http://lod.bco-dmo.org/id/dataset/809272
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
2020-04-13
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Thermovibrio ammonificans HB1 genome manual curation
2020-04-13
publication
2020-04-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-03-18
publication
https://doi.org/10.26008/1912/bco-dmo.809272.1
Donato Giovannelli
Rutgers University
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: Giovannelli, D. (2022) Thermovibrio ammonificans HB1 genome manual curation. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-04-13 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.809272.1 [access date]
Thermovibrio ammonificans HB1 genome manual curation Dataset Description: <p>Thermovibrio ammonificans HB1 genome manual curation. Methods are further described in&nbsp;Giovannelli et al. (2012).</p> Methods and Sampling:
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0939564 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0939564
completed
Donato Giovannelli
Rutgers University
+39 081 679056
Department of Biology, University of Naples Federico II, Monte Sant'Angelo Edificio 7, Stanza 1D-22
Napoli
80126
Italy
donato.giovannelli@unina.it
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Organism
Chromosome
Contig
Gene
Strand
Start
Stop
Called_By
Product
Product_From
Color
Accession
Organism_Name
Positivities
Identities
NR
SPTR
PFAM
TIGRFAM
KEGG
COGs
theme
None, User defined
taxon
No BCO-DMO term
accession number
featureType
BCO-DMO Standard Parameters
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.
Center for Dark Energy Biosphere Investigations
http://www.darkenergybiosphere.org
Center for Dark Energy Biosphere Investigations
The mission of the Center for Dark Energy Biosphere Investigations (C-DEBI) is to explore life beneath the seafloor and make transformative discoveries that advance science, benefit society, and inspire people of all ages and origins.
C-DEBI provides a framework for a large, multi-disciplinary group of scientists to pursue fundamental questions about life deep in the sub-surface environment of Earth. The fundamental science questions of C-DEBI involve exploration and discovery, uncovering the processes that constrain the sub-surface biosphere below the oceans, and implications to the Earth system. What type of life exists in this deep biosphere, how much, and how is it distributed and dispersed? What are the physical-chemical conditions that promote or limit life? What are the important oxidation-reduction processes and are they unique or important to humankind? How does this biosphere influence global energy and material cycles, particularly the carbon cycle? Finally, can we discern how such life evolved in geological settings beneath the ocean floor, and how this might relate to ideas about the origin of life on our planet?
C-DEBI's scientific goals are pursued with a combination of approaches:
(1) coordinate, integrate, support, and extend the research associated with four major programs—Juan de Fuca Ridge flank (JdF), South Pacific Gyre (SPG), North Pond (NP), and Dorado Outcrop (DO)—and other field sites;
(2) make substantial investments of resources to support field, laboratory, analytical, and modeling studies of the deep subseafloor ecosystems;
(3) facilitate and encourage synthesis and thematic understanding of submarine microbiological processes, through funding of scientific and technical activities, coordination and hosting of meetings and workshops, and support of (mostly junior) researchers and graduate students; and
(4) entrain, educate, inspire, and mentor an interdisciplinary community of researchers and educators, with an emphasis on undergraduate and graduate students and early-career scientists.
Note: Katrina Edwards was a former PI of C-DEBI; James Cowen is a former co-PI.
Data Management:
C-DEBI is committed to ensuring all the data generated are publically available and deposited in a data repository for long-term storage as stated in their Data Management Plan (PDF) and in compliance with the NSF Ocean Sciences Sample and Data Policy. The data types and products resulting from C-DEBI-supported research include a wide variety of geophysical, geological, geochemical, and biological information, in addition to education and outreach materials, technical documents, and samples. All data and information generated by C-DEBI-supported research projects are required to be made publically available either following publication of research results or within two (2) years of data generation.
To ensure preservation and dissemination of the diverse data-types generated, C-DEBI researchers are working with BCO-DMO Data Managers make data publicly available online. The partnership with BCO-DMO helps ensure that the C-DEBI data are discoverable and available for reuse. Some C-DEBI data is better served by specialized repositories (NCBI's GenBank for sequence data, for example) and, in those cases, BCO-DMO provides dataset documentation (metadata) that includes links to those external repositories.
C-DEBI
largerWorkCitation
program
Alternative carbon fixation strategies in the model organism Thermovibrio ammonificans: A model system to study energy limitation in the deep biosphere
https://osprey.bco-dmo.org/project/654078
Alternative carbon fixation strategies in the model organism Thermovibrio ammonificans: A model system to study energy limitation in the deep biosphere
<p><em>Project Abstract from C-DEBI:</em><br />
Despite being the largest ecosystem on earth, the deep biosphere is considered to be energy limited. Chemoautotrophy is an important source of organic carbon in the deep biosphere, and significantly contributes to the deep carbon cycle. We investigated the carbon fixation strategies in the model organism Themovibrio ammonificans in relationship to the presence of different terminal electron acceptor. T. ammonicans uses the reverse Tricarboxylic Acid cycle (rTCA) as carbon fixation pathways, however our comparative genomic analysis reveals the presence of an incomplete Wood-Ljungdahl (WL) pathway. Carbon isotopic fractionation value support the rTCA cycle as carbon fixation pathway, however a difference in carbon fractionation is present when growing T. ammonificans with sulfur instead of nitrate as terminal electron acceptor. Transcriptomic analysis showed that the putative carbon monoxide dehydrogenase (type V) is expressed under both conditions. We also identified a putative oxidoreductase involved in the respiration of elemental sulfur, and propose a new pathway of sulfur reduction. The presence of incomplete yet functional alternative pathways of carbon fixation in subsurface organisms may be more widespread that previously thought, and may provide an evolutionary advantage in surviving under energy limiting conditions.</p>
<p>C-DEBI Project Page:<a href="http://https://www.darkenergybiosphere.org/award/alternative-carbon-fixation-strategies-in-the-model-organism-thermovibrio-ammonificans-a-model-system-to-study-energy-limitation-in-the-deep-biosphere/" target="_blank"> </a><a href="https://www.darkenergybiosphere.org/award/alternative-carbon-fixation-strategies-in-the-model-organism-thermovibrio-ammonificans-a-model-system-to-study-energy-limitation-in-the-deep-biosphere/">https://www.darkenergybiosphere.org/award/alternative-carbon-fixation-strategies-in-the-model-organism-thermovibrio-ammonificans-a-model-system-to-study-energy-limitation-in-the-deep-biosphere/</a></p>
Deep Biosphere Energy Limitation
largerWorkCitation
project
eng; USA
oceans
2020-04-13
Deep Biosphere
0
BCO-DMO catalogue of parameters from Thermovibrio ammonificans HB1 genome manual curation
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/809276.rdf
Name: Organism
Units: unitless
Description: <p>taxid of the organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/809277.rdf
Name: Chromosome
Units: unitless
Description: <p>chromosome where the gene is located</p>
http://lod.bco-dmo.org/id/dataset-parameter/809278.rdf
Name: Contig
Units: unitless
Description: <p>chromosome where the gene is located</p>
http://lod.bco-dmo.org/id/dataset-parameter/809279.rdf
Name: Gene
Units: unitless
Description: <p>locus name for the gene</p>
http://lod.bco-dmo.org/id/dataset-parameter/809280.rdf
Name: Strand
Units: unitless
Description: <p>DNA strand where the gene is</p>
http://lod.bco-dmo.org/id/dataset-parameter/809281.rdf
Name: Start
Units: unitless
Description: <p>start position in base pairs</p>
http://lod.bco-dmo.org/id/dataset-parameter/809282.rdf
Name: Stop
Units: unitless
Description: <p>stop position in base pairs</p>
http://lod.bco-dmo.org/id/dataset-parameter/809283.rdf
Name: Called_By
Units: unitless
Description: <p>gene prediction by</p>
http://lod.bco-dmo.org/id/dataset-parameter/809284.rdf
Name: Product
Units: unitless
Description: <p>gene function name</p>
http://lod.bco-dmo.org/id/dataset-parameter/809285.rdf
Name: Product_From
Units: unitless
Description: <p>product called by which database</p>
http://lod.bco-dmo.org/id/dataset-parameter/809286.rdf
Name: Color
Units: unitless
Description: <p>product called by which database</p>
http://lod.bco-dmo.org/id/dataset-parameter/809287.rdf
Name: Accession
Units: unitless
Description: <p>accession number of the match from blastp</p>
http://lod.bco-dmo.org/id/dataset-parameter/809288.rdf
Name: Organism_Name
Units: unitless
Description: <p>name of the organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/809289.rdf
Name: Positivities
Units: unitless
Description: <p>% of positivities in the sequence alignment</p>
http://lod.bco-dmo.org/id/dataset-parameter/809290.rdf
Name: Identities
Units: unitless
Description: <p>% of identities in the sequence alignment</p>
http://lod.bco-dmo.org/id/dataset-parameter/809291.rdf
Name: NR
Units: unitless
Description: <p>function assigned by NCBI NR database</p>
http://lod.bco-dmo.org/id/dataset-parameter/809292.rdf
Name: SPTR
Units: unitless
Description: <p>function assigned by SPTR</p>
http://lod.bco-dmo.org/id/dataset-parameter/809293.rdf
Name: PFAM
Units: unitless
Description: <p>function assigned by PFAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/809294.rdf
Name: TIGRFAM
Units: unitless
Description: <p>function assigned by TIGRFAM</p>
http://lod.bco-dmo.org/id/dataset-parameter/809295.rdf
Name: KEGG
Units: unitless
Description: <p>function assigned by KEGG</p>
http://lod.bco-dmo.org/id/dataset-parameter/809296.rdf
Name: COGs
Units: unitless
Description: <p>COG function assigned</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
853143
https://darchive.mblwhoilibrary.org/bitstream/1912/28212/1/dataset-809272_tam-genome-analysis__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.809272.1
download
onLine
dataset
<p>Manual curation of the genome was performed using blastn and blastp against the non-redundant database, the conserved domain database, the Kyoto Encyclopedia of Genes and Genomes, and the PFAM database. Coding sequence similarities were compared using translated protein sequence. Metabolic pathways were reconstructed on the basis of available genomic, physiologic, and biochemical information and using Kyoto Encyclopedia of Genes and Genomes and SEED pathways as template.</p>
<p>Plots generated using this dataset can be found at:<br />
<a href="http://genomevolution.org/r/9vb3" target="_blank">http://genomevolution.org/r/9vb3</a><br />
<a href="http://genomevolution.org/r/9vb4" target="_blank">http://genomevolution.org/r/9vb4</a><br />
<a href="http://genomevolution.org/r/9vb8" target="_blank">http://genomevolution.org/r/9vb8</a></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