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Strain identifier

BacDive ID: 17017

Type strain: Yes

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)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 884

BacDive-ID: 17017

DSM-Number: 1728

keywords: genome sequence, 16S sequence, Archaea, thermophilic

description: Thermoplasma acidophilum 122-1B2 is a thermophilic archaeon that was isolated from coal refuse pile.

NCBI tax id

NCBI tax idMatching level
273075strain
2303species

strain history

doi: 10.13145/bacdive17017.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/archaea
  • keyword: phylum/euryarchaeota
  • domain: Archaea
  • phylum: Euryarchaeota
  • 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: 99.178

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

@refgrowthtypetemperaturerangeconfidence
884positivegrowth55thermophilic
67770positivegrowth55thermophilic
69480thermophilic99.4

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: anaerobe
  • confidence: 75.61

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 97.807

compound production

  • @ref: 884
  • compound: restriction endonuclease ThaI

halophily

  • @ref: 69480
  • halophily level: non-halophilic
  • confidence: 71.379

observation

  • @ref: 67770
  • observation: quinones: MK-7, MMK-7, MK-7, MMK-7

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
884coal refuse pileUSAUSANorth America
67770Coal refuse pile

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
884Thermoplasma acidophilum 16S rRNA geneM386372914ena2303
884Citrus unshiu DNA, scaffold00261, cultivar: Miyagawa wase, whole genome shotgun sequenceM20822321284ena55188

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thermoplasma acidophilum DSM 1728 DSM1728GCA_000195915completencbi273075
66792Thermoplasma acidophilum DSM 1728638154521completeimg273075
67770Thermoplasma acidophilum DSM 1728 complete genomeAL139299ena273075

GC content

@refGC-contentmethod
88446.8
6777045high performance liquid chromatography (HPLC)
6777045Buoyant density centrifugation (BD)
6777046.9Buoyant density centrifugation (BD)
6777046thermal denaturation, midpoint method (Tm)

External links

@ref: 884

culture collection no.: DSM 1728, ATCC 25905, AMRC C165, JCM 9062, IFO 15155, NBRC 15155

straininfo link

@refpassport
20218http://www.straininfo.net/strains/104667
20218http://www.straininfo.net/strains/104666

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism17827289Structural 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 KYJ Bacteriol10.1128/JB.00713-072007Amino 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/*geneticsEnzymology
Metabolism18309272Crystallization 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 KYJ Microbiol Biotechnol71372008Aminohydrolases/*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/*enzymologyEnzymology
Enzymology19058034Heterologous expression and characterization of an alcohol dehydrogenase from the archeon Thermoplasma acidophilum.Marino-Marmolejo EN, De Leon-Rodriguez A, de la Rosa AP, Santos LMol Biotechnol10.1007/s12033-008-9130-z2008Alcohol 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/*enzymologyMetabolism
Metabolism31640225The Main (Glyco) Phospholipid (MPL) of Thermoplasma acidophilum.Freisleben HJInt J Mol Sci10.3390/ijms202052172019Archaeal Proteins/chemistry/metabolism, Calorimetry, Differential Scanning, Computer Simulation, Differential Thermal Analysis, Glycosylation, Liposomes/metabolism, Phospholipids/chemistry/*metabolism, Thermoplasma/*metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
884Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 1728)https://www.dsmz.de/collection/catalogue/details/culture/DSM-1728
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João 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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)