Strain identifier

BacDive ID: 3894

Type strain: Yes

Species: Deinococcus aerius

Strain Designation: TR0125

Strain history: CIP <- 2009, DSMZ <- A. Yamagishi, Tokyo Univ., Tokyo, Japan: strain TR0125

NCBI tax ID(s): 200253 (species)

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General

@ref: 15498

BacDive-ID: 3894

DSM-Number: 21212

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, coccus-shaped

description: Deinococcus aerius TR0125 is an aerobe, mesophilic, coccus-shaped bacterium that was isolated from air dust collected in the high atmosphere.

NCBI tax id

  • NCBI tax id: 200253
  • Matching level: species

strain history

@refhistory
15498<- A. Yamagishi, Tokyo University of Pharmacy and Life Science; TR0125
67770A. Yamagishi TR0125.
116061CIP <- 2009, DSMZ <- A. Yamagishi, Tokyo Univ., Tokyo, Japan: strain TR0125

doi: 10.13145/bacdive3894.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/deinococcota
  • domain: Bacteria
  • phylum: Deinococcota
  • class: Deinococci
  • order: Deinococcales
  • family: Deinococcaceae
  • genus: Deinococcus
  • species: Deinococcus aerius
  • full scientific name: Deinococcus aerius Yang et al. 2009

@ref: 15498

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus aerius

full scientific name: Deinococcus aerius Yang et al. 2009

strain designation: TR0125

type strain: yes

Morphology

cell morphology

@refcell lengthcell widthcell shapemotilitygram stain
291761.25 µm1.25 µmcoccus-shapedno
116061coccus-shapednopositive

pigmentation

  • @ref: 29176
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15498TGE MEDIUM (DSMZ Medium 1207)yeshttps://mediadive.dsmz.de/medium/1207Name: TGE (DSMZ Medium 1207) Composition: Agar 15.0 g/l Tryptone 10.0 g/l Beef extract 6.0 g/l Glucose 2.0 g/l Distilled water
15498GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484)yeshttps://mediadive.dsmz.de/medium/1484Name: Glycerol-Yeast extract-Peptone Medium (DSMZ Medium 1484) Composition: Agar 15.0 g/l Yeast extract 5.0 g/l Bacto peptone 3.0 g/l Betaine 1.25 g/l Sodium pyruvate 1.25 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l CoSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Pyridoxine hydrochloride 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l (DL)-alpha-Lipoic acid 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Nicotinic acid 5e-05 g/l Riboflavin 5e-05 g/l Thiamine HCl 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Glycerol Distilled water
37913MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
116061CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

@refgrowthtypetemperaturerange
15498positivegrowth28mesophilic
29176positiveoptimum27.5mesophilic
37913positivegrowth30mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29176aerobe
116061facultative anaerobe

spore formation

  • @ref: 29176
  • spore formation: no

murein

  • @ref: 15498
  • murein short key: A21.01
  • type: A3ß L-Orn-Gly2-3

observation

@refobservation
29176aggregates in clumps
67770quinones: MK-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2917616449alanine+carbon source
2917622599arabinose+carbon source
291765417glucosamine+carbon source
2917629987glutamate+carbon source
2917615428glycine+carbon source
2917617306maltose+carbon source
2917618257ornithine+carbon source
2917626271proline+carbon source
2917616634raffinose+carbon source
2917617992sucrose+carbon source
291764853esculin+hydrolysis
11606117632nitrate-reduction
11606116301nitrite-reduction

metabolite production

  • @ref: 116061
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29176alkaline phosphatase+3.1.3.1
29176catalase+1.11.1.6
29176cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
116061oxidase+
116061catalase+1.11.1.6
116061urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116061--++-+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15498air dust collected in the high atmosphereMain IslandJapanJPNAsia
67770Air sample collected from the high atmosphereJapanJPNAsia
116061Environment, Dust samples, high atmosphereJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Air#Outdoor Air
#Environmental#Terrestrial#Dust

taxonmaps

  • @ref: 69479
  • File name: preview.99_23660.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15362;96_3844;97_4737;98_6087;99_23660&stattab=map
  • Last taxonomy: Deinococcus aerius subclade
  • 16S sequence: AB087288
  • Sequence Identity:
  • Total samples: 28
  • soil counts: 4
  • aquatic counts: 2
  • animal counts: 22

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
154981Risk group (German classification)
1160611Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15498
  • description: Deinococcus aerius gene for 16S ribosomal RNA, partial sequence
  • accession: AB087288
  • length: 1468
  • database: ena
  • NCBI tax ID: 200253

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus aerius TR01252895784119draftimg200253
67770Deinococcus aerius TR0125GCA_002897375contigncbi200253

GC content

@refGC-contentmethod
1549870.5high performance liquid chromatography (HPLC)
2917670.5

External links

@ref: 15498

culture collection no.: DSM 21212, CIP 110035, JCM 11750

straininfo link

  • @ref: 73404
  • straininfo: 364125

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19567578Deinococcus aerius sp. nov., isolated from the high atmosphere.Yang Y, Itoh T, Yokobori S, Itahashi S, Shimada H, Satoh K, Ohba H, Narumi I, Yamagishi AInt J Syst Evol Microbiol10.1099/ijs.0.007963-02009*Air Microbiology, Amino Acids/analysis, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Deinococcus/*classification/genetics/*isolation & purification/physiology, Fatty Acids/analysis, Gamma Rays, Japan, Microscopy, Electron, Scanning, Molecular Sequence Data, Peptidoglycan/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ultraviolet RaysGenetics
Genetics29496828Draft Genome Sequence of the Radioresistant Bacterium Deinococcus aerius TR0125, Isolated from the High Atmosphere above Japan.Satoh K, Arai H, Sanzen T, Kawaguchi Y, Hayashi H, Yokobori SI, Yamagishi A, Oono Y, Narumi IGenome Announc10.1128/genomeA.00080-182018Phylogeny

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15498Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21212)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21212
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
29176Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2560028776041
37913Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7848
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
73404Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID364125.1StrainInfo: A central database for resolving microbial strain identifiers
116061Curators of the CIPCollection of Institut Pasteur (CIP 110035)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110035