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)

Website: https://www.bco-dmo.org/dataset/716817
Data Type: Cruise Results
Version:
Version Date: 2017-10-27

Project
» Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation (P Processing by Tricho)
ContributorsAffiliationRole
Dyhrman, Sonya T.Lamont-Doherty Earth Observatory (LDEO)Principal Investigator
Van Mooy, Benjamin A.S.Woods Hole Oceanographic Institution (WHOI)Co-Principal Investigator
Copley, NancyWoods Hole Oceanographic Institution (WHOI BCO-DMO)BCO-DMO Data Manager


Coverage

Spatial Extent: N:24.5 E:178.44 S:-27.41 W:-158.284
Temporal Extent: 2007-03-01 - 2015-07-29

Dataset Description

Trichodesmium 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.

The accessions and further associated metadata are reported at NCBI GenBank as:
PRJNA314461
PRJNA330990
PRJNA381915 - to be made publicly accessible by 2018-10-27


Methods & Sampling

BioProject PRJNA314461; cruises KM0703, X0804, KM1309:Sample acquisition and processing (pdf)

BioProject PRJNA330990; cruise AE1409: Sample acquisition and processing (pdf)

BioProject PRJNA381915; cruise KM1513: Sample acquisition and processing (pdf)


Data Processing Description

BCO-DMO Processing:
Added conventional header with dataset name, PI name, version date.
Modified parameter names to conform with BCO-DMO naming conventions.
Split lat_lon into separate latitude and longitude columns
Added columns: cruise_id, cruise_name
Added links to NCBI GenBank BioProject accession pages


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Data Files

File
tricho_accessions.csv
(Comma Separated Values (.csv), 19.89 KB)
MD5:14e352674262df82258c118bf5d216b2
Primary data file for dataset ID 716817

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Parameters

ParameterDescriptionUnits
cruise_idofficial UNOLS cruise identifier unitless
cruise_nameproject cruise name unitless
sample_namesequencing facility sample identifier unitless
sample_titlelaboratory sample identifier unitless
bioproject_accessioncollection of biological data related to a single initiative unitless
organismcyanobacterium used in this study unitless
strainpopulation of organism that descends from a single organism or pure culture isolate; not applicable to this dataset unitless
isolatespecific individual from which this sample was obtained; not applicable to this dataset unitless
hosthost organism; not applicable to this dataset unitless
isolation_sourcephysical; environmental; geographic source of the sample unitless
collection_datedate sample was obtained year-month-day
geo_loc_namegeographical origin of the sample unitless
sample_typesample type such as: whole organism; mixed culture; cell culture; metagenomic assembly unitless
biomaterial_providerlaboratory and principal investigator where sample came from unitless
collected_bylaboratory and principal investigator where organism was isolated unitless
depthvertical distance below the surface where sample was collected meters
env_biomedescriptor of the broad ecological context of sample unitless
genotypeobserved genotype; not applicable to this dataset unitless
latsample collection latitude; north is positive decimal degrees
lonsample collection longitude; east is positive decimal degrees
passage_historyduration of sample not applicable
samp_sizeamount of sample collected colonies
NCBI_accession_linklink to NCBI GenBank BioProject accession page unitless


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Instruments

Dataset-specific Instrument Name
net
Generic Instrument Name
Plankton Net
Dataset-specific Description
Used to collect Trichodesmium colonies.
Generic 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.

Dataset-specific Instrument Name
Illumina Miseq platform
Generic Instrument Name
Automated DNA Sequencer
Generic Instrument Description
General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

Dataset-specific Instrument Name
Generic Instrument Name
Thermal Cycler
Generic 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)


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Deployments

AE1409

Website
Platform
R/V Atlantic Explorer
Start Date
2014-05-08
End Date
2014-05-26
Description
May 2014 cruise conducted as part of the "Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation" project.

KM1513

Website
Platform
R/V Kilo Moana
Start Date
2015-07-24
End Date
2015-08-05
Description
The objective of the cruise is deploy free-drifting surface drifters in the vicinity of the Hawaii Ocean Time-series (HOT) station (Station ALOHA), which is defined as a circle with a 6 nautical mile radius centered at 22° 45'N, 158°W. The surface drifters will be monitored for the duration of the cruise and the Kilo Moana will conduct water-column sampling using the CTD-rosette alongside one of the drifters for the duration of the cruise. Cruise Plan Cruise Binder

KM0703

Website
Platform
R/V Kilo Moana
Report
Start Date
2007-03-14
End Date
2007-04-18
Description
The cruise began in Townsville, Australia and sampled the Coral Sea, a transect southward toward the Tasman Sea, and a transect northward toward New Caledonia, with twelve hydrostations (001-012). It then made a run eastward to 170 deg W, a northward run to 15 deg S, then a transect to the east before ending in Suva, Fiji after carrying out fourteen stations (013-026). Cruise information and original data are available from the NSF R2R data catalog.

KM1309

Website
Platform
R/V Kilo Moana
Start Date
2013-05-22
End Date
2013-06-05

AE0810

Website
Platform
R/V Atlantic Explorer
Start Date
2008-05-03
End Date
2008-05-25
Description
One in a series of transect cruises to study the biological and biogeochemical aspects of the marine phosphorus cycle. Note the cruise identifiers for the Atlantic Explorer were originally formatted as XYY## (e.g. X0806 was the 6th cruise in 2008).  The data files include cruise IDs of this type.  The vessel operator changed the cruise ID syntax several years after the cruise and the official cruise ID syntax was changed to AEYY##.  For example, AE0810 should be the same cruise as X0810.  One exception for this dataset is that X0804 is cruise ID AE0810 (unclear how the cruise numbering scheme got so confused). Database validation showed that AE0804 was not the correct cruiseid based on information at R2R.  The cruiseid was then updated to reflect the corrected information (the May 2008 cruise was AE0810. Additional Information from R2R Site


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Project Information

Dissolved Phosphorus Processing by Trichodesmium Consortia: Quantitative Partitioning, Role of Microbial Coordination, and Impact on Nitrogen Fixation (P Processing by Tricho)

Coverage: Western Tropical North Atlantic


Description from NSF award abstract:
Colonies of the cyanbacterium Trichodesmium are responsible for a large fraction of N2 fixation in nutrient-poor, open-ocean ecosystems, ultimately fueling primary production in both Trichodesmium and in the broader planktonic community. However, in some parts of the ocean, the scarcity of dissolved phosphorus limits rates of Trichodesmium N2 fixation. Trichodesmium 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.

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 Trichodesmium consortia, and to discern the role of quorum sensing in phosphorus acquisition and partitioning. Results from this study are expected to expand understanding of Trichodesmium 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.



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Funding

Funding SourceAward
NSF Division of Ocean Sciences (NSF OCE)

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