Download URLhttps://www.bco-dmo.org/dataset/781137/data/download
Media Type text/tab-separated-values
Created November 6, 2019
Modified November 22, 2019
State Final no updates expected
Brief Description

Metagenomic data

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.

Processing Description

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


Illumina HiSeq 2500 [Automated DNA Sequencer]

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.

hydraulic piston coring system (HPCS) [Piston Corer]
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.


Cruise_ID [cruise_id]
Cruise ID number
cruise designation; name
Sample_Name [sample]
Sample name

unique sample identification or number; any combination of alpha numeric characters; precise definition is file dependent

Latitude [latitude]
Latitude; positive values = North

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

Longitude [longitude]
Longitude; positive values = East

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datsets as degrees, minutes

Water_depth [depth_w]
Water depth

water depth, in meters

Top_Depth [depth_bsf]
Top depth

depth below seafloor.  Includes mbsf (meters below seafloor) and cmbsf (centimeters below seafloor).

Bottom_Depth [depth_bsf]
Bottom depth

depth below seafloor.  Includes mbsf (meters below seafloor) and cmbsf (centimeters below seafloor).

Sediment_type [sample_descrip]
Sediment type
text description of sample collected
Estimated_Temp [temperature]
Estimated temperature; based on 3 degrees C/m
water temperature at measurement depth
MGRAST_Name [accession number]
Database identifier assigned by repository and linked to GenBank or other repository.
MGRAST_ID [accession number]
Database identifier assigned by repository and linked to GenBank or other repository.
Notes [comment]
free text comments, may only have meaning to submitting PI

Dataset Maintainers

Christopher H. HousePennsylvania State University (PSU)
Leah D. BrandtPennsylvania State University (PSU)
Shannon RauchPennsylvania State University (PSU)
Shannon RauchPennsylvania State University (PSU)
Shannon RauchWoods Hole Oceanographic Institution (WHOI BCO-DMO)

BCO-DMO Project Info

Project Title An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments
Acronym Subvent_Biosphere_Sediments
Created September 1, 2017
Modified November 5, 2019
Project Description

The Iheya North Hydrothermal Field in the Okinawa Backarc Basin represents an ideal environment in which to investigate the biotic temperature fringe of microbial life at depth because of its subsurface hydrothermal activity within its continental margin-type sediment profile. Geographically, the Okinawa Backarc Basin is situated along a continental margin, which is a sediment profile type commonly sampled and studied across the seafloor (e.g. Peru Margin, Costa Rica Margin, Cascadia Margin). The hydrothermal network within the subsurface here supplies an additional temperature obstacle to microbial life existing in the sediments. In particular, the sediment profile at Site C0014 exhibits a transition from hemipelagic ooze with pumiceous volcaniclastic sediments and low temperature (4°C) to a hydrothermally altered sequence of clays within the top ~10 mbsf of sediment. Temperature measurements indicate a gradient of approximately 3°C/m, which is roughly an order of magnitude greater than continental margin sites (e.g. Cascadia Margin, IODP 311 and Costa Rica Margin, IODP 344), but is more gradual than intense, centimeter-scale gradients from other hot, surface sediments. We have focused on the application of culture-independent, molecular methods to understand taxonomic and functional characteristics through this hydrothermal gradient. Confidence in DNA recovery suggests a microbial biosphere extent of approximately 15 mbsf (55°C).

Results from both 16S rRNA gene surveys and metagenomics analyses suggest a temperature-dependent stratigraphy of taxonomic and functional adaptations between the shallowest and deepest sample horizons. Cosmopolitan marine subsurface bacterial and archaeal taxa are present throughout the top 10 mbsf, whereas, hyperthermophilic heterotrophic as well as thermophilic anaerobic methanotrophic archaea appear in varying local abundances in deeper, hydrothermal clay horizons. “An In-Depth analysis of the subvent biosphere within Okinawa Backarc Basin (IODP 331, Iheya North Hydrothermal Field) sediments” encompasses datasets funded through C-DEBI to investigate the microbial communities in IODP 331 Iheya North Hydrothermal Field sediments. Site C0014 at this field site is 500 m away from the active vent and experiences a 3C/m temperature gradient with depth. In the research grant “Investigating the active microbial populations in near hydrothermal vent sediments” and the Research Exchange grant “Learning new RNA extraction techniques”, we used an RNA-based approach to explore the active microbial community. Upon analysis, the RNA dataset does not appear to reflect the same information as the phylogenetic signals coming from both the 16S rRNA gene as well as the metagenomes. The data indicate significant background noise from the RNA extraction process rather than from an indigenous representation of the subsurface biosphere.

The graduate fellowship “An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field” provided an opportunity to bring together metagenomic, 16S rRNA gene amplicon (DNA), and 16S rRNA amplicon datasets from IODP 331 Iheya North Hydrothermal Field sediments to understand the biogeography of this subvent biosphere.

For more information, refer to the following C-DEBI grants/projects.
An in-depth analysis of the subvent biosphere within the Okinawa backarc basin Iheya North hydrothermal field:

Investigating the active microbial populations in near hydrothermal vent sediments: https://www.darkenergybiosphere.org/award/investigating-the-active-microbial-populations-in-near-hydrothermal-vent-sediments/

Learn new RNA extraction techniques: https://www.darkenergybiosphere.org/award/learn-new-rna-extraction-techniques/

Data Project Maintainers
Christopher H. HousePennsylvania State University (PSU)Principal Investigator
Jennifer F. BiddleUniversity of DelawareCo-Principal Investigator