Strain identifier
BacDive ID: 13024
Type strain:
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)
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 id | Matching level |
---|---|
1449349 | strain |
317 | species |
strain history
@ref | history |
---|---|
3983 | <- NCPPB <- K. A. Sabet |
123401 | CIP <- 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
@ref | name | growth | link | composition |
---|---|---|---|---|
3983 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: 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 |
3983 | GLUCOSE YEAST EXTRACT MEDIUM (DSMZ Medium 54) | yes | https://mediadive.dsmz.de/medium/54 | Name: 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 |
36440 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
123401 | CIP Medium 3 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3 | |
123401 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
3983 | positive | growth | 26 | mesophilic |
36440 | positive | growth | 25 | mesophilic |
123401 | positive | growth | 5-30 | |
123401 | no | growth | 37 | mesophilic |
123401 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 123401
- oxygen tolerance: obligate aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
123401 | NaCl | positive | growth | 0-6 % |
123401 | NaCl | no | growth | 8 % |
123401 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | - | assimilation |
68369 | 59640 | N-acetylglucosamine | - | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | + | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | + | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | - | fermentation |
68369 | 27897 | tryptophan | - | energy source |
68369 | 17632 | nitrate | - | reduction |
123401 | 16947 | citrate | + | carbon source |
123401 | 4853 | esculin | + | hydrolysis |
123401 | 17632 | nitrate | - | reduction |
123401 | 16301 | nitrite | - | reduction |
123401 | 17632 | nitrate | - | 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
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
123401 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | cytochrome oxidase | - | 1.9.3.1 |
68369 | gelatinase | + | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
123401 | oxidase | + | |
123401 | beta-galactosidase | - | 3.2.1.23 |
123401 | alcohol dehydrogenase | - | 1.1.1.1 |
123401 | gelatinase | +/- | |
123401 | amylase | - | |
123401 | DNase | - | |
123401 | caseinase | + | 3.4.21.50 |
123401 | catalase | + | 1.11.1.6 |
123401 | tween esterase | - | |
123401 | lecithinase | - | |
123401 | lipase | - | |
123401 | lysine decarboxylase | - | 4.1.1.18 |
123401 | ornithine decarboxylase | - | 4.1.1.17 |
123401 | protease | + | |
123401 | tryptophan deaminase | - | |
123401 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123401 | - | + | + | + | + | + | + | - | + | - | + | + | - | - | - | - | + | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3983 | - | - | - | - | - | + | + | - | + | + | + | + | - | - | + | + | - | + | + | - | - |
3983 | - | - | - | - | - | + | + | - | + | + | + | + | - | - | + | + | - | + | + | - | - |
3983 | - | - | - | - | - | + | + | - | + | + | + | + | - | - | + | + | - | + | + | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123401 | + | + | + | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | + | + | + | + | - | - | - | - | + | - | - | - | - | + | + | + | - | - | + | - | - | - | + | - | - | + | + | - | - | - | - | + | + | + | - | + | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | + | + | - | + | - | + | + | + | - | + | + | + | + | + | + | - | + | - | + | + | + | + | + | + | + | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent |
---|---|---|---|---|---|
3983 | Syringa vulgaris | Syringa vulgaris | United Kingdom | GBR | Europe |
123401 | Syringa 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
@ref | pathogenicity plant | biosafety level | biosafety level comment |
---|---|---|---|
3983 | yes | 1 | Risk group (German classification) |
123401 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pseudomonas syringae strain ATCC 19310 16S ribosomal RNA gene, partial sequence | AF094749 | 1460 | ena | 317 |
20218 | Pseudomonas syringae a41 16S ribosomal RNA gene, partial sequence | AF311988 | 497 | ena | 317 |
20218 | Pseudomonas syringae axB12 16S ribosomal RNA gene, partial sequence | AF311989 | 489 | ena | 317 |
20218 | Pseudomonas syringae partial 16S rRNA gene, type strain ICMP 3023T | AJ308316 | 1371 | ena | 317 |
20218 | Pseudomonas syringae 16S rRNA gene | D84026 | 1454 | ena | 317 |
20218 | Pseudomonas syringae strain ATCC 19310 16S ribosomal RNA gene, partial sequence | FJ971872 | 793 | ena | 317 |
20218 | Pseudomonas syringae pv. syringae culture-collection ICMP:3023 16S ribosomal RNA gene, partial sequence | HM190217 | 1444 | ena | 321 |
20218 | Pseudomonas syringae pv. syringae culture-collection LMG:1247 16S-23S ribosomal RNA intergenic spacer, partial sequence | HM032080 | 526 | ena | 321 |
20218 | Pseudomonas syringae pv. syringae culture-collection LMG:1247 16S-23S ribosomal RNA intergenic spacer, partial sequence | HM032083 | 516 | ena | 321 |
20218 | Pseudomonas syringae pv. syringae culture-collection LMG:1247 16S-23S ribosomal RNA intergenic spacer, partial sequence | HM032084 | 517 | ena | 321 |
20218 | P.syringae 16S rRNA gene | Z76669 | 1494 | ena | 317 |
20218 | Pseudomonas syringae pv. syringae strain NRRL B-1631 16S-23S ribosomal RNA intergenic spacer, partial sequence | AY342181 | 532 | ena | 321 |
3983 | Pseudomonas syringae pv. syringae strain NCPPB 281 16S ribosomal RNA gene, partial sequence | DQ318866 | 1482 | ena | 321 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas syringae pv. syringae ICMP 3023 | GCA_001401075 | scaffold | ncbi | 321 |
66792 | Pseudomonas syringae DSM 10604 | GCA_000597765 | contig | ncbi | 1449349 |
66792 | Pseudomonas syringae DSM 10604 | 1449349.3 | wgs | patric | 1449349 |
66792 | Pseudomonas syringae pv. syringae strain ICMP3023 | 321.65 | wgs | patric | 321 |
66792 | Pseudomonas syringae pv. syringae ICMP 3023 | 2713896866 | draft | img | 321 |
66792 | Pseudomonas syringae DSM 10604 | 2579778699 | draft | img | 1449349 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 89.878 | no |
gram-positive | no | 98.293 | no |
anaerobic | no | 98.204 | no |
halophile | no | 92.495 | no |
spore-forming | no | 93.895 | no |
thermophile | no | 99.718 | yes |
glucose-util | yes | 96.279 | yes |
aerobic | yes | 95.408 | no |
flagellated | yes | 69.461 | no |
glucose-ferment | no | 89.398 | yes |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Genetics | 1898935 | Conservation 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 RE | J Bacteriol | 10.1128/jb.173.2.768-775.1991 | 1991 | Amino 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 Specificity | Enzymology |
Enzymology | 3023282 | Cloning and regulation of Erwinia herbicola pigment genes. | Perry KL, Simonitch TA, Harrison-Lavoie KJ, Liu ST | J Bacteriol | 10.1128/jb.168.2.607-612.1986 | 1986 | *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/genetics | Metabolism |
Metabolism | 18535860 | Surface display of GFP by Pseudomonas syringae truncated ice nucleation protein in attenuated Vibrio anguillarum strain. | Xu Y, Liu Q, Zhou L, Yang Z, Zhang Y | Mar Biotechnol (NY) | 10.1007/s10126-008-9108-7 | 2008 | Bacterial 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 | |
Genetics | 24444998 | Genome sequence and comparative genome analysis of Pseudomonas syringae pv. syringae type strain ATCC 19310. | Park YS, Jeong H, Sim YM, Yi HS, Ryu CM | J Microbiol Biotechnol | 10.4014/jmb.1312.12082 | 2014 | Computational Biology, DNA, Bacterial/*chemistry/*genetics, *Genome, Bacterial, Molecular Sequence Data, Pseudomonas syringae/*genetics/isolation & purification, *Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
3983 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10604) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-10604 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
36440 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/18857 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
82235 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID4542.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123401 | Curators of the CIP | Collection of Institut Pasteur (CIP 106698) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106698 |