Dataset: Metagenome
Deployment: Chikyu-331

Metagenomic data

Principal Investigator:

Christopher House (Pennsylvania State University, PSU)

Scientist:

Leah Brandt (Pennsylvania State University, PSU)

BCO-DMO Data Manager:

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments (Subvent_Biosphere_Sediments)

Current State:

Final no updates expected

Deployment Synonyms:

IODP-331

Data URL:

https://www.bco-dmo.org/dataset-deployment/781142/data

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Description

Next-generation sequencing data across a hydrothermal gradient; Okinawa Backarc Basin IODP 331 – subvent biosphere. The purpose these metagenomic data was to capture a distinct changeover of microbial assemblages between the mesophilic horizons above 10 mbsf and the hottest (55C) hydrothermal clay horizon. In this section of the dynamic Iheya North Hydrothermal system, the temperature gradient was estimated to be ~3C/m. These metagenomes provide functional evidence to this model, demonstrating that molecular signals represent a responsive microbial community to the increasingly demanding environmental conditions.

Methods & Sampling

Dataset acquisition description

Sampling of cores was done in accordance with IODP protocols.

All C0014 samples were cored on 16 September 2010 via via HPCS (hydraulic piston coring system).
All C0015 samples were cored on 18 September 2010 via HPCS.
All C0017 samples were cored on 27 September 2010 via HPCS.

Core sections were kept frozen (-80°C) until DNA extractions. A MoBio® Power Soil kit was used to extract environmental DNA. Metagenomic data was produced from whole genome amplified environmental DNA (REPLI-g Mini Kit, Qiagen).

Sequencing was performed at the Penn State Genomics Core Facility – University Park, PA using the Illumina® HiSeq 2500 (NSF-MRI award DBI-1229046 (Axtell et al., 2012)). The sequencing facility prepared DNA libraries using Nextera XT Library Preparation Kits prior to sequencing. Together, the samples were run on one-half of a sequencing plate. This sequencing run was run using rapid-run model that averages up to 300 million single reads, or 600 million paired reads of ~150 nucleotides per rapid-run.

Data Processing Description

Dataset Processing Description

Data Processing: Data assembly was performed with Ray Meta de novo assembly program using a k-mer of 65 for all samples.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0939564	NSF Division of Ocean Sciences

Instruments

Automated DNA Sequencer

Supplied Name: Illumina HiSeq 2500

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

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.

Piston Corer

Supplied Name: hydraulic piston coring system (HPCS)

Supplied Description:

Instrument Type

Generic Name: Piston Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

The piston corer is a type of bottom sediment sampling device. A long, heavy tube is plunged into the seafloor to extract samples of mud sediment. A piston corer uses a "free fall" of the coring rig to achieve a greater initial force on impact than gravity coring. A sliding piston inside the core barrel reduces inside wall friction with the sediment and helps to evacuate displaced water from the top of the corer. A piston corer is capable of extracting core samples up to 90 feet in length.

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise_ID	Cruise ID number	unitless	cruise_id
Sample_Name	Sample name	unitless	sample
Latitude	Latitude; positive values = North	decimal degrees	lat
Longitude	Longitude; positive values = East	decimal degrees	lon
Water_depth	Water depth	meters	depth_w
Top_Depth	Top depth	meters below seafloor	depth_bsf
Bottom_Depth	Bottom depth	meters below seafloor	depth_bsf
Sediment_type	Sediment type	unitless	sample_descrip
Estimated_Temp	Estimated temperature; based on 3 degrees C/m	degrees Celsius	temp
MGRAST_Name	MGRAST name	unitless	accession_number
MGRAST_ID	MGRAST ID	unitless	accession_number
Notes	Notes	unitless	comment

Database

Contribute Data

Dataset: Metagenome
Deployment: Chikyu-331

Dataset acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: MetagenomeDeployment: Chikyu-331

Dataset acquisition description

Dataset Processing Description

Dataset: Metagenome
Deployment: Chikyu-331