Strain identifier

BacDive ID: 5018

Type strain: Yes

Species: Pectobacterium atrosepticum

Strain Designation: G/39, G39

Strain history: CIP <- 1997, CFBP <- D.C. Graham: strain G39

NCBI tax ID(s): 29471 (species)

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General

@ref: 7378

BacDive-ID: 5018

DSM-Number: 18077

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

description: Pectobacterium atrosepticum G/39 is a facultative anaerobe, mesophilic, Gram-negative plant pathogen that was isolated from Solanum tuberosum.

NCBI tax id

  • NCBI tax id: 29471
  • Matching level: species

strain history

@refhistory
7378<- CFBP <- D. C. Graham; G/39
116545CIP <- 1997, CFBP <- D.C. Graham: strain G39

doi: 10.13145/bacdive5018.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Enterobacterales
  • family: Pectobacteriaceae
  • genus: Pectobacterium
  • species: Pectobacterium atrosepticum
  • full scientific name: Pectobacterium atrosepticum (van Hall 1902) Gardan et al. 2003

  • synonyms

    @refsynonym
    20215Bacillus atrosepticus
    20215Erwinia carotovora subsp. atroseptica
    20215Pectobacterium carotovorum subsp. atrosepticum

@ref: 7378

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Enterobacteriales, not validated

family: Pectobacteriaceae

genus: Pectobacterium

species: Pectobacterium atrosepticum

full scientific name: Pectobacterium atrosepticum (van Hall 1902) Gardan et al. 2003

strain designation: G/39, G39

type strain: yes

Morphology

cell morphology

  • @ref: 116545
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7378NUTRIENT 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
38538MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116545CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
7378positivegrowth30mesophilic
38538positivegrowth30mesophilic
116545positivegrowth5-30
116545nogrowth37mesophilic
116545nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116545
  • oxygen tolerance: facultative anaerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-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
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose+builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
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
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-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
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
116545mannitol+fermentation29864
116545citrate+carbon source16947
116545glucose+fermentation17234
116545lactose+fermentation17716
116545nitrate+reduction17632
116545nitrite-reduction16301
116545malonate-assimilation15792
116545sodium thiosulfate-builds gas from132112
116545glucose+degradation17234

antibiotic resistance

  • @ref: 116545
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836817997dinitrogenyes
6836816301nitriteno
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11654535581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin+
6836835581indole-
11654515688acetoin+
11654517234glucose+

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
116545oxidase-
116545beta-galactosidase+3.2.1.23
116545alcohol dehydrogenase-1.1.1.1
116545gelatinase-
116545catalase+1.11.1.6
116545lysine decarboxylase-4.1.1.18
116545ornithine decarboxylase-4.1.1.17
116545phenylalanine ammonia-lyase-4.3.1.24
116545tryptophan deaminase-
116545urease-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
116545-+-+-+--+-++++-++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
7378+---+----+-+++-+++++--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
116545+/---+++---++++-+-+/-+--+++/-++++-++++/---+---+-------+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116545+++++-+++--+++++++++++++-------+++-------+-++----+---+++---++------------------++-----+--+---------

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
7378Solanum tuberosumSolanum tuberosumUnited KingdomGBREurope
116545Solanum tuberosumUnited KingdomGBREurope

isolation source categories

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

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
7378yes1Risk group (German classification)
1165451Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pectobacterium carotovorum subsp. carotovorum strain ATCC 33260 16S ribosomal RNA gene, partial sequenceFJ595869874ena555
20218Pectobacterium atrosepticum strain CFBP 1526 16S ribosomal RNA gene, partial sequenceJN6003321531ena29471
7378Pectobacterium atrosepticum 16S ribosomal RNA, strain LMG 2386Z960901485ena29471

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pectobacterium atrosepticum NCPPB 549GCA_000749905contigncbi29471
66792Pectobacterium atrosepticum CFBP1526GCA_019056595completencbi29471
66792Pectobacterium atrosepticum strain CFBP152629471.84completepatric29471
66792Pectobacterium atrosepticum strain NCPPB 54929471.26wgspatric29471
66792Pectobacterium atrosepticum NCPPB 5492740892408draftimg29471

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes58.564no
gram-positiveno98.179no
anaerobicno97.333no
aerobicyes75.513no
halophileno89.121no
spore-formingno93.305no
motileyes90.247no
thermophileno98.86yes
glucose-utilyes93.806no
glucose-fermentyes90.257no

External links

@ref: 7378

culture collection no.: DSM 18077, ATCC 33260, CFBP 1526, CIP 105192, NCPPB 549, LMG 2386, ICPB EA 155

straininfo link

  • @ref: 74513
  • straininfo: 2463

literature

topicPubmed-IDtitleauthorsjournalDOIyearmesh
Phylogeny12710602Elevation of three subspecies of Pectobacterium carotovorum to species level: Pectobacterium atrosepticum sp. nov., Pectobacterium betavasculorum sp. nov. and Pectobacterium wasabiae sp. nov.Gardan L, Gouy C, Christen R, Samson RInt J Syst Evol Microbiol10.1099/ijs.0.02423-02003Enterobacteriaceae/*classification/genetics, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/microbiology, RNA, Ribosomal, 16S/analysis, Species Specificity
30716837First Report of Potato Blackleg Disease Caused by Pectobacterium atrosepticum in Guangdong China.She XM, He ZF, Tang YF, Du ZG, Lan GBPlant Dis10.1094/PDIS-03-13-0275-PDN2013

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7378Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18077)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18077
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
38538Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17184
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)
68368Automatically annotated from API 20E
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
74513Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID2463.1StrainInfo: A central database for resolving microbial strain identifiers
116545Curators of the CIPCollection of Institut Pasteur (CIP 105192)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105192