Strain identifier

BacDive ID: 13068

Type strain: Yes

Species: Pseudomonas brassicacearum

Strain Designation: DBK11, DBK 11

Strain history: CIP <- 2001, CFBP <- W. Achouak: strain DBK 11

NCBI tax ID(s): 930166 (species)

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General

@ref: 4970

BacDive-ID: 13068

DSM-Number: 13227

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

description: Pseudomonas brassicacearum DBK11 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizoplane of Brassica napus.

NCBI tax id

  • NCBI tax id: 930166
  • Matching level: species

strain history

@refhistory
4970<- CFBP <- W. Achouak
67770DSM 13227 <-- CFBP 11706 <-- W. Achouak DBK 11.
116996CIP <- 2001, CFBP <- W. Achouak: strain DBK 11

doi: 10.13145/bacdive13068.20230509.8.1

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 brassicacearum
  • full scientific name: Pseudomonas brassicacearum Achouak et al. 2000

@ref: 4970

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas brassicacearum

full scientific name: Pseudomonas brassicacearum Achouak et al. 2000 emend. Ivanova et al. 2009

strain designation: DBK11, DBK 11

type strain: yes

Morphology

cell morphology

  • @ref: 116996
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 116996
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4970REACTIVATION 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
39647MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116996CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4970positivegrowth30mesophilic
39647positivegrowth30mesophilic
67770positivegrowth28mesophilic
116996positivegrowth5-37
116996nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116996
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116996NaClpositivegrowth0-6 %
116996NaClnogrowth8 %
116996NaClnogrowth10 %

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
11699616947citrate+carbon source
1169964853esculin-hydrolysis
11699617632nitrate+reduction
11699616301nitrite+reduction
11699617632nitrate+respiration

antibiotic resistance

  • @ref: 116996
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116996
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
116996oxidase+
116996beta-galactosidase-3.2.1.23
116996alcohol dehydrogenase+1.1.1.1
116996gelatinase+/-
116996amylase-
116996DNase+
116996caseinase-3.4.21.50
116996catalase+1.11.1.6
116996tween esterase+
116996lecithinase-
116996lipase-
116996lysine decarboxylase-4.1.1.18
116996ornithine decarboxylase-4.1.1.17
116996protease-
116996tryptophan deaminase-
116996urease-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
116996-+++-+--+-++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4970++-+--+-+++++-++-++-+
4970---+--+-+++++-++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116996+++++--+-----------+++----+----+++--+--+---++-+-++++-++++--++-+++--+--++++-+++-++++++-+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
4970rhizoplane of Brassica napusBrassica napusDieulouardFranceFRAEurope
59219Rhizoplane of Brassica napusDieulouardFranceFRAEurope
67770Rhizoplane of Brassica napusBrassica napusFranceFRAEurope
116996Rhizoplane of Brassica napusDieulardFranceFRAEurope

isolation source categories

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

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: AF100321
  • Sequence Identity:
  • Total samples: 42314
  • soil counts: 16904
  • aquatic counts: 8731
  • animal counts: 11521
  • plant counts: 5158

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
49701Risk group (German classification)
1169961Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas brassicacearum partial 16S rRNA gene, strain CFBP 11706AJ293858650ena930166
4970Pseudomonas brassicacearum strain DBK11 16S ribosomal RNA gene, partial sequenceAF1003211473ena930166

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas brassicacearum subsp. brassicacearum CCUG 51508GCA_008801605contigncbi86264
66792Pseudomonas brassicacearum strain JCM 11938930166.118wgspatric930166
66792Pseudomonas brassicacearum subsp. brassicacearum strain CCUG 5150886264.4wgspatric86264
67770Pseudomonas brassicacearum JCM 11938GCA_012034345scaffoldncbi930166

GC content

  • @ref: 67770
  • GC-content: 60.8
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.935no
flagellatedyes82.611no
gram-positiveno98.216no
anaerobicno98.163no
halophileno91.041no
spore-formingno95.504no
glucose-utilyes94.695yes
aerobicyes88.892no
thermophileno99.847no
glucose-fermentno88.966yes

External links

@ref: 4970

culture collection no.: DSM 13227, CFBP 11706, CCUG 51508, JCM 11938, CIP 107059, CFBP 5593

straininfo link

  • @ref: 82278
  • straininfo: 49439

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10826782Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana.Achouak W, Sutra L, Heulin T, Meyer JM, Fromin N, Degraeve S, Christen R, Gardan LInt J Syst Evol Microbiol10.1099/00207713-50-1-92000Arabidopsis/*microbiology, Base Composition, Brassica/*microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, Pseudomonas/*classification/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Restriction Mapping, Sequence Analysis, DNA, Siderophores/classificationGenetics
Phylogeny19622656Pseudomonas brassicacearum subsp. neoaurantiaca subsp. nov., orange-pigmented bacteria isolated from soil and the rhizosphere of agricultural plants.Ivanova EP, Christen R, Bizet C, Clermont D, Motreff L, Bouchier C, Zhukova NV, Crawford RJ, Kiprianova EAInt J Syst Evol Microbiol10.1099/ijs.0.009654-02009Base Composition, Crops, Agricultural/*microbiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, Pigmentation, Plant Roots/microbiology, Pseudomonas/classification/genetics/*isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism
Phylogeny32776868Pseudomonas viciae sp. nov., isolated from rhizosphere of broad bean.Zhao H, Ma Y, Wu X, Zhang LInt J Syst Evol Microbiol10.1099/ijsem.0.0043732020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, *Rhizosphere, *Soil Microbiology, Ubiquinone/chemistry, Vicia faba/*microbiologyEnzymology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4970Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13227)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13227
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
39647Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19258
59219Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51508)https://www.ccug.se/strain?id=51508
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
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
82278Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49439.1StrainInfo: A central database for resolving microbial strain identifiers
116996Curators of the CIPCollection of Institut Pasteur (CIP 107059)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107059