http://lod.bco-dmo.org/id/dataset/868323
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
2022-01-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Accession numbers for metagenome-assembled genomes (MAGs) from samples collected in 2018 on R/V Thompson cruise TN350 at the Upper and Lower Cones, Upper Caldera Wall and NW Caldera, Brothers Volcano
2022-01-19
publication
2022-01-19
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-08-24
publication
https://doi.org/10.26008/1912/bco-dmo.868323.1
Anna-Louise Reysenbach
Portland State University
principalInvestigator
Susan Humphris
Woods Hole Oceanographic Institution
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: Reysenbach, A., Humphris, S. (2022) Accession numbers for metagenome-assembled genomes (MAGs) from samples collected in 2018 on R/V Thompson cruise TN350 at the Upper and Lower Cones, Upper Caldera Wall and NW Caldera, Brothers Volcano. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2022-01-19 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.868323.1 [access date]
Brothers Volcano Metagenome-Assembled Genome Accession Numbers Dataset Description: Methods and Sampling: <p>Water samples and hydrothermal vent deposits were collected as described in Reysenbach &amp; St. John et al., 2020. Samples were collected with remotely operated vehicle ROV Jason. Water samples were obtained using major water samplers. Hydrothermal deposits were placed in sealed bioboxes in the ROV sampling basket to restrict flushing of samples by surrounding seawater during the ascent. Once shipboard, 1L of water samples were filtered through a 0.2-μm Sterivex filter (Merck). For the hydrothermal deposits, the outer few millimeters (up to approximately 5 mm) was subsampled for DNA extraction. These exterior samples were homogenized and stored in cryovials at -80 degrees C for subsequent DNA extraction. For the water samples, the DNA was extracted from the sterivex filters as previously described by R. E. Anderson et al. (2017). The DNA was extracted from the homogenized hydrothermal depot samples using the DNeasy PowerSoil kit (Qiagen) All purified environmental DNA was stored at -80 degrees C. After DNA extraction and library preparation, metagenomes were sequenced using the Illumina HiSeq 3000.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1558795 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1558795
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1558356 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1558356
completed
Anna-Louise Reysenbach
Portland State University
503-725-3864
1719 SW 10th Ave. SRTC Room 246
Portland
OR
97201
USA
bwar@pdx.edu
pointOfContact
Susan Humphris
Woods Hole Oceanographic Institution
508-289-3451
360 Woods Hole Rd. McLean 206 MS#08
Woods Hole
MA
02543
USA
shumphris@whoi.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Sample
MAG
Repository
Biosample_accession
WGS_accession
Organism
Collection_location
Collection_date
Latitude
Longitude
Depth
Sequencing_technology
Assembly_program
Binning_program
Illumina HiSeq 3000
theme
None, User defined
sample identification
No BCO-DMO term
NCBI BioSample accession
accession number
taxon
site
date
latitude
longitude
depth
instrument
sampling_method
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
TN350
service
Deployment Activity
Brothers Volcano
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.
Collaborative Research: Hydrothermal and Microbiological Investigations of the Active Brothers Volcano in the Kermadec Arc
https://osprey.bco-dmo.org/project/778733
Collaborative Research: Hydrothermal and Microbiological Investigations of the Active Brothers Volcano in the Kermadec Arc
<p><em>NSF Award Abstract:</em><br />
Nearly one third, or 22,000 km of Earth's submarine volcanic activity, occurs along intraoceanic volcanic arcs. The volcanos and seafloor spreading centers in these areas host significant numbers of hydrothermal systems that vent hot, mineral-charged waters into the oceans and support unique micro- and macrobiological communities that are found nowhere else on Earth. The chemistry of hydrothermal systems found along interoceanic arcs differ substantially from those located at mid-ocean ridges, with arc systems exhibiting strong magmatic signatures. This unique chemistry, coupled with the shallow depths at which the calderas of many of these arc volcanoes occur, result in highly acidic and volatile-enriched fluids that are the precursors to economically metal-rich mineral deposits. Because these systems are difficult to detect unless they are come upon by accident, these systems are relatively unstudied and have unexplored microbiological communities. This research will undertake a 20-day oceanographic research expedition and shore-based laboratory studies of the samples that are collected to characterize one of these unique volcanoes: Brothers Volcano in the Kermadec Arc in the Western Pacific Ocean. This volcano has also been selected as a potential ocean drilling site with science focused on the development of a better understanding of active seafloor hydrothermal systems and their circulation pathways. Goals of the present research program include using remotely operated vehicles to survey and sample the rocks, vent fluids, and microbes in the Brothers Volcano caldera. It also includes an extensive heat flow survey to identify areas of fluid recharge and discharge. Broader impacts of the research include establishing collaborations with New Zealand scientists, graduate student training, support of two investigators whose genders are under-represented in the sciences, and public outreach through the Woods Hole Oceanographic Institution's award-winning Dive and Discover website. Presentations will also be made to the public as opportunities present themselves. There is also the potential for the discovery of new microbiological species with unusual metabolic pathways or enzymes which may have natural products and/or pharmacological utility. The work also has the ability to help us understand the formation of hydrothermal vent related sulfide deposits which commonly are rich in copper, gold, and molybdenum. This research also complements the science agenda of the NSF-funded International Ocean Discovery Program and provides a critical site survey upon which seafloor drilling legs can be based.</p>
<p>This research is focused on documenting and understanding the geology, heat flow, hydrothermal, and microbial characteristics of the Brothers Volcano edifice in the Kermadec Arc in the Western Pacific Ocean. A 20-day sample collection cruise will take place in the caldera of the Brothers Volcano and will be followed up by onshore laboratory geochemical and microbiological work. The research project will test five hypotheses related to hydrothermal circulation at Brothers volcano. Work will include documenting the heat and chemical fluxes coming from the caldera; the role of low pH in these systems; and the influence of magmatic volatile-rich hydrothermal fluids on rock alteration. Research will also involve determining mechanisms and the extent of fluid-rock interaction and mass transfer of carbon, sulfur, metals and metalloids into the ocean; the subseafloor distribution of metals and associated mineral deposits; and the diversity and extent of microbial life in an arc volcano hydrothermal environment. Brothers volcano is ideally suited for such studies because it harbors two different styles of hydrothermal vents within its caldera: (1) high-temperature black smoker-type fluids discharging from Cu-Au-rich sulfide chimneys; and (2) moderate temperature, gassy, acid-sulfate waters where native sulfur chimneys and extensive Fe-oxyhydroxide crusts occur. During the cruise a mapping, sampling, and observational program will take place, consisting of a series of dives by a remotely operated vehicle to four distinct hydrothermal fields within Brothers caldera. Thermal blankets will be deployed in the caldera around the hydrothermal vents to measure heat flow and fluid recharge and discharge zones. Coexisting minerals and fluids associated with the vents and the surrounding caldera will be collected and geochemically analyzed. This research and the resulting caldera survey complements other observational and analytical work carried out over the past decade by NOAA, the National Ocean and Atmospheric Administration, and its corresponding agency associated with the government of New Zealand. One important goal of the survey work is to identify potential sites for ocean drilling for further understanding of seafloor arc volcanic systems.</p>
Brothers Volcano Microbiology
largerWorkCitation
project
eng; USA
oceans
Brothers Volcano
179.051933
179.071443
-34.8823655
-34.8579131
2018-03-01
2018-03-31
Brothers volcano, NE of New Zealand on the Kermadec arc (34.88, 179.08)
0
BCO-DMO catalogue of parameters from Accession numbers for metagenome-assembled genomes (MAGs) from samples collected in 2018 on R/V Thompson cruise TN350 at the Upper and Lower Cones, Upper Caldera Wall and NW Caldera, Brothers Volcano
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/868478.rdf
Name: Sample
Units: unitless
Description: <p>Sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/868479.rdf
Name: MAG
Units: unitless
Description: <p>Metagenome-assembled genome (MAG) identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/868480.rdf
Name: Repository
Units: unitless
Description: <p>Public database where data is deposited</p>
http://lod.bco-dmo.org/id/dataset-parameter/868481.rdf
Name: Biosample_accession
Units: unitless
Description: <p>Genbank Biosample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/868482.rdf
Name: WGS_accession
Units: unitless
Description: <p>Genbank whole genome sequence accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/868483.rdf
Name: Organism
Units: unitless
Description: <p>Genbank-compatable organism name</p>
http://lod.bco-dmo.org/id/dataset-parameter/868484.rdf
Name: Collection_location
Units: unitless
Description: <p>Geographic location of collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/868485.rdf
Name: Collection_date
Units: unitless
Description: <p>Collection date; format: YYYY-MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/868486.rdf
Name: Latitude
Units: decimal degrees North
Description: <p>Collection latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/868487.rdf
Name: Longitude
Units: decimal degrees East
Description: <p>Collection longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/868488.rdf
Name: Depth
Units: meters
Description: <p>Depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/868489.rdf
Name: Sequencing_technology
Units: unitless
Description: <p>Technology used to sequence metagenomes</p>
http://lod.bco-dmo.org/id/dataset-parameter/868490.rdf
Name: Assembly_program
Units: unitless
Description: <p>Software used to assemble contigs from metagenome reads</p>
http://lod.bco-dmo.org/id/dataset-parameter/868491.rdf
Name: Binning_program
Units: unitless
Description: <p>Software used to bin MAGs from contigs</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
130255
https://darchive.mblwhoilibrary.org/bitstream/1912/29258/1/dataset-868323_brothers-volcano-metagenome-assembled-genome-accession-numbers__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.868323.1
download
onLine
dataset
<p>Water samples and hydrothermal vent deposits were collected as described in Reysenbach &amp; St. John et al., 2020. Samples were collected with remotely operated vehicle ROV Jason. Water samples were obtained using major water samplers. Hydrothermal deposits were placed in sealed bioboxes in the ROV sampling basket to restrict flushing of samples by surrounding seawater during the ascent. Once shipboard, 1L of water samples were filtered through a 0.2-μm Sterivex filter (Merck). For the hydrothermal deposits, the outer few millimeters (up to approximately 5 mm) was subsampled for DNA extraction. These exterior samples were homogenized and stored in cryovials at -80 degrees C for subsequent DNA extraction. For the water samples, the DNA was extracted from the sterivex filters as previously described by R. E. Anderson et al. (2017). The DNA was extracted from the homogenized hydrothermal depot samples using the DNeasy PowerSoil kit (Qiagen) All purified environmental DNA was stored at -80 degrees C. After DNA extraction and library preparation, metagenomes were sequenced using the Illumina HiSeq 3000.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
Metagenome reads were trimmed using Trimmomatic, and assembled into contigs with MEGAHIT. Reads were then mapped back to the contigs with Bowtie2 and SAMtools. Metagenome-assembled genomes were binned using MetaBAT, followed by curation of key genomes using Emergent Self Organizing Maps.</p>
<p><strong>Software:</strong><br />
Trimmomatic v.0.36: Trimming software for read processing.</p>
<p>MEGAHIT v.1.1.1-2-g02102e1: Assembly software used to generate contigs from reads.</p>
<p>Bowtie2 v.2.2.9 and SAMtools v.1.3.1: Software used to map reads back to contigs and parse results of the mapping.</p>
<p>MetaBAT v.0.32.4: Binning software, used to group contigs into metagenome-assembled genomes (MAGs).</p>
<p>Emergent Self Organizing Maps (ESOM): manual binning software used to curate genomes of interest.</p>
<p><strong>BCO-DMO Processing:</strong><br />
- removed commas from Collection_location column;<br />
- removed directional letters from the Latitude&nbsp;and Longitude columns and made Latitude values negative to indicate South;<br />
- converted Collection_date field to YYYY-MM format.</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 3000
Illumina HiSeq 3000
PI Supplied Instrument Name: Illumina HiSeq 3000 PI Supplied Instrument Description:Illumina HiSeq 3000: Sequencing platform used to generate metagenome reads 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.
Cruise: TN350
TN350
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN350
Anna-Louise Reysenbach
Portland State University
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel