Strain identifier

BacDive ID: 13024

Type strain: Yes

Species: Pseudomonas syringae

Variant: Isotype of BacDive ID 24420

Strain history: CIP <- 2000, CCUG <- K. Kersters, LMG, Gent, Belgium <- NCPPB <- K. Sabet

NCBI tax ID(s): 1449349 (strain), 317 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 3983

BacDive-ID: 13024

DSM-Number: 10604

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

description: Pseudomonas syringae DSM 10604 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from Syringa vulgaris.

NCBI tax id

NCBI tax idMatching level
1449349strain
317species

strain history

@refhistory
3983<- NCPPB <- K. A. Sabet
123401CIP <- 2000, CCUG <- K. Kersters, LMG, Gent, Belgium <- NCPPB <- K. Sabet

doi: 10.13145/bacdive13024.20230509.8.1

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 syringae
  • full scientific name: Pseudomonas syringae van Hall 1902 (Approved Lists 1980)

@ref: 3983

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas syringae

full scientific name: Pseudomonas syringae van Hall 1902

variant: Isotype of BacDive ID 24420

type strain: yes

Morphology

cell morphology

  • @ref: 123401
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 123401
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3983CASO 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
3983GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54)yeshttps://mediadive.dsmz.de/medium/54Name: GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54) Composition: CaCO3 20.0 g/l Glucose 20.0 g/l Agar 17.0 g/l Yeast extract 10.0 g/l Distilled water
36440MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
123401CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3
123401CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
3983positivegrowth26mesophilic
36440positivegrowth25mesophilic
123401positivegrowth5-30
123401nogrowth37mesophilic
123401nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123401
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
123401NaClpositivegrowth0-6 %
123401NaClnogrowth8 %
123401NaClnogrowth10 %

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
12340116947citrate+carbon source
1234014853esculin+hydrolysis
12340117632nitrate-reduction
12340116301nitrite-reduction
12340117632nitrate-respiration

antibiotic resistance

  • @ref: 123401
  • 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
12340135581indoleno

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
123401oxidase+
123401beta-galactosidase-3.2.1.23
123401alcohol dehydrogenase-1.1.1.1
123401gelatinase+/-
123401amylase-
123401DNase-
123401caseinase+3.4.21.50
123401catalase+1.11.1.6
123401tween esterase-
123401lecithinase-
123401lipase-
123401lysine decarboxylase-4.1.1.18
123401ornithine decarboxylase-4.1.1.17
123401protease+
123401tryptophan deaminase-
123401urease-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
123401-++++++-+-++----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3983-----++-++++--++-++--
3983-----++-++++--++-++--
3983-----++-++++--++-++--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123401+++-+--+----------++++----+----+++--+---+--++----+++-++-----+---------++-+-+++-++++++-+-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
3983Syringa vulgarisSyringa vulgarisUnited KingdomGBREurope
123401Syringa vulgaris

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_108.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_98;99_108&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: Z76669
  • Sequence Identity:
  • Total samples: 1469
  • soil counts: 744
  • aquatic counts: 346
  • animal counts: 234
  • plant counts: 145

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3983yes1Risk group (German classification)
1234011Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas syringae strain ATCC 19310 16S ribosomal RNA gene, partial sequenceAF0947491460ena317
20218Pseudomonas syringae a41 16S ribosomal RNA gene, partial sequenceAF311988497ena317
20218Pseudomonas syringae axB12 16S ribosomal RNA gene, partial sequenceAF311989489ena317
20218Pseudomonas syringae partial 16S rRNA gene, type strain ICMP 3023TAJ3083161371ena317
20218Pseudomonas syringae 16S rRNA geneD840261454ena317
20218Pseudomonas syringae strain ATCC 19310 16S ribosomal RNA gene, partial sequenceFJ971872793ena317
20218Pseudomonas syringae pv. syringae culture-collection ICMP:3023 16S ribosomal RNA gene, partial sequenceHM1902171444ena321
20218Pseudomonas syringae pv. syringae culture-collection LMG:1247 16S-23S ribosomal RNA intergenic spacer, partial sequenceHM032080526ena321
20218Pseudomonas syringae pv. syringae culture-collection LMG:1247 16S-23S ribosomal RNA intergenic spacer, partial sequenceHM032083516ena321
20218Pseudomonas syringae pv. syringae culture-collection LMG:1247 16S-23S ribosomal RNA intergenic spacer, partial sequenceHM032084517ena321
20218P.syringae 16S rRNA geneZ766691494ena317
20218Pseudomonas syringae pv. syringae strain NRRL B-1631 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY342181532ena321
3983Pseudomonas syringae pv. syringae strain NCPPB 281 16S ribosomal RNA gene, partial sequenceDQ3188661482ena321

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas syringae pv. syringae ICMP 3023GCA_001401075scaffoldncbi321
66792Pseudomonas syringae DSM 10604GCA_000597765contigncbi1449349
66792Pseudomonas syringae DSM 106041449349.3wgspatric1449349
66792Pseudomonas syringae pv. syringae strain ICMP3023321.65wgspatric321
66792Pseudomonas syringae pv. syringae ICMP 30232713896866draftimg321
66792Pseudomonas syringae DSM 106042579778699draftimg1449349

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.878no
gram-positiveno98.293no
anaerobicno98.204no
halophileno92.495no
spore-formingno93.895no
thermophileno99.718yes
glucose-utilyes96.279yes
aerobicyes95.408no
flagellatedyes69.461no
glucose-fermentno89.398yes

External links

@ref: 3983

culture collection no.: DSM 10604, ATCC 19310, ICMP 3023, ICPB PS255, NCPPB 281, CIP 106698, CCUG 14279, LMG 1247, DSM 6693, CRBIP25.27, CCEB 760, PDDCC 3023

straininfo link

  • @ref: 82235
  • straininfo: 4542

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Genetics1898935Conservation of the gene for outer membrane protein OprF in the family Pseudomonadaceae: sequence of the Pseudomonas syringae oprF gene.Ullstrom CA, Siehnel R, Woodruff W, Steinbach S, Hancock REJ Bacteriol10.1128/jb.173.2.768-775.19911991Amino Acid Sequence, Bacterial Outer Membrane Proteins/*genetics, Base Sequence, Cloning, Molecular, Escherichia coli/genetics, *Genes, Bacterial, Genotype, Lipid Bilayers, Molecular Sequence Data, Plasmids, *Porins, Pseudomonadaceae/*genetics, Pseudomonas/*genetics, Pseudomonas aeruginosa/genetics, Restriction Mapping, Sequence Homology, Nucleic Acid, Species SpecificityEnzymology
Enzymology3023282Cloning and regulation of Erwinia herbicola pigment genes.Perry KL, Simonitch TA, Harrison-Lavoie KJ, Liu STJ Bacteriol10.1128/jb.168.2.607-612.19861986*Cloning, Molecular, Corynebacterium/genetics, Cyclic AMP/biosynthesis, DNA, Bacterial/analysis/genetics, Erwinia/*genetics/metabolism, Escherichia coli/genetics, *Gene Expression Regulation, *Genes, Bacterial, Glucose/pharmacology, Pigments, Biological/biosynthesis/*genetics, Plasmids, Pseudomonas/genetics, Rhizobium/genetics, Sequence Homology, Nucleic Acid, Xanthomonas/geneticsMetabolism
Metabolism18535860Surface display of GFP by Pseudomonas syringae truncated ice nucleation protein in attenuated Vibrio anguillarum strain.Xu Y, Liu Q, Zhou L, Yang Z, Zhang YMar Biotechnol (NY)10.1007/s10126-008-9108-72008Bacterial Outer Membrane Proteins/genetics/*metabolism, Gene Expression, Green Fluorescent Proteins/genetics/*metabolism, Plasmids, Protein Engineering, Pseudomonas syringae/genetics/*metabolism, Recombinant Fusion Proteins/genetics/*metabolism, Vibrio/genetics/*metabolism
Genetics24444998Genome sequence and comparative genome analysis of Pseudomonas syringae pv. syringae type strain ATCC 19310.Park YS, Jeong H, Sim YM, Yi HS, Ryu CMJ Microbiol Biotechnol10.4014/jmb.1312.120822014Computational Biology, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Molecular Sequence Data, Pseudomonas syringae/*genetics/isolation & purification, *Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3983Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10604)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10604
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
36440Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18857
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
82235Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4542.1StrainInfo: A central database for resolving microbial strain identifiers
123401Curators of the CIPCollection of Institut Pasteur (CIP 106698)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106698