Strain identifier

BacDive ID: 2053

Type strain: Yes

Species: Cupriavidus pinatubonensis

Strain Designation: 1245

Strain history: CIP <- 2005, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain 1245

NCBI tax ID(s): 248026 (species)

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General

@ref: 8170

BacDive-ID: 2053

DSM-Number: 19553

keywords: 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped, colony-forming

description: Cupriavidus pinatubonensis 1245 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from volcanic ash deposits.

NCBI tax id

  • NCBI tax id: 248026
  • Matching level: species

strain history

@refhistory
8170<- H. Ohta, Ibaraki University, Japan
383042005, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain 1245
121833CIP <- 2005, H. Ohta, Ibaraki Univ., Ibaraki, Japan: strain 1245

doi: 10.13145/bacdive2053.20230509.8.1

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 pinatubonensis
  • full scientific name: Cupriavidus pinatubonensis Sato et al. 2006

@ref: 8170

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Cupriavidus

species: Cupriavidus pinatubonensis

full scientific name: Cupriavidus pinatubonensis Sato et al. 2006

strain designation: 1245

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
23160negative0.8-1.6 µm0.3-0.6 µmrod-shaped
121833negativerod-shapedyes

colony morphology

@refcolony colorcolony shapemedium used
23160whitecircular100-fold diluted NB agar
121833

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8170REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
23160100-fold diluted NB agaryes
38304MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121833CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
8170positivegrowth28mesophilic
23160positivegrowth27-41
38304positivegrowth30mesophilic
60075positivegrowth37mesophilic
121833positivegrowth25-37mesophilic
121833nogrowth5psychrophilic
121833nogrowth15psychrophilic
121833nogrowth41thermophilic
121833nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
23160aerobe
60075aerobe
121833obligate aerobe

spore formation

  • @ref: 23160
  • spore formation: no

halophily

  • @ref: 121833
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2316022599arabinose-assimilation
2316029749ferulate-assimilation
2316015740formate-assimilation
2316017234glucose-assimilation
2316028591guaiacol-assimilation
2316017306maltose-assimilation
2316029864mannitol-assimilation
2316037684mannose-assimilation
23160506227N-acetylglucosamine-assimilation
2316017992sucrose-assimilation
2316016632vanillate-assimilation
2316017234glucose-builds acid from
2316027897tryptophan-energy source
2316030762salicylate+assimilation
2316036241protocatechuate+assimilation
23160178794-hydroxybenzoate+assimilation
2316030089acetate+assimilation
2316017128adipate+assimilation
2316027689decanoate+assimilation
2316018135catechol+assimilation
2316016947citrate+assimilation
2316015824D-fructose+assimilation
2316024265gluconate+assimilation
2316029987glutamate+assimilation
2316024996lactate+assimilation
2316025115malate+assimilation
2316015882phenol+assimilation
2316018401phenylacetate+assimilation
23160trimethoxybenzoate+assimilation
2316017632nitrate+reduction
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
12183316947citrate+carbon source
1218334853esculin-hydrolysis
121833606565hippurate+hydrolysis
12183317632nitrate-builds gas from
12183317632nitrate+reduction
12183316301nitrite+builds gas from
12183316301nitrite-reduction
12183315792malonate+assimilation
12183317632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
2316035581indoleno
6836935581indoleno
12183335581indoleno

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
2316035581indole-
6836935581indole-
12183315688acetoin-
12183317234glucose-

enzymes

@refvalueactivityec
23160beta-galactosidase-3.2.1.23
23160beta-glucosidase-3.2.1.21
23160catalase+1.11.1.6
23160cytochrome oxidase+1.9.3.1
23160tryptophan deaminase-4.1.99.1
23160urease+3.5.1.5
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
121833oxidase+
121833beta-galactosidase-3.2.1.23
121833alcohol dehydrogenase-1.1.1.1
121833gelatinase-
121833amylase-
121833DNase-
121833caseinase-3.4.21.50
121833catalase-1.11.1.6
121833tween esterase-
121833gamma-glutamyltransferase+2.3.2.2
121833lecithinase-
121833lipase-
121833lysine decarboxylase-4.1.1.18
121833ornithine decarboxylase-4.1.1.17
121833phenylalanine ammonia-lyase-4.3.1.24
121833tryptophan deaminase-
121833urease+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
121833-+++-++---++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
8170+-------------+++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121833-+-----------------------------------------+++---+++++----+-++++++++-+-----++++++++----+++++-+++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
8170volcanic ash depositsMt. PinatuboPhilippinesPHLAsia
23160volcanic mudflow deposits derived from the eruption of Mt. Pinatubo1991
60075Volcanic mudflowMt PinatuboPhilippinesPHLAsia1998
121833Environment, Volcanic mudflowMount PinatuboPhilippinesPHLAsia1998

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Dust
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Terrestrial#Volcanic

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
81701Risk group (German classification)
1218331Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8170
  • description: Cupriavidus pinatubonensis gene for 16S ribosomal RNA, strain: 1245
  • accession: AB121221
  • length: 1524
  • database: ena
  • NCBI tax ID: 248026

GC content

  • @ref: 23160
  • GC-content: 65.9

External links

@ref: 8170

culture collection no.: DSM 19553, CIP 108725, PNCM 10346, CCUG 53907, KCTC 22125

straininfo link

  • @ref: 71700
  • straininfo: 290966

literature

  • topic: Phylogeny
  • Pubmed-ID: 16627640
  • title: Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the Philippines.
  • authors: Sato Y, Nishihara H, Yoshida M, Watanabe M, Rondal JD, Concepcion RN, Ohta H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63922-0
  • year: 2006
  • mesh: Bacterial Proteins/analysis, Bacterial Typing Techniques, Base Composition, Burkholderiaceae/chemistry/*classification/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Flagella/physiology, Genes, rRNA/genetics, Hydrogen/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Philippines, Phylogeny, Proteome/analysis, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil Microbiology, *Volcanic Eruptions
  • topic2: Enzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8170Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19553)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19553
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
23160Yoshinori Sato, Hirofumi Nishihara, Masao Yoshida, Makiko Watanabe, Jose D. Rondal, Rogelio N. Concepcion, Hiroyuki Ohta10.1099/ijs.0.63922-0Cupriavidus pinatubonensis sp. nov. and Cupriavidus laharis sp. nov., novel hydrogen-oxidizing, facultatively chemolithotrophic bacteria isolated from volcanic mudflow deposits from Mt. Pinatubo in the PhilippinesIJSEM 56: 973-978 200616627640
38304Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6386
60075Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53907)https://www.ccug.se/strain?id=53907
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
71700Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID290966.1StrainInfo: A central database for resolving microbial strain identifiers
121833Curators of the CIPCollection of Institut Pasteur (CIP 108725)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108725