http://lod.bco-dmo.org/id/dataset/544279
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
2014-12-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Accession numbers for sequences generated from hydrothermal plume samples collected on R/V New Horizon cruises GoCAL1, GoCAL2, GoCAL3 in the Guaymas Basin, Gulf of California from 2005-2014 (Guaymas plumes project)
2015-01-12
publication
2015-01-12
revision
BCO-DMO Linked Data URI
2015-01-12
creation
http://lod.bco-dmo.org/id/dataset/544279
Gregory J. Dick
University of Michigan
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: Dick, G. J. (2015) Accession numbers for sequences generated from hydrothermal plume samples collected on R/V New Horizon cruises GoCAL1, GoCAL2, GoCAL3 in the Guaymas Basin, Gulf of California from 2005-2014 (Guaymas plumes project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 12 Jan 2015) Version Date 2015-01-12 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/544279 [access date]
Accession numbers for sequences generated from hydrothermal plume samples. Dataset Description: <p>Accession numbers and links are provided for DNA sequence data. Samples were collected in the Guaymas and Carmen Basins, Gulf of California.</p>
<p><em>The following publications are associated with this data:</em><br />
Anantharaman, K.A., M.B. Duhaime, J.A. Breier, K. Wendt, B.M. Toner, and G.J. Dick (2014). Sulfur oxidation genes in diverse deep-sea viruses. Science 344: 757-760. doi:<a href="http://dx.doi.org/10.1126/science.1252229" target="_blank">10.1126/science.1252229 </a></p>
<p>Li, M., B.M. Toner, B.J. Baker, J.A. Breier, C.S. Sheik, and G.J. Dick (2014). Microbial iron uptake as a mechanism for dispersing iron from deep-sea hydrothermal vents. Nature Communications 5: 3192. doi:<a href="http://dx.doi.org/10.1038/ncomms4192" target="_blank">10.1038/ncomms4192</a></p>
<p>Li, M., S. Jain, B.J. Baker, C. Taylor, and G.J. Dick (2014). Novel hydrocarbon monooxygenase genes in the metatranscriptome of a natural deep-sea hydrocarbon plume. Environmental Microbiology 16: 60-71. doi:<a href="http://dx.doi.org/10.1111/1462-2920.12182" target="_blank">10.1111/1462-2920.12182</a></p>
<p>Sheik, C.S. 2, S. Jain, and G.J. Dick (2014). Metabolic flexibility of enigmatic SAR324 revealed through metagenomics and metatranscriptomics. Environmental Microbiology 16: 304-317. doi:<a href="http://dx.doi.org/10.1111/1462-2920.12165" target="_blank">10.1111/1462-2920.12165</a></p>
<p>Baker, B.J., C.S. Sheik, C.A. Taylor, S. Jain, A. Bhasi, J.D. Cavalcoli, and G.J. Dick (2013). Community transcriptomic assembly reveals microbes that contribute to deep-sea carbon and nitrogen cycling. The ISME Journal 7: 1962-1973. doi:<a href="http://dx.doi.org/10.1038/ismej.2013.85" target="_blank">10.1038/ismej.2013.85</a></p>
<p>Dick, G.J., K. Anantharaman, B.J. Baker, M. Li, D.C. Reed, and C.S. Sheik (2013). Hydrothermal vent plume microbiology: ecological and biogeographic linkages to seafloor and water column habitats. Frontiers in Microbiology 4: 124. doi:<a href="http://dx.doi.org/10.3389/fmicb.2013.00124" target="_blank">10.3389/fmicb.2013.00124 </a></p>
<p>Anantharaman, K., J.A. Breier, C.S. Sheik, and G.J. Dick (2013). Evidence for hydrogen oxidation and metabolic plasticity in widespread deep-sea bacteria. Proceedings of the National Academy of Sciences 110: 330-335. doi:<a href="http://dx.doi.org/10.1073/pnas.1215340110" target="_blank">10.1073/pnas.1215340110</a></p>
<p>Baker, B.J., R.A. Lesniewski, and G.J. Dick. Genome-enabled transcriptomics reveals archaeal populations that drive nitrification in a deep-sea hydrothermal plume (2012). The ISME Journal 6: 2269-2279. doi:<a href="http://dx.doi.org/10.1038/ismej.2012.64" target="_blank">10.1038/ismej.2012.64</a></p>
<p>Lesniewski, R.A., S. Jain, P.D. Schloss, K. Anantharaman,and G.J. Dick (2012). The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and chemolithotrophs. The ISME Journal 6: 2257-2268. doi:<a href="http://dx.doi.org/10.1038/ismej.2012.63" target="_blank">10.1038/ismej.2012.63</a></p> Methods and Sampling:
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1029242 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1029242
Funding provided by Gordon and Betty Moore Foundation (GBMF) Award Number: GBMF2609 Award URL: http://www.moore.org/grants/list/GBMF2609
completed
Gregory J. Dick
University of Michigan
734-763-3228
Department of Earth and Environmental Sciences 1100 N. University Ave., 2534 CC Little Building
Ann Arbor
MI
48109-1005
USA
gdick@umich.edu
pointOfContact
asNeeded
Dataset Version: 12 Jan 2015
Unknown
database
accession_num
description
URL
theme
None, User defined
No BCO-DMO term
accession number
sample description
featureType
BCO-DMO Standard Parameters
GoCAL1
GoCAL2
GoCAL3
service
Deployment Activity
Guaymas Basin, Gulf of California
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.
Linking biogeochemistry and microbial community dynamics in deep-sea hydrothermal plumes
http://www.earth.lsa.umich.edu/geomicrobiology/Guaymas.html
Linking biogeochemistry and microbial community dynamics in deep-sea hydrothermal plumes
<p><em>Description from NSF award abstract:</em><br />
Deep-sea hydrothermal vent plumes are globally distributed along the 60,000-km mid-ocean ridge system and are hot spots of microbial biogeochemistry in the deep oceans. These plumes play host to important interactions between microbial communities and hydrothermal inputs; hydrothermal energy sources stimulate enhanced microbial activity and productivity, and microorganisms mediate the flux of elements and energy from deep-sea hydrothermal vents into the oceans. This hydrothermal flux is a significant source of two key micronutrients, iron and manganese, for the oceans. Despite this importance, microbial communities in deep sea-hydrothermal plumes have been understudied relative to those inhabiting near-vent and subsurface environments. The overall goal of this project is to reveal the microbial community dynamics responsible for enhanced microbial activities and mediation of geochemical processes that has been observed in deep-sea hydrothermal plumes. This research project is focused on plumes in the Guaymas Basin (Gulf of California), where previous results showed dramatic enhancement of microbial activity and enzymatic manganese (II) oxidation relative to the ambient deep sea. Cutting-edge DNA sequencing technologies will be utilized to characterize the microbial diversity, metabolic potential and physiological state of plume versus background communities through metagenomics and metatranscriptomics. The specific objectives are:<br />
(1) to utilize hundreds of thousands of rRNA gene sequences available from DNA and RNA to compare community structure and population-specific activity in plumes versus background;<br />
(2) to reconstruct composite genomes from the most abundant deep-sea microbial populations and evaluate their metabolic capabilities and nutritional needs; and<br />
(3) to quantitatively compare gene content and expression profiles in plume and background, with a focus on uncovering metabolic shifts towards chemolithoautotrophy.</p>
<p>Overall, results are expected to shed light on the nature of microbial players and processes in plumes: is plume biogeochemistry mediated by indigenous deep-sea microorganisms that have been stimulated by hydrothermal inputs, or by plume-specific groups that were entrained from near-vent environments?</p>
Guaymas plumes
largerWorkCitation
project
eng; USA
biota
oceans
Guaymas Basin, Gulf of California
2015-01-12
Guaymas Basin and Carmen Basin, Gulf of California
0
BCO-DMO catalogue of parameters from Accession numbers for sequences generated from hydrothermal plume samples collected on R/V New Horizon cruises GoCAL1, GoCAL2, GoCAL3 in the Guaymas Basin, Gulf of California from 2005-2014 (Guaymas plumes 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
http://lod.bco-dmo.org/id/dataset-parameter/544288.rdf
Name: database
Units: text
Description: <p>Name of the database/repository where the sequence data are located.</p>
http://lod.bco-dmo.org/id/dataset-parameter/544289.rdf
Name: accession_num
Units: alphanumeric
Description: <p>Sequence accession number (or Taxon Object ID for DOE JGI-IMG/MER).</p>
http://lod.bco-dmo.org/id/dataset-parameter/544290.rdf
Name: description
Units: text
Description: <p>Description of the type of sequence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/544291.rdf
Name: URL
Units: text
Description: <p>Hyperlink to the database/repository for the accession number.</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
5036
https://datadocs.bco-dmo.org/file/vmmwMWRCWWZPxk/sequence_accessions.csv
sequence_accessions.csv
Primary data file for dataset ID 544279
download
https://osprey.bco-dmo.org/dataset/544279/data/download
download
onLine
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
Cruise: GoCAL1
GoCAL1
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
GoCAL1
Brian N. Popp
University of Hawai'i
Cruise: GoCAL2
GoCAL2
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
GoCAL2
Brian N. Popp
University of Hawai'i
Cruise: GoCAL3
GoCAL3
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel
GoCAL3
Brian N. Popp
University of Hawai'i
R/V New Horizon
Community Standard Description
International Council for the Exploration of the Sea
R/V New Horizon
vessel