taxonomic group or entity. This may be a family, class, genus, species, etc.; usually this parameter will contain a mixture of taxonomic entities.
URL | https://www.bco-dmo.org/dataset/809272 |
---|---|
Download URL | https://www.bco-dmo.org/dataset/809272/data/download |
Media Type | text/tab-separated-values |
Created | April 13, 2020 |
Modified | July 8, 2020 |
State | Final no updates expected |
Brief Description | Thermovibrio ammonificans HB1 genome manual curation |
Processing Description
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.
Plots generated using this dataset can be found at:
http://genomevolution.org/r/9vb3
http://genomevolution.org/r/9vb4
http://genomevolution.org/r/9vb8
Parameters
taxonomic group or entity. This may be a family, class, genus, species, etc.; usually this parameter will contain a mixture of taxonomic entities.
Dataset Maintainers
Name | Affiliation | Contact |
---|---|---|
Donato Giovannelli | Rutgers University | ✓ |
Shannon Rauch | Rutgers University | ✓ |
BCO-DMO Project Info
Project Title | Alternative carbon fixation strategies in the model organism Thermovibrio ammonificans: A model system to study energy limitation in the deep biosphere |
---|---|
Acronym | Deep Biosphere Energy Limitation |
URL | https://www.bco-dmo.org/project/654078 |
Created | August 15, 2016 |
Modified | April 13, 2020 |
Project Description
Project Abstract from C-DEBI:
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.
C-DEBI Project Page: 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/
Data Project Maintainers
Name | Affiliation | Role |
---|---|---|
Donato Giovannelli | Rutgers University (Rutgers IMCS) | Lead Principal Investigator |