Strain identifier

BacDive ID: 13140

Type strain: Yes

Species: Pseudomonas marginalis

Strain history: CIP <- 2004, J. Chun, Seoul, Republic of Korea: strain CG20106

NCBI tax ID(s): 298 (species)

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General

@ref: 7580

BacDive-ID: 13140

DSM-Number: 18529

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

description: Pseudomonas marginalis DSM 18529 is an aerobe, mesophilic, Gram-negative plant pathogen that was isolated from rusty root lesions of Korean ginseng.

NCBI tax id

  • NCBI tax id: 298
  • Matching level: species

strain history

@refhistory
7580<- KCTC <- J. Chun, Natl. Univ., Seoul
382802004, J. Chun, Seoul, Republic of Korea: strain CG20106
67771<- J. Chun, Seoul National Univ.
121525CIP <- 2004, J. Chun, Seoul, Republic of Korea: strain CG20106

doi: 10.13145/bacdive13140.20230509.8.1

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 marginalis
  • full scientific name: Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Bacterium marginale
    20215Pseudomonas panacis

@ref: 7580

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas panacis

full scientific name: Pseudomonas panacis Park et al. 2005

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31450negativerod-shapedyes
67771negative
69480yes96.315
69480negative99.998
121525negativerod-shapedyes

pigmentation

@refproductionname
31450yes
121525noPyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7580NUTRIENT 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
7580TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
38280MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121525CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7580positivegrowth30mesophilic
31450positivegrowth04-35
31450positiveoptimum19.5psychrophilic
38280positivegrowth30mesophilic
67771positivegrowth30mesophilic
121525positivegrowth10-30
121525nogrowth5psychrophilic
121525nogrowth37mesophilic
121525nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31450aerobe
67771aerobe
121525obligate aerobe

spore formation

@refspore formationconfidence
31450no
69481no100
69480no99.985

halophily

@refsaltgrowthtested relationconcentration
31450NaClpositivegrowth<5 %
31450NaClpositiveoptimum2.5 %
121525NaClpositivegrowth0-4 %
121525NaClnogrowth6 %
121525NaClnogrowth8 %
121525NaClnogrowth10 %

observation

  • @ref: 31450
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3145021217L-alaninamide+carbon source
3145016449alanine+carbon source
3145022599arabinose+carbon source
3145018403L-arabitol+carbon source
3145022653asparagine+carbon source
3145035391aspartate+carbon source
3145027689decanoate+carbon source
3145017126DL-carnitine+carbon source
3145016947citrate+carbon source
3145028757fructose+carbon source
3145028260galactose+carbon source
3145024265gluconate+carbon source
3145017234glucose+carbon source
3145029987glutamate+carbon source
3145017754glycerol+carbon source
3145027570histidine+carbon source
3145017596inosine+carbon source
3145024996lactate+carbon source
3145025017leucine+carbon source
3145025115malate+carbon source
3145015792malonate+carbon source
3145029864mannitol+carbon source
3145037684mannose+carbon source
3145028053melibiose+carbon source
3145051850methyl pyruvate+carbon source
3145018257ornithine+carbon source
3145017272propionate+carbon source
3145017822serine+carbon source
3145030911sorbitol+carbon source
3145030031succinate+carbon source
3145017992sucrose+carbon source
3145027082trehalose+carbon source
3145016704uridine+carbon source
3145027248urocanic acid+carbon source
314504853esculin+hydrolysis
3145017632nitrate+reduction
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate+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
12152516947citrate+carbon source
1215254853esculin+hydrolysis
12152517632nitrate+reduction
12152516301nitrite-reduction
12152517632nitrate-respiration

antibiotic resistance

  • @ref: 121525
  • 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
12152535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
31450acid phosphatase+3.1.3.2
31450alkaline phosphatase+3.1.3.1
31450catalase+1.11.1.6
31450gelatinase+
31450cytochrome 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
121525oxidase+
121525beta-galactosidase-3.2.1.23
121525alcohol dehydrogenase+1.1.1.1
121525gelatinase+/-
121525amylase+
121525DNase-
121525caseinase-3.4.21.50
121525catalase+1.11.1.6
121525tween esterase-
121525lecithinase+
121525lipase-
121525lysine decarboxylase-4.1.1.18
121525ornithine decarboxylase-4.1.1.17
121525protease-
121525tryptophan deaminase-
121525urease-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
121525--++-+--+-++----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7580+--+-++-++++++/-++-++-+
7580+--+-++-+++++-++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121525+++++-------------++++----+----+++--+--++--++---+++++++++++++-+++-----++++-++++++++++-+++++++++++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
7580rusty root lesions of Korean ginsengRepublic of KoreaKORAsia
67771From GinsengRepublic of KoreaKORAsia
121525Plant, Rusty root of Korea ginsengRepublic of KoreaKORAsia2004

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Other#Wound
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_199.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_199&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AY787208
  • Sequence Identity:
  • Total samples: 8172
  • soil counts: 874
  • aquatic counts: 1631
  • animal counts: 3216
  • plant counts: 2451

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
7580yes1Risk group (German classification)
1215251Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7580
  • description: Pseudomonas panacis strain CG20106 16S ribosomal RNA gene, partial sequence
  • accession: AY787208
  • length: 1499
  • database: ena
  • NCBI tax ID: 307251

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas marginalis DSM 18529GCA_007858175contigncbi298
66792Pseudomonas panacis strain DSM 18529307251.4wgspatric307251

GC content

  • @ref: 31450
  • GC-content: 61.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.383yes
anaerobicno98.418yes
halophileno92.247no
spore-formingno95.593yes
glucose-utilyes94.507yes
motileyes91.868yes
flagellatedyes80.49no
aerobicyes94.182yes
thermophileno99.87yes
glucose-fermentno89.232yes

External links

@ref: 7580

culture collection no.: DSM 18529, CIP 108524, IMSNU 14100, KCTC 12330, CG 20106, IMSNU 14101

straininfo link

  • @ref: 82348
  • straininfo: 232819

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014508Pseudomonas panacis sp. nov., isolated from the surface of rusty roots of Korean ginseng.Park YD, Lee HB, Yi H, Kim Y, Bae KS, Choi JE, Jung HS, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.63592-02005Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Panax/*microbiology, Phenotype, Phylogeny, Plant Roots/*microbiology, Pseudomonas/chemistry/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny35507398Genome analysis of Pseudomonas species reveals that Pseudomonas panacis Park et al. 2005 is a later heterotypic synonym of Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980).Kujur RRA, Deb S, Das SKInt J Syst Evol Microbiol10.1099/ijsem.0.0053542022Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Nucleic Acid Hybridization, Phylogeny, *Pseudomonas/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7580Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18529)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18529
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
31450Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2775328776041
38280Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6156
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
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
82348Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID232819.1StrainInfo: A central database for resolving microbial strain identifiers
121525Curators of the CIPCollection of Institut Pasteur (CIP 108524)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108524