| Contributors | Affiliation | Role |
|---|---|---|
| Dyhrman, Sonya T. | Lamont-Doherty Earth Observatory (LDEO) | Principal Investigator |
| Van Mooy, Benjamin A.S. | Woods Hole Oceanographic Institution (WHOI) | Co-Principal Investigator |
| Copley, Nancy | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
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
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)
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
| File |
|---|
tricho_accessions.csv (Comma Separated Values (.csv), 19.89 KB) MD5:14e352674262df82258c118bf5d216b2 Primary data file for dataset ID 716817 |
| Parameter | Description | Units |
| cruise_id | official UNOLS cruise identifier | unitless |
| cruise_name | project cruise name | unitless |
| sample_name | sequencing facility sample identifier | unitless |
| sample_title | laboratory sample identifier | unitless |
| bioproject_accession | collection of biological data related to a single initiative | unitless |
| organism | cyanobacterium used in this study | unitless |
| strain | population of organism that descends from a single organism or pure culture isolate; not applicable to this dataset | unitless |
| isolate | specific individual from which this sample was obtained; not applicable to this dataset | unitless |
| host | host organism; not applicable to this dataset | unitless |
| isolation_source | physical; environmental; geographic source of the sample | unitless |
| collection_date | date sample was obtained | year-month-day |
| geo_loc_name | geographical origin of the sample | unitless |
| sample_type | sample type such as: whole organism; mixed culture; cell culture; metagenomic assembly | unitless |
| biomaterial_provider | laboratory and principal investigator where sample came from | unitless |
| collected_by | laboratory and principal investigator where organism was isolated | unitless |
| depth | vertical distance below the surface where sample was collected | meters |
| env_biome | descriptor of the broad ecological context of sample | unitless |
| genotype | observed genotype; not applicable to this dataset | unitless |
| lat | sample collection latitude; north is positive | decimal degrees |
| lon | sample collection longitude; east is positive | decimal degrees |
| passage_history | duration of sample | not applicable |
| samp_size | amount of sample collected | colonies |
| NCBI_accession_link | link to NCBI GenBank BioProject accession page | unitless |
| 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 | 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 | |
| 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) |
| 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. |
| 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 |
| 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. |
| Website | |
| Platform | R/V Kilo Moana |
| Start Date | 2013-05-22 |
| End Date | 2013-06-05 |
| 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 |
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.
| Funding Source | Award |
|---|---|
| NSF Division of Ocean Sciences (NSF OCE) |