http://lod.bco-dmo.org/id/dataset/3791
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 sequences from marine bacterioplankton from Sapelo Island, GA (En-Gen DMSP Cycling project)
2012-11-23
publication
2012-11-23
revision
BCO-DMO Linked Data URI
2012-11-23
creation
http://lod.bco-dmo.org/id/dataset/3791
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., Kiene, R. P., Whitman, W. (2012) Links to published dmdA sequences from marine bacterioplankton from Sapelo Island, GA (En-Gen DMSP Cycling project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 23 Nov 2012) Version Date 2012-11-23 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/3791 [access date]
Links to published dmdA sequences from marine bacterioplankton from Sapelo Island, GA. Dataset Description: <p>Links are provided to published dimethylsulfoniopropionate (DMSP) demethylase protein, DmdA, sequence data from marine bacterioplankton that has been deposited in the NCBI GenBank Short Read Archive (SRA).</p>
<p><strong>Experimental design, methods, and results are further described in:</strong><br />
<strong>Varaljay, V. A</strong>., 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> Methods and Sampling: <p>See Varaljay et al. 2010 for detailed methods, which are paraphrased below.</p>
<p>"Surface water was collected between October 2000 and April 2005 at two sampling sites at the <a href="http://simo.marsci.uga.edu/index.htm" target="_blank">Sapelo Island Microbial Observatory</a> (SIMO) in coastal Georgia: the Dean Creek site (a salt marsh tidal creek) and the Doboy Sound (a coastal ocean inlet). Approximately 20 liters of water was filtered sequentially through 8.0-um, 1.0-um, and 0.2-um pore size polycarbonate membrane filters, with two replicate samples obtained at each site. Cells captured on the 1.0-um (particle associated) and 0.2-um filter (free-living) were stored at -20 degrees C until DNA extraction using a PowerMax Soil DNA Isolation kit (MO BIO Laboratories, Inc.). 76 DNA extracts were used in the study, representing 38 samples of each size fraction. Samples were separately pooled by size fraction in equal amounts to produce composite free-living and particle-associated DNA samples.</p>
<p>Primer pairs giving single amplicons of the correct size from the composite SIMO DNA were chosen for analysis by sequencing. Amplicons suitable for 454 sequencing were prepared by modifying each primer pair with an adaptor sequence at the 5 end of the forward primer according to the method of Huber et al. Additional four-base key sequences in between the adaptor and primer sequence were used to distinguish inosine and degenerate primer sequences. PCRs were carried out in duplicate using 24 ng template DNA and then pooled before sequencing. Amplicons were cleaned using the AMPure purification method (Agencourt Bioscience Corp., Beverly, MA) according to the 454 Life Sciences protocol (Roche Diagnostics Corp., Branford, CT), with modifications to the volume of purified PCR products (30.0 l) and AMPure beads (50.4 l). Products were quantified spectrophotometrically and combined in equal concentrations in four separate pools based on primer and size fraction. Four-region 454 FLX LR70 sequencing was carried out at the University of South Carolina EnGenCore facility. Amplicon sequences were annotated by BLASTx analysis. This analysis was used to distinguish correct target sequences from closely related paralogous sequences and to classify amplicons by clade."</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: 23 Nov 2012
Unknown
site_desc
taxon
accession_number
site
lat
lon
theme
None, User defined
site description
taxon
accession number
site
latitude
longitude
featureType
BCO-DMO Standard Parameters
DMSP_Sapelo_Island
service
Deployment Activity
Coastal Georgia
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
Coastal Georgia
2012-11-23
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 sequences from marine bacterioplankton from Sapelo Island, GA (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/30886.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/30887.rdf
Name: taxon
Units: text
Description: <p>Description of the taxon of study.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30888.rdf
Name: accession_number
Units: unitless
Description: <p>Accession number and link to NCBI's Short Read Archive (SRA).</p>
http://lod.bco-dmo.org/id/dataset-parameter/30889.rdf
Name: site
Units: text
Description: <p>Name of the sampling site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30890.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of the sampling site. North = positive.</p>
http://lod.bco-dmo.org/id/dataset-parameter/30891.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of the sampling site. East = positive.</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
389
https://datadocs.bco-dmo.org/file/xooy0XRhB1N8Lz/bacterioplankton_dmdA_sequences.csv
bacterioplankton_dmdA_sequences.csv
Primary data file for dataset ID 3791
download
https://osprey.bco-dmo.org/dataset/3791/data/download
download
onLine
dataset
<p>See Varaljay et al. 2010 for detailed methods, which are paraphrased below.</p>
<p>"Surface water was collected between October 2000 and April 2005 at two sampling sites at the <a href="http://simo.marsci.uga.edu/index.htm" target="_blank">Sapelo Island Microbial Observatory</a> (SIMO) in coastal Georgia: the Dean Creek site (a salt marsh tidal creek) and the Doboy Sound (a coastal ocean inlet). Approximately 20 liters of water was filtered sequentially through 8.0-um, 1.0-um, and 0.2-um pore size polycarbonate membrane filters, with two replicate samples obtained at each site. Cells captured on the 1.0-um (particle associated) and 0.2-um filter (free-living) were stored at -20 degrees C until DNA extraction using a PowerMax Soil DNA Isolation kit (MO BIO Laboratories, Inc.). 76 DNA extracts were used in the study, representing 38 samples of each size fraction. Samples were separately pooled by size fraction in equal amounts to produce composite free-living and particle-associated DNA samples.</p>
<p>Primer pairs giving single amplicons of the correct size from the composite SIMO DNA were chosen for analysis by sequencing. Amplicons suitable for 454 sequencing were prepared by modifying each primer pair with an adaptor sequence at the 5 end of the forward primer according to the method of Huber et al. Additional four-base key sequences in between the adaptor and primer sequence were used to distinguish inosine and degenerate primer sequences. PCRs were carried out in duplicate using 24 ng template DNA and then pooled before sequencing. Amplicons were cleaned using the AMPure purification method (Agencourt Bioscience Corp., Beverly, MA) according to the 454 Life Sciences protocol (Roche Diagnostics Corp., Branford, CT), with modifications to the volume of purified PCR products (30.0 l) and AMPure beads (50.4 l). Products were quantified spectrophotometrically and combined in equal concentrations in four separate pools based on primer and size fraction. Four-region 454 FLX LR70 sequencing was carried out at the University of South Carolina EnGenCore facility. Amplicon sequences were annotated by BLASTx analysis. This analysis was used to distinguish correct target sequences from closely related paralogous sequences and to classify amplicons by clade."</p>
Specified by the Principal Investigator(s)
<p>"To account for differences in the number of amplicons sequenced for each primer pair (ranging from 2,000 to 12,000 sequences), a resampling approach was used in which 1,000 sample populations of the same size were randomly drawn from the amplicon pools being compared. This approach was used to normalize the number of 90% dmdA clusters in comparisons between primer pairs and size fractions." (Varaljay et al. 2010)</p>
<p>BCO-DMO added the site coordinates, which were obtained from the <a href="http://simo.marsci.uga.edu/index.htm" target="_blank">Sapelo Island Microbial Observatory</a> (SIMO) website.</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
Deployment: DMSP_Sapelo_Island
DMSP_Sapelo_Island
shoreside Sapelo Island Microbial Observatory
shoreside Sapelo Island Microbial Observatory
island
DMSP_Sapelo_Island
Mary Ann Moran
University of Georgia
shoreside Sapelo Island Microbial Observatory
shoreside Sapelo Island Microbial Observatory
island