Strain identifier

BacDive ID: 13060

Type strain: Yes

Species: Pseudomonas flavescens

Strain Designation: B62

Strain history: CIP <- 1994, M. Hendson, California Univ., Berkeley, CA, USA: strain B62 <- D.C. Hildebrand, CA, USA

NCBI tax ID(s): 1215099 (strain), 29435 (species)

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General

@ref: 4595

BacDive-ID: 13060

DSM-Number: 12071

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile, plant pathogen

description: Pseudomonas flavescens B62 is an aerobe, mesophilic, motile plant pathogen that was isolated from canker tissue of Juglans regia.

NCBI tax id

NCBI tax idMatching level
1215099strain
29435species

strain history

@refhistory
4595<- NCPPB <- D.C. Hildebrand; B62
67770IAM 15128 <-- CIP 104204 <-- M. Hendson <-- D. C. Hildebrand.
119373CIP <- 1994, M. Hendson, California Univ., Berkeley, CA, USA: strain B62 <- D.C. Hildebrand, CA, USA

doi: 10.13145/bacdive13060.20230509.8.1

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 flavescens
  • full scientific name: Pseudomonas flavescens Hildebrand et al. 1994

@ref: 4595

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas flavescens

full scientific name: Pseudomonas flavescens Hildebrand et al. 1994

strain designation: B62

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.866
6948099.995negative
119373yesnegativerod-shaped

pigmentation

  • @ref: 119373
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4595NUTRIENT 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
38160MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
119373CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4595positivegrowth28mesophilic
38160positivegrowth30mesophilic
58633positivegrowth22-35
67770positivegrowth30mesophilic
119373positivegrowth30mesophilic
119373nogrowth5psychrophilic
119373nogrowth41thermophilic
119373nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58633aerobe
119373obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.978

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
11937316947citrate+carbon source
1193734853esculin-hydrolysis
11937317632nitrate-reduction
11937316301nitrite-reduction
11937317632nitrate-respiration

antibiotic resistance

  • @ref: 119373
  • 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
11937335581indoleno

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
119373oxidase+
119373alcohol dehydrogenase-1.1.1.1
119373gelatinase-
119373catalase+1.11.1.6
119373lysine decarboxylase-4.1.1.18
119373ornithine decarboxylase-4.1.1.17
119373urease-3.5.1.5

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4595--------++++--++-++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119373+++++--+------------+----------+-+---------+---++++--+------+++++--+--++++-+++-++---+--+++++-+++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
4595canker tissue of Juglans regiaJuglans regiaCalifornia, OrindaUSAUSANorth America
58633Walnut tree,canker tissueCA,OrindaUSAUSANorth America
67770Walnut blight cankers
119373Plant, Canker tissue on a walnut treeOrinda, CaliforniaUnited States of AmericaUSANorth America

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_4640.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_64;98_2761;99_4640&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: U01916
  • Sequence Identity:
  • Total samples: 120
  • soil counts: 4
  • aquatic counts: 30
  • animal counts: 60
  • plant counts: 26

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
4595yes1Risk group (German classification)
1193731Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4595
  • description: Pseudomonas flavescens B62 16S ribosomal RNA
  • accession: U01916
  • length: 1529
  • database: ena
  • NCBI tax ID: 29435

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas flavescens NBRC 103044 strain NBRC 1030441215099.3wgspatric1215099
66792Pseudomonas flavescens strain LMG 1838729435.6wgspatric29435
66792Pseudomonas flavescens LMG 183872663762794draftimg29435
67770Pseudomonas flavescens NBRC 103044GCA_002091575contigncbi1215099
67770Pseudomonas flavescens LMG 18387GCA_900100535scaffoldncbi29435

GC content

@refGC-contentmethod
459563thermal denaturation, midpoint method (Tm)
6777063high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes90.716no
gram-positiveno98.642no
anaerobicno97.892yes
aerobicyes93.431no
halophileno84.343no
spore-formingno94.981no
thermophileno99.531no
glucose-utilyes93.035yes
flagellatedyes78.695no
glucose-fermentno90.729yes

External links

@ref: 4595

culture collection no.: DSM 12071, NCPPB 3063, CCUG 49622, CIP 104204, ATCC 51555, LMG 18387, CFBP 5586, JCM 21586, IAM 15128, ICMP 13539, NBRC 103044

straininfo link

  • @ref: 82270
  • straininfo: 12040

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny7520732Pseudomonas flavescens sp. nov., isolated from walnut blight cankers.Hildebrand DC, Palleroni NJ, Hendson M, Toth J, Johnson JLInt J Syst Bacteriol10.1099/00207713-44-3-4101994DNA, Bacterial/genetics, Flagella/ultrastructure, Microscopy, Electron, Molecular Sequence Data, Pigments, Biological/analysis, Pseudomonas/classification/genetics/*isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Species Specificity, Terminology as Topic, Trees/*microbiologyGenetics
Phylogeny9490074Structural investigation of the exopolysaccharide produced by Pseudomonas flavescens strain B62--degradation by a fungal cellulase and isolation of the oligosaccharide repeating unit.Cescutti P, Toffanin R, Fett WF, Osman SF, Pollesello P, Paoletti SEur J Biochem10.1046/j.1432-1327.1998.2510971.x1998Carbohydrate Conformation, Carbohydrate Sequence, Cellulase/*metabolism, Chromatography, Gas, Chromatography, Gel, Molecular Sequence Data, Nuclear Magnetic Resonance, Biomolecular, Oligosaccharides/*chemistry/isolation & purification, Penicillium/*enzymology, Polysaccharides, Bacterial/biosynthesis/*chemistry/isolation & purification, Pseudomonas/immunology/*metabolismMetabolism
Phylogeny18319482Pseudomonas marincola sp. nov., isolated from marine environments.Romanenko LA, Uchino M, Tebo BM, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.65406-02008Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Echinodermata/*microbiology, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, *Seawater, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitle
4595Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12071)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12071
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
38160Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16086
58633Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49622)https://www.ccug.se/strain?id=49622
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
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82270Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID12040.1StrainInfo: A central database for resolving microbial strain identifiers
119373Curators of the CIPCollection of Institut Pasteur (CIP 104204)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104204