http://lod.bco-dmo.org/id/dataset/3792
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)
Links to published dmdA, cDNA, and RNA sequences from the Dauphin Island Cubitainer Experiment (DICE) from samples collected on R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling project)
2014-06-20
publication
2014-06-20
revision
BCO-DMO Linked Data URI
2014-06-20
creation
http://lod.bco-dmo.org/id/dataset/3792
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. (2014) Links to published dmdA, cDNA, and RNA sequences from the Dauphin Island Cubitainer Experiment (DICE) from samples collected on R/V E.O. Wilson in the Gulf of Mexico, Alabama (En-Gen DMSP Cycling project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 20 June 2014) Version Date 2014-06-20 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3792 [access date]
Links to published dmdA, cDNA, and RNA sequences from the Dauphin Island Cubitainer Experiment (DICE). Dataset Description: <p>Links are provided to published&nbsp; dmdA amplicon, cDNA transcript, and mircoarray sequences resulting from Dauphin Island Cubitainer Experiments (DICE) as part of the project "En-Gen: A Functional Genomics Approach to Organic Sulfur Cycling in the Ocean".</p>
<p><strong>Experimental design, methods, and results are further described in:</strong><br />
<strong>E. C. Howard</strong>, S. Sun, C. R. Reisch, D. A. del Valle, R. P. Kiene, and M. A. Moran (2010). Changes in DMSP Demethylase Gene Assemblages in Response to an Induced Phytoplankton Bloom. Applied and Environmental Microbiology, vol. 77, p. 524.<strong> </strong>DOI: <a href="http://dx.doi.org/10.1128/AEM.01457-10" target="_blank">10.1128/AEM.01457-10</a><br />
<strong>Rinta-Kanto</strong>, H. Burgmann, S. M. Gifford, S. Sun, S. Sharma, R. P. Kiene, and M. A. Moran (2011). Analysis of Sulfur-Related Gene Expression by Roseobacter Communities Using a Taxon-Specific Functional Gene Microarray. Environmental Microbiology, vol. 13, p. 453. DOI: <a href="http://dx.doi.org/10.1111/j.1462-2920.2010.02350.x" target="_blank">10.1111/j.1462-2920.2010.02350.x</a><br />
<strong>J. M. Rinta-Kanto</strong>, S. Sun, S. Sharma, R. P. Kiene, and M. A. Moran (2012). Bacterial Community Transcription Patterns During a Marine Phytoplankton Bloom", Environmental Microbiology, vol. 14, p. 228. DOI: <a href="http://dx.doi.org/10.1111/j.1462-2920.2011.02602.x" target="_blank">10.1111/j.1462-2920.2011.02602.x</a><strong> </strong></p> Methods and Sampling: <p>See Howard et al. (2010), Rinta-Kanto et al. (2011), and Rinta-Kanto et al. (2012) for detailed methods, which are paraphrased below:</p>
<p>"In October 2006, seawater was collected from near-surface waters in the Gulf of Mexico off the coast of Dauphin Island (temp = 27 degrees C, salinity = 34) by lowering a clean bucket ~10 cm below the surface. Water was filtered through a 200 micrometer mesh into six 20-liter polyethylene Cubitainers (Fold-A-Carrier; Reliance Products, Ltd.). Three experimental Cubitainer microcosms were amended with sodium nitrate (10 uM) and potassium phosphate (0.6 uM) to induce bloom conditions; three control microcosms received no nutrient amendments. The microcosms were incubated at 27 degrees C with a 12-h-on/12-h-off light cycle (200 umol quanta per square meter per second) for the duration of the experiment. At the initial time point (T = 0), the full contents of one control and one experimental microcosm (20 liters each) were sacrificed for detailed chemical and biological measurements."</p>
<p><strong>Howard et al. (2010):</strong><br />
"For DNA samples, water from each time point was sequentially filtered through 8-um and 3-um prefilters, and&nbsp; particles were collected on 0.2-um pore-size polycarbonate filters. DNA was extracted using the PowerMax soil DNA isolation kit (MoBio Laboratories, Inc.). Concentrations were estimated by absorbance on a NanoDrop spectrophotometer (Thermo Scientific). DNA extracted from duplicate control and experimental samples was used as template for PCRs, followed by pyrosequencing of amplicons. Universal dmdA primers were modified from the work of Varaljay et al (2010). PCR products were run on 1% (dmdA amplicons) or 2% (bacterial and archaeal 16S rRNA amplicons) agarose gels, followed by purification using the Qiagen QIAquick gel extraction kit. Products were cleaned using the Ampure system (Agencourt Bioscience Corporation). Two separate pools were assembled, and these were sequenced on separate halves of the PicoTiterPlate (454 Life Sciences). 1,300 ng DNA was used in Roche GS FLX LR70 pyrosequencing at the University of South Carolina Environmental Genomics Facility (Columbia, SC).</p>
<p>For reads of high quality, adaptor and key sequences were removed and sequences were clustered using the CD-HIT program. For analysis of dmdA amplicons, reference sequences (the longest read in the cluster) were analyzed via&nbsp; BLASTX against an in-house DmdA database. rRNA sequences were deposited in the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) database with project ID CAM-PROJ_DICE (sample CAM_S_A001= experimental microcosms; sample CAM_S_A002 = control microcosms). dmdA amplicon sequences were deposited in the NCBI Short Read Archive with project ID 49967."</p>
<p><strong>Rinta-Kanto et al. (2011):</strong><br />
"The microarray was designed based on<em> R. pomeroyi</em> DSS-3 genes and their orthologs in 12 other Roseobacter&nbsp; genomes (<a href="http://www.roseobase.org" target="_blank">http://www.roseobase.org</a>). The gene encoding DMSP demethylase (dmdA) was included on the array. Genes involved in DMSP cleavage to DMS (discovered in Roseobacter genomes subsequent to microarray final design) were not included on the array. Once a list of <em>R. pomeroyi</em> DSS-3 genes was compiled, orthologs for these genes in the other 12 Roseobacter genomes were identified using reciprocal BLASTs. Probes were designed from the orthologs using the Hierarchical Probe Design algorithm. The best probes selected by the program were queried against NCBI’s nr database using BLASTN, and only those probes with a best hit to a Roseobacter gene were retained. The final array consisted of 1578 probes targeting 431 genes. The complete list of probes is deposited in NCBI’s Gene Expression Omnibus database under accession number GPL10323. (The identifier codes for each probe begin with the<em> R. pomeroyi </em>DSS-3 locus tag followed by a number generated by the probe design algorithm describing the placement of the probe in the&nbsp; tree generated during design.)"</p>
<p><strong>Rinta-Kanto et al. (2012):</strong><br />
"RNA samples were collected from the microcosms on Day 5 by prefiltering ~1 L subsamples through 8.0 and 3.0 um poresize polycarbonate filters and collecting bacterioplankton on 0.2-um polycarbonate filters. Filters were placed in sterile 15 ml polypropylene tubes with lysis/binding buffer from the Ambion RNAqueous-kit. Cells were lysed using the Ambion RNAqueous Midi-kit (Applied Biosystems, Austin, TX). RNA was extracted from the lysate using Qiagen RNeasy kit. RNA was quantified after the extraction using a Nanodrop spectrometer.</p>
<p>Samples were processed as described in Poretsky et al. (2009) with some modifications (see Rinta-Kanto et al. 2012). Resulting amplified antisense RNAs were converted to doublestranded cDNA using Universal RiboClone cDNA Synthesis System (Promega). Concentrations of mRNA, amplified RNA and cDNA were measured using a Nanodrop spectrometer, and quality of the mRNA and cDNA was assessed using an Experion Automated Electrophoresis Station (Bio-Rad). Five ug of cDNA from each sample was used for pyrosequencing with the GS FLX sequencing system (Roche). Transcript libraries were deposited in the CAMERA database with a project ID CAM_PROJ_DICE."</p>
<p><strong>References:</strong><br />
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:&nbsp;<a href="http://dx.doi.org/10.1002/9781118010518.ch63" target="_blank">10.1002/9781118010518.ch63</a><br />
Varaljay, V. A., E. C. Howard, S. Sun, M. A. Moran (2009). Deep Sequencing of a DMSP-Degrading Gene (dmdA) Using PCR Primer Pairs Designed from Marine Metagenomic Data. Applied and Environmental Microbiology, vol. 76, p. 609. DOI: <a href="http://dx.doi.org/10.1128/AEM.01258-09" target="_blank">10.1128/AEM.01258-09</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: 20 June 2014
Unknown
taxon
site_desc
lat
lon
month
year
descrip
repository
project_id
sample_accession
bucket
Spectrometer
theme
None, User defined
taxon
site description
latitude
longitude
month of year
year
sample description
No BCO-DMO term
project
accession number
featureType
BCO-DMO Standard Parameters
bucket
Spectrometer
instrument
BCO-DMO Standard Instruments
DMSP_Dauphin_Island
service
Deployment Activity
Gulf of Mexico, Alabama
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
oceans
Gulf of Mexico, Alabama
2014-06-20
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 Links to published dmdA, cDNA, and RNA sequences from the Dauphin Island Cubitainer Experiment (DICE) from samples collected on R/V E.O. Wilson in the Gulf of Mexico, Alabama (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/31951.rdf
Name: taxon
Units: text
Description: <p>Description of the taxon of study.</p>
http://lod.bco-dmo.org/id/dataset-parameter/31952.rdf
Name: site_desc
Units: text
Description: <p>Description of the general location where samples were collected.</p>
http://lod.bco-dmo.org/id/dataset-parameter/31953.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of the sampling site. North = positive.</p>
http://lod.bco-dmo.org/id/dataset-parameter/31954.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of the sampling site. East = positive.</p>
http://lod.bco-dmo.org/id/dataset-parameter/31955.rdf
Name: month
Units: mm (01 to 12)
Description: <p>2-digit month when sampling occurred.</p>
http://lod.bco-dmo.org/id/dataset-parameter/31956.rdf
Name: year
Units: YYYY
Description: <p>4-digit year when sampling occurred.</p>
http://lod.bco-dmo.org/id/dataset-parameter/31957.rdf
Name: descrip
Units: text
Description: <p>Sample description.</p>
http://lod.bco-dmo.org/id/dataset-parameter/31958.rdf
Name: repository
Units: text
Description: <p>Name of the repository where sequences can be accessed.</p>
http://lod.bco-dmo.org/id/dataset-parameter/31959.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/31960.rdf
Name: sample_accession
Units: unitless
Description: <p>Sample accession number and link to repostiory.</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
2127
https://datadocs.bco-dmo.org/file/yppz4YVU2GPKp1/DICE_sequences.csv
DICE_sequences.csv
Primary data file for dataset ID 3792
download
https://osprey.bco-dmo.org/dataset/3792/data/download
download
onLine
dataset
<p>See Howard et al. (2010), Rinta-Kanto et al. (2011), and Rinta-Kanto et al. (2012) for detailed methods, which are paraphrased below:</p>
<p>"In October 2006, seawater was collected from near-surface waters in the Gulf of Mexico off the coast of Dauphin Island (temp = 27 degrees C, salinity = 34) by lowering a clean bucket ~10 cm below the surface. Water was filtered through a 200 micrometer mesh into six 20-liter polyethylene Cubitainers (Fold-A-Carrier; Reliance Products, Ltd.). Three experimental Cubitainer microcosms were amended with sodium nitrate (10 uM) and potassium phosphate (0.6 uM) to induce bloom conditions; three control microcosms received no nutrient amendments. The microcosms were incubated at 27 degrees C with a 12-h-on/12-h-off light cycle (200 umol quanta per square meter per second) for the duration of the experiment. At the initial time point (T = 0), the full contents of one control and one experimental microcosm (20 liters each) were sacrificed for detailed chemical and biological measurements."</p>
<p><strong>Howard et al. (2010):</strong><br />
"For DNA samples, water from each time point was sequentially filtered through 8-um and 3-um prefilters, and&nbsp; particles were collected on 0.2-um pore-size polycarbonate filters. DNA was extracted using the PowerMax soil DNA isolation kit (MoBio Laboratories, Inc.). Concentrations were estimated by absorbance on a NanoDrop spectrophotometer (Thermo Scientific). DNA extracted from duplicate control and experimental samples was used as template for PCRs, followed by pyrosequencing of amplicons. Universal dmdA primers were modified from the work of Varaljay et al (2010). PCR products were run on 1% (dmdA amplicons) or 2% (bacterial and archaeal 16S rRNA amplicons) agarose gels, followed by purification using the Qiagen QIAquick gel extraction kit. Products were cleaned using the Ampure system (Agencourt Bioscience Corporation). Two separate pools were assembled, and these were sequenced on separate halves of the PicoTiterPlate (454 Life Sciences). 1,300 ng DNA was used in Roche GS FLX LR70 pyrosequencing at the University of South Carolina Environmental Genomics Facility (Columbia, SC).</p>
<p>For reads of high quality, adaptor and key sequences were removed and sequences were clustered using the CD-HIT program. For analysis of dmdA amplicons, reference sequences (the longest read in the cluster) were analyzed via&nbsp; BLASTX against an in-house DmdA database. rRNA sequences were deposited in the Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis (CAMERA) database with project ID CAM-PROJ_DICE (sample CAM_S_A001= experimental microcosms; sample CAM_S_A002 = control microcosms). dmdA amplicon sequences were deposited in the NCBI Short Read Archive with project ID 49967."</p>
<p><strong>Rinta-Kanto et al. (2011):</strong><br />
"The microarray was designed based on<em> R. pomeroyi</em> DSS-3 genes and their orthologs in 12 other Roseobacter&nbsp; genomes (<a href="http://www.roseobase.org" target="_blank">http://www.roseobase.org</a>). The gene encoding DMSP demethylase (dmdA) was included on the array. Genes involved in DMSP cleavage to DMS (discovered in Roseobacter genomes subsequent to microarray final design) were not included on the array. Once a list of <em>R. pomeroyi</em> DSS-3 genes was compiled, orthologs for these genes in the other 12 Roseobacter genomes were identified using reciprocal BLASTs. Probes were designed from the orthologs using the Hierarchical Probe Design algorithm. The best probes selected by the program were queried against NCBI’s nr database using BLASTN, and only those probes with a best hit to a Roseobacter gene were retained. The final array consisted of 1578 probes targeting 431 genes. The complete list of probes is deposited in NCBI’s Gene Expression Omnibus database under accession number GPL10323. (The identifier codes for each probe begin with the<em> R. pomeroyi </em>DSS-3 locus tag followed by a number generated by the probe design algorithm describing the placement of the probe in the&nbsp; tree generated during design.)"</p>
<p><strong>Rinta-Kanto et al. (2012):</strong><br />
"RNA samples were collected from the microcosms on Day 5 by prefiltering ~1 L subsamples through 8.0 and 3.0 um poresize polycarbonate filters and collecting bacterioplankton on 0.2-um polycarbonate filters. Filters were placed in sterile 15 ml polypropylene tubes with lysis/binding buffer from the Ambion RNAqueous-kit. Cells were lysed using the Ambion RNAqueous Midi-kit (Applied Biosystems, Austin, TX). RNA was extracted from the lysate using Qiagen RNeasy kit. RNA was quantified after the extraction using a Nanodrop spectrometer.</p>
<p>Samples were processed as described in Poretsky et al. (2009) with some modifications (see Rinta-Kanto et al. 2012). Resulting amplified antisense RNAs were converted to doublestranded cDNA using Universal RiboClone cDNA Synthesis System (Promega). Concentrations of mRNA, amplified RNA and cDNA were measured using a Nanodrop spectrometer, and quality of the mRNA and cDNA was assessed using an Experion Automated Electrophoresis Station (Bio-Rad). Five ug of cDNA from each sample was used for pyrosequencing with the GS FLX sequencing system (Roche). Transcript libraries were deposited in the CAMERA database with a project ID CAM_PROJ_DICE."</p>
<p><strong>References:</strong><br />
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:&nbsp;<a href="http://dx.doi.org/10.1002/9781118010518.ch63" target="_blank">10.1002/9781118010518.ch63</a><br />
Varaljay, V. A., E. C. Howard, S. Sun, M. A. Moran (2009). Deep Sequencing of a DMSP-Degrading Gene (dmdA) Using PCR Primer Pairs Designed from Marine Metagenomic Data. Applied and Environmental Microbiology, vol. 76, p. 609. DOI: <a href="http://dx.doi.org/10.1128/AEM.01258-09" target="_blank">10.1128/AEM.01258-09</a></p>
Specified by the Principal Investigator(s)
<p>BCO-DMO added the site coordinates obtained from the CAMERA repository.</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
bucket
bucket
PI Supplied Instrument Name: bucket PI Supplied Instrument Description:Water was collected in the field using a clean bucket. Instrument Name: bucket Instrument Short Name:bucket Instrument Description: A bucket used to collect surface sea water samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0536/
Spectrometer
Spectrometer
PI Supplied Instrument Name: Spectrometer PI Supplied Instrument Description:RNA (post-extraction), mRNA, amplified RNA (aRNA), and cDNA were quantified using a Nanodrop spectrometer. Instrument Name: Spectrometer Instrument Short Name:Spectrometer Instrument Description: A spectrometer is an optical instrument used to measure properties of light over a specific portion of the electromagnetic spectrum. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0460/
Cruise: DMSP_Dauphin_Island
DMSP_Dauphin_Island
R/V E.O. Wilson
R/V E.O. Wilson
vessel
DMSP_Dauphin_Island
Mary Ann Moran
University of Georgia
R/V E.O. Wilson
R/V E.O. Wilson
vessel