http://lod.bco-dmo.org/id/dataset/3793
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
2012-11-23
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Link to published bacterial cDNA sequences from the Bermuda Atlantic Time Series (BATS) Station, Sargasso Sea, 2008 (En-Gen DMSP Cycling project)
2018-04-26
publication
2018-04-26
revision
BCO-DMO Linked Data URI
2018-04-26
creation
http://lod.bco-dmo.org/id/dataset/3793
Mary Ann Moran
University of Georgia
principalInvestigator
Ronald P. Kiene
Dauphin Island Sea Lab
principalInvestigator
William Whitman
University of Georgia
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: Moran, M., Whitman, W., Kiene, R. P. (2018) Link to published bacterial cDNA sequences from the Bermuda Atlantic Time Series (BATS) Station, Sargasso Sea, 2008 (En-Gen DMSP Cycling project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 26 April 2018) Version Date 2018-04-26 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3793 [access date]
Link to published bacterial cDNA sequences from BATS station. Dataset Description: <p>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).</p>
<p><strong>Experimental design, methods, and results are further described in:</strong><br />
<strong>Vila-Costa</strong>, 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.<strong> </strong>doi: <a href="http://dx.doi.org/10.1038/ismej.2010.62" target="_blank">10.1038/ismej.2010.62</a><strong> </strong></p> Methods and Sampling: <p>See Vila-Costa et al. (2010) for detailed methodology, which is paraphrased below:</p>
<p>"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.</p>
<p>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.</p>
<p>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."</p>
<p><strong>References:</strong><br />
<strong>Poretsky</strong>, 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:&nbsp;<a href="http://dx.doi.org/10.1002/9781118010518.ch63" target="_blank">10.1002/9781118010518.ch63</a></p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0724017 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0724017
completed
Mary Ann Moran
University of Georgia
706-542-6481
Department of Marine Sciences
Athens
GA
30602
USA
mmoran@uga.edu
pointOfContact
Ronald P. Kiene
Dauphin Island Sea Lab
pointOfContact
William Whitman
University of Georgia
706-542-4219
Depmartment of Microbiogy 541 Biological Sciences
Athens
GA
30602
USA
whitman@uga.edu
pointOfContact
asNeeded
Dataset Version: 26 April 2018
Unknown
taxon
site_desc
lat
lon
day
month
year
project_id
repository
Niskin bottle
theme
None, User defined
taxon
site description
latitude
longitude
day of month
month of year
year
No BCO-DMO term
accession number
featureType
BCO-DMO Standard Parameters
Niskin bottle
instrument
BCO-DMO Standard Instruments
DMSP_Sargasso_Sea
service
Deployment Activity
BATS Station, Sargasso Sea
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.
En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean
https://osprey.bco-dmo.org/project/2244
En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean
<p>The recent discovery of key genes that mediate competing pathways at a critical juncture in the marine sulfur cycle has allowed biogeochemists to make rapid advances in understanding where and when sulfur transformations occur in the ocean, and most importantly, what factors regulate them. This project describes an environmental functional genomics project that will rapidly increase our knowledge of the role that bacterioplankton play in dimethylsulfoniopropionate (DMSP) cycling in ocean surface waters, focusing particularly on biological controls of volatile sulfur exchange across the ocean/atmosphere boundary.</p>
<p>The investigators have asked three critical hypotheses to explain the regulation of bacterial DMSP degradation: that involve investigations on the energy constraints of DMSP cycling, the role that DMSP concentration in the oceans plays, and the sulfur requirements for bacterial growth. These research areas serve as the focus for hypothesis-driven laboratory and field studies using functional genomics approaches that will track patterns in gene expression in relation to sulfur metabolism. The hypotheses will be tested with:<br />
1) chemostat systems with a model marine bacterium Silicibacter pomeroyi;<br />
2) microcosm experiments with Gulf of Mexico seawater; and<br />
3) field studies at various sites in the Gulf of Mexico. Marine bacterioplankton play a key role in regulating the flux of DMSP-derived sulfur to the atmosphere, a process of great importance for global climate regulation and marine productivity.</p>
<p>The investigators will also be involved in graduate and undergraduate student education, and two post-doctoral associates will be trained to address multidisciplinary challenges in environmental microbiology. High school biology students in Athens, GA will participate in marine microbial biology research that includes bacterial diversity and discovery studies in coastal Georgia, follow-up training in molecular tools and bioinformatics in their own classroom, and summer internships at the University of Georgia and Dauphin Island Sea Laboratory.</p>
<p>(The description above is from the NSF Award Abstract).</p>
En-Gen DMSP Cycling
largerWorkCitation
project
eng; USA
biota
oceans
BATS Station, Sargasso Sea
-64.132
-64.132
31.668
31.668
2018-04-26
Sapelo Island, GA, USA, 31.4° N Lat, 81.3° W Lon / Dauphin Island, AL, USA, 30.3 ° N Lat, 88.1° W Lon
0
BCO-DMO catalogue of parameters from Link to published bacterial cDNA sequences from the Bermuda Atlantic Time Series (BATS) Station, Sargasso Sea, 2008 (En-Gen DMSP Cycling 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/30892.rdf
Name: taxon
Units: text
Description: <p>Description of the taxonomic group of study.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30893.rdf
Name: site_desc
Units: text
Description: <p>Description of the sampling site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30894.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sampling site. North = positive.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30895.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of the sampling site. East = positive.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30896.rdf
Name: day
Units: dd (01 to 31)
Description: <p>2-digit day of month when field sampling occurred.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30897.rdf
Name: month
Units: mm (01 to 12)
Description: <p>2-digit month of year when field sampling occurred.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30898.rdf
Name: year
Units: YYYY
Description: <p>4-digit year when field sampling occurred.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30899.rdf
Name: project_id
Units: text
Description: <p>The identifier assigned to the project in the repository.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30900.rdf
Name: repository
Units: text
Description: <p>Name of and link to the repository where sequences can be accessed.</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
234
https://datadocs.bco-dmo.org/file/933jz4kcxgNkoj/BATS_cDNA_sequences.csv
BATS_cDNA_sequences.csv
Primary data file for dataset ID 3793
download
https://osprey.bco-dmo.org/dataset/3793/data/download
download
onLine
dataset
<p>See Vila-Costa et al. (2010) for detailed methodology, which is paraphrased below:</p>
<p>"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.</p>
<p>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.</p>
<p>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."</p>
<p><strong>References:</strong><br />
<strong>Poretsky</strong>, 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:&nbsp;<a href="http://dx.doi.org/10.1002/9781118010518.ch63" target="_blank">10.1002/9781118010518.ch63</a></p>
Specified by the Principal Investigator(s)
<p>2018.04.26: Updated the link and repository location for sequences: CAMERA data has been migrated to iMicrobe.</p>
<p>BCO-DMO added coordinates of the BATS station and the sampling date from Vila-Costa et al. (2010).</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
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:Samples were collected in 10-L Niskin bottles. Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: DMSP_Sargasso_Sea
DMSP_Sargasso_Sea
Bermuda Atlantic Time Series Vessel
vessel
DMSP_Sargasso_Sea
Mary Ann Moran
University of Georgia
Bermuda Atlantic Time Series Vessel
vessel