Strain identifier

BacDive ID: 13167

Type strain: No

Species: Pseudomonas amygdali

Strain Designation: 2

Strain history: CIP <- 2000, NCPPB <- C. Ogimi, strain: 2

NCBI tax ID(s): 86176 (species)

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General

@ref: 2804

BacDive-ID: 13167

DSM-Number: 6759

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

description: Pseudomonas amygdali 2 is an aerobe, mesophilic, Gram-negative plant pathogen that was isolated from china berry .

NCBI tax id

  • NCBI tax id: 86176
  • Matching level: species

strain history

@refhistory
2804<- ATCC <- C. Ogimi; 2
116350CIP <- 2000, NCPPB <- C. Ogimi, strain: 2

doi: 10.13145/bacdive13167.20230509.8.1

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 amygdali
  • full scientific name: Pseudomonas amygdali Psallidas and Panagopoulos 1975 (Approved Lists 1980)

  • synonyms

    • @ref: 20215
    • synonym: Pseudomonas meliae

@ref: 2804

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas amygdali

full scientific name: Pseudomonas amygdali Psallidas and Panagopoulos 1975

strain designation: 2

type strain: no

Morphology

cell morphology

  • @ref: 116350
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 116350
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
2804REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b)yeshttps://mediadive.dsmz.de/medium/535bName: REACTIVATION WITH LIQUID MEDIUM (DSMZ Medium 535b) Composition: Trypticase soy broth 30.0 g/l Casein peptone 17.0 g/l Agar 15.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l K2HPO4 2.5 g/l D(+)-Glucose 2.5 g/l Distilled water
39560MEDIUM 328- for nutrient agaryesDistilled water make up to (1000.000 ml);Agar (15.000 g);Peptone (5.000g);Beef extract (3.000 g)
116350CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
2804positivegrowth28mesophilic
39560positivegrowth25mesophilic
59214positivegrowth20-30

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
59214aerobe
116350obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116350NaClpositivegrowth0 %
116350NaClnogrowth2 %
116350NaClnogrowth4 %
116350NaClnogrowth6 %
116350NaClnogrowth8 %
116350NaClnogrowth10 %

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
11635016947citrate+carbon source
1163504853esculin-hydrolysis
11635017632nitrate-reduction
11635016301nitrite-reduction
11635017632nitrate-respiration

antibiotic resistance

  • @ref: 116350
  • 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
11635035581indoleno

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
116350oxidase+
116350beta-galactosidase-3.2.1.23
116350alcohol dehydrogenase-1.1.1.1
116350gelatinase-
116350amylase-
116350DNase-
116350caseinase-3.4.21.50
116350catalase+1.11.1.6
116350tween esterase-
116350lecithinase-
116350lipase-
116350lysine decarboxylase-4.1.1.18
116350ornithine decarboxylase-4.1.1.17
116350protease-
116350tryptophan deaminase-
116350urease-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
116350-+++-+----++----+---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
2804--------+-----+-----+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116350++-++--+--+--------++----------+------+----++---++---+------+------------+----+++--------+++++-----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
2804china berry (Melia azedarach)Melia azedarach
59214China berry (Melia azedarch)
116350Melia azedarachOkinawaJapanJPNAsia1974

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: HF558390
  • 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
2804yes1Risk group (German classification)
1163501Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Pseudomonas meliae partial 16S rRNA gene, strain Ogimi 2
  • accession: HF558390
  • length: 1512
  • database: ena
  • NCBI tax ID: 86176

External links

@ref: 2804

culture collection no.: DSM 6759, ATCC 33050, NCPPB 3033, CCUG 51503, CIP 106733, ICMP 6289, LMG 2220

straininfo link

  • @ref: 82375
  • straininfo: 4157

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2804Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6759)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6759
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
39560Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18896
59214Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51503)https://www.ccug.se/strain?id=51503
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
82375Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4157.1StrainInfo: A central database for resolving microbial strain identifiers
116350Curators of the CIPCollection of Institut Pasteur (CIP 106733)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106733