq instrument

Supplied Description:

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.

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.

CTD Sea-Bird SBE 911plus

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD Sea-Bird SBE 911plus

Acronym: CTD SBE 911plus

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/

Generic Description:

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

Niskin bottle

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

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.

Sediment Trap

Supplied Name: HOE-DYLAN 5 sediment trap

Supplied Description:

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.

Instrument Type

Generic Name: Sediment Trap

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/33/

Generic Description:

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.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
lat	latitude (positive north)	decimal degrees	lat
lon	longitude (positive east)	decimal degrees	lon
sample	sample ID	dimensionless	sample
depth	depth	meters	depth
date	date	YYYYMMDD	date
BioProject	NCBI BioProject accession number	dimensionless	accession_number
SRX	NCBI SRX accession number	dimensionless	accession_number
BioSample	NCBI BioSample accession number	dimensionless	accession_number

Database

Contribute Data

Dataset: Sedtrap Metagenomes
Deployment: KM1219

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: Sedtrap MetagenomesDeployment: KM1219

Dataset acquisition description

Dataset Processing Description

Dataset: Sedtrap Metagenomes
Deployment: KM1219