Strain identifier

BacDive ID: 4402

Type strain: Yes

Species: Erwinia persicina

Strain Designation: HK 204, 9108-82

Strain history: CIP <- 1997, CFBP, Erwinia persicinus <- ATCC <- D.J. Brenner, CDC: strain 9108-82 <- K. Komagata and N. Okada: strain HK 204

NCBI tax ID(s): 1219360 (strain), 55211 (species)

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General

@ref: 8048

BacDive-ID: 4402

DSM-Number: 19328

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

description: Erwinia persicina HK 204 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from tomato plant.

NCBI tax id

NCBI tax idMatching level
55211species
1219360strain

strain history

@refhistory
8048<- IAM <- M. V. Hao and K. Komagata; HK 204
67770K. Komagata HK 204.
121688CIP <- 1997, CFBP, Erwinia persicinus <- ATCC <- D.J. Brenner, CDC: strain 9108-82 <- K. Komagata and N. Okada: strain HK 204

doi: 10.13145/bacdive4402.20230509.8.1

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 persicina
  • full scientific name: Erwinia persicina corrig. Hao et al. 1990

  • synonyms

    • @ref: 20215
    • synonym: Erwinia persicinus

@ref: 8048

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Erwiniaceae

genus: Erwinia

species: Erwinia persicina

full scientific name: Erwinia persicina Hao et al. 1990

strain designation: HK 204, 9108-82

type strain: yes

Morphology

cell morphology

  • @ref: 121688
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8048NUTRIENT 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
39228MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8048TRYPTICASE 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
121688CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
8048positivegrowth30mesophilic
39228positivegrowth25mesophilic
67770positivegrowth37mesophilic
121688positivegrowth5-30
121688nogrowth37mesophilic
121688nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 121688
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate+builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
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-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol+builds acid from17924
68371D-mannitol+builds acid from16899
68371galactitol-builds acid from16813
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
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
121688mannitol+fermentation29864
121688citrate+carbon source16947
121688glucose+fermentation17234
121688lactose-fermentation17716
121688nitrate+reduction17632
121688nitrite-reduction16301
121688malonate+assimilation15792
121688sodium thiosulfate-builds gas from132112
121688glucose+degradation17234

antibiotic resistance

  • @ref: 121688
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenno
6836816301nitriteyes
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
12168835581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
12168815688acetoin+
12168817234glucose-

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
121688oxidase-
121688beta-galactosidase+3.2.1.23
121688alcohol dehydrogenase-1.1.1.1
121688gelatinase-
121688catalase+1.11.1.6
121688lysine decarboxylase-4.1.1.18
121688ornithine decarboxylase-4.1.1.17
121688phenylalanine ammonia-lyase-4.3.1.24
121688tryptophan deaminase-
121688urease-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
121688-+---+----++-+------

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
8048+---+----+-+++++++++-+-

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121688+/-+/--++----++++-+/--+/-++---++++++-+/-+/-+/---+---+-------+/--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121688+++++-++++++++++-++++--+-------+++--++--+--------+++-+++++-++--------------+--+++-----+--++++++----

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
8048tomato plantJapanJPNAsia
67770Tomato
121688Tomato, Lycopersicon esculentumJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_4284.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_6;96_7;97_502;98_2340;99_4284&stattab=map
  • Last taxonomy: Erwinia
  • 16S sequence: Z96086
  • Sequence Identity:
  • Total samples: 12606
  • soil counts: 935
  • aquatic counts: 1231
  • animal counts: 9059
  • plant counts: 1381

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
8048yes1Risk group (German classification)
1216881Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
8048Erwinia persicinus 16S ribosomal RNA gene, partial sequenceU802051456ena55211
67770Erwinia persicinus LMG 11254 16S ribosomal RNAZ960861496ena55211

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Erwinia persicina NBRC 1024181219360.3wgspatric1219360
66792Erwinia persicina NBRC 1024182731957625draftimg1219360
67770Erwinia persicina NBRC 102418GCA_001571305contigncbi1219360

GC content

  • @ref: 67770
  • GC-content: 54
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.909no
gram-positiveno98.553no
anaerobicno97.876no
aerobicno56.142no
halophileno89.217no
spore-formingno95.29no
thermophileno99.421yes
glucose-utilyes95.764no
flagellatedno64.054no
glucose-fermentyes89.313yes

External links

@ref: 8048

culture collection no.: DSM 19328, ATCC 35998, CDC 9108-82, IAM 12843, JCM 3704, AJ 2716, CFBP 3622, CIP 105199, ICMP 12532, LMG 11254, NBRC 102418, NCIMB 13181, NCPPB 3774

straininfo link

  • @ref: 73893
  • straininfo: 11848

literature

topicPubmed-IDtitleauthorsjournalDOIyearmesh
Phylogeny2275853Erwinia persicinus, a new species isolated from plants.Hao MV, Brenner DJ, Steigerwalt AG, Kosako Y, Komagata KInt J Syst Bacteriol10.1099/00207713-40-4-3791990Base Composition, DNA, Bacterial/analysis, Erwinia/*classification/genetics, Nucleic Acid Hybridization, Phylogeny, Plants/*microbiology, Species Specificity
30727103First Report of Erwinia persicinus Causing Wilting of Medicago sativa Sprouts in China.Zhang ZF, Nan ZBPlant Dis10.1094/PDIS-10-11-09092012
30781193Erwinia persicina Causing Chlorosis and Necrotic Spots in Leaves and Tendrils of Pisum sativum in Southeastern Spain.Gonzalez AJ, Tello JC, Rodicio MRPlant Dis10.1094/PDIS-91-4-0460A2007

Reference

@idauthorscataloguedoi/urltitle
8048Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19328)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19328
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
39228Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17192
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/
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
73893Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID11848.1StrainInfo: A central database for resolving microbial strain identifiers
121688Curators of the CIPCollection of Institut Pasteur (CIP 105199)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105199