Strain identifier

BacDive ID: 4389

Type strain: Yes

Species: Erwinia rhapontici

Strain Designation: CP/28, CP 28

Strain history: CIP <- 1997, CFBP <- J.J. Panes: strain CP 28

NCBI tax ID(s): 55212 (species)

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General

@ref: 1697

BacDive-ID: 4389

DSM-Number: 4484

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

description: Erwinia rhapontici CP/28 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from rhubarb.

NCBI tax id

  • NCBI tax id: 55212
  • Matching level: species

strain history

@refhistory
1697<- ATCC <- M.P. Starr, ICPB <- NCPPB <- J. Panes, CP/28
122195CIP <- 1997, CFBP <- J.J. Panes: strain CP 28

doi: 10.13145/bacdive4389.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Erwiniaceae
  • genus: Erwinia
  • species: Erwinia rhapontici
  • full scientific name: Erwinia rhapontici (Millard 1924) Burkholder 1948 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Phytomonas rhapontica
    20215Pectobacterium rhapontici

@ref: 1697

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Erwinia

species: Erwinia rhapontici

full scientific name: Erwinia rhapontici (Millard 1924) Burkholder 1948 emend. Hauben et al. 1998

strain designation: CP/28, CP 28

type strain: yes

Morphology

cell morphology

  • @ref: 122195
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
1697REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)yeshttps://mediadive.dsmz.de/medium/1aName: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39230MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
122195CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
1697positivegrowth30mesophilic
39230positivegrowth25mesophilic
122195positivegrowth5-41

Physiology and metabolism

oxygen tolerance

  • @ref: 122195
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371gluconate+builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose+builds acid from62318
68371turanose+builds acid from32528
68371gentiobiose+builds acid from28066
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose+builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose+builds acid from28053
68371lactose+builds acid from17716
68371maltose+builds acid from17306
68371cellobiose+builds acid from17057
68371salicin+builds acid from17814
68371esculin+builds acid from4853
68371arbutin+builds acid from18305
68371amygdalin+builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol+builds acid from17268
68371L-rhamnose+builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose+builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol+builds acid from17754
68368nitrate+reduction17632
68368L-arabinose+fermentation30849
68368amygdalin+fermentation27613
68368melibiose+fermentation28053
68368sucrose+fermentation17992
68368L-rhamnose+fermentation62345
68368sorbitol-fermentation30911
68368myo-inositol+fermentation17268
68368D-mannitol+fermentation16899
68368D-glucose+fermentation17634
68368gelatin-hydrolysis5291
68368tryptophan-energy source27897
68368urea-hydrolysis16199
68368citrate+assimilation16947
68368ornithine-degradation18257
68368lysine-degradation25094
68368arginine-hydrolysis29016
122195mannitol+fermentation29864
122195citrate+carbon source16947
122195glucose+fermentation17234
122195lactose+fermentation17716
122195nitrate+reduction17632
122195nitrite+reduction16301
122195malonate+assimilation15792
122195sodium thiosulfate-builds gas from132112
122195glucose+degradation17234

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteyes
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12219535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12219515688acetoin+
12219517234glucose+

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase+3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)-
68382alkaline phosphatase+3.1.3.1
68368cytochrome oxidase-1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase-3.2.1.23
122195oxidase-
122195beta-galactosidase+3.2.1.23
122195alcohol dehydrogenase-1.1.1.1
122195gelatinase-
122195catalase+1.11.1.6
122195lysine decarboxylase-4.1.1.18
122195ornithine decarboxylase-4.1.1.17
122195phenylalanine ammonia-lyase-4.3.1.24
122195tryptophan deaminase-
122195urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122195-+---+----++-+-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
1697----+----+-+++-+++++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122195+--++----++++-++/-++--+/-+++++++++++-++--+/-+++-----++/-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122195+++++-++++++-++++++++-++-+--++-+++++---+-+-------++--+++++-++--------------+--+++-+---+--++++++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
1697rhubarb
122195Rhubarb, Rheum rhabarbarumUnited KingdomGBREurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_20464.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_502;98_2340;99_20464&stattab=map
  • Last taxonomy: Erwinia
  • 16S sequence: Z96087
  • Sequence Identity:
  • Total samples: 19365
  • soil counts: 1082
  • aquatic counts: 1814
  • animal counts: 15272
  • plant counts: 1197

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
1697yes1Risk group (German classification)
1221951Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Erwinia rhapontici strain ATCC 29283 16S-23S intergenic spacer region and tRNA-Glu gene, complete sequenceAF232678376ena55212
20218Erwinia rhapontici 16S ribosomal RNA gene, partial sequenceU802061458ena55212
20218Erwinia rhapontici 16S rRNA gene (strain DSM 4484)AJ2334171497ena55212
20218Erwinia rhapontici LMG 2688 16S ribosomal RNAZ960871498ena55212

External links

@ref: 1697

culture collection no.: DSM 4484, ATCC 29283, ICPB ER 102, NCPPB 1578, CIP 105202, CFBP 3618, ICMP 1582

straininfo link

  • @ref: 73880
  • straininfo: 92240

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Biotechnology17113282Application of response surface methodology to cell immobilization for the production of palatinose.Mundra P, Desai K, Lele SSBioresour Technol10.1016/j.biortech.2006.09.0462006Chromatography, High Pressure Liquid, Erwinia/*metabolism, Isomaltose/*analogs & derivatives/analysis/biosynthesisMetabolism
Phylogeny26637820Erwinia endophytica sp. nov., isolated from potato (Solanum tuberosum L.) stems.Ramirez-Bahena MH, Salazar S, Cuesta MJ, Tejedor C, Igual JM, Fernandez-Pascual M, Peix AInt J Syst Evol Microbiol10.1099/ijsem.0.0008202015

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1697Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 4484)https://www.dsmz.de/collection/catalogue/details/culture/DSM-4484
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
39230Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17195
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
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
73880Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID92240.1StrainInfo: A central database for resolving microbial strain identifiers
122195Curators of the CIPCollection of Institut Pasteur (CIP 105202)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105202