Strain identifier

BacDive ID: 13160

Type strain: Yes

Species: Pseudomonas chlororaphis

Strain Designation: 292

Strain history: CIP <- 1963, O. Lysenko, Inst. Biol., Prague, Czechoslovakia, Pseudomonas chlororaphis: strain 292 <- R.Y. Stanier, Inst. Pasteur, Paris, France: strain 30, Pseudomonas fluorescens, biotype D

NCBI tax ID(s): 587753 (species)

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General

@ref: 12633

BacDive-ID: 13160

DSM-Number: 50083

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

description: Pseudomonas chlororaphis 292 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from plate contaminant.

NCBI tax id

  • NCBI tax id: 587753
  • Matching level: species

strain history

@refhistory
12633<- ICPB <- NRRL <- W.H. Schmidt
67770K. Komagata KS 0015 <-- AJ 2066.
118245CIP <- 1963, O. Lysenko, Inst. Biol., Prague, Czechoslovakia, Pseudomonas chlororaphis: strain 292 <- R.Y. Stanier, Inst. Pasteur, Paris, France: strain 30, Pseudomonas fluorescens, biotype D

doi: 10.13145/bacdive13160.20230509.8.1

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 chlororaphis
  • full scientific name: Pseudomonas chlororaphis (Guignard and Sauvageau 1894) Bergey et al. 1930 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Bacillus chlororaphis

@ref: 12633

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas chlororaphis

full scientific name: Pseudomonas chlororaphis (Guignard and Sauvageau 1894) Bergey et al. 1930 emend. Peix et al. 2007

strain designation: 292

type strain: yes

Morphology

cell morphology

  • @ref: 118245
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 44227
  • incubation period: 1 day

pigmentation

  • @ref: 118245
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37700MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
12633NUTRIENT AGAR (DSMZ Medium 1)yesName: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/1
118245CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
37700positivegrowth30mesophilic
44227positivegrowth30-37mesophilic
12633positivegrowth26mesophilic
67770positivegrowth26mesophilic
118245positivegrowth30-41
118245nogrowth5psychrophilic
118245nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
44227aerobe
118245obligate aerobe

compound production

@refcompound
12633DAHP synthetase
126332 keto-L-gulonic acid
12633polyhydroxyalkanoic acids
12633chlororaphin
126336 aminopenicillanic acid
12633L carnitine
20216Chlororaphin

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
11824516947citrate+carbon source
1182454853esculin-hydrolysis
11824517632nitrate+reduction
11824516301nitrite-reduction
11824515882phenol+degradation
11824517632nitrate-respiration

antibiotic resistance

  • @ref: 118245
  • 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
67770168082-dehydro-D-gluconateyes
67770chlororaphinyes
11824535581indoleno

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
118245oxidase+
118245beta-galactosidase-3.2.1.23
118245alcohol dehydrogenase+1.1.1.1
118245gelatinase+
118245amylase-
118245caseinase+3.4.21.50
118245catalase+1.11.1.6
118245tween esterase+
118245lecithinase-
118245lysine decarboxylase-4.1.1.18
118245ornithine decarboxylase-4.1.1.17
118245tryptophan deaminase-
118245urease-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
44227-+++-++---++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
12633+--+--+-+-+++-++-++-+
44227+--+--+-+-+++-++-++-+
12633+--+--+-+-+++-++-++-+
12633+--+--+-+-+++-++-++-+
12633+--+--+-+-+++-++-++-+

Isolation, sampling and environmental information

isolation

@refsample type
12633plate contaminant
44227Plate contaminant
67770Plate contaminant
118245Plate contaminant

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Laboratory
  • Cat3: #Contaminant

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
126331Risk group (German classification)
1182451Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas chlororaphis strain ATCC 9446 16S ribosomal RNA gene, partial sequenceAF0947231458ena587753
20218Pseudomonas chlororaphis partial 16S rRNA gene, type strain ICMP 13613TAJ3083011371ena587753
20218Pseudomonas chlororaphis strain ATCC 9446 16S ribosomal RNA (rrsA) gene, partial sequenceFJ6526101459ena587753
20218Pseudomonas chlororaphis strain DSM 50083 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceDQ023306566ena587753
20218Pseudomonas chlororaphis subsp. chlororaphis strain DSM 50083 16S ribosomal RNA gene, partial sequenceFJ5445751359ena333
20218P.chlororaphis (strain DSM 50083T) 16S rRNA geneZ766731492ena333
20218Pseudomonas chlororaphis gene for 16S rRNAD840111531ena587753
20218Pseudomonas chlororaphis gene for 16S ribosomal RNA, partial sequence, strain: IFO 3904D860041329ena587753
20218P.chlororaphis (strain LMG 5004T) 16S rRNA geneZ766571493ena333
20218Pseudomonas chlororaphis subsp. chlororaphis gene for 16S rRNA, partial sequence, strain: NBRC 3904AB6801661462ena333

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas chlororaphis subsp. chlororaphis DSM 50083GCA_003945765completencbi333
66792Pseudomonas chlororaphis DSM 50083GCA_016803445scaffoldncbi587753
66792Pseudomonas chlororaphis subsp. chlororaphis LMG 5004GCA_001269625contigncbi333
66792Pseudomonas chlororaphis strain DSM 50083587753.91wgspatric587753
66792Pseudomonas chlororaphis subsp. chlororaphis NBRC 3904 strain NBRC 39041215096.5wgspatric1215096
66792Pseudomonas chlororaphis subsp. chlororaphis strain ATCC 9446333.6wgspatric333
66792Pseudomonas chlororaphis subsp. chlororaphis strain DSM 50083333.12wgspatric333
66792Pseudomonas chlororaphis subsp. chlororaphis strain DSM 50083333.10completepatric333
66792Pseudomonas chlororaphis subsp. chlororaphis strain LMG 5004333.4wgspatric333
66792Pseudomonas chlororaphis chlororaphis NBRC 39042917093585draftimg1215096
66792Pseudomonas chlororaphis chlororaphis ATCC 94462617270790draftimg587753
66792Pseudomonas chlororaphis chlororaphis LMG 50042713897223draftimg333
66792Pseudomonas chlororaphis chlororaphis DSM 500832875542621completeimg333
67770Pseudomonas chlororaphis subsp. chlororaphis NBRC 3904GCA_002091535contigncbi1215096
67770Pseudomonas chlororaphis subsp. chlororaphis ATCC 9446GCA_002095925contigncbi333
67770Pseudomonas chlororaphis subsp. chlororaphis NCTC11032GCA_900625015contigncbi333
67770Pseudomonas chlororaphis subsp. chlororaphis DSM 50083GCA_007858335contigncbi333
66792Pseudomonas chlororaphis ATCC 9446GCA_028747405completencbi587753

GC content

  • @ref: 12633
  • GC-content: 64.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes78.383no
gram-positiveno98.437no
anaerobicno98.623no
aerobicyes92.51yes
halophileno91.875no
spore-formingno94.057no
glucose-utilyes94.74yes
thermophileno99.847no
motileyes91.135no
glucose-fermentno90.585no

External links

@ref: 12633

culture collection no.: DSM 50083, ATCC 9446, CCM 1975, ICPB 2392, IFO 3904, NBRC 3904, NCIB 9392, NRRL B-560, CCUG 552 B, LMG 6220, CCM 292, CIP 63.22, JCM 2778, AJ 2066, BCRC 11566, CCUG 552, CECT 4470, CFBP 2132, HAMBI 2011, IAM 12354, IAM 1511, ICMP 13613, LMG 5004, LMG 6457, NCCB 76041, NCIMB 9392, NCPPB 1798, NCTC 13002, VKM B-1246, VKM B-897, VTT E-95581, IMET 10404, NRRL: B-560

straininfo link

  • @ref: 82368
  • straininfo: 311044

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism10919812Degradation of triphenyltin by a fluorescent pseudomonad.Inoue H, Takimura O, Fuse H, Murakami K, Kamimura K, Yamaoka YAppl Environ Microbiol10.1128/AEM.66.8.3492-3498.20002000Biodegradation, Environmental, Culture Media, *Fluorescence, Geologic Sediments/microbiology, Organotin Compounds/*metabolism, Pseudomonas/classification/isolation & purification/*metabolism, Soil MicrobiologyCultivation
Phylogeny11098840The complex structure of ferri-ferribactins.Taraz K, Seipold L, Amann C, Budzikiewicz HZ Naturforsch C J Biosci10.1515/znc-2000-9-10272000Gallium, Iron, Iron Chelating Agents/*chemistry/isolation & purification, Models, Molecular, Molecular Conformation, Nuclear Magnetic Resonance, Biomolecular, Oligopeptides/*chemistry/isolation & purification, Pseudomonas/*chemistry, Pseudomonas fluorescens/chemistry, Siderophores/*chemistry/isolation & purification, Species SpecificityEnzymology
Metabolism12571007Tin-carbon cleavage of organotin compounds by pyoverdine from Pseudomonas chlororaphis.Inoue H, Takimura O, Kawaguchi K, Nitoda T, Fuse H, Murakami K, Yamaoka YAppl Environ Microbiol10.1128/AEM.69.2.878-883.20032003Bacterial Proteins/chemistry/metabolism, Biodegradation, Environmental, Carbon/metabolism, Catalysis, *Oligopeptides, Organotin Compounds/*metabolism, Pigments, Biological/chemistry/*metabolism, Pseudomonas/*metabolism, Siderophores/chemistry/metabolism, Substrate Specificity, Tin/metabolism
Enzymology14729308Two azurins with unusual redox and spectroscopic properties isolated from the Pseudomonas chlororaphis strains DSM 50083T and DSM 50135.Pinho D, Besson S, Brondino CD, Pereira E, de Castro B, Moura IJ Inorg Biochem10.1016/j.jinorgbio.2003.10.0232004Animals, Azurin/*chemistry/isolation & purification, Electrochemistry, Electrophoresis, Polyacrylamide Gel, Hydrogen-Ion Concentration, Oxidation-Reduction, Pseudomonas/*chemistry, Spectrophotometry, AtomicPhylogeny
Phylogeny17551044Reclassification of Pseudomonas aurantiaca as a synonym of Pseudomonas chlororaphis and proposal of three subspecies, P. chlororaphis subsp. chlororaphis subsp. nov., P. chlororaphis subsp. aureofaciens subsp. nov., comb. nov. and P. chlororaphis subsp. aurantiaca subsp. nov., comb. nov.Peix A, Valverde A, Rivas R, Igual JM, Ramirez-Bahena MH, Mateos PF, Santa-Regina I, Rodriguez-Barrueco C, Martinez-Molina E, Velazquez EInt J Syst Evol Microbiol10.1099/ijs.0.64621-02007Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/chemistry/*classification/genetics, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidGenetics
Genetics28596401Draft Genome Sequence of Pseudomonas chlororaphis ATCC 9446, a Nonpathogenic Bacterium with Bioremediation and Industrial Potential.Moreno-Avitia F, Lozano L, Utrilla J, Bolivar F, Escalante AGenome Announc10.1128/genomeA.00474-172017
Pathogenicity30798087Occurrence of non-toxic bioemulsifiers during polyhydroxyalkanoate production by Pseudomonas strains valorizing crude glycerol by-product.Kourmentza C, Araujo D, Sevrin C, Roma-Rodriques C, Lia Ferreira J, Freitas F, Dionisio M, Baptista PV, Fernandes AR, Grandfils C, Reis MAMBioresour Technol10.1016/j.biortech.2019.02.0662019Cell Line, Tumor, Cell Proliferation/drug effects, Glycerol/*metabolism, Humans, Melanoma/pathology, Polyhydroxyalkanoates/*biosynthesis, Pseudomonas/*metabolismMetabolism
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
32984920Metabolic reconstruction of Pseudomonas chlororaphis ATCC 9446 to understand its metabolic potential as a phenazine-1-carboxamide-producing strain.Moreno-Avitia F, Utrilla J, Bolivar F, Nogales J, Escalante AAppl Microbiol Biotechnol10.1007/s00253-020-10913-42020Hydrogen Peroxide, Phenazines, Pseudomonas/genetics, *Pseudomonas chlororaphis/genetics
33466508Screening for Microbial Metal-Chelating Siderophores for the Removal of Metal Ions from Solutions.Hofmann M, Heine T, Malik L, Hofmann S, Joffroy K, Senges CHR, Bandow JE, Tischler DMicroorganisms10.3390/microorganisms90101112021
Metabolism35365429Regulation of phenazine-1-carboxamide production by quorum sensing in type strains of Pseudomonas chlororaphis subsp. chlororaphis and Pseudomonas chlororaphis subsp. piscium.Morohoshi T, Yabe N, Yaguchi N, Xie X, Someya NJ Biosci Bioeng10.1016/j.jbiosc.2022.03.0042022Acyl-Butyrolactones, *Bacterial Proteins/genetics/metabolism, Phenazines/metabolism, Pseudomonas, *Quorum Sensing/physiologyBiotechnology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12633Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 50083)https://www.dsmz.de/collection/catalogue/details/culture/DSM-50083
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
20216Curators of the HKIhttp://www.leibniz-hki.de/de/Collection Description Leibniz-Institut für Naturstoff-Forschung und Infektionsbiologie e. V. Hans-Knöll-Institut (HKI)
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
37700Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10028
44227Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 552 B)https://www.ccug.se/strain?id=552
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
82368Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID311044.1StrainInfo: A central database for resolving microbial strain identifiers
118245Curators of the CIPCollection of Institut Pasteur (CIP 63.22)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2063.22