http://lod.bco-dmo.org/id/dataset/767265
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
2019-05-10
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
GenBank Short Read Archive (SRA) sequence accession numbers metatranscriptomic data from the gills of Alviniconcha species from R/V Falkor in the Lau Basin from April to May 2016
2019-05-10
publication
2019-05-10
revision
BCO-DMO Linked Data URI
2019-05-10
creation
http://lod.bco-dmo.org/id/dataset/767265
Roxanne A. Beinart
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: Beinart, R. A. (2019) GenBank Short Read Archive (SRA) sequence accession numbers metatranscriptomic data from the gills of Alviniconcha species from R/V Falkor in the Lau Basin from April to May 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2019-05-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/767265 [access date]
GenBank Short Read Archive (SRA) sequence accession numbers metatranscriptomic data from the gills of Alviniconcha species from R/V Falkor in the Eastern Lau Spreading Center, Lau Basin Dataset Description: <p>GenBank Short Read Archive (SRA) sequence accession numbers metatranscriptomic data from the gills of <em>Alviniconcha</em> species</p> Methods and Sampling: <p>Gill tissue pieces were quickly excised and homogenized in Trizol preservative using a Tissue-Tearor. Homogenates were stored at -80C until extraction with the Direct-zol RNA extraction kit (Zymo Research, Inc.). RNA was sequenced with Illumina NovaSeq using the RNAtag-Seq method with rRNA-depletion.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1536331 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1536331
onGoing
Roxanne A. Beinart
Woods Hole Oceanographic Institution
401-874-6492
215 South Ferry Road
Narragansett
RI
02882
USA
rbeinart@uri.edu
pointOfContact
asNeeded
Unknown
Illumina MiSeq.
theme
None, User defined
Automated DNA Sequencer
instrument
BCO-DMO Standard Instruments
FK160407
service
Deployment Activity
Tonga and Fiji
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: Ecosystem dynamics of Western Pacific hydrothermal vent communities associated with polymetallic sulfide deposits
https://osprey.bco-dmo.org/project/670478
Collaborative Research: Ecosystem dynamics of Western Pacific hydrothermal vent communities associated with polymetallic sulfide deposits
<p><em>Description from NSF award abstract:</em><br />
Hydrothermal vents are common in the Western Pacific, and are markedly different in many geological, geochemical, and biological aspects from the much better known hydrothermal vents on mid-ocean ridges. The processes that structure western Pacific vent communities, such as the extent to which physical and chemical conditions change over time, the dispersal of organisms among hydrothermal vent fields, and the physiological capacities of the symbionts and their animal host are poorly understood. And yet, large-scale industrial mining of polymetallic sulfide deposits at active hydrothermal vents is imminent in the Western Pacific. In 2005 and 2006, 19 long term study sites were established on the Eastern Lau Spreading Center by generating high resolution photomosaics of animal communities in both active and inactive flow areas and on both sulfide chimneys and on lavas, and mapping spatially discrete physical and chemical environmental measurements on to these photomosaics. Revisiting these study sites and acquiring data of comparable resolution in the coming year, combined with detailed studies of the physiology of key species, will significantly increase our understanding of the physiology of the fauna and how these communities respond to change. The resulting data will provide crucial information on the fauna and communities endemic to this region that is critical for predicting and mitigating the effects of mining activities on these ecosystems, and for informing plans for monitoring potential recovery post-mining. To ensure that Western Pacific Islanders are engaged throughout the duration of our program, local scientists will be included in the fieldwork, in-country presentations to students and the general public will be given in association with port stops, and findings will be communicated to local resource managers through the Geoscience Division of the Secretariat of the Pacific Community (SPC). The principal investigators are also proponents of fostering greater "open access and collaboration" among oceanographers, and telepresence will be used during this expedition to experiment on two different models of collaboration, which - along with the resulting scientific insights - will be published to disseminate the results of this effort. Finally, in collaboration with the Harvard Museum of Natural History (HMNH), an exhibit module and course curricula will be developed presenting the effects of both natural and anthropogenic disturbance on biodiversity. It will feature high-resolution imagery, animal and mineralogical samples, and deep-sea research technologies. Web-enabled kiosks will allow visitors to delve deeper into the subject material. The HMNH attracts 200,000 visitors each year, including 33,000 students (K-12) and their teachers, as well as visitors from around the world.</p>
<p>The funded interlinked studies of holobiont (symbionts and their animal host) physiology and distribution, community structure and change over time, genetic connectivity, and holobiont ecosystem engineering will significantly increase our understanding of the processes structuring hydrothermal vent ecosystems in general, and those of the Western Pacific in particular. Vent fields in the proposed study area within the Lau Basin are located in relative proximity to one another with no known barriers to biological dispersal and span a pronounced regional gradient in both geological setting and physico-chemical conditions. This natural laboratory, that is home to a significant diversity of vent fauna and where long-term study sites were established a decade ago, presents an opportunity to gain broad new insights into the ecological and physiological characteristics of the vent fauna and the processes that structure these communities. Accordingly, the project will A) determine the rates and patterns of natural physical, chemical, and biological changes at vents in the Lau Basin over a decadal time period by acquiring new high-resolution, co-registered geological, chemical and biological maps and comparing these with data of comparable resolution acquired in 2005, 2006, and 2009; B) evaluate the role of symbiont physiology -in particular their use of key energy sources not previously measured- in the realized distribution of the holobionts by coupling genetic characterization of host and symbionts with shipboard physiological measurements and gene expression studies, and physico-chemical microhabitat characterization; C) quantify the effects of different holobionts on the surrounding environment by coupling repeated spatially integrated measurements of physico-chemical conditions to all collections and; D) assess the influence of genetic connectivity of populations in the Lau Basin on the distribution of holobionts across regional gradients in geology and geochemistry. They will provide new and generally applicable insights on the role of multiple symbionts in both the distribution of their animal hosts and in structuring associated communities. These efforts will also constrain the roles of genetic connectivity, environmental chemistry, and holobiont capabilities in structuring communities along this spreading center. Moreover, through co-registered animal collections and in situ geochemical measurements, the investigators will develop first-order estimates of the extent to which holobiont aggregations affect geochemical flux from diffuse flows, which accounts for ~50% of all vent geochemical flux. Ultimately, this effort will provide critical and robust data on the dynamics of vent fields and communities in the western Pacific biogeographic province, as well as on the underlying physiological and ecological factors governing these patterns.</p>
<p><strong>Datasets at the Marine Geoscience Data System (MGDS):</strong></p>
<p>1. Processed ship-based multibeam data files: <a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24306">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24306</a><br />
2. Raw ROV-based multibeam data files: <a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24317">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24317</a><br />
3. CTD data from ROV: Conductivity, Temperature and Depth records from the ROV dives: <a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24206">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24206</a><br />
4. ROPOS event logs: Event logs from the ROV dives: <a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24146">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24146</a><br />
5. ROPOS navigation: Navigation records from the ROV dives: <a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24165">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24165</a><br />
6. Geo-referenced photo mosaics of the study sites:<a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24031">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24031</a><br />
7. Low-resolution photo mosaics of the study sites:<br />
<a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24046">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24046</a><br />
8. IRLS photos: This includes 3,534 sea floor images taken from the ROV with a Nikon D700 digital camera in a pressure housing: <a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24151">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24151</a><br />
9. Highlight photographs from the expedition:<br />
<a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24047">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24047</a><br />
10. Links to the ship based navigation data held at the Rolling Deck to Repository Website (R2R):<a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=23926">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=23926</a><br />
11. Links to the raw ship-based multibeam held at NOAA:<a href="http://www.marine-geo.org/tools/search/DataSets.php?data_set_uids=23951,23952">http://www.marine-geo.org/tools/search/DataSets.php?data_set_uids=23951,23952</a><br />
12. The final GIS products linking the photomosaics to the chem/temp data: <a href="http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24502">http://www.marine-geo.org/tools/search/Files.php?data_set_uid=24502</a></p>
<p>Due to PI transfer award OCE-1819530 was added to this project in March 2019</p>
Eco Dyn W Pacific Vents
largerWorkCitation
project
eng; USA
oceans
Tonga and Fiji
2016-04-13
2016-05-01
Lau basin (21S, 176W)
0
BCO-DMO catalogue of parameters from GenBank Short Read Archive (SRA) sequence accession numbers metatranscriptomic data from the gills of Alviniconcha species from R/V Falkor in the Lau Basin from April to May 2016
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
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
https://osprey.bco-dmo.org/dataset/767265/data/download
download
onLine
dataset
<p>Gill tissue pieces were quickly excised and homogenized in Trizol preservative using a Tissue-Tearor. Homogenates were stored at -80C until extraction with the Direct-zol RNA extraction kit (Zymo Research, Inc.). RNA was sequenced with Illumina NovaSeq using the RNAtag-Seq method with rRNA-depletion.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing Notes:<br />
-&nbsp;added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added lat and&nbsp;lon&nbsp;columns<br />
- converted date from m/d/yy to yyyy-mm-dd ISO convention</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 MiSeq.
Illumina MiSeq.
PI Supplied Instrument Name: Illumina MiSeq. PI Supplied Instrument Description:16S rRNA genes were amplified from the extracted DNA with the 515F/926R primers (Walters et al., 2015) and PE 251bp reads were sequenced using Illumina MiSeq. 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: FK160407
FK160407
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK160407
Charles Fisher
Pennsylvania State University
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel