Strain identifier

BacDive ID: 13051

Type strain: Yes

Species: Pseudomonas amygdali

Strain Designation: AL1

Strain history: CIP <- 2000, NCPPB <- C.G. Panagopoulos and P.G. Psallidas: strain AL1

NCBI tax ID(s): 47877 (species)

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General

@ref: 3102

BacDive-ID: 13051

DSM-Number: 7298

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

description: Pseudomonas amygdali AL1 is an obligate aerobe, mesophilic, Gram-negative plant pathogen that was isolated from almond, Prunus dulcis.

NCBI tax id

  • NCBI tax id: 47877
  • Matching level: species

strain history

@refhistory
3102<- ICPB <- C. G. Panagopoulos, AL1
116351CIP <- 2000, NCPPB <- C.G. Panagopoulos and P.G. Psallidas: strain AL1

doi: 10.13145/bacdive13051.20230509.8.1

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: 3102

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: AL1

type strain: yes

Morphology

cell morphology

  • @ref: 116351
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 116351
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3102NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1; with strain-specific modifications) Composition: Agar 15.0 g/l Glucose 10.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39564MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
116351CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
116351CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
3102positivegrowth27mesophilic
39564positivegrowth25mesophilic
116351positivegrowth5-30
116351nogrowth37mesophilic
116351nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116351
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116351NaClpositivegrowth0-4 %
116351NaClnogrowth6 %
116351NaClnogrowth8 %
116351NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1163514853esculin-hydrolysis
11635117632nitrate-reduction
11635116301nitrite-reduction
11635117632nitrate-respiration

antibiotic resistance

  • @ref: 116351
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 116351
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116351oxidase-
116351beta-galactosidase-3.2.1.23
116351alcohol dehydrogenase-1.1.1.1
116351gelatinase-
116351amylase-
116351DNase-
116351caseinase-3.4.21.50
116351catalase+1.11.1.6
116351tween esterase+
116351lecithinase-
116351lipase-
116351lysine decarboxylase-4.1.1.18
116351ornithine decarboxylase-4.1.1.17
116351tryptophan deaminase-
116351urease-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
116351-+++-+--+-++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116351++--+--+------------++----+------+--+------+-----+---+------+------------+-----++--------+++--+----

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationisolation date
3102almond, Prunus dulcisPrunus dulcisGreeceGRCEurope
116351Prunus dulcisGreeceGRCEuropeCrete1967

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_266.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_226;99_266&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: Z76654
  • Sequence Identity:
  • Total samples: 1423
  • soil counts: 435
  • aquatic counts: 325
  • animal counts: 369
  • plant counts: 294

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
3102yes1Risk group (German classification)
1163511Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas amygdali 16S rRNA geneD840071449ena47877
20218P.amygdali 16S rRNA geneZ766541494ena47877

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas amygdali ICMP 3918GCA_002699855scaffoldncbi47877
66792Pseudomonas amygdali ICMP3918GCA_001400115scaffoldncbi47877
66792Pseudomonas amygdali strain ICMP 391847877.9wgspatric47877
66792Pseudomonas amygdali strain ICMP391847877.4wgspatric47877
66792Pseudomonas amygdali ICMP 39182713896844draftimg47877

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes70.378no
gram-positiveno98.161no
anaerobicno97.949no
aerobicyes94.106no
halophileno93.987no
spore-formingno94.237no
glucose-utilyes96.419no
thermophileno99.702yes
motileyes90.769no
glucose-fermentno89.518no

External links

@ref: 3102

culture collection no.: DSM 7298, ATCC 33614, ICMP 3918, NCPPB 2607, CIP 106734, LMG 2123

straininfo link

  • @ref: 82261
  • straininfo: 3913

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3102Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7298)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7298
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
39564Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18897
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)
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
82261Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID3913.1StrainInfo: A central database for resolving microbial strain identifiers
116351Curators of the CIPCollection of Institut Pasteur (CIP 106734)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106734