Strain identifier

BacDive ID: 13099

Type strain: Yes

Species: Pseudomonas umsongensis

Strain Designation: Ps 3-10

Strain history: CIP <- 2005, KACC <- Nat. Inst. Agricult. Biotechn., Korea: strain Ps 3-10

NCBI tax ID(s): 198618 (species)

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General

@ref: 6521

BacDive-ID: 13099

DSM-Number: 16611

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

description: Pseudomonas umsongensis Ps 3-10 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from agricultural soil.

NCBI tax id

  • NCBI tax id: 198618
  • Matching level: species

strain history

@refhistory
6521<- S. W. Kwon; Ps 3-10
67770KACC 10847 <-- S.-W. Kwon Ps 3-10.
123722CIP <- 2005, KACC <- Nat. Inst. Agricult. Biotechn., Korea: strain Ps 3-10

doi: 10.13145/bacdive13099.20230509.8.1

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 umsongensis
  • full scientific name: Pseudomonas umsongensis Kwon et al. 2003

@ref: 6521

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas umsongensis

full scientific name: Pseudomonas umsongensis Kwon et al. 2003

strain designation: Ps 3-10

type strain: yes

Morphology

cell morphology

  • @ref: 123722
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 123722
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6521CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
33259MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123722CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6521positivegrowth30mesophilic
33259positivegrowth30mesophilic
60270positivegrowth30mesophilic
67770positivegrowth30mesophilic
123722positivegrowth5-37
123722nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60270aerobe
123722obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
123722NaClpositivegrowth0-4 %
123722NaClnogrowth6 %
123722NaClnogrowth8 %
123722NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+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
12372216947citrate+carbon source
1237224853esculin-hydrolysis
12372217632nitrate+reduction
12372216301nitrite-reduction
12372217632nitrate-respiration

antibiotic resistance

  • @ref: 123722
  • 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
12372235581indoleno

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
123722oxidase+
123722beta-galactosidase-3.2.1.23
123722alcohol dehydrogenase-1.1.1.1
123722gelatinase-
123722amylase-
123722DNase-
123722caseinase-3.4.21.50
123722catalase+1.11.1.6
123722tween esterase-
123722lecithinase-
123722lipase-
123722lysine decarboxylase-4.1.1.18
123722ornithine decarboxylase-4.1.1.17
123722protease-
123722tryptophan deaminase-
123722urease-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
123722--++-++-+-+---------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6521+--+----+++---++-++++
6521+--+----++++++++-++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123722+++-+--------------+++---------+-----------++---++++-++++-+-+++++--+-++++++++++++++++-+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6521agricultural soilUmsong regionRepublic of KoreaKORAsia
60270Soil,agriculturalRepublic of KoreaKORAsia
67770Soil of Umsong Region in Korea
123722Environment, SoilUmsong RegionRepublic of KoreaKORAsia2000

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_444.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_444&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AF468450
  • Sequence Identity:
  • Total samples: 636
  • soil counts: 197
  • aquatic counts: 124
  • animal counts: 162
  • plant counts: 153

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65211Risk group (German classification)
1237221Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6521
  • description: Pseudomonas sp. Ps 3-10 16S ribosomal RNA gene, partial sequence
  • accession: AF468450
  • length: 1455
  • database: ena
  • NCBI tax ID: 198618

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas umsongensis strain DSM 16611198618.6wgspatric198618
66792Pseudomonas umsongensis strain DSM 16611198618.7wgspatric198618
66792Pseudomonas umsongensis LMG 213172639762618draftimg198618
66792Pseudomonas umsongensis DSM 166112917099900draftimg198618
67770Pseudomonas umsongensis DSM 16611GCA_002236105contigncbi198618
66792Pseudomonas umsongensis LMG 21317GCA_900105285chromosomencbi198618

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.838no
glucose-fermentno89.834no
flagellatedyes79.151no
gram-positiveno98.294no
anaerobicno98.025no
aerobicyes90.828yes
halophileno83.881no
spore-formingno96.029no
thermophileno99.839yes
glucose-utilyes89.853no

External links

@ref: 6521

culture collection no.: DSM 16611, KACC 10847, LMG 21317, CCUG 54631, JCM 16394, BCRC 17504, CIP 108618

straininfo link

  • @ref: 82309
  • straininfo: 86037

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656147Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea.Kwon SW, Kim JS, Park IC, Yoon SH, Park DH, Lim CK, Go SJInt J Syst Evol Microbiol10.1099/ijs.0.02326-02003Agriculture, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species SpecificityGenetics
Genetics28963215Draft Genome Sequence of the Type Strain Pseudomonas umsongensis DSM 16611.Furmanczyk EM, Kaminski MA, Dziembowski A, Lipinski L, Sobczak AGenome Announc10.1128/genomeA.01038-172017

Reference

@idauthorscataloguedoi/urltitle
6521Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16611)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16611
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
33259Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6267
60270Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54631)https://www.ccug.se/strain?id=54631
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
82309Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID86037.1StrainInfo: A central database for resolving microbial strain identifiers
123722Curators of the CIPCollection of Institut Pasteur (CIP 108618)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108618