Strain identifier

BacDive ID: 13044

Type strain: Yes

Species: Pseudomonas corrugata

Strain Designation: 939/1

Strain history: CIP <- 1998, CFBP <- G.F. Slade: strain 939/1

NCBI tax ID(s): 47879 (species)

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General

@ref: 3063

BacDive-ID: 13044

DSM-Number: 7228

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

description: Pseudomonas corrugata 939/1 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from Lycopersicon esculentum.

NCBI tax id

  • NCBI tax id: 47879
  • Matching level: species

strain history

@refhistory
3063<- NCPPB <- G.F. Slade
118757CIP <- 1998, CFBP <- G.F. Slade: strain 939/1

doi: 10.13145/bacdive13044.20230509.8.1

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 corrugata
  • full scientific name: Pseudomonas corrugata Roberts and Scarlett 1981

@ref: 3063

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas corrugata

full scientific name: Pseudomonas corrugata Roberts and Scarlett 1981 emend. Sutra et al. 1997

strain designation: 939/1

type strain: yes

Morphology

cell morphology

  • @ref: 118757
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 118757
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3063REACTIVATION 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
32736MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
118757CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118757CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3063positivegrowth26mesophilic
32736positivegrowth25mesophilic
118757positivegrowth5-37
118757nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118757
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
118757NaClpositivegrowth0-6 %
118757NaClnogrowth8 %
118757NaClnogrowth10 %

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
11875716947citrate-carbon source
1187574853esculin-hydrolysis
11875717632nitrate+reduction
11875716301nitrite-reduction
11875717632nitrate+respiration

antibiotic resistance

  • @ref: 118757
  • 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
11875735581indoleno

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
118757oxidase+
118757beta-galactosidase-3.2.1.23
118757alcohol dehydrogenase-1.1.1.1
118757gelatinase+/-
118757amylase-
118757DNase-
118757caseinase+3.4.21.50
118757catalase+1.11.1.6
118757tween esterase-
118757lecithinase-
118757lipase-
118757lysine decarboxylase-4.1.1.18
118757ornithine decarboxylase-4.1.1.17
118757protease+
118757tryptophan deaminase-
118757urease-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
118757--++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3063+-----+-+++++-++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118757+++++--+-----------+++---------+++---------++----+++-+++---++-+++-----++++++++++++-++-+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
3063Lycopersicon esculentumLycopersicon esculentumUnited KingdomGBREurope
118757Lycopersicon esculentumUnited KingdomGBREurope

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_555.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_555&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: D84012
  • Sequence Identity:
  • Total samples: 42314
  • soil counts: 16904
  • aquatic counts: 8731
  • animal counts: 11521
  • plant counts: 5158

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3063yes1Risk group (German classification)
1187571Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas corrugata 16S rRNA geneD840121454ena47879
20218Pseudomonas corrugata DNA for 16S ribosomal RNA, 23S ribosomal RNA, partial sequenceD87087553ena47879
20218Pseudomonas corrugata culture-collection CFBP:2431 16S ribosomal RNA gene, partial sequenceHM1902301442ena47879

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas corrugata DSM 7228GCA_001269905contigncbi47879
66792Pseudomonas corrugata NCPPB2445GCA_001411965scaffoldncbi47879
66792Pseudomonas corrugata NCPPB2445GCA_003699065scaffoldncbi47879
66792Pseudomonas corrugata strain DSM 722847879.38wgspatric47879
66792Pseudomonas corrugata strain NCPPB244547879.35wgspatric47879
66792Pseudomonas corrugata strain NCPPB244547879.43wgspatric47879
66792Pseudomonas corrugata NCPPB24452563366525draftimg47879
66792Pseudomonas corrugata DSM 72282713897228draftimg47879

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes81.514no
gram-positiveno98.243no
anaerobicno98.447no
aerobicyes92.799no
halophileno90.135no
spore-formingno95.358no
glucose-utilyes94.766yes
thermophileno99.791yes
motileyes90.788no
glucose-fermentno90.041yes

External links

@ref: 3063

culture collection no.: DSM 7228, ATCC 29736, NCPPB 2445, CIP 105514, CFBP 2431

straininfo link

  • @ref: 82255
  • straininfo: 86474

literature

  • topic: Phylogeny
  • Pubmed-ID: 35072599
  • title: Pseudomonas canavaninivorans sp. nov., isolated from bean rhizosphere.
  • authors: Hauth F, Buck H, Hartig JS
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.005203
  • year: 2022
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Germany, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Transcriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3063Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7228)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7228
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
32736Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17542
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
82255Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID86474.1StrainInfo: A central database for resolving microbial strain identifiers
118757Curators of the CIPCollection of Institut Pasteur (CIP 105514)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105514