http://lod.bco-dmo.org/id/dataset/861683
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
2021-09-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sequence read accession (SRA) numbers for bacterial and archaeal 16S rRNA gene amplicons from the DeepCCZ and Abyssline programs
2023-10-25
publication
2023-10-25
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2024-06-13
publication
https://doi.org/10.26008/1912/bco-dmo.861683.1
Matthew J. Church
University of Montana
principalInvestigator
Jeffrey C. Drazen
University of Hawaiʻi at Mānoa
principalInvestigator
Craig R. Smith
University of Hawaiʻi at Mānoa
principalInvestigator
Emma Wear
University of Montana
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: Church, M. J., Drazen, J. C., Smith, C. R., Wear, E. (2024) Sequence read accession (SRA) numbers for bacterial and archaeal 16S rRNA gene amplicons from the DeepCCZ and Abyssline programs. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2023-10-25 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.861683.1 [access date]
Microbial 16S rRNA gene amplicon SRA numbers Dataset Description: <p>This sample set includes 16S rRNA gene amplicon sequences from both samples newly collected on the DeepCCZ cruise in the western Clarion-Clipperton Zone and re-sequenced, archival samples from the Abyssline01 and Abyssline02 cruises in the northeastern Clarion-Clipperton Zone.</p> Methods and Sampling: <p>On the DeepCCZ cruise, benthic samples (sediments and nodules) were collected using the ROV Lu'ukai, using push corers and the ROV's manipulator arm. On the Abyssline cruises, benthic samples were collected with box corers and megacorers. On both cruises, water samples were collected with Niskin bottles mounted on a sampling rosette.</p>
<p>Sediment samples were sectioned into depth horizons and stored frozen at -80 degrees Celsius (C). Nodules were rinsed with 0.2-µm-filtered seawater and frozen whole at -80C. On DeepCCZ, seawater was sequentially collected on 3 µm and 0.2 µm pore-size filters; on the Abyssline cruises, seawater was collected on 0.2 micrometer (µm) pore-size filters. Filters were stored frozen at -80C.</p>
<p>Genomic DNA was extracted from seawater filters using a DNeasy Plant Mini Kit (Qiagen) with modifications as described in Shulse et al. (2017; doi: <a href="http://dx.doi.org/10.1002/mbo3.428" target="_blank">10.1002/mbo3.428</a>). Genomic DNA was extracted from subsamples of sediments and nodules using the FastDNA Spin Kit for Soil, modified as described in Shulse et al. (2017). gDNA was concentrated using the Zymo Clean &amp; Concentrator-5 kit.</p>
<p>The V4-V5 region of the 16S rRNA gene was amplified using primers 515F-Y and 926R as recommended by Parada et al. (2016; doi: <a href="http://dx.doi.org/10.1111/1462-2920.13023" target="_blank">10.1111/1462-2920.13023</a>), with a multiplexing index on the forward primer following the design of the Earth Microbiome Project (<a href="https://earthmicrobiome.org/protocols-and-standards/16s/" target="_blank">https://earthmicrobiome.org/protocols-and-standards/16s/</a>). Triplicate amplifications were combined and cleaned with an ENZA Cycle Pure Kit (Omega Bio-Tek) and then pooled at approximately equimolar proportions into two libraries. Libraries were sequenced at the University of Montana on an Illumina MiSeq using paired-end 250 v2 chemistry. Samples were demultiplexed by the sequencing facility.</p>
<p><strong>Problem Report:</strong><br />
On DeepCCZ, sediments were not collected from the seamount in APEI 1 due to ROV constraints.</p>
Funding provided by Gordon and Betty Moore Foundation (GBMF) Award Number: GBMF5596 Award URL: https://www.moore.org/grant-detail?grantId=GBMF5596
Funding provided by National Oceanic and Atmospheric Administration (NOAA) Award Number: NA17OAR0110209
completed
Matthew J. Church
University of Montana
(406) 982-3301
Flathead Lake Biological Station, University of Montana 321225 Bio Station Lane
Polson
MT
59860-6815
USA
matt.church@flbs.umt.edu
pointOfContact
Jeffrey C. Drazen
University of Hawaiʻi at Mānoa
808-956-6567
Department of Oceanography, SOEST 1000 Pope Road
Honolulu
HI
96822
USA
jdrazen@hawaii.edu
pointOfContact
Craig R. Smith
University of Hawaiʻi at Mānoa
808-956-7776
Department of Oceanography 1000 Pope Road
Honolulu
HI
96822
USA
craigsmi@hawaii.edu
pointOfContact
Emma Wear
University of Montana
815-540-6478
Department of Biology 615 S. Palatine Hill Road
Portland
OR
97219
USA
ekwear.oceans@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
bioproject_accession
sample_name
SRA_run_ID
design_description
Cruise
Isolation_Source
latitude
longitude
CCZ_region
benthic_structure
bottom_depth
sample_depth
date_collected
filter_size_range
sample_size
sample_size_extracted
box corers
megacorers
Niskin bottle
push corers
ROV Lu'ukai
theme
None, User defined
accession number
sample identification
NCBI SRA run accession (SRR)
sampling_method
Cruise identfier
sample description
latitude
longitude
region
site description
depth_bottom
depth
date
filter_size
volume
featureType
BCO-DMO Standard Parameters
Box Corer
Multi Corer
Niskin bottle
Push Corer
Remotely Operated Vehicle
Thermal Cycler
instrument
BCO-DMO Standard Instruments
KM1808
MV1313
TN319
service
Deployment Activity
Western Clarion-Clipperton Zone of the North Pacific Subtropical Gyre
Eastern Clarion-Clipperton Zone of the North Pacific Subtropical Gyre
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.
DeepCCZ
https://oceanexplorer.noaa.gov/explorations/18ccz/welcome.html
DeepCCZ
<p><strong><em>GBMF Grant Name:</em></strong> Closing Gaps in Knowledge About Biodiversity and Ecology of the Deep Sea to Better Assess the Impacts of Deep-Sea Mining</p>
<p><em><strong>GBMF Grant Statement: </strong></em> To generate a better understanding of the biodiversity oand ecology of a large deep-sea ecosystem prior to mining</p>
<p><em><strong>Expected Measurements: </strong></em></p>
<ul>
<li>Shipboard underway data: meteorological data, navigation data, and processed multibeam mapping data,</li>
<li>processed CTD water-column environmental data (e.g., water temperature, pH, salinity, light),</li>
<li>raw ROV video records and associated environmental sensor data</li>
<li>raw free vehicle baited video and still imagery</li>
<li>specimen capture records (ROV and trap - location, date, time, and all body measurements)</li>
<li>processed DNA sequence data for captured animal specimens</li>
<li>processed metagenomic DNA sequence data for microbial assemblages in sediment and water samples</li>
<li>sediment community respiration and nutrient regeneration data</li>
<li>isotopic data for sediment infaunal organisms</li>
</ul>
<p><strong><em>Anticipated Derived Data Products:</em></strong></p>
<ul>
<li>Biodiversity, abundance, and species composition of benthic megafauna, mobile scavengers, and sediment microbes at each study location</li>
<li>Sediment community function (respiration, nutrient regeneration, detrital processing) at each study location</li>
<li>Genetic connectivity at species and population levels for key megafaunal and mobile scavenger species between study locations.</li>
</ul>
DeepCCZ
largerWorkCitation
project
eng; USA
oceans
Western Clarion-Clipperton Zone of the North Pacific Subtropical Gyre; Eastern Clarion-Clipperton Zone of the North Pacific Subtropical Gyre
-153.7464
-116.4598
4.8879
19.4724
2013-10-08
2018-06-13
Western Clarion-Clipperton Zone of the North Pacific Subtropical Gyre (~5N 142 W to ~11N 154 W)
0
BCO-DMO catalogue of parameters from Sequence read accession (SRA) numbers for bacterial and archaeal 16S rRNA gene amplicons from the DeepCCZ and Abyssline programs
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/861902.rdf
Name: bioproject_accession
Units: unitless
Description: <p>NCBI SRA BioProject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/861903.rdf
Name: sample_name
Units: unitless
Description: <p>sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/861904.rdf
Name: SRA_run_ID
Units: unitless
Description: <p>NCBI SRA run ID</p>
http://lod.bco-dmo.org/id/dataset-parameter/861905.rdf
Name: design_description
Units: unitless
Description: <p>basic description of how sequences were generated</p>
http://lod.bco-dmo.org/id/dataset-parameter/861906.rdf
Name: Cruise
Units: unitless
Description: <p>name of cruise on which sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/861907.rdf
Name: Isolation_Source
Units: unitless
Description: <p>physical substrate from which DNA was sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/861908.rdf
Name: latitude
Units: decimal degrees North
Description: <p>latitude, in degrees north</p>
http://lod.bco-dmo.org/id/dataset-parameter/861909.rdf
Name: longitude
Units: decimal degrees East
Description: <p>longitude (negative values = West)</p>
http://lod.bco-dmo.org/id/dataset-parameter/861910.rdf
Name: CCZ_region
Units: unitless
Description: <p>administrative region where sample was collected, following the terminology of the International Seabed Authority</p>
http://lod.bco-dmo.org/id/dataset-parameter/861911.rdf
Name: benthic_structure
Units: unitless
Description: <p>bathymetric feature where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/861912.rdf
Name: bottom_depth
Units: m
Description: <p>total depth of water column where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/861913.rdf
Name: sample_depth
Units: m or cm or descriptive
Description: <p>depth where sample was collected (seawater samples: depth in water column in m; sediment and nodule samples: depth (range) in sediments where collected)</p>
http://lod.bco-dmo.org/id/dataset-parameter/861914.rdf
Name: date_collected
Units: unitless
Description: <p>date sample was collected from the field (UTC); format: YYYY-MM-DD</p>
http://lod.bco-dmo.org/id/dataset-parameter/861915.rdf
Name: filter_size_range
Units: um
Description: <p>size range of filter cut-offs on which DNA was collected (water column samples only)</p>
http://lod.bco-dmo.org/id/dataset-parameter/861916.rdf
Name: sample_size
Units: L or mL or descriptive
Description: <p>amount of sample collected from the environment (seawater samples: volume filtered in L; sediment: volume frozen in mL)</p>
http://lod.bco-dmo.org/id/dataset-parameter/861917.rdf
Name: sample_size_extracted
Units: L or g
Description: <p>volume or mass of sample from which DNA was extracted (large nodules were extracted multiple times and resulting gDNA was combined with weighting by extraction mass)</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
154952
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/2b80618b-a73a-4bff-8031-13673dd82b3b/content
download
https://doi.org/10.26008/1912/bco-dmo.861683.1
download
onLine
dataset
<p>On the DeepCCZ cruise, benthic samples (sediments and nodules) were collected using the ROV Lu'ukai, using push corers and the ROV's manipulator arm. On the Abyssline cruises, benthic samples were collected with box corers and megacorers. On both cruises, water samples were collected with Niskin bottles mounted on a sampling rosette.</p>
<p>Sediment samples were sectioned into depth horizons and stored frozen at -80 degrees Celsius (C). Nodules were rinsed with 0.2-µm-filtered seawater and frozen whole at -80C. On DeepCCZ, seawater was sequentially collected on 3 µm and 0.2 µm pore-size filters; on the Abyssline cruises, seawater was collected on 0.2 micrometer (µm) pore-size filters. Filters were stored frozen at -80C.</p>
<p>Genomic DNA was extracted from seawater filters using a DNeasy Plant Mini Kit (Qiagen) with modifications as described in Shulse et al. (2017; doi: <a href="http://dx.doi.org/10.1002/mbo3.428" target="_blank">10.1002/mbo3.428</a>). Genomic DNA was extracted from subsamples of sediments and nodules using the FastDNA Spin Kit for Soil, modified as described in Shulse et al. (2017). gDNA was concentrated using the Zymo Clean &amp; Concentrator-5 kit.</p>
<p>The V4-V5 region of the 16S rRNA gene was amplified using primers 515F-Y and 926R as recommended by Parada et al. (2016; doi: <a href="http://dx.doi.org/10.1111/1462-2920.13023" target="_blank">10.1111/1462-2920.13023</a>), with a multiplexing index on the forward primer following the design of the Earth Microbiome Project (<a href="https://earthmicrobiome.org/protocols-and-standards/16s/" target="_blank">https://earthmicrobiome.org/protocols-and-standards/16s/</a>). Triplicate amplifications were combined and cleaned with an ENZA Cycle Pure Kit (Omega Bio-Tek) and then pooled at approximately equimolar proportions into two libraries. Libraries were sequenced at the University of Montana on an Illumina MiSeq using paired-end 250 v2 chemistry. Samples were demultiplexed by the sequencing facility.</p>
<p><strong>Problem Report:</strong><br />
On DeepCCZ, sediments were not collected from the seamount in APEI 1 due to ROV constraints.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong><br />
Demultiplexing was conducted by the sequencing facility.</p>
<p>&nbsp;</p>
Specified by the Principal Investigator(s)
- Imported original file named "DeepCCZ_DNA_metadata_for_BCODMO_v2.xlsx" into the BCO-DMO system.
- Changed date format to YYYY-MM-DD.
- Converted longitude from positive degrees west to negative degrees east.
- Replaced mu symbol with u.
- Saved the final file as "861683_v1_sra.csv".
Specified by BCO-DMO Data Managers
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
box corers
box corers
PI Supplied Instrument Name: box corers Instrument Name: Box Corer Instrument Short Name:Box Corer Instrument Description: General description of a box corer:
A box corer is a marine geological tool that recovers undisturbed soft surface sediments. It is designed for minimum disturbance of the sediment surface by bow wave effects. Traditionally, it consists of a weighted stem fitted to a square sampling box. The corer is lowered vertically until it impacts with the seabed. At this point the instrument is triggered by a trip as the main coring stem passes through its frame. While pulling the corer out of the sediment a spade swings underneath the sample to prevent loss. When hauled back on board, the spade is under the box. (definition from the SeaVox Device Catalog)
Box corers are one of the simplest and most commonly used types of sediment corers. The stainless steel sampling box can contain a surface sediment block as large as 50cm x 50cm x 75cm with negligible disturbance. Once the sediment is recovered onboard, the sediment box can be detached from the frame and taken to a laboratory for subsampling and further analysis. The core sample size is controlled by the speed at which the corer is lowered into the ocean bottom. When the bottom is firm, a higher speed is required to obtain a complete sample. A depth pinger or other depth indicator is generally used to determine when the box is completely filled with sediment. Once the core box is filled with sediment, the sample is secured by moving the spade-closing lever arm to lower the cutting edge of the spade into the sediment, until the spade completely covers the bottom of the sediment box. (definition from Woods Hole Oceanographic Institution). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
megacorers
megacorers
PI Supplied Instrument Name: megacorers Instrument Name: Multi Corer Instrument Short Name:Multi Corer Instrument Description: The Multi Corer is a benthic coring device used to collect multiple, simultaneous, undisturbed sediment/water samples from the seafloor. Multiple coring tubes with varying sampling capacity depending on tube dimensions are mounted in a frame designed to sample the deep ocean seafloor. For more information, see Barnett et al. (1984) in Oceanologica Acta, 7, pp. 399-408. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/51/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:Water samples were collected with Niskin bottles mounted on a sampling rosette. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
push corers
push corers
PI Supplied Instrument Name: push corers Instrument Name: Push Corer Instrument Short Name: Instrument Description: Capable of being performed in numerous environments, push coring is just as it sounds. Push coring is simply pushing the core barrel (often an aluminum or polycarbonate tube) into the sediment by hand. A push core is useful in that it causes very little disturbance to the more delicate upper layers of a sub-aqueous sediment.
Description obtained from: http://web.whoi.edu/coastal-group/about/how-we-work/field-methods/coring/
ROV Lu'ukai
ROV Lu'ukai
PI Supplied Instrument Name: ROV Lu'ukai PI Supplied Instrument Description:See: https://www.soest.hawaii.edu/UMC/cms/Luukai.php
SOEST took delivery of the ROV Lu'ukai in 2013. It is a two-part, "top hat" system, consisting of the vehicle itself, performing science operations on the seabed or in the water column, and a Tether Management System (TMS) which hovers above the working vehicle and relays power and data to and from the support ship on the surface. The two components are launched, recovered and transported to the ocean floor as a stacked unit. Upon arrival at the work site, the ROV vehicle is "undocked" from the TMS and piloted to the seabed to commence a mission. Upon completion of the mission, the vehicle is docked to the TMS and the "stack" is then recovered to deck. Instrument Name: Remotely Operated Vehicle Instrument Short Name:ROV Instrument Description: Remotely operated underwater vehicles (ROVs) are unoccupied, highly maneuverable underwater robots operated by a person aboard a surface vessel. They are linked to the ship by a group of cables that carry electrical signals back and forth between the operator and the vehicle. Most are equipped with at least a video camera and lights. Additional equipment is commonly added to expand the vehicle’s capabilities. These may include a still camera, a manipulator or cutting arm, water samplers, and instruments that measure water clarity, light penetration, and temperature.
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument 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)
Cruise: KM1808
KM1808
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM1808
Craig R. Smith
University of Hawaiʻi at Mānoa
Cruise: MV1313
MV1313
R/V Melville
Community Standard Description
International Council for the Exploration of the Sea
R/V Melville
vessel
MV1313
Craig R. Smith
University of Hawaiʻi at Mānoa
Cruise: TN319
TN319
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN319
Craig R. Smith
University of Hawaiʻi at Mānoa
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
R/V Melville
Community Standard Description
International Council for the Exploration of the Sea
R/V Melville
vessel
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel