http://lod.bco-dmo.org/id/dataset/626613
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
2015-11-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
16S rRNA gene clones and accessions from bacterioplankton in the NE Pacific Ocean from R/V Thomas G. Thompson TN268 in the Northeast Pacific from August to September 2011 (Sulfur Oxidizers project)
2015-11-17
publication
2015-11-17
revision
BCO-DMO Linked Data URI
2015-11-17
creation
http://lod.bco-dmo.org/id/dataset/626613
Robert Morris
University of Washington
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: Morris, R. (2015) 16S rRNA gene clones and accessions from bacterioplankton in the NE Pacific Ocean from R/V Thomas G. Thompson TN268 in the Northeast Pacific from August to September 2011 (Sulfur Oxidizers project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version final) Version Date 2015-11-17 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/626613 [access date]
16S rRNA gene clones from bacterioplankton in the NE Pacific Ocean Dataset Description: <p>16S rRNA gene clones from bacterioplankton in the northeastern Pacific Ocean.</p>
<p>These data are reported and discussed in <a href="http://www.nature.com/ismej/journal/v7/n12/full/ismej2013113a.html" target="_blank">Mattes et al., 2013</a>.&nbsp; doi:10.1038/ismej.2013.113</p> Methods and Sampling: <p>Bacterial 16S rRNA gene clone libraries were constructed by amplifying community 16S rRNA genes with bacterial primers 27F_B and 1492R (5′-GGYTACCTTGTTACGACTT -3′) as described previously (Morris et al 2012). Briefly, amplifications were performed using community genomic DNA extracted from (CTD17, 1 450 m) and (CTD7, 2 850m), Apex Taq polymerase (Genesee Scientific, San Diego, CA), and the following conditions: 35 cycles, annealing at 55ºC for 1 min, elongation at 72ºC for 2 min, and denaturation at 94ºC for 30 s. Amplicons were purified and cloned using the pGEM-T-Easy vector (Promega, Madison, WI) following the manufacturer’s instructions. The resulting transformations were sent to High Throughput Sequencing (HTSeq.org, Seattle, WA), where clones were isolated and sequenced by Sanger sequencing using the M13F (5'-TGTAAAACGACGGCCAGT-3') and M13R (5'-CAGGAAACAGCTATGAC-3') primers. (See Data).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1232840 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1232840
completed
Robert Morris
University of Washington
206-221-7228
School of Oceanography Box 357940
Seattle
WA
98195-7940
USA
morrisrm@uw.edu
pointOfContact
asNeeded
Dataset Version: final
Unknown
clone_ID_predicted
lat
lon
HaeIII_TRF_bp_predicted
NCBI_accession
SILVA_class
Bayesian_class
theme
None, User defined
sample identification
latitude
longitude
No BCO-DMO term
accession number
featureType
BCO-DMO Standard Parameters
TN268
service
Deployment Activity
North Pacific
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.
Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade
http://morrislab.ocean.washington.edu/
Mixotrophic bacteria and the cryptic marine sulfur cycle: Mechanisms of carbon assimilation and sulfur oxidation in the Arctic96BD-19 GSO clade
<p><em>Description from NSF award abstract:</em><br />
The ocean serves an immense reservoir of carbon, nitrogen, phosphorus, sulfur, and other elements required for all life. The active and diverse microbial populations that inhabit the oceans are responsible for mediating nutrient transformations that maintain the chemistry of seawater. A recent study identified a ubiquitous group of marine bacteria from the Arctic96BD-19 gamma-proteobacterial sulfur oxidizer (GSO) lineage that is closely related to known sulfur oxidizing species that fix inorganic carbon and oxidize sulfide in low-oxygen waters. The potential for GSOs to use reduced forms of sulfur in oxygenated waters suggests that they are a keystone species that link the marine carbon and sulfur cycles. The only known isolates from the Arctic96BD-19 lineage of GSOs are now in culture, allowing fundamental questions about their roles in carbon and sulfur cycling to be investigated. Preliminary data suggest that they use energy from the oxidation of sulfur to assimilate carbon. This project seek to address the overarching hypothesis that sulfur transformations provide the Arctic96BD- 19 lineage of GSOs with energy for organic and inorganic carbon cycling throughout the water column.</p>
<p>Three specific hypotheses will be tested.<br />
1. Arctic96BD-19 cells assimilate either organic carbon or fixes inorganic carbon, depending on environmental conditions.<br />
2. Arctic96BD-19 cells oxidize thiosulfate via formation of a tetrathionate intermediate, or using the branched thiosulfate oxidation pathway.<br />
3. Arctic96BD-19 cells are ubiquitous sulfur oxidizers that assimilate organic and inorganic carbon through the Pacific Northwest.</p>
<p>A combination of laboratory growth studies of the investigator's pure cultures and comparative genomic analyses will be used. The genomic data will be used to determine whether the Arctic96BD-19 cultures possess the genetic potential to oxidize reduced sulfur to sulfate (based on possession of known core and ancillary sulfur oxidation genes), which potential oxidation pathways are used, and whether they can fix inorganic carbon. These data will help guide the physiology studies by determining the most likely forms of inorganic and organic compounds that can be utilized.</p>
<p>Marine bacteria are critical players in global nutrient cycles, but many of their individual and community functions in the ecosystem are not well understood. Future oceanographers will need to use cultivation-dependent and cultivation-independent methods to identify metabolic process that shape microbial communities and impact biogeochemical cycles. Student education, scientific advancement, and public awareness are all important components of this project.</p>
Sulfur Oxidizers
largerWorkCitation
project
eng; USA
biota
oceans
North Pacific
-130.0138
-127.9353
45.8602
45.934
2015-11-17
North Pacific Ocean
0
BCO-DMO catalogue of parameters from 16S rRNA gene clones and accessions from bacterioplankton in the NE Pacific Ocean from R/V Thomas G. Thompson TN268 in the Northeast Pacific from August to September 2011 (Sulfur Oxidizers 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/628981.rdf
Name: clone_ID_predicted
Units: text
Description: <p>sample identification; includes the CTD and station number(if available) and the depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/628982.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/628983.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude; West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/628984.rdf
Name: HaeIII_TRF_bp_predicted
Units: number of base pairs
Description: <p>predicted length of the terminal restriction fragment after digestion by the HaeIII enzyme</p>
http://lod.bco-dmo.org/id/dataset-parameter/628985.rdf
Name: NCBI_accession
Units: link
Description: <p>link to NCBI GenBank</p>
http://lod.bco-dmo.org/id/dataset-parameter/628986.rdf
Name: SILVA_class
Units: text
Description: <p>Classification of rRNA sequences using SILVA database (<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2175337" target="_blank">Pruesse et al.(2007)</a>)</p>
http://lod.bco-dmo.org/id/dataset-parameter/628987.rdf
Name: Bayesian_class
Units: text
Description: <p>Bayesian Classification; classification of rRNA sequences using a naive Bayesian classification (<a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1950982" target="_blank">Wang et al.(2007)</a>; p-values at each taxonomic level shown are greater than 0.7</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
31467
https://datadocs.bco-dmo.org/file/N77GrPGFPxDZPM/16S_rRNA_NP.csv
16S_rRNA_NP.csv
Primary data file for dataset ID 626613
download
https://osprey.bco-dmo.org/dataset/626613/data/download
download
onLine
dataset
<p>Bacterial 16S rRNA gene clone libraries were constructed by amplifying community 16S rRNA genes with bacterial primers 27F_B and 1492R (5′-GGYTACCTTGTTACGACTT -3′) as described previously (Morris et al 2012). Briefly, amplifications were performed using community genomic DNA extracted from (CTD17, 1 450 m) and (CTD7, 2 850m), Apex Taq polymerase (Genesee Scientific, San Diego, CA), and the following conditions: 35 cycles, annealing at 55ºC for 1 min, elongation at 72ºC for 2 min, and denaturation at 94ºC for 30 s. Amplicons were purified and cloned using the pGEM-T-Easy vector (Promega, Madison, WI) following the manufacturer’s instructions. The resulting transformations were sent to High Throughput Sequencing (HTSeq.org, Seattle, WA), where clones were isolated and sequenced by Sanger sequencing using the M13F (5'-TGTAAAACGACGGCCAGT-3') and M13R (5'-CAGGAAACAGCTATGAC-3') primers. (See Data).</p>
Specified by the Principal Investigator(s)
<p>Nearly full-length 16S rRNA gene sequences were obtained for frequently occuring lineages by selecting and purifying a subset of clones using the Qiagen plasmid mini-prep kit (QIAGEN, Germantown, MD). Sequencing was performed using the following primer pairs (M13R-, 519F (5′-CAGC(A/G)GCCGCGGTAATAC-3′), 338F (5′-ACTCCTACGGGAGGCAGC-3′), and 926R (5′-CCGTCAATTC(A/C)TTT (A/G)AGTTT-3′)) by GeneWiz, Inc. (LaJolla, CA). Sequences were assembled with the CAP3 Sequence Assembly Program (Huang and Madan 1999) and annotated by using the Bayesian method of (Wang et al 2007), which contained a custom training set augmented with marine environmental clades (Iverson et al 2012), and by using the SILVA least common ancestor classification tool (Pruesse et al 2007). In silico restriction analysis and other DNA sequence manipulation operations were performed with the Sequence Manipulation Suite (Stothard 2000). Restriction fragments were verified for a subset of clones to confirm predicted fragment sizes. Bacterial 16S rRNA sequences generated during this study were submitted to Genbank (accession numbers KC522839- KC522949 -- See Data).</p>
<p>&nbsp;</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
Cruise: TN268
TN268
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel
TN268
Dr John R. Delaney
University of Washington
R/V Thomas G. Thompson
Community Standard Description
International Council for the Exploration of the Sea
R/V Thomas G. Thompson
vessel