Strain identifier

BacDive ID: 13059

Type strain: Yes

Species: Pseudomonas agarici

Strain Designation: 71A

Strain history: CIP <- 2000, LMG <- NCPPB <- J. Young

NCBI tax ID(s): 690598 (strain), 46677 (species)

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General

@ref: 4497

BacDive-ID: 13059

DSM-Number: 11810

keywords: genome sequence, 16S sequence, Bacteria, obligate aerobe, mesophilic, motile, plant pathogen

description: Pseudomonas agarici 71A is an obligate aerobe, mesophilic, motile plant pathogen that was isolated from mushroom .

NCBI tax id

NCBI tax idMatching level
46677species
690598strain

strain history

@refhistory
4497<- NCPPB <- J.M. Young; 71A
67770DSM 11810 <-- NCPPB 2289 <-- J. M. Young 71A.
116148CIP <- 2000, LMG <- NCPPB <- J. Young

doi: 10.13145/bacdive13059.20230509.8.1

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 agarici
  • full scientific name: Pseudomonas agarici Young 1970 (Approved Lists 1980)

@ref: 4497

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas agarici

full scientific name: Pseudomonas agarici Young 1970

strain designation: 71A

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes98.101
6948099.999negative
116148yesnegativerod-shaped

pigmentation

  • @ref: 116148
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4497NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
38640MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116148CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
4497positivegrowth30mesophilic
38640positivegrowth25mesophilic
67770positivegrowth30mesophilic
116148positivegrowth5-30
116148nogrowth37mesophilic
116148nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116148
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.938

halophily

@refsaltgrowthtested relationconcentration
116148NaClpositivegrowth0-8 %
116148NaClnogrowth10 %

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
11614816947citrate-carbon source
1161484853esculin-hydrolysis
11614817632nitrate-reduction
11614816301nitrite-reduction
11614817632nitrate-respiration

antibiotic resistance

  • @ref: 116148
  • 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
11614835581indoleno

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
116148oxidase+
116148beta-galactosidase-3.2.1.23
116148alcohol dehydrogenase-1.1.1.1
116148gelatinase-
116148amylase-
116148DNase-
116148caseinase-3.4.21.50
116148catalase+1.11.1.6
116148tween esterase-
116148lecithinase-
116148lipase-
116148lysine decarboxylase-4.1.1.18
116148ornithine decarboxylase-4.1.1.17
116148protease-
116148tryptophan deaminase-
116148urease-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
116148-+++-+--+-++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
4497-----------+--++-++-+
4497-----------+--++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116148+---+--------------+------+----+-+--------------+++--+------+-+----+---+++-+++-+++-----+++++++-++--

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentisolation date
4497mushroom (Agaricus bisporus)Agaricus bisporusNew ZealandNZLAustralia and Oceania
67770Mushroom (Agaricus bisporus)Agaricus bisporus
116148Agaricus bisporus, drippy gillsNew ZealandNZLAustralia and Oceania1969

isolation source categories

  • Cat1: #Host
  • Cat2: #Fungi
  • Cat3: #Mushroom

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
4497yes1Risk group (German classification)
1161481Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas agarici 16S ribosomal RNA gene, partial sequence; internal transcribed spacer 1, complete sequence; tRNA-Ile and tRNA-Ala genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF127589557ena46677
20218Pseudomonas agarici 16S rRNA geneD840051453ena46677
20218Pseudomonas agarici partial 16S rRNA gene, strain ICMP 2656TAJ3082981370ena46677
4497P.agarici 16S rRNA geneZ766521491ena46677

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas agarici NCPPB 2289690598.6wgspatric690598
66792Pseudomonas agarici strain IPO374046677.12wgspatric46677
66792Pseudomonas agarici strain LMG 211246677.9wgspatric46677
66792Pseudomonas agarici NCPPB 22892505679085draftimg690598
66792Pseudomonas agarici LMG 21122667527210draftimg46677
67770Pseudomonas agarici NCPPB 2289GCA_000280785scaffoldncbi690598
67770Pseudomonas agarici LMG 2112GCA_900109755scaffoldncbi46677

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.508no
anaerobicno98.91no
halophileno87.978no
spore-formingno96.302no
glucose-utilyes93.815no
thermophileno99.566yes
flagellatedyes83.349no
motileyes90.672no
aerobicyes87.98no
glucose-fermentno88.722yes

External links

@ref: 4497

culture collection no.: DSM 11810, ATCC 25941, ICMP 2656, ICPB PA144, NCPPB 2289, JCM 12566, BCRC 15817, CCUG 23365, CCUG 32769, CECT 4467, CFBP 2063, CIP 106703, LMG 2112, VTT E-94513

straininfo link

  • @ref: 82269
  • straininfo: 13750

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4497Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 11810)https://www.dsmz.de/collection/catalogue/details/culture/DSM-11810
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
38640Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18862
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
82269Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13750.1StrainInfo: A central database for resolving microbial strain identifiers
116148Curators of the CIPCollection of Institut Pasteur (CIP 106703)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106703