Dataset: Assembled metagenome sequences > 500 bp

Name: Assembled metagenome sequences collected on the R/V Melville (MGLN10MV) and R/V Atlantis (Alvin AT11-07) cruises in the Loihi Seamount, Hawaiian archipelago and East Pacific Rise from 2011-2013 (EPR and Loihi basalt genomes project)
Published: 2016-01-14
Keywords: biota, oceans

Cite This Dataset

Spatial Extent: N:18.47 E:-104.16 S:9.725 W:-155.18

Project:

Metagenomic signatures in seafloor rocks and subsurface sediments: East Pacific Rise and Loihi Seamount (EPR and Loihi basalt genomes)

Program:

Center for Dark Energy Biosphere Investigations (C-DEBI)

Lead Principal Investigator:

Katrina Edwards (University of Southern California, USC)

Principal Investigator:

Esther Singer (University of Southern California, USC)

Contact:

Esther Singer (University of Southern California, USC)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

2016-01-14

Version Date:

2016-01-14

Validated:

Yes

Current State:

Final no updates expected

Assembled metagenome sequences collected on the R/V Melville (MGLN10MV) and R/V Atlantis (Alvin AT11-07) cruises in the Loihi Seamount, Hawaiian archipelago and East Pacific Rise from 2011-2013 (EPR and Loihi basalt genomes project)

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Description

This dataset includes FASTA formatted files of the metagenomes from the East Pacific Rise seafloor basalt, the Loi'hi Seamount seafloor basalt, and negative control of sterile water.

The sequence data has been submitted to NCBI under Bioproject number PRJNA302671:
- Biosamples SUB1190178 (blank)
- SUB1190153 (Lo'ihi)
- SUB1190159 (EPR)

This dataset is the result of a C-DEBI Graduate Student Fellowship award (2011).

Methods & Sampling

Methodology:

EPR: Rock material was collected from the EPR at 9.725 N, 104.16 W (2,674 m depth) aboard the R/V Atlantis using the submarine Alvin (cruise AT11-07, dive 3968) in 2004. DNA was extracted from basalt chips using a phenol-chloroform extraction including a negative control. DNA was amplified using the illustrate GenomiPhi V2 DNA Multiple Displacement Amplification (MDA) kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA). Final DNA samples and the control were sent to the core genomics center at University of Pennsylvania for whole genome shotgun sequencing on a Roche GS-FLX Titanium 454 sequencer (454 Life Sciences, Branford, CT, USA).

Loi'hi: Two seafloor basalt samples (J2-243 R2-F, J-246 R2) were collected from the Lō’ihi Seamount (18.47 N, 155.18 W) at a depth of 5,000 m aboard the R/V Melville using the ROV Jason II in 2006. DNA was amplified using the illustrate GenomiPhi V2 DNA Multiple Displacement Amplification (MDA) kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA). Final DNA samples and the control were sent to the core genomics center at University of Pennsylvania for whole genome shotgun sequencing on a Roche GS-FLX Titanium 454 sequencer (454 Life Sciences, Branford, CT, USA).

Negative control: DNA was extracted from sterile MilliQ water using a phenol-chloroform extraction. DNA was amplified using the illustrate GenomiPhi V2 DNA Multiple Displacement Amplification (MDA) kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA). Final DNA was sent to the core genomics center at University of Pennsylvania for whole genome shotgun sequencing on a Roche GS-FLX Titanium 454 sequencer (454 Life Sciences, Branford, CT, USA).

Data Processing Description

All seafloor basalts were stored frozen at -80°C for XRD analysis and DNA extraction. Bulk mineralogy analysis, i.e. quantitative determination of rock-forming minerals and total clay minerals, was determined on all three seafloor basalts via X-ray Diffraction (XRD) analysis at KT GeoServices, Inc. Detection limits were at 1-5 wt%. For the two Lō’ihi seafloor basalts, average values were used.

Raw sequence reads were evaluated with FastQC version 0.11.3 (Schmieder and Edwards, 2011a), quality trimmed (minimum quality score – 25, maximum length – 450 bp, maximum homopolymer length – 9 bp, max N-tail – 1 bp), and filtered (removal of technical duplicates, minimum length – 60 bp) with Prinseq 0.20.4 (Schmieder and Edwards, 2011b) and MG-RAST (Meyer et al., 2008). We obtained 1,191,651 sequences in the EPR dataset; 1,102,191 sequences in the Lo’ihi dataset; and 58,188 sequences in the negative control dataset. Quality-filtered reads were assembled denovo using standard 454 settings in mira 3.4.1.1 (Chevreux et al., 1999). Padded (i.e. including potential gaps) contigs > 500 bp were filtered using mira 3.4.1.1 (convert_project) (Chevreux et al., 1999). Seafloor basalt contigs were screened for contamination using a combination of BBMap (bbduk.sh with parameters mcf=0.25, k=31) and the BLASTN algorithm (Altschul et al., 1990). The BBMap algorithm identified 4 potentially contaminant contigs in the EPR metagenome dataset (total of 4,290 bp) and 10 potentially contaminant contigs in the Lo’ihi (total of 12,423 bp). Community richness was estimated using the Chao1 index, diversity analysis was calculated using the Shannon index in QIIME 1.9.1 (alpha_diversity.py) based on BLASTX assignments of contigs. Phylosift was used to assess community diversity using the core molecular marker set of genes, which includes ~40 three-domain protein coding genes, single-copy eukaryote specific nuclear orthologs, ribosomal RNA genes (16S/18S), mitochondrial genes (mtDNA markers), and plastid and viral markers identified through Markov-clustering algorithms applied to genome datasets (Darling et al., 2014).

BCO-DMO Processing:

version 2015-11-06: replaced version 2015-10-23. Added site, lat, lon, and date columns.

Data Files

File
metagenomes_fasta3.csv (Comma Separated Values (.csv), 881 bytes) MD5:35cbd4801daa4764e76569d58305fb00 Primary data file for dataset ID 616326

More Information about this dataset

Funding Sources

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

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
MGLN10MV	FEMO-1	2006-10-24	R/V Melville	Craig L. Moyer (Chief Scientist)	data info
AT11-07		2004-01-28	R/V Atlantis	Dr Hans Schouten (Chief Scientist)	data info
AT11-07_Alvin_Dives		2014-02-03	Alvin	Daniel Fornari (Scientist)	data info

Instruments

Automated DNA Sequencer

Supplied Name:

Supplied Description:

Roche GS-FLX Titanium 454 sequencer (454 Life Sciences, Branford, CT, USA) at the core genomics center at University of Pennsylvania.

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.

ROV Jason

Supplied Name: Jason II

Supplied Description:

Jason dives 243 and 246 (18.47 N, 155.18 W).

Instrument Type

Generic Name: ROV Jason

Generic Description:

The Remotely Operated Vehicle (ROV) Jason is operated by the Deep Submergence Laboratory (DSL) at Woods Hole Oceanographic Institution (WHOI). WHOI engineers and scientists designed and built the ROV Jason to give scientists access to the seafloor that didn't require them leaving the deck of the ship. Jason is a two-body ROV system. A 10-kilometer (6-mile) fiber-optic cable delivers electrical power and commands from the ship through Medea and down to Jason, which then returns data and live video imagery. Medea serves as a shock absorber, buffering Jason from the movements of the ship, while providing lighting and a bird’s eye view of the ROV during seafloor operations. During each dive (deployment of the ROV), Jason pilots and scientists work from a control room on the ship to monitor Jason’s instruments and video while maneuvering the vehicle and optionally performing a variety of sampling activities. Jason is equipped with sonar imagers, water samplers, video and still cameras, and lighting gear. Jason’s manipulator arms collect samples of rock, sediment, or marine life and place them in the vehicle’s basket or on "elevator" platforms that float heavier loads to the surface. More information is available from the operator site at URL.

Thermal Cycler

Supplied Name:

Supplied Description:

DNA was amplified using the illustrate GenomiPhi V2 DNA Multiple Displacement Amplification (MDA) kit (GE Healthcare Life Sciences, Pittsburgh, PA, USA)

Instrument Type

Generic Name: Thermal Cycler

Generic Description:

A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.

(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)

X-ray diffractometer

Supplied Name: X-ray diffractometer (XRD)

Supplied Description:

X-ray Diffraction (XRD) analysis at KT GeoServices, Inc.

Instrument Type

Generic Name: X-ray diffractometer

Acronym: XRD

Generic Description:

Instruments that identify crystalline solids by measuring the characteristic spaces between layers of atoms or molecules in a crystal.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
NCBI_accession	link to NCBI GenBank accession page	unitless	accession_number
site	Site name: EPR = East Pacific Rise: Loihi = Loi'hi Seamount Hawaii.	unitless	site
day	day of sample collection	DD	day
lat	latitude; north is positive	decimal degrees	lat
Fasta_file_link	Link to FASTA metagenome files	unitless	file_link
lon	longitude;east is positive	decimal degrees	lon
month	month of sample collection	MM	month
sample_type	type of sample	unitless	sample_type
year	year of sample collection	YYYY	year

Status message

Database

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Dataset: Assembled metagenome sequences > 500 bp