Strain identifier

BacDive ID: 1997

Type strain: Yes

Species: Cupriavidus basilensis

Strain Designation: RK1

Strain history: CIP <- 2000, P. Steinle, Ciba, Pratteln, Switzerland: strain RK1

NCBI tax ID(s): 68895 (species)

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General

@ref: 4512

BacDive-ID: 1997

DSM-Number: 11853

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Cupriavidus basilensis RK1 is an aerobe, mesophilic, motile bacterium that was isolated from laboratory fixed-bed reactor.

NCBI tax id

  • NCBI tax id: 68895
  • Matching level: species

strain history

@refhistory
4512<- P. Steinle; RK1
405992000, P. Steinle, Ciba, Pratteln, Switzerland: strain RK1
116737CIP <- 2000, P. Steinle, Ciba, Pratteln, Switzerland: strain RK1

doi: 10.13145/bacdive1997.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Cupriavidus
  • species: Cupriavidus basilensis
  • full scientific name: Cupriavidus basilensis (Steinle et al. 1999) Vandamme and Coenye 2004

  • synonyms

    @refsynonym
    20215Ralstonia basilensis
    20215Wautersia basilensis

@ref: 4512

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus basilensis

full scientific name: Cupriavidus basilensis (Steinle et al. 1999) Vandamme and Coenye 2004

strain designation: RK1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes93.647
6948099.994negative
116737nonegativerod-shaped

multimedia

@refmultimedia contentintellectual property rightscaption
4512https://www.dsmz.de/microorganisms/photos/DSM_11853.jpg© Leibniz-Institut DSMZ
4512https://www.dsmz.de/microorganisms/photos/DSM_11853-1.jpgLeibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbHIridescence (metallic) of DSM 11853 on medium 1 at 28 °C

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4512NUTRIENT 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
4512MINERAL MEDIUM (NAGEL AND ANDREESEN) (DSMZ Medium 461)yeshttps://mediadive.dsmz.de/medium/461Name: MINERAL MEDIUM (NAGEL AND ANDREESEN) (DSMZ Medium 461) Composition: Na2HPO4 x 2 H2O 1.44135 g/l MgSO4 x 7 H2O 0.497018 g/l NH4Cl 0.298211 g/l KH2PO4 0.248509 g/l NaCl 0.0497018 g/l MnSO4 0.00994036 g/l CaCl2 0.00994036 g/l HCl 0.00248509 g/l FeCl2 x 4 H2O 0.00149105 g/l Thiamine-HCl x 2 H2O 0.000248509 g/l p-Aminobenzoic acid 0.000248509 g/l Vitamin B12 0.000248509 g/l Pantothenic acid 0.000248509 g/l Riboflavin 0.000248509 g/l alpha-lipoic acid 0.000248509 g/l CoCl2 x 6 H2O 0.000188867 g/l Nicotine amide 0.000124254 g/l Nicotinic acid 0.000124254 g/l Folic acid 9.94036e-05 g/l Biotin 9.94036e-05 g/l MnCl2 x 4 H2O 9.94036e-05 g/l ZnCl2 6.95825e-05 g/l Pyridoxamine hydrochloride 4.97018e-05 g/l Na2MoO4 x 2 H2O 3.57853e-05 g/l NiCl2 x 6 H2O 2.38569e-05 g/l H3BO3 5.96421e-06 g/l CuCl2 x 2 H2O 1.98807e-06 g/l Distilled water
40599MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116737CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4512positivegrowth30mesophilic
40599positivegrowth25mesophilic
58517positivegrowth28mesophilic
116737positivegrowth5-37
116737nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58517aerobe
116737obligate aerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.959

halophily

@refsaltgrowthtested relationconcentration
116737NaClpositivegrowth0-6 %
116737NaClnogrowth8 %
116737NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11673716947citrate+carbon source
1167374853esculin-hydrolysis
11673717632nitrate-reduction
11673716301nitrite-reduction
11673717632nitrate-respiration

antibiotic resistance

  • @ref: 116737
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11673735581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
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
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
116737oxidase+
116737beta-galactosidase-3.2.1.23
116737alcohol dehydrogenase-1.1.1.1
116737gelatinase-
116737amylase-
116737DNase-
116737caseinase-3.4.21.50
116737catalase+1.11.1.6
116737tween esterase+
116737lecithinase-
116737lipase-
116737lysine decarboxylase-4.1.1.18
116737ornithine decarboxylase-4.1.1.17
116737protease-
116737tryptophan deaminase-
116737urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    58517C14:04.414
    58517C15:00.415
    58517C16:026.316
    58517C17:00.417
    58517C18:00.518
    58517C14:0 2OH0.815.205
    58517C14:0 3OH/C16:1 ISO I6.515.485
    58517C16:0 2OH0.817.233
    58517C16:1 2OH2.317.047
    58517C16:1 ω7c30.915.819
    58517C17:0 CYCLO516.888
    58517C18:1 2OH2.519.088
    58517C18:1 ω7c /12t/9t18.317.824
    58517C19:0 CYCLO ω8c0.418.9
    58517Unidentified0.518.132
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116737-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4512--------------+++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116737-+-----------------------------+-----------++-++-+++-+-++---++++++++-+---+-+++-++++----+++++-+-+-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4512laboratory fixed-bed reactorSchweizerhalleSwitzerlandCHEEurope
58517Sediment of a freshwater pond enriched in ...AmponvilleFranceFRAEurope
116737Environment, Sediment of a fresh water pondAmponvilleFranceFRAEurope1996

isolation source categories

Cat1Cat2
#Engineered#Bioreactor
#Engineered#Laboratory

taxonmaps

  • @ref: 69479
  • File name: preview.99_3685.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_409;97_464;98_534;99_3685&stattab=map
  • Last taxonomy: Cupriavidus
  • 16S sequence: AF312022
  • Sequence Identity:
  • Total samples: 6080
  • soil counts: 2258
  • aquatic counts: 1798
  • animal counts: 1650
  • plant counts: 374

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
45121Risk group (German classification)
1167371Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Ralstonia basilensis strain DSM 11853 16S ribosomal RNA gene, partial sequenceAF3120221484ena68895
4512Ralstonia basilensis 16S rRNA geneAJ0023021457ena68895

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cupriavidus basilensis DSM 11853GCA_008801925completencbi68895
66792Cupriavidus basilensis strain CCUG 4934068895.15wgspatric68895

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes86.566no
motileyes86.566no
flagellatedno56.094no
flagellatedno56.094no
gram-positiveno98.508no
gram-positiveno98.508no
anaerobicno98.874yes
anaerobicno98.874yes
aerobicyes92.844no
aerobicyes92.844no
halophileno94.813no
halophileno94.813no
spore-formingno94.031no
spore-formingno94.031no
thermophileno99.527no
thermophileno99.527no
glucose-utilyes51.888no
glucose-utilyes51.888no
glucose-fermentno91.082yes
glucose-fermentno91.082yes

External links

@ref: 4512

culture collection no.: DSM 11853, CCUG 49340, LMG 19474, LMG 18990, ATCC BAA 699, CIP 106792

straininfo link

  • @ref: 71644
  • straininfo: 12956

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545472Taxonomy of the genus Cupriavidus: a tale of lost and found.Vandamme P, Coenye TInt J Syst Evol Microbiol10.1099/ijs.0.63247-02004Bacterial Proteins/analysis/isolation & purification, Base Composition, Burkholderiaceae/*classification/genetics/physiology, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Genes, rRNA/genetics, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Proteome/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny15570416Chlorinated aliphatic hydrocarbon-induced degradation of trichloroethylene in Wautersia numadzuensis sp. nov.Kageyama C, Ohta T, Hiraoka K, Suzuki M, Okamoto T, Ohishi KArch Microbiol10.1007/s00203-004-0746-52004Biodegradation, Environmental, Burkholderiaceae/*classification/isolation & purification/*metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Dichloroethylenes/metabolism, *Enzyme Induction, Genes, rRNA, Hydrocarbons, Chlorinated/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Ralstonia/genetics, Sequence Analysis, DNA, Soil Microbiology, Tetrachloroethylene/metabolism, Trichloroethylene/*metabolismMetabolism
Phylogeny25690136Cupriavidus yeoncheonense sp. nov., isolated from soil of ginseng.Singh P, Kim YJ, Nguyen NL, Hoang VA, Sukweenadhi J, Farh Mel-A, Yang DCAntonie Van Leeuwenhoek10.1007/s10482-014-0369-z2015Aerobiosis, Anti-Bacterial Agents/pharmacology, Bacterial Typing Techniques, Base Composition, Ceftazidime/pharmacology, Cluster Analysis, Culture Media/chemistry, Cupriavidus/*classification/genetics/*isolation & purification/physiology, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Glycolipids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Panax/growth & development, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Temperature, Tetracycline/pharmacologyGenetics
Phylogeny30317454Cupriavidus lacunae sp. nov., isolated from pond-side soil.Feng T, Kim KH, Oh J, Jeon COAntonie Van Leeuwenhoek10.1007/s10482-018-1187-52018Bacterial Typing Techniques, Base Composition, Cupriavidus/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/chemistry/metabolism, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Soil/chemistry, *Soil MicrobiologyMetabolism
Genetics33986075Complete Multipartite Genome Sequence of the Cupriavidus basilensis Type Strain, a 2,6-Dichlorophenol-Degrading Bacterium.Salva-Serra F, Donoso RA, Cho KH, Yoo JA, Lee K, Yoon SH, Pineiro-Iglesias B, Moore ERB, Perez-Pantoja DMicrobiol Resour Announc10.1128/MRA.00134-212021

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4512Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11853)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11853
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
40599Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18961
58517Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49340)https://www.ccug.se/strain?id=49340
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
68369Automatically annotated from API 20NE
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
71644Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12956.1StrainInfo: A central database for resolving microbial strain identifiers
116737Curators of the CIPCollection of Institut Pasteur (CIP 106792)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106792