Strain identifier

BacDive ID: 12817

Type strain: Yes

Species: Pseudomonas cichorii

Strain Designation: PC 1

Strain history: CIP <- 2000, LMG <- NCPPB <- ICPB <- NRRL <- W. Kotte

NCBI tax ID(s): 36746 (species)

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General

@ref: 12688

BacDive-ID: 12817

DSM-Number: 50259

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

description: Pseudomonas cichorii PC 1 is an aerobe, mesophilic, Gram-negative plant pathogen of the family Pseudomonadaceae.

NCBI tax id

  • NCBI tax id: 36746
  • Matching level: species

strain history

@refhistory
12688<- H. Stolp <- ATCC <- B.A. Friedman <- W.H. Burkholder; PC 1
118278CIP <- 2000, LMG <- NCPPB <- ICPB <- NRRL <- W. Kotte

doi: 10.13145/bacdive12817.20230509.8.1

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 cichorii
  • full scientific name: Pseudomonas cichorii (Swingle 1925) Stapp 1928 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Phytomonas cichorii

@ref: 12688

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas cichorii

full scientific name: Pseudomonas cichorii (Swingle 1925) Stapp 1928

strain designation: PC 1

type strain: yes

Morphology

cell morphology

  • @ref: 118278
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 118278
  • production: no
  • name: Pyocyanin

multimedia

  • @ref: 12688
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_50259.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12688TRYPTICASE 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
12688NUTRIENT 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
12688GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54)yeshttps://mediadive.dsmz.de/medium/54Name: GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54) Composition: CaCO3 20.0 g/l Glucose 20.0 g/l Agar 17.0 g/l Yeast extract 10.0 g/l Distilled water
39558MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
12688PSEUDOMONAS AGAR F (DSMZ Medium 907)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium907.pdf
12688CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium220.pdf
118278CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
118278CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
12688positivegrowth28mesophilic
12688positivegrowth27mesophilic
39558positivegrowth25mesophilic
51176positivegrowth28mesophilic
118278positivegrowth5-30
118278nogrowth37mesophilic
118278nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
51176aerobe
118278obligate aerobe

compound production

@refcompound
126886 aminopenicillanic acid
12688poly(ß-hydroxyalkanoic acids)
12688omega transaminase

halophily

@refsaltgrowthtested relationconcentration
118278NaClpositivegrowth0-6 %
118278NaClnogrowth8 %
118278NaClnogrowth10 %

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
11827816947citrate+carbon source
1182784853esculin+hydrolysis
11827817632nitrate-reduction
11827816301nitrite-reduction
11827817632nitrate-respiration

antibiotic resistance

  • @ref: 118278
  • 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
11827835581indoleno

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
118278oxidase+
118278beta-galactosidase-3.2.1.23
118278alcohol dehydrogenase-1.1.1.1
118278gelatinase-
118278amylase-
118278DNase-
118278caseinase-3.4.21.50
118278catalase+1.11.1.6
118278tween esterase-
118278lecithinase-
118278lipase-
118278lysine decarboxylase-4.1.1.18
118278ornithine decarboxylase-4.1.1.17
118278protease-
118278tryptophan deaminase-
118278urease-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
118278-+++-+--+-++----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
12688--------++-+--++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118278+++-+-------------++++----+----+++---------+++++++++-++++---+-+++-----++++-+++-++++++---+++++++++-+

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typesampling dateisolation date
39558GermanyDEUEurope
51176GermanyDEUEuropeCichorium endivia1929
118278GermanyDEUEuropeCichorium endiva1929

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5400.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_2240;99_5400&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: Z76658
  • Sequence Identity:
  • Total samples: 8710
  • soil counts: 1846
  • aquatic counts: 1730
  • animal counts: 3377
  • plant counts: 1757

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
12688yes1Risk group (German classification)
1182781Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas cichorii gene for 16S rRNA, strain: ATCC 10857AB0213981505ena36746
20218Pseudomonas cichorii partial 16S rRNA gene, type strain ICMP 5707TAJ3083021371ena36746
20218Pseudomonas cichorii culture-collection CFBP:2101 16S ribosomal RNA gene, partial sequenceHM1902281444ena36746
20218Pseudomonas cichorii strain BC2595 16S ribosomal RNA gene, partial sequenceJX9137841408ena36746
20218P.cichorii 16S rRNA geneZ766581494ena36746

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas cichorii DSM 50259GCA_018343775completencbi36746
66792Pseudomonas cichorii LMG 2162GCA_015471425contigncbi36746
66792Pseudomonas cichorii ATCC 10857GCA_900104015scaffoldncbi36746
66792Pseudomonas cichorii strain ATCC 1085736746.17wgspatric36746
66792Pseudomonas cichorii strain DSM 5025936746.30completepatric36746
66792Pseudomonas cichorii strain LMG 216236746.26wgspatric36746
66792Pseudomonas cichorii NCPPB 9432667527209draftimg36746

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes79.882no
gram-positiveno98.707no
anaerobicno98.649yes
aerobicyes94.796no
halophileno91.258no
spore-formingno96.175no
thermophileno99.712yes
glucose-utilyes94.983yes
motileyes89.638no
glucose-fermentno89.739no

External links

@ref: 12688

culture collection no.: DSM 50259, ATCC 10857, CCUG 32776, NCPPB 943, LMG 2162, ATCC 19303, ATCC 19474, CIP 106704, NRRL B-832, ICPB PC1

straininfo link

  • @ref: 82027
  • straininfo: 3986

literature

Pubmed-IDtitleauthorsjournalDOIyeartopicmeshtopic2
30786539First Report of Bacterial Leaf Spot Caused by Pseudomonas cichorii on Phlox paniculata in Italy.Garibaldi A, Bertetti D, Scortichini M, Gullino MLPlant Dis10.1094/PD-89-0912C2005
31559681Loss of wbpL disrupts O-polysaccharide synthesis and impairs virulence of plant-associated Pseudomonas strains.Kutschera A, Schombel U, Wrobel M, Gisch N, Ranf SMol Plant Pathol10.1111/mpp.128642019MetabolismArabidopsis/*microbiology, Bacterial Proteins/*metabolism, Gene Knockout Techniques, Lycopersicon esculentum/*microbiology, Multigene Family, Plant Diseases/*microbiology, Polysaccharides/*biosynthesis, Pseudomonas/*pathogenicity, Pseudomonas syringae/pathogenicity, Virulence
34424837Pseudomonas capsici sp. nov., a plant-pathogenic bacterium isolated from pepper leaf in Georgia, USA.Zhao M, Koirala S, Chen HC, Gitaitis R, Kvitko B, Dutta BInt J Syst Evol Microbiol10.1099/ijsem.0.0049712021PhylogenyBacterial Typing Techniques, Base Composition, Capsicum/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Georgia, Nucleic Acid Hybridization, *Phylogeny, Plant Leaves/microbiology, *Pseudomonas/classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12688Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50259)https://www.dsmz.de/collection/catalogue/details/culture/DSM-50259
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
39558Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18863
51176Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32776)https://www.ccug.se/strain?id=32776
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)
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
82027Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3986.1StrainInfo: A central database for resolving microbial strain identifiers
118278Curators of the CIPCollection of Institut Pasteur (CIP 106704)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106704