Strain identifier

BacDive ID: 13070

Type strain: Yes

Species: Pseudomonas kilonensis

Strain Designation: 520-20

Strain history: CIP <- 2001, CFBP <- J. Sikorski, Oldenburg Univ., Oldenburg, Germany

NCBI tax ID(s): 132476 (species)

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General

@ref: 4940

BacDive-ID: 13070

DSM-Number: 13647

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

description: Pseudomonas kilonensis 520-20 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from agricultural soil.

NCBI tax id

  • NCBI tax id: 132476
  • Matching level: species

strain history

@refhistory
4940<- J. Sikorski, Univ. Oldenburg; 520-20
67770DSM 13647 <-- J. Sikorski 520-20.
120413CIP <- 2001, CFBP <- J. Sikorski, Oldenburg Univ., Oldenburg, Germany

doi: 10.13145/bacdive13070.20230509.8.1

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 kilonensis
  • full scientific name: Pseudomonas kilonensis Sikorski et al. 2001

@ref: 4940

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas kilonensis

full scientific name: Pseudomonas kilonensis Sikorski et al. 2001

strain designation: 520-20

type strain: yes

Morphology

cell morphology

  • @ref: 120413
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 120413
  • production: yes
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4940NUTRIENT 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
4940LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
33765MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120413CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4940positivegrowth28mesophilic
33765positivegrowth30mesophilic
67770positivegrowth28mesophilic
120413positivegrowth5-37
120413nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 120413
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120413NaClpositivegrowth0-2 %
120413NaClnogrowth4 %
120413NaClnogrowth6 %
120413NaClnogrowth8 %
120413NaClnogrowth10 %

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
12041316947citrate+carbon source
1204134853esculin-hydrolysis
12041317632nitrate+reduction
12041316301nitrite+reduction
12041317632nitrate+respiration

antibiotic resistance

  • @ref: 120413
  • 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
12041335581indoleno

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
120413oxidase+
120413beta-galactosidase-3.2.1.23
120413alcohol dehydrogenase-1.1.1.1
120413gelatinase-
120413amylase-
120413DNase-
120413caseinase-3.4.21.50
120413catalase+1.11.1.6
120413tween esterase+
120413lecithinase-
120413lipase-
120413lysine decarboxylase-4.1.1.18
120413ornithine decarboxylase-4.1.1.17
120413protease-
120413tryptophan deaminase-
120413urease-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
120413--++-++-+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4940+-----+-++++--++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120413+++++--+-----------+++----+----+++--+------++-+-++++-+++----+-+++------+++-+++-+++-++-+-+++++++++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
4940agricultural soilKielGermanyDEUEurope
67770Agricultural soilnear KielGermanyDEUEurope
120413Environment, SoilGermanyDEUEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#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: AJ292426
  • 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
49401Risk group (German classification)
1204131Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4940
  • description: Pseudomonas kilonensis 16S rRNA gene, strain 520-20
  • accession: AJ292426
  • length: 1528
  • database: ena
  • NCBI tax ID: 132476

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas kilonensis strain DSM 13647132476.6wgspatric132476
66792Pseudomonas kilonensis DSM 136472713897225draftimg132476
66792Pseudomonas kilonensis DSM 136472639762655draftimg132476
67770Pseudomonas kilonensis DSM 13647GCA_001269885contigncbi132476
66792Pseudomonas kilonensis DSM 13647GCA_900105635contigncbi132476

GC content

@refGC-contentmethod
494059.9
6777059.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes92.043no
gram-positiveno98.401no
anaerobicno98.483no
halophileno91.883no
spore-formingno95.744no
glucose-utilyes94.44yes
aerobicyes91.258no
flagellatedyes85.26no
thermophileno99.84no
glucose-fermentno88.749yes

External links

@ref: 4940

culture collection no.: DSM 13647, CFBP 5372, JCM 11939, CIP 107321

straininfo link

  • @ref: 82280
  • straininfo: 49503

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11491357Pseudomonas kilonensis sp. nov., a bacterium isolated from agricultural soil.Sikorski J, Stackebrandt E, Wackernagel WInt J Syst Evol Microbiol10.1099/00207713-51-4-15492001Base Composition, Base Sequence, DNA, Bacterial/chemistry/genetics, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Random Amplified Polymorphic DNA Technique, Ribotyping, *Soil MicrobiologyGenetics
Phylogeny32776868Pseudomonas viciae sp. nov., isolated from rhizosphere of broad bean.Zhao H, Ma Y, Wu X, Zhang LInt J Syst Evol Microbiol10.1099/ijsem.0.0043732020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, *Rhizosphere, *Soil Microbiology, Ubiquinone/chemistry, Vicia faba/*microbiologyEnzymology
Phylogeny33528346Pseudomonas bijieensis sp. nov., isolated from cornfield soil.Liang J, Wang S, Yiming A, Fu L, Ahmad I, Chen G, Zhu BInt J Syst Evol Microbiol10.1099/ijsem.0.0046762021
Phylogeny35072599Pseudomonas canavaninivorans sp. nov., isolated from bean rhizosphere.Hauth F, Buck H, Hartig JSInt J Syst Evol Microbiol10.1099/ijsem.0.0052032022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome
Phylogeny35442877Pseudomonas uvaldensis sp. nov., a bacterial pathogen causing onion bulb rot.Khanal M, Timilsina S, Bhatta BP, Bophela K, Coutinho T, Cochran K, Malla SInt J Syst Evol Microbiol10.1099/ijsem.0.0053112022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Genes, Bacterial, *Onions/microbiology, Phylogeny, Pseudomonas, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitle
4940Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13647)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13647
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
33765Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4744
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
82280Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49503.1StrainInfo: A central database for resolving microbial strain identifiers
120413Curators of the CIPCollection of Institut Pasteur (CIP 107321)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107321