|Moran, Mary Ann||University of Georgia (UGA)||Principal Investigator|
|Kiene, Ronald||Dauphin Island Sea Lab (DISL)||Co-Principal Investigator|
|Whitman, William||University of Georgia (UGA)||Co-Principal Investigator|
|Rauch, Shannon||Woods Hole Oceanographic Institution (WHOI BCO-DMO)||BCO-DMO Data Manager|
A link is provided to published bacterial cDNA sequences from samples from the Bermuda Atlantic Time Series (BATS) station. Metatranscriptomic sequencing was used to analyze the gene expression profiles of the bacterial assemblage with and without short-term enrichment of dimethylsulfoniopropionate (DMSP).
Experimental design, methods, and results are further described in:
Vila-Costa, M., J. M. Rinta-Kanto, S. Sun, S. Sharma, R. Poretsky, and M. A. Moran. (2010). Transcriptomic analysis of a marine bacterial community enriched with dimethylsulfoniopropionate. ISME Journal, vol. 4, p. 1410. doi: 10.1038/ismej.2010.62
See Vila-Costa et al. (2010) for detailed methodology, which is paraphrased below:
"Sampling was carried out on 15 April 2008 at the Bermuda Atlantic Time-series Study (BATS) station at a depth of 10m using 10-L Niskin bottles. A 2 L subsample of unfiltered water was collected to measure in situ concentrations of Chl-a and total DMSP. The remaining seawater was prefiltered by gravity through 3 mm pore-size polycarbonate filters (142mm, Millipore, Billerica, MA, USA) to exclude eukaryotes and large particles. Water was dispensed into 20 L polycarbonate carboys and maintained in a temperature-controlled room in the dark at in situ temperature for 3 h before beginning the experiment to allow time for adaptation to any DMSP released from the cells during filtration.
DMSP was added to experimental carboys to a final concentration of 25 nM. Control carboys remained untreated. Bacterial cells were collected after 30 minutes by filtering the water through 0.2 um pore-size polycarbonate filter. Filters were placed in 15 ml RNAse-free tubes containing 2 ml of Buffer RLT (RNeasy kit, Qiagen, Valencia, CA, USA) plus 10 ml of b-mercaptoethanol per ml. Messenger RNA (mRNA) extraction, enrichment, amplification, and conversion to complementary DNA was performed as described by Poretsky et al. (2009) with few modifications (see Supplementary Material in Vila-Costa et al. 2010). Only one replicate from the experimental and control treatments yielded RNA of sufficient quality for processing.
Complementary DNA libraries were sequenced with Roche GS FLX sequencing (Branford, CT, USA), yielding 606 286 reads (209-bp average length). The sequences were deposited in the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) database with the Genome Project ID CAM_PROJ_SargassoSea."
Poretsky, R.S., Hewson, I., Sun, S.L., Allen, A.E., Zehr, J.P., and Moran, M.A. (2009) Comparative day/night metatranscriptomic analysis of microbial communities in the North Pacific subtropical gyre. Environ Microbiol 11: 1358–1375. DOI: 10.1002/9781118010518.ch63
2018.04.26: Updated the link and repository location for sequences: CAMERA data has been migrated to iMicrobe.
BCO-DMO added coordinates of the BATS station and the sampling date from Vila-Costa et al. (2010).
|taxon||Description of the taxonomic group of study.||text|
|site_desc||Description of the sampling site.||text|
|lat||Latitude of sampling site. North = positive.||decimal degrees|
|lon||Longitude of the sampling site. East = positive.||decimal degrees|
|day||2-digit day of month when field sampling occurred.||dd (01 to 31)|
|month||2-digit month of year when field sampling occurred.||mm (01 to 12)|
|year||4-digit year when field sampling occurred.||YYYY|
|project_id||The identifier assigned to the project in the repository.||text|
|repository||Name of and link to the repository where sequences can be accessed.||text|
|Dataset-specific Instrument Name|| |
|Generic Instrument Name|| |
|Dataset-specific Description|| |
Samples were collected in 10-L Niskin bottles.
|Generic Instrument Description|| |
A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24 or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.
Bermuda Atlantic Time Series Vessel
|Start Date|| |
|End Date|| |
Sampling for the project "En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean" was carried out at the Bermuda Atlantic Time-series Study (BATS) station (31 40.1N, 64 7.9W) at a depth of 10m using 10-l Niskin bottles on 15 April 2008.
This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database. 2020-02-24 16:01:22