http://lod.bco-dmo.org/id/dataset/716817
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
2017-10-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
BioProject accession information for Trichodesmium colonies from R/V Atlantic Explorer AE1409, R/V Kilo Moana KM1513 and other cruises in the N. Atlantic, S. Pacific and N. Pacific, 2007-2015 (P Processing by Tricho project)
2017-10-27
publication
2017-10-27
revision
BCO-DMO Linked Data URI
2017-10-27
creation
http://lod.bco-dmo.org/id/dataset/716817
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
principalInvestigator
Benjamin A.S. Van Mooy
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: Dyhrman, S. T., Van Mooy, B. A. (2017) BioProject accession information for Trichodesmium colonies from R/V Atlantic Explorer AE1409, R/V Kilo Moana KM1513 and other cruises in the N. Atlantic, S. Pacific and N. Pacific, 2007-2015 (P Processing by Tricho project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2017-10-27 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/716817 [access date]
GenBank Trichodesmium accessions and associated metadata Dataset Description: <p>Trichodesmium&nbsp;field sample sequence data from the July 2015 SCOPE cruise (R/V Kilo Moana KM1513) in the NW Pacific, the May 2014 PABST cruise (R/V Atlantic Explorer AE1409) in the Sargasso Sea, and other cruises in March 2007, May 2008, and August 2012 in North and South Pacific Subtropical Gyres, the and North Atlantic Subtropical Gyre. Links to the NCBI GenBank BioProjects are provided.</p>
<p>The accessions and further associated metadata are reported at NCBI GenBank as:<br />
<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA314461" target="_blank">PRJNA314461</a><br />
<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA330990" target="_blank">PRJNA330990</a><br />
<a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA381915" target="_blank">PRJNA381915</a>&nbsp;- to be made publicly accessible by 2018-10-27</p> Methods and Sampling: <p>BioProject <strong>PRJNA314461</strong>; cruises KM0703, X0804, KM1309:<a href="http://dmoserv3.bco-dmo.org/data_docs/P_Processing_by_Tricho/PRJNA314461_methods.pdf" target="_blank">Sample acquisition and processing (pdf)</a></p>
<p>BioProject <strong>PRJNA330990</strong>; cruise AE1409: <a href="http://dmoserv3.bco-dmo.org/data_docs/P_Processing_by_Tricho/Sample_Acquisition_and_Processing_AE1409.pdf" target="_blank">Sample acquisition and processing (pdf)</a></p>
<p>BioProject <strong>PRJNA381915</strong>; cruise KM1513:<strong> </strong><a href="http://dmoserv3.bco-dmo.org/data_docs/P_Processing_by_Tricho/Sample_Acquisition_and_Processing_KM1513.pdf" target="_blank">Sample acquisition and processing (pdf)</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1332912 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1332912
completed
Sonya T. Dyhrman
Lamont-Doherty Earth Observatory
845-365-8465
102E Geoscience 61 Route 9W, PO Box 1000
Palisades
NY
10964
USA
dyhrman@ldeo.columbia.edu
pointOfContact
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
(508) 289 2322
Department of Marine Chemistry and Geochemistry, MS #4, Fye 117 Woods Hole Oceanographic Institution
Woods Hole
MA
02543
USA
bvanmooy@whoi.edu
pointOfContact
asNeeded
Unknown
cruise_id
cruise_name
sample_name
sample_title
bioproject_accession
organism
strain
isolate
host
isolation_source
collection_date
geo_loc_name
sample_type
biomaterial_provider
collected_by
depth
env_biome
genotype
lat
lon
passage_history
samp_size
NCBI_accession_link
Illumina Miseq platform
net
theme
None, User defined
Cruise identfier
cruise name
sample identification
accession number
taxon
region
date
sample description
laboratory
depth
site description
No BCO-DMO term
latitude
longitude
duration
count
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Plankton Net
Thermal Cycler
instrument
BCO-DMO Standard Instruments
AE1409
KM1513
KM0703
KM1309
AE0810
service
Deployment Activity
Western Tropical North Atlantic
Near Hawaii (22.75 N, 158 W)
Tropical and subtropical Southwest Pacific
North of Hawaiian Islands, Pacific Ocean
Western Sargasso Sea roughly 38-20N and 66-43W, Water depths always exceeded 4200m
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.
Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation
https://osprey.bco-dmo.org/project/565176
Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation
<p><em>Description from NSF award abstract:</em><br />
Colonies of the cyanbacterium <em>Trichodesmium</em> are responsible for a large fraction of N2 fixation in nutrient-poor, open-ocean ecosystems, ultimately fueling primary production in both <em>Trichodesmium</em> and in the broader planktonic community. However, in some parts of the ocean, the scarcity of dissolved phosphorus limits rates of <em>Trichodesmium </em>N2 fixation. <em>Trichodesmium</em> colonies employ an arsenal of strategies to mitigate the effects of phosphorus limitation, and the consortia of epibiotic bacteria in the colonies may play a significant role in phosphorus acquisition.</p>
<p>In this study, researchers from Woods Hole Oceanographic Institution and Columbia University will use metagenomic and metatranscriptomic sequencing to investigate how phosphorus metabolism is coordinated in <em>Trichodesmium </em>consortia, and to discern the role of quorum sensing in phosphorus acquisition and partitioning. Results from this study are expected to expand understanding of <em>Trichodesmium</em> from a monospecific colony whose primary function is fixing CO2 and N2 toward a unique planktonic consortium with a diverse, complex, and highly coordinated overall metabolism that exerts profound control over the cycling of inorganic and organic nutrients in the oligotrophic upper ocean.</p>
P Processing by Tricho
largerWorkCitation
project
eng; USA
biota
oceans
Western Tropical North Atlantic; Near Hawaii (22.75 N, 158 W); Tropical and subtropical Southwest Pacific; North of Hawaiian Islands, Pacific Ocean; Western Sargasso Sea roughly 38-20N and 66-43W, Water depths always exceeded 4200m
-158.284
178.44
-27.41
24.5
2007-03-01
2015-07-29
Western Tropical North Atlantic
0
BCO-DMO catalogue of parameters from BioProject accession information for Trichodesmium colonies from R/V Atlantic Explorer AE1409, R/V Kilo Moana KM1513 and other cruises in the N. Atlantic, S. Pacific and N. Pacific, 2007-2015 (P Processing by Tricho 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/716918.rdf
Name: cruise_id
Units: unitless
Description: <p>official UNOLS cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/716919.rdf
Name: cruise_name
Units: unitless
Description: <p>project cruise name</p>
http://lod.bco-dmo.org/id/dataset-parameter/716920.rdf
Name: sample_name
Units: unitless
Description: <p>sequencing facility sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/716921.rdf
Name: sample_title
Units: unitless
Description: <p>laboratory sample identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/716922.rdf
Name: bioproject_accession
Units: unitless
Description: <p>collection of biological data related to a single initiative</p>
http://lod.bco-dmo.org/id/dataset-parameter/716923.rdf
Name: organism
Units: unitless
Description: <p>cyanobacterium used in this study</p>
http://lod.bco-dmo.org/id/dataset-parameter/716924.rdf
Name: strain
Units: unitless
Description: <p>population of organism that descends from a single organism or pure culture isolate; not applicable to this dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/716925.rdf
Name: isolate
Units: unitless
Description: <p>specific individual from which this sample was obtained; not applicable to this dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/716926.rdf
Name: host
Units: unitless
Description: <p>host organism; not applicable to this dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/716927.rdf
Name: isolation_source
Units: unitless
Description: <p>physical; environmental; geographic source of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/716928.rdf
Name: collection_date
Units: year-month-day
Description: <p>date sample was obtained</p>
http://lod.bco-dmo.org/id/dataset-parameter/716929.rdf
Name: geo_loc_name
Units: unitless
Description: <p>geographical origin of the sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/716930.rdf
Name: sample_type
Units: unitless
Description: <p>sample type such as: whole organism; mixed culture; cell culture; metagenomic assembly</p>
http://lod.bco-dmo.org/id/dataset-parameter/716931.rdf
Name: biomaterial_provider
Units: unitless
Description: <p>laboratory and principal investigator where sample came from</p>
http://lod.bco-dmo.org/id/dataset-parameter/716932.rdf
Name: collected_by
Units: unitless
Description: <p>laboratory and principal investigator where organism was isolated</p>
http://lod.bco-dmo.org/id/dataset-parameter/716933.rdf
Name: depth
Units: meters
Description: <p>vertical distance below the surface where sample was collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/716934.rdf
Name: env_biome
Units: unitless
Description: <p>descriptor of the broad ecological context of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/716935.rdf
Name: genotype
Units: unitless
Description: <p>observed genotype; not applicable to this dataset</p>
http://lod.bco-dmo.org/id/dataset-parameter/716936.rdf
Name: lat
Units: decimal degrees
Description: <p>sample collection latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/716937.rdf
Name: lon
Units: decimal degrees
Description: <p>sample collection longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/716938.rdf
Name: passage_history
Units: not applicable
Description: <p>duration of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/716939.rdf
Name: samp_size
Units: colonies
Description: <p>amount of sample collected</p>
http://lod.bco-dmo.org/id/dataset-parameter/716940.rdf
Name: NCBI_accession_link
Units: unitless
Description: <p>link to NCBI GenBank BioProject accession 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
20364
https://datadocs.bco-dmo.org/file/YVVZwWxcLzkX93/tricho_accessions.csv
tricho_accessions.csv
Primary data file for dataset ID 716817
download
https://osprey.bco-dmo.org/dataset/716817/data/download
download
onLine
dataset
<p>BioProject <strong>PRJNA314461</strong>; cruises KM0703, X0804, KM1309:<a href="http://dmoserv3.bco-dmo.org/data_docs/P_Processing_by_Tricho/PRJNA314461_methods.pdf" target="_blank">Sample acquisition and processing (pdf)</a></p>
<p>BioProject <strong>PRJNA330990</strong>; cruise AE1409: <a href="http://dmoserv3.bco-dmo.org/data_docs/P_Processing_by_Tricho/Sample_Acquisition_and_Processing_AE1409.pdf" target="_blank">Sample acquisition and processing (pdf)</a></p>
<p>BioProject <strong>PRJNA381915</strong>; cruise KM1513:<strong> </strong><a href="http://dmoserv3.bco-dmo.org/data_docs/P_Processing_by_Tricho/Sample_Acquisition_and_Processing_KM1513.pdf" target="_blank">Sample acquisition and processing (pdf)</a></p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
Added conventional header with dataset name, PI name, version date.<br />
Modified parameter names to conform with BCO-DMO naming conventions.<br />
Split lat_lon into separate latitude and longitude columns<br />
Added columns: cruise_id, cruise_name<br />
Added links to NCBI GenBank BioProject accession pages</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 platform
Illumina Miseq platform
PI Supplied Instrument Name: Illumina Miseq platform 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.
net
net
PI Supplied Instrument Name: net PI Supplied Instrument Description:Used to collect Trichodesmium colonies. Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
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: AE1409
AE1409
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1409
Benjamin A.S. Van Mooy
Woods Hole Oceanographic Institution
Cruise: KM1513
KM1513
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM1513
Samuel T. Wilson
University of Hawai'i
Cruise: KM0703
KM0703
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM0703
Jonathan P. Zehr
University of California-Santa Cruz
http://www.rvdata.us/catalog/KM0703
Report describing KM0703
Cruise: KM1309
KM1309
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel
KM1309
Dr Karin Björkman
University of Hawai'i
Cruise: AE0810
AE0810
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE0810
Michael W. Lomas
Bermuda Institute of Ocean Sciences
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
R/V Kilo Moana
Community Standard Description
International Council for the Exploration of the Sea
R/V Kilo Moana
vessel