Strain identifier

BacDive ID: 13144

Type strain: Yes

Species: Xanthomonas cissicola

Strain Designation: PC1

Strain history: CIP <- 2000, CCM <- M. Goto: strain PC1, Agrobacterium sp.

NCBI tax ID(s): 86186 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 15429

BacDive-ID: 13144

DSM-Number: 21306

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, plant pathogen

description: Xanthomonas cissicola PC1 is an obligate aerobe, mesophilic, motile plant pathogen that was isolated from Leaf spot of Cissus japonica.

NCBI tax id

  • NCBI tax id: 86186
  • Matching level: species

strain history

@refhistory
15429<- CCM <- M. Goto, Shizuoka University, Japan
67770CIP 106723 <-- CCM 2888 <-- M. Goto PC1.
118291CIP <- 2000, CCM <- M. Goto: strain PC1, Agrobacterium sp.

doi: 10.13145/bacdive13144.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Lysobacteraceae
  • genus: Xanthomonas
  • species: Xanthomonas cissicola
  • full scientific name: Xanthomonas cissicola (Takimoto 1939) Rudra and Gupta 2021

  • synonyms

    @refsynonym
    20215Aplanobacter cissicola
    20215Pseudomonas cissicola

@ref: 15429

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas cissicola

full scientific name: Pseudomonas cissicola (Takimoto 1939) Burkholder 1948

strain designation: PC1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.664
6948099.994negative
118291yesnegativerod-shaped

pigmentation

  • @ref: 118291
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15429R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
40329MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118291CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
15429positivegrowth28mesophilic
40329positivegrowth25mesophilic
67770positivegrowth25mesophilic
118291positivegrowth25-30mesophilic
118291nogrowth5psychrophilic
118291nogrowth10psychrophilic
118291nogrowth37mesophilic
118291nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118291
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentration
118291NaClpositivegrowth0 %
118291NaClnogrowth4 %
118291NaClnogrowth6 %
118291NaClnogrowth8 %
118291NaClnogrowth10 %

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
11829116947citrate+carbon source
1182914853esculin+hydrolysis
11829117632nitrate-reduction
11829116301nitrite-reduction
11829117632nitrate-respiration

antibiotic resistance

  • @ref: 118291
  • 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
11829135581indoleno

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
118291oxidase-
118291beta-galactosidase+3.2.1.23
118291alcohol dehydrogenase-1.1.1.1
118291gelatinase+
118291amylase+
118291DNase+
118291caseinase+3.4.21.50
118291catalase+1.11.1.6
118291tween esterase+
118291lecithinase-
118291lipase+
118291lysine decarboxylase-4.1.1.18
118291ornithine decarboxylase-4.1.1.17
118291protease+
118291tryptophan deaminase-
118291urease-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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    46911C14:0214
    46911C15:01.815
    46911C16:03.516
    46911C10:0 3OH1.711.423
    46911C11:0 ISO 3OH3.212.09
    46911C13:0 ISO 3OH2.314.11
    46911C15:0 ANTEISO814.711
    46911C15:0 ISO42.614.621
    46911C16:0 10-methyl7.116.433
    46911C16:1 ω7c19.415.819
    46911C16:1 ω9c1.315.774
    46911C17:0 iso5.316.629
    46911unknown 11.7981.911.798
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
118291-++++++++-++-+--++--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
46911-----++++-+-+----++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118291+++++-++-------++-+--+--+------+-------+---------+++-+-----+--+----------------++-+---------++--+-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
15429Leaf spot of Cissus japonicaCissus japonica
46911Leaf spotJapanJPNAsia
67770Leaf spot of Cissus japonicaCissus japonicaJapanJPNAsia
118291Plant, Leaf spot of Cissus japonicaJapanJPNAsia1974

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Leaf (Phyllosphere)

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
15429yes1Risk group (German classification)
1182911Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15429
  • description: [Pseudomonas] cissicola gene for 16S rRNA, strain: ATCC 33616
  • accession: AB021399
  • length: 1503
  • database: ena
  • NCBI tax ID: 86186

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792[Pseudomonas] cissicola strain LMG2171986186.3wgspatric86186
66792[Pseudomonas] cissicola strain CCUG 1883986186.4wgspatric86186
66792Pseudomonas cissicola LMG217192791355361draftimg86186
67770Xanthomonas cissicola LMG21719GCA_002019225contigncbi86186
67770Xanthomonas cissicola CCUG 18839GCA_008801575contigncbi86186

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes79.613no
flagellatedno84.016no
gram-positiveno98.084no
anaerobicno99.057no
halophileno95.185no
spore-formingno95.052no
glucose-utilyes94.112no
aerobicyes95.407no
thermophileno98.967yes
glucose-fermentno90.22yes

External links

@ref: 15429

culture collection no.: DSM 21306, ATCC 33616, CCM 2888, CCUG 18839, CIP 106723, ICMP 8561, LMG 2167, NCPPB 2982, JCM 13362, CIP 105155, LMG 21719

Reference

@idauthorscataloguedoi/urltitle
15429Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21306)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21306
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
40329Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18885
46911Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 18839)https://www.ccug.se/strain?id=18839
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
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
118291Curators of the CIPCollection of Institut Pasteur (CIP 106723)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106723