http://lod.bco-dmo.org/id/dataset/654170
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
2016-08-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Roseobacter isolate Sulfitobacter sp. CB2047 and three of its infecting phage accessions at NCBI GenBank
2016-09-06
publication
2016-09-06
revision
BCO-DMO Linked Data URI
2016-09-06
creation
http://lod.bco-dmo.org/id/dataset/654170
Alison Buchan
University of Tennessee Knoxville
principalInvestigator
Shawn R. Campagna
University of Tennessee Knoxville
principalInvestigator
Steven W. Wilhelm
University of Tennessee Knoxville
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: Buchan, A., Campagna, S. R., Wilhelm, S. W. (2016) Roseobacter isolate Sulfitobacter sp. CB2047 and three of its infecting phage accessions at NCBI GenBank. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-09-06 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/654170 [access date]
Sulfitobacter phage accessions Dataset Description: <p><strong>Related Reference:</strong> Ankrah, N. Y. D., A. L. May, J. L., Middleton, D. R. Jones, M. Hadden, J. R. Gooding, G. R. LeCleir, S. W. Wilhelm, S. R. Campagna and A. Buchan. (2014 Phage infection of an environmentally relevant marine bacterium alters host metabolism and lysate composition. International Society for Microbial Ecology Journal (2014) 8, 1089-1100; doi:10.1038/ismej.2013.216; published online 5 December 2013</p>
<p>See also, <a href="http://dmoserv3.bco-dmo.org/data_docs/Roseophage_Model/Ankrah_Supplemental_Buchan.pdf" target="_blank">Supplemental Material (PDF)</a></p> Methods and Sampling: <p>Phage DNA was submitted to the Broad Institute and sequenced under the Gordon and Betty Moore Foundation’s Marine Phage, Virus, and Virome Sequencing Project. The Broad Institute sequencing data were assembled using the Lasergene SeqMan Pro. The assemblies resulted in the generation of single contigs for each phage genome.</p>
<p>The genome of Sulfitobacter sp. strain CB2047was sequenced using Illumina technology with an average sequencing coverage of approximately 600 x. The genome was assembled into 12 contigs, ranging in size from 18 kb to 2.3 Mb, using CLC Assembly Cell (CLC bio, Cambridge, MA, USA). The genome of CB2047 was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm .nih.gov/genome/annotation_prok/) and the KAAS genome annotation and pathway reconstruction server.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1061352 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1061352
completed
Alison Buchan
University of Tennessee Knoxville
865-974-5234
Department of Microbiology M409 WLS
Knoxville
TN
37996
USA
abuchan@utk.edu
pointOfContact
Shawn R. Campagna
University of Tennessee Knoxville
865-974-7337
Dept of Chemistry 618 Buehler Hall
Knoxville
TN
37996
USA
campagna@utk.edu
pointOfContact
Steven W. Wilhelm
University of Tennessee Knoxville
865-974-0665
1499 Circle Dr Room 637
Knoxville
TN
37996
USA
wilhelm@utk.edu
pointOfContact
asNeeded
Unknown
taxon
strain
description
date
lat
lon
accession_NCBI
comment
theme
None, User defined
taxon
sample description
date
latitude
longitude
accession number
comments
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Buchan_lab
service
Deployment Activity
University of Tennesee - Knoxville
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.
Biogeochemical implications of marine phage: Roseophage as a relevant and tractable model
https://osprey.bco-dmo.org/project/554427
Biogeochemical implications of marine phage: Roseophage as a relevant and tractable model
<p><em>Description from NSF award abstract:</em><br />
Prokaryotic viruses (phage) have long been hypothesized to influence microbial community composition, nutrient biogeochemistry and both the flux and character of carbon in the world's oceans. Model estimates indicate that > 25% of the daily carbon production in marine surface waters is shunted to the dissolved organic matter (DOM) pool by viral activity. Through this process viruses redistribute nutrient elements from large biological particles (i.e., bacteria, algae) into biologically inactive (dead) particulate and dissolved pools of organic compounds. Many of these compounds contain macro- and micronutrients (e.g., P, N, Fe) that can be rapidly recycled back into the food web. While we now have a better (yet far from complete) appreciation of the role of viruses in the regeneration of nutrient elements, we remain almost completely ignorant to, and have almost no data for, the role of viruses in the regeneration of organic carbon, the subsequent partitioning of this carbon by size (e.g. dissolved vs particulate) and bioavailability (labile vs recalcitrant). Understanding the contribution of virus activity to the various carbon pools and the rates associated with this process is an absolute necessity if we are to develop accurate marine and global carbon models.</p>
<p>There is little doubt that the global-scale influence of viruses is determined by host-phage interactions, yet our understanding of these interactions and their quantitative effects on system processes is in its infancy. To address these questions, it is imperative that we examine ecologically relevant model systems. To that end, this project focuses on phage that infect the Roseobacter clade, a numerically abundant and biogeochemically active group of heterotrophic marine bacteria. Despite the recognized importance of lineage members to the global cycling of elements (particularly carbon), we know little of the viruses ("roseophage") that infect them, the influence viruses have on host processes and the effects of this interaction on other members of the marine microbial community. As such this project is transformative in that it will exploit recently characterized virus-host models for biogeochemical and molecular studies of a major heterotrophic bacterioplankton lineage that is truly ecologically relevant.</p>
<p>The overall objectives of the project are to: (i) examine the distribution, diversity and production of roseophage, (ii) assess the composition and bioavailability of Roseobacter cell lysis-derived DOM and (iii) to track the subsequent uptake and metabolism of Roseobacter-derived carbon and nitrogen by marine surface water microbial communities. These objectives will be achieved through a combination of lab and field-based experiments: molecular tools will be developed to quantify specific rates of roseophage production and Roseobacter mortality under three different environmental regimes (a naturally productive open ocean regime, a near shore to off-shore gradient and induced phytoplankton blooms from mesocosms). The PIs will specifically determine the character and biological availability of carbon from lysates of Roseobacter in lab trials with model microbes. They will examine the rates of assimilation of radiolabeled Roseobacter lysate by natural communities which, when coupled with data on the composition, bioavailability and fate of the DOM released, will form the baseline for a model of Roseobacter-phage C-cycling through the microbial foodweb. Finally, complementary metabolomics studies of lysate consuming populations (in the lab and field) will provide unprecedented insight into how microbes perceive and process viral-lysed material. Collectively, these data will provide critical information on the interplay of phage with a major marine bacterial lineage and the ensuing influence these interactions have on microbial food webs.</p>
Roseophage as a Model
largerWorkCitation
project
eng; USA
biota
oceans
University of Tennesee - Knoxville
2016-09-06
0
BCO-DMO catalogue of parameters from Roseobacter isolate Sulfitobacter sp. CB2047 and three of its infecting phage accessions at NCBI GenBank
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/658260.rdf
Name: taxon
Units: unitless
Description: <p>taxonomic name of sequenced organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/658261.rdf
Name: strain
Units: unitless
Description: <p>bacterial strain</p>
http://lod.bco-dmo.org/id/dataset-parameter/658262.rdf
Name: description
Units: unitless
Description: <p>type of genetic information</p>
http://lod.bco-dmo.org/id/dataset-parameter/658263.rdf
Name: date
Units: year-month-day
Description: <p>collection date</p>
http://lod.bco-dmo.org/id/dataset-parameter/658264.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/658265.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/658266.rdf
Name: accession_NCBI
Units: unitless
Description: <p>Linked NCBI GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/658267.rdf
Name: comment
Units: unitless
Description: <p>comments</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
758
https://datadocs.bco-dmo.org/file/nGGlAnBTXqokg/Sulfitobacter_accessions.csv
Sulfitobacter_accessions.csv
Primary data file for dataset ID 654170
download
https://osprey.bco-dmo.org/dataset/654170/data/download
download
onLine
dataset
<p>Phage DNA was submitted to the Broad Institute and sequenced under the Gordon and Betty Moore Foundation’s Marine Phage, Virus, and Virome Sequencing Project. The Broad Institute sequencing data were assembled using the Lasergene SeqMan Pro. The assemblies resulted in the generation of single contigs for each phage genome.</p>
<p>The genome of Sulfitobacter sp. strain CB2047was sequenced using Illumina technology with an average sequencing coverage of approximately 600 x. The genome was assembled into 12 contigs, ranging in size from 18 kb to 2.3 Mb, using CLC Assembly Cell (CLC bio, Cambridge, MA, USA). The genome of CB2047 was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (http://www.ncbi.nlm .nih.gov/genome/annotation_prok/) and the KAAS genome annotation and pathway reconstruction server.&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- created a BCO-DMO servable table of accessions and associated metadata obtained from the GenBank source information.</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: PI Supplied Instrument Description:Illumina HiSeq2000 at Center for Pediatric Genome Medicine Children's Mercy Hospitals and Clinics in Kansas City, MO. 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: PI Supplied Instrument Description:DNA Engine Thermo cycler (PTC-200) 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)
Deployment: Buchan_lab
Buchan_lab
UTenn
laboratory
Buchan_lab
Alison Buchan
University of Tennessee Knoxville
UTenn
laboratory