Strain identifier

BacDive ID: 13063

Type strain: Yes

Species: Pseudomonas frederiksbergensis

Strain Designation: JAJ28

Strain history: CIP <- 2001, S.M. Andersen, Geological Survey of Denmark and Greenland, Copenhagen, Denmark: strain JAJ28

NCBI tax ID(s): 104087 (species)

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General

@ref: 4874

BacDive-ID: 13063

DSM-Number: 13022

keywords: 16S sequence, Bacteria, obligate aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Pseudomonas frederiksbergensis JAJ28 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from soil from a gasification site.

NCBI tax id

  • NCBI tax id: 104087
  • Matching level: species

strain history

@refhistory
4874<- S. M. Andersen, GEUS, Geological Survey of Denmark and Greenland; JAJ28
406542001, S.M. Andersen, Geological Survey of Denmark and Greenland, Copenhagen, Denmark: strain JAJ28
119448CIP <- 2001, S.M. Andersen, Geological Survey of Denmark and Greenland, Copenhagen, Denmark: strain JAJ28

doi: 10.13145/bacdive13063.20230509.8.1

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 frederiksbergensis
  • full scientific name: Pseudomonas frederiksbergensis Andersen et al. 2000

@ref: 4874

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas frederiksbergensis

full scientific name: Pseudomonas frederiksbergensis Andersen et al. 2000

strain designation: JAJ28

type strain: yes

Morphology

cell morphology

  • @ref: 119448
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 119448
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4874REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)yeshttps://mediadive.dsmz.de/medium/535bName: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water
4874MEDIUM WITH FLUORANTHENE OR PHENANTHRENE (DSMZ Medium 457b)yeshttps://mediadive.dsmz.de/medium/457bName: MEDIUM WITH FLUORANTHENE (DSMZ Medium 457b; with strain-specific modifications) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l Casamino acids 0.3 g/l Tween 80 0.2 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
40654MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119448CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4874positivegrowth30mesophilic
40654positivegrowth30mesophilic
119448positivegrowth5-30
119448nogrowth37mesophilic
119448nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119448
  • oxygen tolerance: obligate aerobe

compound production

  • @ref: 4874
  • compound: phenylmethyl sulfoxide

halophily

@refsaltgrowthtested relationconcentration
119448NaClpositivegrowth0-2 %
119448NaClnogrowth6 %
119448NaClnogrowth8 %
119448NaClnogrowth10 %

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
11944816947citrate+carbon source
1194484853esculin-hydrolysis
11944817632nitrate+reduction
11944816301nitrite+reduction
11944817632nitrate+respiration

antibiotic resistance

  • @ref: 119448
  • 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
11944835581indoleno

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
119448oxidase+
119448beta-galactosidase-3.2.1.23
119448alcohol dehydrogenase-1.1.1.1
119448gelatinase-
119448amylase-
119448DNase-
119448caseinase-3.4.21.50
119448catalase+1.11.1.6
119448tween esterase-
119448lecithinase-
119448lipase-
119448lysine decarboxylase-4.1.1.18
119448ornithine decarboxylase-4.1.1.17
119448protease-
119448tryptophan deaminase-
119448urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase-
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119448--++-+----+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4874+-------+++++-++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119448+++++--+----------+++-----+----+++---------++---++++-++++--++-+++--+--++++-+++-++++++-+-+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4874soil from a gasification siteCopenhagenDenmarkDNKEurope
119448Environment, Soil from a gasification siteCopenhagenDenmarkDNKEurope1994

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_555.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_555&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: FR750403
  • Sequence Identity:
  • Total samples: 42314
  • soil counts: 16904
  • aquatic counts: 8731
  • animal counts: 11521
  • plant counts: 5158

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
48741Risk group (German classification)
1194481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas frederiksbergensis partial 16S rRNA gene, type strain DSM 13022TFR7504031527ena104087
4874Pseudomonas frederiksbergensis 16S rRNA gene, strain JAJ28AJ2493821503ena104087

External links

@ref: 4874

culture collection no.: CCUG 51506, DSM 13022, CCM 8424, CIP 106887

straininfo link

  • @ref: 82273
  • straininfo: 14971

literature

  • topic: Phylogeny
  • Pubmed-ID: 11155968
  • title: Pseudomonas frederiksbergensis sp. nov., isolated from soil at a coal gasification site.
  • authors: Andersen SM, Johnsen K, Sorensen J, Nielsen P, Jacobsen CS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/00207713-50-6-1957
  • year: 2000
  • mesh: Bacterial Typing Techniques, Base Composition, *Coal Mining, DNA, Ribosomal/analysis, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phenanthrenes/*metabolism, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4874Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13022)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13022
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
40654Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19067
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
82273Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14971.1StrainInfo: A central database for resolving microbial strain identifiers
119448Curators of the CIPCollection of Institut Pasteur (CIP 106887)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106887