Strain identifier

BacDive ID: 3855

Type strain: Yes

Species: Deinococcus geothermalis

Strain Designation: AG-3a

Strain history: CIP <- 1998, A.C. Ferreira, Coimbra Univ., Coimbra, Portugal: strain AG-3a

NCBI tax ID(s): 319795 (strain), 68909 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 4287

BacDive-ID: 3855

DSM-Number: 11300

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, thermophilic, Gram-positive, sphere-shaped

description: Deinococcus geothermalis AG-3a is an obligate aerobe, thermophilic, Gram-positive bacterium that was isolated from hot springs.

NCBI tax id

NCBI tax idMatching level
68909species
319795strain

strain history

@refhistory
4287<- M.S. da Costa, AG-3a
119604CIP <- 1998, A.C. Ferreira, Coimbra Univ., Coimbra, Portugal: strain AG-3a

doi: 10.13145/bacdive3855.20230509.8.1

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 geothermalis
  • full scientific name: Deinococcus geothermalis Ferreira et al. 1997

@ref: 4287

domain: Bacteria

phylum: Deinococcus-Thermus

class: Deinococci

order: Deinococcales

family: Deinococcaceae

genus: Deinococcus

species: Deinococcus geothermalis

full scientific name: Deinococcus geothermalis Ferreira et al. 1997

strain designation: AG-3a

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell shapemotilityconfidence
23350positive1.2-2.0 µmsphere-shapedno
69480positive98.957
119604positivecoccus-shapedno

colony morphology

@refcolony sizecolony colorincubation periodmedium used
233500.2 mmorange3 daysDegryse medium 162
119604

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4287NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
4287THERMUS 162 MEDIUM (DSMZ Medium 878)yeshttps://mediadive.dsmz.de/medium/878Name: THERMUS 162 MEDIUM (DSMZ Medium 878) Composition: Agar 28.0 g/l Na2HPO4 x 12 H2O 4.3 g/l Yeast extract 1.0 g/l Tryptone 1.0 g/l KH2PO4 0.544 g/l MgCl2 x 6 H2O 0.2 g/l Nitrilotriacetic acid 0.1 g/l CaSO4 x 2 H2O 0.04 g/l Fe(III) citrate 0.00122472 g/l MnSO4 x H2O 0.00114 g/l ZnSO4 x 7 H2O 0.00025 g/l H3BO3 0.00025 g/l CoCl2 x 6 H2O 2.25e-05 g/l CuSO4 x 5 H2O 1.25e-05 g/l Na2MoO4 x 2 H2O 1.25e-05 g/l H2SO4 Distilled water
32766MEDIUM 302 - for Deinococcus geothermalisyesDistilled water make up to (800.000 ml);Magnesium chloride hexahydrate (0.200 g);Nitrilotriacetic acid (0.100 g);Agar (28.000 g);Yeast extract (2.500 g);Ferric citrate (4.070 g);Tryptone (2.500 g);Calcium sulphate solution - M0551 (100.000 ml);Mineral sol
119604CIP Medium 302yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=302

culture temp

@refgrowthtypetemperaturerange
4287positivegrowth45thermophilic
4287positivegrowth45-50thermophilic
23350positivegrowth30-55
23350positiveoptimum47thermophilic
32766positivegrowth45thermophilic
119604positivegrowth30-45
119604nogrowth10psychrophilic
119604nogrowth25mesophilic

culture pH

@refabilitytypepH
23350positiveoptimum8.0
23350positiveoptimum6.5
23350nogrowth4.0
23350nogrowth9.0

Physiology and metabolism

oxygen tolerance

  • @ref: 119604
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
23350no
69481no90
69480no99.687

halophily

@refsaltgrowthtested relationconcentration
119604NaClpositivegrowth0-2 %
119604NaClnogrowth4 %
119604NaClnogrowth6 %
119604NaClnogrowth8 %
119604NaClnogrowth10 %

murein

  • @ref: 4287
  • murein short key: A21.01
  • type: A3ß L-Orn-Gly2-3

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2335016947citrate-assimilation
2335028053melibiose-assimilation
2335016634raffinose-assimilation
2335030849L-arabinose-assimilation
2335017268myo-inositol-assimilation
2335015963ribitol-assimilation
2335017632nitrate-reduction
23350yeast extract-required for growth
2335017057cellobiose+assimilation
2335015824D-fructose+assimilation
2335012936D-galactose+assimilation
2335017634D-glucose+assimilation
2335016899D-mannitol+assimilation
2335016024D-mannose+assimilation
2335017924D-sorbitol+assimilation
2335016551D-trehalose+assimilation
2335065327D-xylose+assimilation
2335017754glycerol+assimilation
2335017196L-asparagine+assimilation
2335029985L-glutamate+assimilation
2335018050L-glutamine+assimilation
2335017203L-proline+assimilation
2335062345L-rhamnose+assimilation
2335017115L-serine+assimilation
2335017716lactose+assimilation
2335025115malate+assimilation
2335017306maltose+assimilation
2335015361pyruvate+assimilation
2335030031succinate+assimilation
2335017992sucrose+assimilation
2335018305arbutin+degradation
23350casein+degradation
233505291gelatin+degradation
23350606565hippurate+degradation
2335028017starch+degradation
2335016467L-arginineassimilation
119604606565hippurate+hydrolysis
11960417632nitrate-reduction
11960416301nitrite-reduction

metabolite production

  • @ref: 119604
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11960415688acetoin-
11960417234glucose-

enzymes

@refvalueactivityec
23350alpha-galactosidase+3.2.1.22
23350beta-galactosidase+3.2.1.23
23350catalase+1.11.1.6
23350cytochrome 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
119604beta-galactosidase-3.2.1.23
119604alcohol dehydrogenase-1.1.1.1
119604gelatinase+/-
119604amylase+
119604DNase-
119604caseinase+3.4.21.50
119604catalase+1.11.1.6
119604tween esterase-
119604gamma-glutamyltransferase-2.3.2.2
119604lecithinase-
119604lipase+
119604lysine decarboxylase-4.1.1.18
119604ornithine decarboxylase-4.1.1.17
119604phenylalanine ammonia-lyase-4.3.1.24
119604protease-
119604tryptophan deaminase-
119604urease-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
119604-++++-----++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119604++-++--+-++----+---+-+++--+----+-+-++------------+---------+--+----------------++-----+------+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4287hot springsnear Naples, Termi di AgnanoItalyITAEurope
119604Environment, Hot springNaplesItalyITAEurope1995

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Thermal spring
#Condition#Thermophilic (>45°C)

taxonmaps

  • @ref: 69479
  • File name: preview.99_2804.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15362;96_1491;97_1779;98_2174;99_2804&stattab=map
  • Last taxonomy: Deinococcus geothermalis subclade
  • 16S sequence: Y13038
  • Sequence Identity:
  • Total samples: 3020
  • soil counts: 339
  • aquatic counts: 569
  • animal counts: 1857
  • plant counts: 255

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
42871Risk group (German classification)
1196041Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4287
  • description: D.geothermalis 16S rRNA gene, isolate AG-3aT
  • accession: Y13038
  • length: 1473
  • database: ena
  • NCBI tax ID: 319795

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Deinococcus geothermalis DSM 11300GCA_000196275completencbi319795
66792Deinococcus geothermalis DSM 11300319795.16completepatric319795
66792Deinococcus geothermalis DSM 11300319795.26plasmidpatric319795
66792Deinococcus geothermalis DSM 11300319795.25plasmidpatric319795
66792Deinococcus geothermalis DSM 11300641228488completeimg319795

GC content

  • @ref: 23350
  • GC-content: 65.9
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno90no
motileno91.896yes
flagellatedno97.508yes
gram-positiveyes79.537no
anaerobicno98.049no
aerobicyes89.613no
halophileno94.257no
spore-formingno93.326yes
thermophileyes88.54yes
glucose-utilyes89.218yes
glucose-fermentno85.703no

External links

@ref: 4287

culture collection no.: DSM 11300, CIP 105573

straininfo link

  • @ref: 73365
  • straininfo: 49070

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336890Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., two extremely radiation-resistant and slightly thermophilic species from hot springs.Ferreira AC, Nobre MF, Rainey FA, Silva MT, Wait R, Burghardt J, Chung AP, da Costa MSInt J Syst Bacteriol10.1099/00207713-47-4-9391997Base Composition, DNA, Bacterial/*analysis, Genes, Bacterial/genetics, Glucose/analysis, Gram-Positive Cocci/chemistry/*classification/*genetics/growth & development/ultrastructure, Hydrogen-Ion Concentration, Lipids/analysis, Microscopy, Electron, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/*genetics, Radiation Tolerance, TemperatureGenetics
Enzymology16980504Characterization of adhesion threads of Deinococcus geothermalis as type IV pili.Saarimaa C, Peltola M, Raulio M, Neu TR, Salkinoja-Salonen MS, Neubauer PJ Bacteriol10.1128/JB.00608-062006Bacterial Adhesion, Bacterial Proteins/chemistry/isolation & purification, Deinococcus/chemistry/*physiology/ultrastructure, Electrophoresis, Polyacrylamide Gel, Fimbriae Proteins/chemistry/genetics, Fimbriae, Bacterial/chemistry/*ultrastructure, Glycoconjugates/analysis, Glycosylation, Metalloproteases/chemistry/genetics, Microscopy, Confocal, Microscopy, Electron, Plant Lectins/metabolism, Protein Binding, Ribosome Inactivating Proteins, Sequence Analysis, Protein, Sequence Homology, Amino Acid, Serine Endopeptidases/chemistry/genetics, Staining and LabelingTranscriptome
Metabolism19443548A novel carotenoid 1,2-hydratase (CruF) from two species of the non-photosynthetic bacterium Deinococcus.Sun Z, Shen S, Wang C, Wang H, Hu Y, Jiao J, Ma T, Tian B, Hua YMicrobiology (Reading)10.1099/mic.0.027623-02009Biosynthetic Pathways, Carotenoids/metabolism, DNA, Bacterial/analysis/genetics/metabolism, Deinococcus/*enzymology/genetics, Evolution, Molecular, Gene Deletion, Gene Expression, Genes, Bacterial, *Hydro-Lyases/genetics/metabolism, Phylogeny, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidPhylogeny
Phylogeny22012026Characterization of Deinococcus sahariens sp. nov., a radiation-resistant bacterium isolated from a Saharan hot spring.Bouraoui H, Aissa MB, Abbassi F, Touzel JP, O'donohue M, Manai MArch Microbiol10.1007/s00203-011-0762-12011Base Composition, DNA, Bacterial/chemistry, Deinococcus/*classification/isolation & purification/*radiation effects, Fatty Acids/analysis, Hot Springs/*microbiology, Phylogeny, *Radiation Tolerance, Tunisia, Ultraviolet RaysEnzymology
Metabolism22112416Biosynthesis of (+)-catechin glycosides using recombinant amylosucrase from Deinococcus geothermalis DSM 11300.Cho HK, Kim HH, Seo DH, Jung JH, Park JH, Baek NI, Kim MJ, Yoo SH, Cha J, Kim YR, Park CSEnzyme Microb Technol10.1016/j.enzmictec.2011.05.0072011Bacterial Proteins/genetics/metabolism, Catechin/*analogs & derivatives/biosynthesis/chemistry, Chromatography, High Pressure Liquid, Chromatography, Thin Layer, Deinococcus/*enzymology/genetics, Glucosyltransferases/genetics/*metabolism, Glycosides/*biosynthesis/chemistry, Glycosylation, Molecular Structure, Nuclear Magnetic Resonance, Biomolecular, Recombinant Proteins/genetics/metabolism, Sucrose/metabolismEnzymology
Metabolism25209745Experimental and statistical analysis of nutritional requirements for the growth of the extremophile Deinococcus geothermalis DSM 11300.Bornot J, Aceves-Lara CA, Molina-Jouve C, Uribelarrea JL, Gorret NExtremophiles10.1007/s00792-014-0671-82014Biomass, Culture Media/*chemistry, Deinococcus/*growth & development/metabolism, Fermentation, Glucose/metabolism, Hot Temperature, Industrial Microbiology/*methods, Oxygen/metabolismStress
Genetics28775794High-quality genome sequence of the radioresistant bacterium Deinococcus ficus KS 0460.Matrosova VY, Gaidamakova EK, Makarova KS, Grichenko O, Klimenkova P, Volpe RP, Tkavc R, Ertem G, Conze IH, Brambilla E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Daligault H, Davenport K, Erkkila T, Goodwin LA, Gu W, Munk C, Teshima H, Xu Y, Chain P, Woolbert M, Gunde-Cimerman N, Wolf YI, Grebenc T, Gostincar C, Daly MJStand Genomic Sci10.1186/s40793-017-0258-y2017
Enzymology30369110Sustainable Production of Dihydroxybenzene Glucosides Using Immobilized Amylosucrase from Deinococcus geothermalis.Lee HS, Kim TS, Parajuli P, Pandey RP, Sohng JKJ Microbiol Biotechnol10.4014/jmb.1805.050542018Bacterial Proteins/genetics/*metabolism, Deinococcus/*enzymology/genetics, Enzymes, Immobilized/genetics/*metabolism, Escherichia coli/enzymology/genetics/metabolism, Glucosides/analysis/*biosynthesis/chemistry, Glucosyltransferases/genetics/*metabolism, Glycosides/analysis/biosynthesis/chemistry, Glycosylation, Hydrogen-Ion Concentration, Industrial Microbiology/*methods, Phenols/analysis/chemistry, Recombinant Proteins/genetics/isolation & purification/metabolism, Substrate Specificity, Sucrose/metabolism, TemperatureMetabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4287Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11300)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11300
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
23350Ana Cristina Ferreira, M. Fernanda Nobre, Fred A. Rainey, Manuel T. Silva, Robin Wait, Jutta Burghardt, Ana Paula Chung, Milton S. Da Costa10.1099/00207713-47-4-939Deinococcus geothermalis sp. nov. and Deinococcus murrayi sp. nov., Two Extremely Radiation-Resistant and Slightly Thermophilic Species from Hot SpringsIJSEM 47: 939-947 19979336890
32766Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17607
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
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73365Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49070.1StrainInfo: A central database for resolving microbial strain identifiers
119604Curators of the CIPCollection of Institut Pasteur (CIP 105573)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105573