Strain identifier
BacDive ID: 17017
Type strain: 
Species: Thermoplasma acidophilum
Strain Designation: 122-1B2
Strain history: IFO 15155 <-- T. Itoh <-- ATCC 25905 <-- R. G. Wittler <-- T. D. Brock <-- G. Darland 122-1B2.
NCBI tax ID(s): 273075 (strain), 2303 (species)
version 8.1 (current version)
General
@ref: 884
BacDive-ID: 17017
DSM-Number: 1728
keywords: genome sequence, 16S sequence, Archaea, anaerobe, thermophilic, Gram-negative
description: Thermoplasma acidophilum 122-1B2 is an anaerobe, thermophilic, Gram-negative archaeon that was isolated from coal refuse pile.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 273075 | strain |
| 2303 | species |
strain history
| @ref | history |
|---|---|
| 884 | <- W. Zillig <- E.A. Freundt, AMRC, C165 <- ATCC <- R.G. Wittler, 122-1B2 <- T.D. Brock <- G. Darland |
| 67770 | IFO 15155 <-- T. Itoh <-- ATCC 25905 <-- R. G. Wittler <-- T. D. Brock <-- G. Darland 122-1B2. |
doi: 10.13145/bacdive17017.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/archaea
- keyword: phylum/methanobacteriota
- domain: Archaea
- phylum: Methanobacteriota
- class: Thermoplasmata
- order: Thermoplasmatales
- family: Thermoplasmataceae
- genus: Thermoplasma
- species: Thermoplasma acidophilum
- full scientific name: Thermoplasma acidophilum corrig. Darland et al. 1970 (Approved Lists 1980)
synonyms
- @ref: 20215
- synonym: Thermoplasma acidophila
@ref: 884
domain: Archaea
phylum: Euryarchaeota
class: Thermoplasmata
order: Thermoplasmatales
family: Thermoplasmataceae
genus: Thermoplasma
species: Thermoplasma acidophilum
full scientific name: Thermoplasma acidophilum Darland et al. 1970
strain designation: 122-1B2
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.993
Culture and growth conditions
culture medium
- @ref: 884
- name: THERMOPLASMA ACIDOPHILUM MEDIUM (DSMZ Medium 158)
- growth: yes
- link: https://mediadive.dsmz.de/medium/158
- composition: Name: THERMOPLASMA ACIDOPHILUM MEDIUM (DSMZ Medium 158) Composition: Glucose 20.0 g/l Yeast extract 2.0 g/l (NH4)2SO4 1.32 g/l KH2PO4 0.372 g/l MgSO4 x 7 H2O 0.247 g/l CaCl2 x 2 H2O 0.074 g/l FeCl3 x 6 H2O 0.0193 g/l Na2B4O7 x 10 H2O 0.0045 g/l MnCl2 x 4 H2O 0.0018 g/l ZnSO4 x 7 H2O 0.00022 g/l CuCl2 x 2 H2O 5e-05 g/l VOSO4 x 5 H2O 3.8e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l CoSO4 x 7 H2O 2e-05 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range | confidence |
|---|---|---|---|---|---|
| 884 | positive | growth | 55 | thermophilic | |
| 67770 | positive | growth | 55 | thermophilic | |
| 69480 | thermophilic | 99.999 |
Physiology and metabolism
oxygen tolerance
- @ref: 69480
- oxygen tolerance: anaerobe
- confidence: 96.888
spore formation
- @ref: 69480
- spore formation: no
- confidence: 99.978
compound production
- @ref: 884
- compound: restriction endonuclease ThaI
observation
- @ref: 67770
- observation: quinones: MK-7, MMK-7, MK-7, MMK-7
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent |
|---|---|---|---|---|
| 884 | coal refuse pile | USA | USA | North America |
| 67770 | Coal refuse pile |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Engineered | #Other | #Mine |
| #Engineered | #Waste | #Solid waste |
taxonmaps
- @ref: 69479
- File name: preview.99_187333.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_17823;96_68848;97_89494;98_121774;99_187333&stattab=map
- Last taxonomy: Thermoplasma
- 16S sequence: M38637
- Sequence Identity:
- Total samples: 38
- aquatic counts: 38
Safety information
risk assessment
- @ref: 884
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 884 | Thermoplasma acidophilum 16S rRNA gene | M38637 | 2914 | ena | 2303 |
| 884 | Citrus unshiu DNA, scaffold00261, cultivar: Miyagawa wase, whole genome shotgun sequence | M20822 | 321284 | ena | 55188 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Thermoplasma acidophilum DSM 1728 | GCA_000195915 | complete | ncbi | 273075 |
| 66792 | Thermoplasma acidophilum DSM 1728 | 638154521 | complete | img | 273075 |
| 66792 | Thermoplasma acidophilum DSM 1728 | 273075.10 | complete | patric | 273075 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 884 | 46.8 | |
| 67770 | 45 | high performance liquid chromatography (HPLC) |
| 67770 | 45 | Buoyant density centrifugation (BD) |
| 67770 | 46.9 | Buoyant density centrifugation (BD) |
| 67770 | 46 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 72 | no |
| motile | no | 88.531 | no |
| flagellated | no | 98.101 | no |
| gram-positive | no | 93.086 | no |
| anaerobic | yes | 80.625 | no |
| aerobic | no | 91.301 | no |
| halophile | no | 85.815 | no |
| spore-forming | no | 94.406 | no |
| thermophile | yes | 100 | yes |
| glucose-util | yes | 86.965 | no |
| glucose-ferment | no | 64.767 | no |
External links
@ref: 884
culture collection no.: DSM 1728, ATCC 25905, AMRC C165, JCM 9062, IFO 15155, NBRC 15155
straininfo link
- @ref: 86018
- straininfo: 38714
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 17827289 | Structural and mutational analysis of tRNA intron-splicing endonuclease from Thermoplasma acidophilum DSM 1728: catalytic mechanism of tRNA intron-splicing endonucleases. | Kim YK, Mizutani K, Rhee KH, Nam KH, Lee WH, Lee EH, Kim EE, Park SY, Hwang KY | J Bacteriol | 10.1128/JB.00713-07 | 2007 | Amino Acid Sequence, Archaeal Proteins/chemistry/genetics/metabolism, Catalysis, Endonucleases/genetics/*metabolism, Introns/*genetics, Models, Molecular, Mutation/*genetics, Protein Conformation, *RNA Splicing, RNA, Bacterial/genetics, RNA, Transfer/*genetics, Thermoplasma/classification/*enzymology/*genetics | Enzymology |
| Metabolism | 18309272 | Crystallization and preliminary X-ray diffraction analysis of 5,10- methylenetetrahydrofolate dehydrogenase/cyclohydrolase from Thermoplasma acidophilum DSM 1728. | Kim JH, Sung MW, Lee EH, Nam KH, Hwang KY | J Microbiol Biotechnol | 7137 | 2008 | Aminohydrolases/*chemistry/metabolism, Archaeal Proteins/*chemistry/metabolism, Crystallization, Crystallography, X-Ray, Escherichia coli/genetics/metabolism, Methylenetetrahydrofolate Dehydrogenase (NADP)/*chemistry/metabolism, Multienzyme Complexes/*chemistry/metabolism, Thermoplasma/chemistry/*enzymology | Enzymology |
| Enzymology | 19058034 | Heterologous expression and characterization of an alcohol dehydrogenase from the archeon Thermoplasma acidophilum. | Marino-Marmolejo EN, De Leon-Rodriguez A, de la Rosa AP, Santos L | Mol Biotechnol | 10.1007/s12033-008-9130-z | 2008 | Alcohol Dehydrogenase/*chemistry/genetics/*metabolism, Alcohols/metabolism, Amino Acid Sequence, Escherichia coli/genetics, Hydrogen-Ion Concentration, Kinetics, Molecular Sequence Data, Recombinant Proteins/*chemistry/genetics/*metabolism, Sequence Analysis, DNA, Substrate Specificity, Temperature, Thermoplasma/*enzymology | Metabolism |
| Metabolism | 31640225 | The Main (Glyco) Phospholipid (MPL) of Thermoplasma acidophilum. | Freisleben HJ | Int J Mol Sci | 10.3390/ijms20205217 | 2019 | Archaeal Proteins/chemistry/metabolism, Calorimetry, Differential Scanning, Computer Simulation, Differential Thermal Analysis, Glycosylation, Liposomes/metabolism, Phospholipids/chemistry/*metabolism, Thermoplasma/*metabolism |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 884 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1728) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-1728 | |||
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 69479 | João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 86018 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID38714.1 | StrainInfo: A central database for resolving microbial strain identifiers |