Strain identifier

BacDive ID: 23212

Type strain: No

Species: Pseudomonas alcaliphila

Strain Designation: JAB1

Strain history: <- O. Uhlik, Inst. of Chem. Technol., Prague; JAB1 <- M. Macková, Inst. of Chem. Technol., Prague, Czech Republic

NCBI tax ID(s): 101564 (species)

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General

@ref: 18897

BacDive-ID: 23212

DSM-Number: 26533

keywords: genome sequence, Bacteria, mesophilic, motile

description: Pseudomonas alcaliphila JAB1 is a mesophilic, motile bacterium that was isolated from PCB contaminated soil.

NCBI tax id

  • NCBI tax id: 101564
  • Matching level: species

strain history

  • @ref: 18897
  • history: <- O. Uhlik, Inst. of Chem. Technol., Prague; JAB1 <- M. Macková, Inst. of Chem. Technol., Prague, Czech Republic

doi: 10.13145/bacdive23212.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Pseudomonadaceae
  • genus: Pseudomonas
  • species: Pseudomonas alcaliphila
  • full scientific name: Pseudomonas alcaliphila Yumoto et al. 2001

@ref: 18897

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas alcaliphila

full scientific name: Pseudomonas alcaliphila Yumoto et al. 2001

strain designation: JAB1

type strain: no

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes98.647
6948099.998negative

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18897REACTIVATION 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
18897MINERAL 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

culture temp

  • @ref: 18897
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.933

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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

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

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
18897+-------+-++++++-++-+

Isolation, sampling and environmental information

isolation

  • @ref: 18897
  • sample type: PCB contaminated soil
  • geographic location: Jablonné nad Orlici
  • country: Czech Republic
  • origin.country: CZE
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Engineered#Contamination
#Environmental#Terrestrial#Soil

Safety information

risk assessment

  • @ref: 18897
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas alcaliphila JAB1GCA_001941865completencbi741155
66792Pseudomonas alcaliphila JAB1741155.4completepatric741155
66792Pseudomonas alcaliphila JAB12806311029completeimg741155

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes88.458no
gram-positiveno98.61no
anaerobicno97.289no
halophileno81.4no
spore-formingno95.085no
glucose-utilyes88.869no
aerobicyes89.417no
thermophileno99.803yes
motileyes91.546no
glucose-fermentno91.592yes

External links

@ref: 18897

culture collection no.: DSM 26533

straininfo link

  • @ref: 87440
  • straininfo: 402140

literature

  • topic: Genetics
  • Pubmed-ID: 29435100
  • title: Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants.
  • authors: Ridl J, Suman J, Fraraccio S, Hradilova M, Strejcek M, Cajthaml T, Zubrova A, Macek T, Strnad H, Uhlik O
  • journal: Stand Genomic Sci
  • DOI: 10.1186/s40793-017-0306-7
  • year: 2018

Reference

@idauthorscataloguedoi/urltitle
18897Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26533)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26533
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
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)
68369Automatically annotated from API 20NE
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
87440Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID402140.1StrainInfo: A central database for resolving microbial strain identifiers