Strain identifier

BacDive ID: 13016

Type strain: Yes

Species: Pseudomonas viridiflava

Strain Designation: PV6

Variant: Isotype of BacDive ID 24401

Strain history: CIP <- 2000, CCUG <- J.M. Young, ICMP, Auckland, New Zealand <- D.W. Dye <- NCPPB <- W.H. Burkholder

NCBI tax ID(s): 33069 (species)

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General

@ref: 4216

BacDive-ID: 13016

DSM-Number: 11124

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

description: Pseudomonas viridiflava PV6 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from dwarf or runner bean.

NCBI tax id

  • NCBI tax id: 33069
  • Matching level: species

strain history

@refhistory
4216<- ATCC <- W. H. Burkholder; PV6
123865CIP <- 2000, CCUG <- J.M. Young, ICMP, Auckland, New Zealand <- D.W. Dye <- NCPPB <- W.H. Burkholder

doi: 10.13145/bacdive13016.20230509.8.1

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 viridiflava
  • full scientific name: Pseudomonas viridiflava (Burkholder 1930) Dowson 1939 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Phytomonas viridiflava

@ref: 4216

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas viridiflava

full scientific name: Pseudomonas viridiflava (Burkholder 1930) Dowson 1939

strain designation: PV6

variant: Isotype of BacDive ID 24401

type strain: yes

Morphology

cell morphology

  • @ref: 123865
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 123865
  • production: yes
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4216CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
32999MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123865CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4216positivegrowth28mesophilic
32999positivegrowth25mesophilic
123865positivegrowth5-30
123865nogrowth37mesophilic
123865nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123865
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
123865NaClpositivegrowth0-4 %
123865NaClnogrowth6 %
123865NaClnogrowth8 %
123865NaClnogrowth10 %

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
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
12386516947citrate+carbon source
1238654853esculin+hydrolysis
12386517632nitrate-reduction
12386516301nitrite-reduction
12386517632nitrate-respiration

antibiotic resistance

  • @ref: 123865
  • 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
12386535581indoleno

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
123865oxidase-
123865beta-galactosidase-3.2.1.23
123865alcohol dehydrogenase-1.1.1.1
123865gelatinase-
123865amylase-
123865DNase-
123865caseinase+3.4.21.50
123865catalase+1.11.1.6
123865tween esterase-
123865lecithinase-
123865lipase-
123865lysine decarboxylase-4.1.1.18
123865ornithine decarboxylase-4.1.1.17
123865protease-
123865tryptophan deaminase-
123865urease-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
123865-+++-+--+-++----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4216-----++/--++-+--++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123865+++-+-------------++++----+----+++--+--++--++-++++++-+++----+-+++-----++-+-+-+-+++++--+-++++++++++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentisolation date
4216dwarf or runner beanSwitzerlandCHEEurope
123865Dwarf or runner beanSwitzerlandCHEEurope1927

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Shrub (Scrub)

taxonmaps

  • @ref: 69479
  • File name: preview.99_910.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_718;99_910&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: Z76671
  • Sequence Identity:
  • Total samples: 736
  • soil counts: 184
  • aquatic counts: 147
  • animal counts: 195
  • plant counts: 210

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
4216yes1Risk group (German classification)
1238651Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas viridiflava strain ATCC 13223 16S ribosomal RNA gene, partial sequenceAF0947511461ena33069
20218Pseudomonas viridiflava culture-collection CFBP:2107 16S ribosomal RNA gene, partial sequenceHM1902291442ena33069
20218P.viridiflava 16S rRNA geneZ766711492ena33069

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas viridiflava DSM 6694GCA_001305955contigncbi33069
66792Pseudomonas viridiflava strain DSM 669433069.8wgspatric33069
66792Pseudomonas viridiflava DSM 66942639762757draftimg33069

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.303no
anaerobicno98.442no
halophileno93.011no
spore-formingno94.029no
glucose-utilyes95.048yes
flagellatedyes71.035no
aerobicyes95.14no
thermophileno99.754no
motileyes90.117no
glucose-fermentno89.603no

External links

@ref: 4216

culture collection no.: DSM 11124, ATCC 13223, DSM 6694, NCPPB 635, CIP 106699, CCUG 23371, LMG 2352, NRRL B895

straininfo link

@refstraininfo
822266872
82227377524

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny29148362Pseudomonas floridensis sp. nov., a bacterial pathogen isolated from tomato.Timilsina S, Minsavage GV, Preston J, Newberry EA, Paret ML, Goss EM, Jones JB, Vallad GEInt J Syst Evol Microbiol10.1099/ijsem.0.0024452017Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Lycopersicon esculentum/*microbiology, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, Plant Diseases/microbiology, Pseudomonas/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Solanum tuberosum/microbiology, Tobacco/microbiologyTranscriptome
Phylogeny34800898Pseudomonas alliivorans sp. nov., a plant-pathogenic bacterium isolated from onion foliage in Georgia, USA.Zhao M, Tyson C, Chen HC, Paudel S, Gitaitis R, Kvitko B, Dutta BSyst Appl Microbiol10.1016/j.syapm.2021.1262782021Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Georgia, Nucleic Acid Hybridization, *Onions, Phylogeny, *Pseudomonas/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4216Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11124)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11124
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
32999Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18858
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
82226Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID6872.1StrainInfo: A central database for resolving microbial strain identifiers
82227Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID377524.1StrainInfo: A central database for resolving microbial strain identifiers
123865Curators of the CIPCollection of Institut Pasteur (CIP 106699)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106699