Strain identifier

BacDive ID: 13155

Type strain: Yes

Species: Pseudomonas knackmussii

Strain Designation: B13

Strain history: CIP <- 2007, DSMZ <- K.J. Knackmus, Germany: strain B13

NCBI tax ID(s): 1301098 (strain), 65741 (species)

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General

@ref: 2933

BacDive-ID: 13155

DSM-Number: 6978

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

description: Pseudomonas knackmussii B13 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sewage plant.

NCBI tax id

NCBI tax idMatching level
1301098strain
65741species

strain history

@refhistory
2933<- K.-J. Knackmuss
120452CIP <- 2007, DSMZ <- K.J. Knackmus, Germany: strain B13

doi: 10.13145/bacdive13155.20230509.8.1

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 knackmussii
  • full scientific name: Pseudomonas knackmussii Stolz et al. 2007

@ref: 2933

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas knackmussii

full scientific name: Pseudomonas knackmussii Stolz et al. 2007

strain designation: B13

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31984negativerod-shapedyes
120452negativerod-shapedyes

pigmentation

  • @ref: 31984
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2933NUTRIENT 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
2933MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)yeshttps://mediadive.dsmz.de/medium/457Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 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
37774MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120452CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
2933positivegrowth30mesophilic
31984positivegrowth20-41
31984positiveoptimum30.5mesophilic
37774positivegrowth30mesophilic
60389positivegrowth30-37mesophilic

culture pH

@refabilitytypepH
31984positivegrowth6.0-8.3
31984positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60389aerobe
120452obligate aerobe

compound production

  • @ref: 2933
  • compound: muconat cycloisomerase II

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31984370543-hydroxybutyrate+carbon source
31984178794-hydroxybenzoate+carbon source
3198417128adipate+carbon source
3198416449alanine+carbon source
3198435391aspartate+carbon source
3198416947citrate+carbon source
3198428757fructose+carbon source
3198424265gluconate+carbon source
3198417234glucose+carbon source
3198427570histidine+carbon source
3198417240itaconate+carbon source
3198424996lactate+carbon source
3198425017leucine+carbon source
3198425115malate+carbon source
3198418257ornithine+carbon source
3198418401phenylacetate+carbon source
3198426271proline+carbon source
3198417148putrescine+carbon source
3198415361pyruvate+carbon source
319849300suberic acid+carbon source
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
12045217632nitrate+reduction
12045216301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12045235581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31984catalase+1.11.1.6
31984cytochrome oxidase+1.9.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6
120452oxidase+
120452catalase+1.11.1.6
120452urease-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
120452-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2933+--+----+-----++-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
2933sewage plantGöttingenGermanyDEUEurope
120452Environment, Sewage treatment plantGöttingenGermanyDEUEurope

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Water treatment plant

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
29331Risk group (German classification)
1204521Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas sp. partial 16S rRNA gene, isolate B13AJ272544612ena1301098
20218Pseudomonas knackmussii strain B13 16S ribosomal RNA gene, partial sequenceHM0071541441ena1301098
20218Pseudomonas sp. B13(2012) 16S ribosomal RNA gene, partial sequenceJF3130491517ena1156300
20218Pseudomonas sp. B13(2012b) 16S ribosomal RNA gene, partial sequenceJQ9515211483ena1207912
20218Pseudomonas sp. 16S ribosomal RNA (rRNA)L40412559ena306
31984Pseudomonas knackmussii strain B13 small subunit ribosomal RNA gene, complete sequenceAF0394891528nuccore1301098

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas knackmussii B13GCA_000689415completencbi1301098
66792Pseudomonas knackmussii B131301098.3completepatric1301098
66792Pseudomonas knackmussii B132579778852completeimg1301098

GC content

@refGC-contentmethod
293367.0thermal denaturation, midpoint method (Tm)
3198466.8-67.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.885yes
flagellatedyes82.847no
gram-positiveno98.082no
anaerobicno97.839yes
halophileno83.453no
spore-formingno95.133no
glucose-utilyes88.588yes
aerobicyes91.271yes
thermophileno99.537yes
glucose-fermentno89.958no

External links

@ref: 2933

culture collection no.: DSM 6978, CCUG 54928, CIP 109584, DSM 624, LMG 23759

straininfo link

  • @ref: 82363
  • straininfo: 48342

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17329787Pseudomonas knackmussii sp. nov.Stolz A, Busse HJ, Kampfer PInt J Syst Evol Microbiol10.1099/ijs.0.64761-02007DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Pseudomonas/chemistry/*classification/genetics/physiology, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny18523175Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site.Gupta SK, Kumari R, Prakash O, Lal RInt J Syst Evol Microbiol10.1099/ijs.0.65401-02008Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
2933Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6978)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6978
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
31984Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128238
37774Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7343
60389Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54928)https://www.ccug.se/strain?id=54928
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
82363Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48342.1StrainInfo: A central database for resolving microbial strain identifiers
120452Curators of the CIPCollection of Institut Pasteur (CIP 109584)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109584