PROJECT INFORMATION | |
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GOLD Project ID
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Gp0316967
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Project Name
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Carboxydocella thermautotrophica 041
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Other Names
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Legacy GOLD ID
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NCBI BioProject Name | Carboxydocella thermautotrophica 041 genome sequencing |
NCBI BioProject Accession
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PRJEB11520 |
NCBI Locus Tag
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CTH
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NCBI BioSample Accession
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SAMN07757920 |
PI | |
Added By |
JGI automated process
on 2018-05-24 |
Last Modified By |
JGI automated process
on 2018-05-25 |
Project Comments |
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Project Status
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Complete and Published
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Project Relevance
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Sequencing Center
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Baltic Federal University
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Collaborating Institute
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Funding Agency
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Project Description
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Genus Carboxydocella forms a deeply branching family Incertae Sedis XVI in the class Clostridia and is represented by.three species capable of different modes of anaerobic metabolism, autotrophic or organotrophic. The type strain of the type species, Carboxydocella thermautotrophica, was first described as an obligate chemolithoautotroph growing exclusively by hydrogenogenic CO-oxidation. Here we describe a novel strain of C. thermautotrophica designated 019 isolated form a core sample taken at a thermal field at Uzon Caldera, Kamchatka. Metabolism of new isolate is much more versatile, together with the ability to hydrogengenic CO oxidation sharing some features with other Сarboxydocella species, e.g., the ability to organotrophic growth, acetogenesis, nitrate and Fe(III) reduction, the capacities absent in the type strain of this species. Ferric iron-containing silicate minerals glauconite and diatomite could also be used as the electron acceptors for strain 019, Fe being reduced to Fe(II) in the form of siderite. To give insights into these important metabolic features of C. thermautotrtophica, genomes of both strains of the species were sequenced using Illumina and PGM technologies. Genome analysis revealed both strains to possess gene clusters encoding an energy-converting hydrogenase and a CO-dehydrogenase (CODH), similar to those previously described in thermophilic hydrogenogenic carboxydothrophs. Six different CODH-encoding genes (maximum among known prokaryotic genomes) have been identified in each strain suggesting crucial role of CO for the metabolism of this organism. Also, a set of ca. 40 multiheme c-type cytochromes highly similar in both genomes has been identified, while only one 17-heme cytochrome gene exclusively appeared in the Fe(III)-reducing strain 019. This gene is proposed to represent a novel type of determinants of dissimilatory Fe(III) reduction in prokaryotes. Our results represent the first genome analysis of the deep phylogenetic branch Clostridia Incertae Sedis XVI family and gives insights into metabolic diversity of Carboxydocella thermautotrophica with special emphasis on its energy metabolism which might have significant ecological implications in hot terrestrial sedimentary habitats.
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Is JGI Project |
No
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Project Information Visibility
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Public |
PROJECT TYPE | |
Specimen
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Organism |
Nucleic Acid
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DNA |
Sequencing Strategy
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Whole Genome Sequencing
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EXTERNAL PROJECT LINKS | |
JGI Data Utilization Status
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JGI Award DOI
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Genome Publications
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Other Publications
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Ignored Publications
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Unassigned Publications
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International Journal of Systematic and Evolutionary Microbiology
52(Pt 6):1961-7
Carboxydocella thermautotrophica gen. nov., sp. nov., a novel anaerobic, CO-utilizing thermophile from a Kamchatkan hot spring.
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SRA Experiment |
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PROJECT COMPOSITION | |
Study |
Carboxydocella thermautotrophica 041 genome sequencing |
Organism |
Carboxydocella thermautotrophica 041 |
Analysis Projects |
Carboxydocella thermautotrophica 041 |
Number of Analysis Projects (AP) |
1 |
Number of Derived Analyis Projects (DAP) |
0
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SEQUENCING INFORMATION | |
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Sequencing Status
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Complete |
Sequencing Quality (MIGS-31) |
Level 6: Finished |
Finishing Goal
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Contamination Screening Input
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DNA Amplification Method
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Single Cell Lysis Protocol
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Single Cell Lysis Approach
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Sequencing Comments
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DNA Amplification Kit
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Sequencing Technology
(MIGS-29)
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Illumina MiSeq |
Library Method
(MIGS-28)
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Library Layout
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Library Screening Method
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Number Of Reads
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Read Size
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Vector
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GC Percent |
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Chromosome Count |
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Plasmid Count |
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ORGANISM NAME | |
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GOLD Organism ID |
Go0452546 |
Organism Name |
Carboxydocella thermautotrophica 041
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Other names (alias, synonyms, short names, common names) |
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Organism Domain |
BACTERIAL
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Phylogeny |
FIRMICUTES
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Genus |
Carboxydocella
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Genus Synonyms |
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Species |
Carboxydocella thermautotrophica
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Subspecies |
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Species Synonyms |
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Strain |
041
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Strain Synonyms |
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Serovar/Cultivar |
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Culture Collection ID |
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Type Strain |
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Exemplar DOI |
10.1601/ex.4486
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Exemplar Name |
Carboxydocella thermautotrophica
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Taxon DOI |
10.1601/tx.4486
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Biosafety Level |
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Organism Comments |
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Cultured |
Yes
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Culture Type |
Isolate
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Organism Type |
Natural
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Uncultured Type |
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Commercial Strain |
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Commercial Strain Comments |
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ORGANISM TAXONOMY
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NCBI Taxonomy ID |
178899 |
NCBI Superkingdom |
Bacteria
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NCBI Kingdom |
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NCBI Phylum |
Firmicutes
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NCBI Class |
Clostridia
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NCBI Order |
Eubacteriales
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NCBI Family |
Clostridiales Family XVI. Incertae Sedis
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NCBI Genus |
Carboxydocella
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NCBI Species |
Carboxydocella thermautotrophica
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ISOLATION CLASSIFICATION | |
Ecosystem |
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Ecosystem Category |
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Ecosystem Type |
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Ecosystem Subtype |
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Specific Ecosystem |
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ORGANISM EXTERNAL REFERENCES | |
Strain Info ID |
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Genbank 16S ID |
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GENERAL PROPERTIES | |
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Oxygen Requirement |
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Cell Shape |
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Motility |
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Sporulation |
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Temperature Range |
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Salinity |
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pH |
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Cell Diameter |
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Cell Length |
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Color |
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Gram Staining |
Gram+
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Biotic Relationships |
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Symbiotic Physical Interaction |
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Symbiotic Relationship |
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Symbiont Name |
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Symbiont Taxon ID |
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Cell Arrangements |
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Diseases |
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Known Habitats |
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Metabolisms |
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Phenotypes |
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Energy Sources |
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