http://lod.bco-dmo.org/id/dataset/628767
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
2015-12-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
The complete genome sequence of Candidatus Thioglobus singularis strain PS1, the first cultured mixotrophic representative from the SUP05 clade.
2015-12-08
publication
2015-12-08
revision
BCO-DMO Linked Data URI
2015-12-08
creation
http://lod.bco-dmo.org/id/dataset/628767
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) The complete genome sequence of Candidatus Thioglobus singularis strain PS1, the first cultured mixotrophic representative from the SUP05 clade. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version final) Version Date 2015-12-08 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/628767 [access date]
Complete genome sequence - first cultured mixotroph from SUP05 clade Dataset Description: <p>The complete genome sequence of <em>Candidatus</em>&nbsp;Thioglobus singularis strain PS1, the first cultured mixotrophic representative from the SUP05 clade.</p>
<p>See <a href="http://dmoserv3.bco-dmo.org/data_docs/SulfurOxidizers/Genome_Announc_2015_Marshall.pdf">Announcement</a>.</p>
<p><strong>N.B.: </strong>In bacterial nomenclature, <em><strong>Candidatus</strong></em>&nbsp; is a component of the taxonomic name for a bacterium that cannot be maintained in a bacteriology culture collection.&nbsp; Candidatus status may be used when a species or genus is well characterized but yet-uncultured. (Murray and Schleifer, 1994)&nbsp;&nbsp; With today's technology much information is obtained by 16S ribosomal RNA or even near-complete genomes with modern metagenomics techniques. [<span style="font-size:10px">paraphrased from Wikipedia</span>]</p> Methods and Sampling: <p>Cultures of <em>T. singularis</em> were grown in one-liter polycarbonate bottles of filter sterilized seawater media as&nbsp; described in&nbsp;<a href="http://dmoserv3.bco-dmo.org/data_docs/SulfurOxidizers/Marshall_2012_Tsingular.pdf" target="_blank">Marshall and Morris, 2012</a>. . Cells were then filtered onto sterile 0.2 µm polyethersulfone filters (Pall, Port Washington, NY), placed in 15 mL Teflon tubes containing 2 ml of sucrose lysis buffer (SLB), and flash frozen in liquid nitrogen. Cells were later lysed by adding 100 µL of 1mg/mL lysozyme and incubating at 4 °C for 60 minutes, then by adding 465 µL of 10% SDS and 250 µL of proteinase K and incubating at 55 °C for 2 hours. DNA was extracted and purified from cell lysates using DNeasy Blood and Tissue and Minelute kits according the manufacturers instructions, respectively (QIAGEN, Germantown, MD). A total of 20.35 µg of DNA was used to construct a mate pair library according to the SOLiD™v3.0 mate-pair protocol (Life Technologies, Foster City, CA).</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
entry
GenBank_accession
lat
lon
depth
month
year
description
theme
None, User defined
sample identification
accession number
latitude
longitude
depth
month_local
year
brief description
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
oceans
North Pacific
-122.404
-122.402
47.687
47.687
2009-11-10
2009-11-10
North Pacific Ocean
0
BCO-DMO catalogue of parameters from The complete genome sequence of Candidatus Thioglobus singularis strain PS1, the first cultured mixotrophic representative from the SUP05 clade.
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/628830.rdf
Name: entry
Units: text
Description: <p>name of bacteria</p>
http://lod.bco-dmo.org/id/dataset-parameter/628831.rdf
Name: GenBank_accession
Units: link
Description: <p>link to NCBI GenBank</p>
http://lod.bco-dmo.org/id/dataset-parameter/628832.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/628833.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude; West is negative</p>
http://lod.bco-dmo.org/id/dataset-parameter/628834.rdf
Name: depth
Units: meters
Description: <p>Sampling depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/628835.rdf
Name: month
Units: text
Description: <p>month sampling took place</p>
http://lod.bco-dmo.org/id/dataset-parameter/628836.rdf
Name: year
Units: number
Description: <p>year sampling took place</p>
http://lod.bco-dmo.org/id/dataset-parameter/628837.rdf
Name: description
Units: text
Description: <p>name of GenBank file with complete genome</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
366
https://datadocs.bco-dmo.org/file/P66GwREUpZDyO/T_singularis_PS1.csv
T_singularis_PS1.csv
Primary data file for dataset ID 628767
download
https://osprey.bco-dmo.org/dataset/628767/data/download
download
onLine
dataset
<p>Cultures of <em>T. singularis</em> were grown in one-liter polycarbonate bottles of filter sterilized seawater media as&nbsp; described in&nbsp;<a href="http://dmoserv3.bco-dmo.org/data_docs/SulfurOxidizers/Marshall_2012_Tsingular.pdf" target="_blank">Marshall and Morris, 2012</a>. . Cells were then filtered onto sterile 0.2 µm polyethersulfone filters (Pall, Port Washington, NY), placed in 15 mL Teflon tubes containing 2 ml of sucrose lysis buffer (SLB), and flash frozen in liquid nitrogen. Cells were later lysed by adding 100 µL of 1mg/mL lysozyme and incubating at 4 °C for 60 minutes, then by adding 465 µL of 10% SDS and 250 µL of proteinase K and incubating at 55 °C for 2 hours. DNA was extracted and purified from cell lysates using DNeasy Blood and Tissue and Minelute kits according the manufacturers instructions, respectively (QIAGEN, Germantown, MD). A total of 20.35 µg of DNA was used to construct a mate pair library according to the SOLiD™v3.0 mate-pair protocol (Life Technologies, Foster City, CA).</p>
Specified by the Principal Investigator(s)
<p>The <em>T. singularis</em> genome was assembled using SEAStAR v. 0.4.17 as described in Iverson et al (2012). The initial assembly was 97% complete and contained 177 gaps with a mean gap length of 198 bp. Gaps were closed by PCR with custom primers designed using Geneious 7.0.4 (Biomatters, Auckland, NZ). Amplification products were visualized, gel purified, and sequenced by Genewiz (Foster City, CA). The complete genome sequence (1,714,148bp) was confirmed by performing additional PCR reactions to resolve any irregularities in the assembly and by comparing read coverage, physical coverage and insert sizes of mate pairs covering the genome. Annotations were performed using the NCBI Prokaryotic Genome Automatic Annotation Pipeline and were checked against RAST annotations, IMG annotations , and in some cases by phylogenetic analyses. Discrepancies were corrected and final annotations were submitted to NCBI.</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