http://lod.bco-dmo.org/id/dataset/636430
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2016-01-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Metegenomic sequences from Lau Basin low temperature vents and Loihi Seamount; from R/V Roger Revelle and R/V Thomas G. Thompson cruises RR1211 and TN225 in the Northeast Lau Basin, Loihi Seamount from 2008-2012
2016-01-25
publication
2016-01-25
revision
BCO-DMO Linked Data URI
2016-01-25
creation
http://lod.bco-dmo.org/id/dataset/636430
Bradley M. Tebo
Oregon Health & Science University
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Tebo, B. M. (2016) Metegenomic sequences from Lau Basin low temperature vents and Loihi Seamount; from R/V Roger Revelle and R/V Thomas G. Thompson cruises RR1211 and TN225 in the Northeast Lau Basin, Loihi Seamount from 2008-2012. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 25 Jan 2016) Version Date 2016-01-25 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/636430 [access date]
Metegenomic sequences from Lau Basin low temperature vents and Loihi Seamount. Dataset Description: <p>Metegenomic sequences from Lau Basin low temperature vents and Loihi Seamount; collected on the 2012 "Submarine Ring of Fire" (SRoF) cruise and the 2008 FeMO cruise.</p> Methods and Sampling: <p>Samples were collected with a closable PVC scoop sampler that was designed to sample mat material along with bottom waters while minimizing cross-contamination from other samples or with ambient seawater. The sampler was constructed with 3"&nbsp;PVC pipe and was washed with 70% ethanol before being rinsed and filled with filter-sterilized deionized water and sealed with a ball valve before deployment. The valve was opened immediately prior to sampling and closed directly after the sample collected and remained sealed until the sample was recovered on the ship. All samples were allowed to settle at 4 degrees&nbsp;C for approximately 2 hours before the overlying seawater was decanted and the mat material frozen at -80 degrees&nbsp;C until DNA was extracted in the lab.</p>
<p>Note:&nbsp;The J2-373 dive video can be found on the virtual van (<a href="http://4dgeo.whoi.edu/jason/">http://4dgeo.whoi.edu/jason/</a>).</p>
<p><strong>DNA extraction: </strong>Total genomic DNA (gDNA) was extracted from each sample in duplicate using the FastDNA Spin Kit for Soil following the manufacturer's protocol (Qbiogene, Irvine, CA). Extracted gDNA from each sample was pooled, cleaned, and concentrated using Montáge PCR centrifugal filter devices (Millipore, Bedford, MA). The gDNAs were then quantified using a Nanodrop ND-1000 spectrophotometer and were diluted to 10 ng DNA/ml using filter sterilized 10 mM Tris 0.1 mM EDTA (pH 8.0).</p>
<p><strong>Metagenome sequencing: </strong>Two micrograms of gDNA was sheared using a Covaris S2 sonicator and 400bp fragments were size selected for library construction. The library was constructed using the TruSeq DNA sample prep kit (Illumina) following the manufactures protocol. Sequencing was performed using an Illumina HiSeq 2000 sequencer.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1129553 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1129553
completed
Bradley M. Tebo
Oregon Health & Science University
503-346-3438
Division of Environmental and Biomolecular Systems 20000 NW Walker Road
Beaverton
OR
97006
USA
tebob@ohsu.edu
pointOfContact
asNeeded
Dataset Version: 25 Jan 2016
Unknown
cruise
description
BioProject
location
dive
sample
date
lat
lon
depth
BioProject_URL
Illumina HiSeq 2000 sequencer
Nanodrop ND-1000 spectrophotometer
Covaris S2 sonicator
theme
None, User defined
Cruise identfier
brief description
accession number
site description
No BCO-DMO term
sample identification
date
latitude
longitude
depth
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
ROV Jason
Spectrophotometer
ultrasonic cell disrupter (sonicator)
instrument
BCO-DMO Standard Instruments
RR1211
TN225
service
Deployment Activity
Northeast Lau Basin
Loihi Seamount
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Understanding microbial manganese-oxidizing communities and physiological mechanisms in metal oxide-rich hydrothermal sediments using a metagenomic and metatranscriptomic approach
https://osprey.bco-dmo.org/project/527494
Understanding microbial manganese-oxidizing communities and physiological mechanisms in metal oxide-rich hydrothermal sediments using a metagenomic and metatranscriptomic approach
<p><em>Project description from the NSF award abstract:</em><br />
Hydrothermal systems are important sources of dissolved Mn to the oceans. Upon oxidation of Mn(II), Mn(III,IV) oxides are deposited at the sea floor as crusts, nodules and sediments both near and far from the sources. Microbial activity has long been recognized as being important to the fate of Mn in these hydrothermal systems, yet we know very little about the organisms that catalyze Mn oxidation, the mechanisms by which Mn is oxidized or the physiological function that Mn oxidation serves. The overarching goals of this project are to reveal the organisms and mechanism(s) underlying Mn(II) oxidation, to evaluate whether hydrothermal Mn oxidizers may obtain energy from Mn oxidation, and test whether thermophilic Mn oxidizers exist. Specifically, the project will: 1) evaluate whether we can identify certain genomic sequences that correlate to the presence/concentration of Mn oxides (and hence Mn(II)- oxidizing bacteria) by comparing the metagenomes of ferromanganese (containing both Mn and Fe oxides) microbial mats with ferruginous (Fe oxide only) mats from Lau Basin and Loihi Seamount; 2) use peptide probes bound to magnetic particles for selectively binding and capturing Mn oxide particles and characterizing the particles using phylogenetic and functional gene (PCR and FISH) and transcriptomic analysis; 3) assess the main pathways of carbon fixation in ferromanganese microbial mats as compared to ferruginous mats as a possible indicator of Mn-based auto/mixotrophy using genomic approaches and substrate stimulated (e.g., addition of Mn(II)) CO2 fixation measurements and stable isotope probing (SIP) genomic analysis; and 4) isolate and characterize Mn(II)-oxidizing bacteria and determine whether thermophilic Mn oxidizers exist.</p>
<p>The results of this research will increase our understanding of Mn(II) oxidation in hydrothermal sediments, identify microorganisms that are the environmentally relevant Mn oxidizers and begin to address the long standing question of whether Mn auto/mixotrophy exists using approaches not based on the biases associated with cultivation. Ultimately this information is critical to our understanding of biogeochemical cycles (Mn oxidation and Mn oxides impact many other elemental cycles, including carbon, sulfur, and heavy metals) and the natural attenuation of toxic metal and organic compounds; this may lead to improved technologies for environmental remediation. Because Mn oxides are believed to be an analog to the ancestral Mn centers in photosystem II, this research may also lend new insights into ancient biogeochemistry occurring before the Great Oxidation Event.</p>
Vent Mn-Fe Microbes
largerWorkCitation
project
eng; USA
oceans
Northeast Lau Basin; Loihi Seamount
2016-01-25
Northeast Lau Basin
0
BCO-DMO catalogue of parameters from Metegenomic sequences from Lau Basin low temperature vents and Loihi Seamount; from R/V Roger Revelle and R/V Thomas G. Thompson cruises RR1211 and TN225 in the Northeast Lau Basin, Loihi Seamount from 2008-2012
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/636452.rdf
Name: cruise
Units: dimensionless
Description: <p>Cruise identifier. TN225 also known as FeMO-3. RR1211 also known as SRoF-12.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636453.rdf
Name: description
Units: dimensionless
Description: <p>Description of sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636454.rdf
Name: BioProject
Units: dimensionless
Description: <p>NCBI's BioProject ID number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636455.rdf
Name: location
Units: dimensionless
Description: <p>Description of location.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636456.rdf
Name: dive
Units: dimensionless
Description: <p>Dive number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636457.rdf
Name: sample
Units: dimensionless
Description: <p>Sample number.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636458.rdf
Name: date
Units: YYYYmmdd
Description: <p>Date (year, month, and day) of sampling.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636459.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636460.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636461.rdf
Name: depth
Units: meters
Description: <p>Depth of sample.</p>
http://lod.bco-dmo.org/id/dataset-parameter/636462.rdf
Name: BioProject_URL
Units: dimensionless
Description: <p>Hyperlink to NCBI BioProject page.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
822
https://datadocs.bco-dmo.org/file/EKKygDDHlzoOVy/metagenomes.csv
metagenomes.csv
Primary data file for dataset ID 636430
download
https://osprey.bco-dmo.org/dataset/636430/data/download
download
onLine
dataset
<p>Samples were collected with a closable PVC scoop sampler that was designed to sample mat material along with bottom waters while minimizing cross-contamination from other samples or with ambient seawater. The sampler was constructed with 3"&nbsp;PVC pipe and was washed with 70% ethanol before being rinsed and filled with filter-sterilized deionized water and sealed with a ball valve before deployment. The valve was opened immediately prior to sampling and closed directly after the sample collected and remained sealed until the sample was recovered on the ship. All samples were allowed to settle at 4 degrees&nbsp;C for approximately 2 hours before the overlying seawater was decanted and the mat material frozen at -80 degrees&nbsp;C until DNA was extracted in the lab.</p>
<p>Note:&nbsp;The J2-373 dive video can be found on the virtual van (<a href="http://4dgeo.whoi.edu/jason/">http://4dgeo.whoi.edu/jason/</a>).</p>
<p><strong>DNA extraction: </strong>Total genomic DNA (gDNA) was extracted from each sample in duplicate using the FastDNA Spin Kit for Soil following the manufacturer's protocol (Qbiogene, Irvine, CA). Extracted gDNA from each sample was pooled, cleaned, and concentrated using Montáge PCR centrifugal filter devices (Millipore, Bedford, MA). The gDNAs were then quantified using a Nanodrop ND-1000 spectrophotometer and were diluted to 10 ng DNA/ml using filter sterilized 10 mM Tris 0.1 mM EDTA (pH 8.0).</p>
<p><strong>Metagenome sequencing: </strong>Two micrograms of gDNA was sheared using a Covaris S2 sonicator and 400bp fragments were size selected for library construction. The library was constructed using the TruSeq DNA sample prep kit (Illumina) following the manufactures protocol. Sequencing was performed using an Illumina HiSeq 2000 sequencer.</p>
Specified by the Principal Investigator(s)
<p><strong>Metagenome quality control and assembly:</strong> Sequences were quality controlled and trimmed using the program Sickle. The trimmed sequences were then digitally normalized using the program Khmer utilizing a two-pass strategy. The sequences were first normalized by median to reduce sequences with high-abundance kmers using a kmer size of 20bp and a maximum coverage overlap value of 20. The sequences were then filtered to remove low-abundance kmers and Illumina sequencing artifacts using the Khmer script filter-below-abund with a minimum overlap of 2 kmers. The remaining sequences after preprocessing were used for sequence assembly.</p>
<p>The normalized reads were assembled using the de Bruijn graph-based assembler Velvet. Four independent assemblies were constructed with kmer sizes of 41, 51, 61, and 71. The contigs were assembled into "supercontigs"&nbsp;using the program Geneious with a minimum overlap of 25bp. Contigs longer than 1000bp were exported and used in further analysis.</p>
<p>The sequence data has been submitted to NCBI under Bioproject numbers PRJNA298367 (Lau sequences) and PRJNA297446 (Loihi sequences).</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina HiSeq 2000 sequencer
Illumina HiSeq 2000 sequencer
PI Supplied Instrument Name: Illumina HiSeq 2000 sequencer Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: Instrument Name: ROV Jason Instrument Short Name:ROV Jason Instrument 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. https://ndsf.whoi.edu/jason/
Nanodrop ND-1000 spectrophotometer
Nanodrop ND-1000 spectrophotometer
PI Supplied Instrument Name: Nanodrop ND-1000 spectrophotometer Instrument Name: Spectrophotometer Instrument Short Name:Spectrophotometer Instrument Description: An instrument used to measure the relative absorption of electromagnetic radiation of different wavelengths in the near infra-red, visible and ultraviolet wavebands by samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB20/
Covaris S2 sonicator
Covaris S2 sonicator
PI Supplied Instrument Name: Covaris S2 sonicator Instrument Name: ultrasonic cell disrupter (sonicator) Instrument Short Name: Instrument Description: Instrument that applies sound energy to agitate particles in a sample.
Cruise: RR1211
RR1211
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
RR1211
Joseph A. Resing
University of Washington
http://dmoserv3.whoi.edu/data_docs/Vent_Mn-Fe_Microbes/SRoF12-cruisereport-final.pdf
Report describing RR1211
Cruise: TN225
TN225
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN225
Craig L. Moyer
Western Washington University
R/V Roger Revelle
Community Standard Description
International Council for the Exploration of the Sea
R/V Roger Revelle
vessel
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel