http://lod.bco-dmo.org/id/dataset/632875
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
2016-01-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial culture collection, strain IDs, locations and depths R/V F.G. Walton Smith (WS1209) cruise in the Yucatan Carribean and Mexico during 2012 (CEMSB project)
2016-01-19
publication
2016-01-19
revision
BCO-DMO Linked Data URI
2016-01-19
creation
http://lod.bco-dmo.org/id/dataset/632875
Paul Jensen
University of California-San Diego Scripps
principalInvestigator
Gregory Rouse
University of California-San Diego Scripps
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: Jensen, P., Rouse, G. (2016) Microbial culture collection, strain IDs, locations and depths R/V F.G. Walton Smith (WS1209) cruise in the Yucatan Carribean and Mexico during 2012 (CEMSB project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2016-01-19) Version Date 2016-01-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/632875 [access date]
Microbial culture collection, strain IDs, locations and depth from cruise WB1209 Dataset Description: <p>This dataset includes microbial Salinispora strains and co-occurring bacteria found in samples from WS1209, their associated collection information, and links to GenBank accession pages. The collections were made from sediments off of Yucatan in the Mexican Caribbean Sea. Bacteria were cultured from marine sediments and identified based on 16S sequence analysis.</p>
<p>Coordinates (this study) or year of isolation are given for each strain, as well as sample depth if known. BC stands for Banco Chinchorro, which divided into North (N), Middle (M), and South (S) locations.<br />
The following are also flagged in the data:<br />
* Genome sequence available.<br />
+ Strains used in secondary assays to determine the temporal onset of antagonism.</p>
<p><strong>Related Reference:</strong></p>
<p>Patin,NV; Duncan,KR; Dorrestein,PC; Jensen,PR. (2012) Competitive strategies differentiate closely related species of marine actinobacteria. ISME J 10:478-490. doi:10.1038/ismej.2015.128</p> Methods and Sampling: <p><a href="http://dmoserv3.bco-dmo.org/data_docs/CEMSB/WS1209_strains_methods.pdf" target="_blank">Methodolody</a> (pdf)</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1235142 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1235142
completed
Paul Jensen
University of California-San Diego Scripps
8585347322
9500 Gilman Drive
LA JOLLA
CA
92093-0204
pjensen@ucsd.edu
pointOfContact
Gregory Rouse
University of California-San Diego Scripps
858-534-7973
9500 Gilman Drive Mail Code: 0202
La Jolla
CA
92093
USA
grouse@ucsd.edu
pointOfContact
asNeeded
Dataset Version: 2016-01-19
Unknown
sample
species_strain
GenBank_accession
BLAST_pcent
seq_avail_flag
study_2_flag
site
lat
lon
year
depth
theme
None, User defined
sample identification
species
accession number
No BCO-DMO term
flag
site
latitude
longitude
year
depth
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
WS1209
service
Deployment Activity
Mexico, Yucatan Carribean
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.
The Chemical Ecology of Marine Sediment Bacteria
https://osprey.bco-dmo.org/project/536445
The Chemical Ecology of Marine Sediment Bacteria
<p>This project explores the ecological functions of bacterial secondary metabolites as agents of chemical defense. It targets marine sediments, a major and poorly explored marine biome. The aims are to test three hypotheses related to the effects of bacterial secondary metabolites on co-occurring microorganisms and protistan grazers. The focus is on the bacterial genus Salinispora, which is well defined in terms of its diversity and distributions in marine sediments, and well characterized at the genomic level and in terms of secondary metabolite production. A genetic system recently developed for these bacteria will be employed to establish links between biological activities and specific secondary metabolites. By employing a variety of innovative methodologies including imaging mass spectrometry, it will be possible for the first time to gain insight into the potential roles of Salinispora secondary metabolites in structuring marine sediment microbial communities. The results will have broad implications for our understanding of the factors that regulate the diversity and distributions of bacteria in the marine environment. They will additionally address the supplemental hypothesis that secondary metabolites represent ecotype-defining traits that delineate Salinispora species.</p>
<p>The hypotheses to be tested are:<br />
H1: Secondary metabolites inhibit microbial competitors,<br />
H2: Secondary metabolites affect bacterial community composition, and<br />
H3: Secondary metabolites function as invertebrate feeding deterrents.</p>
<p>A large collection of diverse, co-occurring microbes will be tested for sensitivity to Salinispora secondary metabolites using a direct challenge assay. These types of assays are highly informative in that they can detect behavioral and morphological responses in addition to toxicity. A recently developed imaging mass spectrometry technique will be used to visualize secondary metabolites associated with any observed biological activities. The results will be linked to existing genome sequences and used to aide in compound identification. The associated pathways will be knocked out to provide experimental support for the biological activities of specific compounds.</p>
<p>Given that most marine bacteria are not readily cultured, these experiments will additionally address the effects of secondary metabolites on the sediment bacterial community by employing culture independent techniques. In situ growth chambers and next generation sequencing technologies will be used to test extracts and pure compounds against a natural assemblages of sediment bacteria. The results will inform future cultivation efforts and provide a more comprehensive assessment of the organisms targeted by native chemical defenses. Finally, a robust feeding assay using two model protists will be developed and used to test the roles of bacterial secondary metabolites as invertebrate feeding deterrents. In situ experiments will provide insight into the natural assemblage of invertebrates affected by these defenses. The overall results of these studies have the potential to profoundly impact our understanding of the ecological functions of microbial secondary metabolites and the extent to which these compounds affect community composition.</p>
CEMSB
largerWorkCitation
project
eng; USA
biota
oceans
Mexico, Yucatan Carribean
2016-01-19
The Mexican Yucatan, Fiji (South coast of Viti Levu), Belize (Smithsonian Field station, Carrie Bow Cay)
0
BCO-DMO catalogue of parameters from Microbial culture collection, strain IDs, locations and depths R/V F.G. Walton Smith (WS1209) cruise in the Yucatan Carribean and Mexico during 2012 (CEMSB 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/633167.rdf
Name: sample
Units: unitless
Description: <p>sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/633168.rdf
Name: species_strain
Units: unitless
Description: <p>species and strain</p>
http://lod.bco-dmo.org/id/dataset-parameter/633169.rdf
Name: GenBank_accession
Units: unitless
Description: <p>GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/633170.rdf
Name: BLAST_pcent
Units: percent
Description: <p>BLAST result</p>
http://lod.bco-dmo.org/id/dataset-parameter/633171.rdf
Name: seq_avail_flag
Units: unitless
Description: <p>genome sequence available</p>
http://lod.bco-dmo.org/id/dataset-parameter/633172.rdf
Name: study_2_flag
Units: unitless
Description: <p>flag denoting strains used in secondary assays to determine the temporal onset of antagonism</p>
http://lod.bco-dmo.org/id/dataset-parameter/633173.rdf
Name: site
Units: unitless
Description: <p>collection site</p>
http://lod.bco-dmo.org/id/dataset-parameter/633174.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/633175.rdf
Name: lon
Units: decimal degrees
Description: <p>lonitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/633176.rdf
Name: year
Units: yyyy
Description: <p>year of Isolation</p>
http://lod.bco-dmo.org/id/dataset-parameter/633177.rdf
Name: depth
Units: meters
Description: <p>collection depth</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
25483
https://datadocs.bco-dmo.org/file/VJJWD1LsXWKGvA/WS1209_strains_16S.csv
WS1209_strains_16S.csv
Primary data file for dataset ID 632875
download
https://osprey.bco-dmo.org/dataset/632875/data/download
download
onLine
dataset
<p><a href="http://dmoserv3.bco-dmo.org/data_docs/CEMSB/WS1209_strains_methods.pdf" target="_blank">Methodolody</a> (pdf)</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong></p>
<p>- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- added hyperlinks to GenBank accessions<br />
- changed '&lt;1' to 'lt_1'<br />
- split collection year and location into 2 columns, adding 'nd' in empty cells<br />
- replaced empty cells with 'nd' (no data)<br />
- replaced blanks with underscores</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
PI Supplied Instrument Name: Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Cruise: WS1209
WS1209
R/V F.G. Walton Smith
Community Standard Description
International Council for the Exploration of the Sea
R/V F.G. Walton Smith
vessel
WS1209
Joseph Pawlik
University of North Carolina - Wilmington
R/V F.G. Walton Smith
Community Standard Description
International Council for the Exploration of the Sea
R/V F.G. Walton Smith
vessel