Strain identifier

BacDive ID: 13066

Type strain: Yes

Species: Pseudomonas thivervalensis

Strain history: CIP <- 2008, CFBP <- W. Achouak, UMR 163 CNRS-CEA, Saint-Paul-les-Durance, France: strain CFBP 11261

NCBI tax ID(s): 86265 (species)

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General

@ref: 4964

BacDive-ID: 13066

DSM-Number: 13194

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

description: Pseudomonas thivervalensis CCUG 54622 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizoplane of Brassica napus.

NCBI tax id

  • NCBI tax id: 86265
  • Matching level: species

strain history

@refhistory
4964<- CFBP <- W. Achouak
67770DSM 13194 <-- CFBP 11261 <-- W. Achouak.
123529CIP <- 2008, CFBP <- W. Achouak, UMR 163 CNRS-CEA, Saint-Paul-les-Durance, France: strain CFBP 11261

doi: 10.13145/bacdive13066.20230509.8.1

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

@ref: 4964

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas thivervalensis

full scientific name: Pseudomonas thivervalensis Achouak et al. 2000

type strain: yes

Morphology

cell morphology

  • @ref: 123529
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4964REACTIVATION 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
37857MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123529CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
123529CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4964positivegrowth30mesophilic
37857positivegrowth25mesophilic
60264positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60264aerobe
123529obligate aerobe

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
12352917632nitrate+reduction
12352916301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12352935581indoleno

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
123529oxidase+
123529catalase+1.11.1.6
123529urease-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
123529--++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4964+-----+-+++++-++-++-+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
4964rhizoplane of Brassica napusBrassica napusSexy-les-BoisFranceFRAEurope
60264Rhizoplane of Brassica napusFranceFRAEurope
67770Rhizoplane of Brassica napusBrassica napusFranceFRAEurope
123529Environment, Brassica napus, rhizosphere

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: AF100323
  • 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
49641Risk group (German classification)
1235291Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4964
  • description: Pseudomonas thivervalensis 16S ribosomal RNA gene, partial sequence
  • accession: AF100323
  • length: 1430
  • database: ena
  • NCBI tax ID: 86265

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas thivervalensis strain DSM 1319486265.3wgspatric86265
66792Pseudomonas thivervalensis strain LMG 2162686265.5wgspatric86265
66792Pseudomonas thivervalensis LMG 216262744054620draftimg86265
66792Pseudomonas thivervalensis DSM 131942639762509draftimg86265
66792Pseudomonas thivervalensis DSM 131942675903515draftimg86265
67770Pseudomonas thivervalensis DSM 13194GCA_001269655contigncbi86265
67770Pseudomonas thivervalensis LMG 21626GCA_001637285contigncbi86265
66792Pseudomonas thivervalensis DSM 13194GCA_900102295chromosomencbi86265

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.086no
flagellatedyes81.996no
gram-positiveno98.356no
anaerobicno98.452no
aerobicyes93.55no
halophileno91.395no
spore-formingno95.742no
glucose-fermentno89.163yes
thermophileno99.839no
glucose-utilyes95.317yes

External links

@ref: 4964

culture collection no.: CCUG 54622, DSM 13194, CFBP 11261, JCM 11941, LMG 21626, CIP 109843, CFBP 5754

straininfo link

  • @ref: 82276
  • straininfo: 49436

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
Metabolism27007713Pyoverdine and histicorrugatin-mediated iron acquisition in Pseudomonas thivervalensis.Matthijs S, Brandt N, Ongena M, Achouak W, Meyer JM, Budzikiewicz HBiometals10.1007/s10534-016-9929-12016Iron/chemistry/*metabolism, Oligopeptides/*biosynthesis/chemistry, Pseudomonas/genetics/*metabolism, Siderophores/*biosynthesis/chemistry
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
Phylogeny33528346Pseudomonas bijieensis sp. nov., isolated from cornfield soil.Liang J, Wang S, Yiming A, Fu L, Ahmad I, Chen G, Zhu BInt J Syst Evol Microbiol10.1099/ijsem.0.0046762021
Phylogeny35072599Pseudomonas canavaninivorans sp. nov., isolated from bean rhizosphere.Hauth F, Buck H, Hartig JSInt J Syst Evol Microbiol10.1099/ijsem.0.0052032022Bacterial 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 MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitle
4964Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 13194)https://www.dsmz.de/collection/catalogue/details/culture/DSM-13194
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
37857Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7633
60264Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 54622)https://www.ccug.se/strain?id=54622
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
82276Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID49436.1StrainInfo: A central database for resolving microbial strain identifiers
123529Curators of the CIPCollection of Institut Pasteur (CIP 109843)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109843