Strain identifier

BacDive ID: 13049

Type strain: Yes

Species: Pseudomonas asplenii

Strain Designation: 6801

Strain history: CIP <- 2000, CCUG <- D. Janssens, LMG, Ghent, Belgium <- PDDCC <- A. Tanii: strain 6801

NCBI tax ID(s): 50340 (species)

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General

@ref: 3066

BacDive-ID: 13049

DSM-Number: 7231

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Pseudomonas asplenii 6801 is an aerobe, mesophilic, motile bacterium that was isolated from Oriza sativa.

NCBI tax id

  • NCBI tax id: 50340
  • Matching level: species

strain history

@refhistory
3066<- NCPPB <- ICMP <- A. Tanii, 6801
119500CIP <- 2000, CCUG <- D. Janssens, LMG, Ghent, Belgium <- PDDCC <- A. Tanii: strain 6801

doi: 10.13145/bacdive13049.20230509.8.1

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 asplenii
  • full scientific name: Pseudomonas asplenii (Ark and Tompkins 1946) Savulescu 1947 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Phytomonas asplenii
    20215Pseudomonas fuscovaginae

@ref: 3066

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas asplenii

full scientific name: Pseudomonas asplenii (Ark and Tompkins 1946) Savulescu 1947 emend. Tvrzová et al. 2006

strain designation: 6801

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes97.535
6948099.998negative
119500yesnegativerod-shaped

pigmentation

  • @ref: 119500
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
3066YPGA (DSMZ Medium 1015)yeshttps://mediadive.dsmz.de/medium/1015Name: YPGA (DSMZ Medium 1015) Composition: Agar 15.0 g/l Glucose 7.0 g/l Bacto peptone 7.0 g/l Yeast extract 7.0 g/l Distilled water
3066TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
3066NUTRIENT 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
3066GLUCOSE 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
39527MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
119500CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperaturerange
3066positivegrowth28mesophilic
39527positivegrowth30mesophilic
51179positivegrowth22psychrophilic
51179positivegrowth28mesophilic
119500positivegrowth5-30
119500nogrowth37mesophilic
119500nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
51179aerobe
119500obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.99

halophily

@refsaltgrowthtested relationconcentration
119500NaClpositivegrowth0-4 %
119500NaClnogrowth6 %
119500NaClnogrowth8 %
119500NaClnogrowth10 %

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
11950016947citrate+carbon source
1195004853esculin-hydrolysis
11950017632nitrate-reduction
11950016301nitrite-reduction
11950017632nitrate-respiration

antibiotic resistance

  • @ref: 119500
  • 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
11950035581indoleno

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
119500oxidase+
119500beta-galactosidase-3.2.1.23
119500alcohol dehydrogenase+1.1.1.1
119500gelatinase+/-
119500amylase-
119500DNase-
119500caseinase+3.4.21.50
119500catalase+1.11.1.6
119500tween esterase-
119500lecithinase+
119500lipase+
119500lysine decarboxylase-4.1.1.18
119500ornithine decarboxylase-4.1.1.17
119500protease-
119500tryptophan deaminase-
119500urease-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
119500-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
3066---+----++++--++-++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119500+++++--------------++-----+----+-+---------++--+++++-+++----+-+++-----++-+-+++-++++++++-+++++++++++

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinent
3066Oriza sativaOriza sativaJapanJPNAsia
51179Oryza sativaJapanJPNAsia
119500Oryza sativaJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Plants
  • Cat3: #Herbaceous plants (Grass,Crops)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
30661Risk group (German classification)
1195001Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Pseudomonas fuscovaginae strain ICMP 5940 16S ribosomal RNA gene, partial sequence
  • accession: FJ483519
  • length: 1395
  • database: ena
  • NCBI tax ID: 50340

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas fuscovaginae LMG 2158GCA_900108595chromosomencbi50340
66792Pseudomonas fuscovaginae ICMP 5940 ICMP5940GCA_000467065contigncbi1367451
66792Pseudomonas fuscovaginae ICMP 59401367451.3wgspatric1367451
66792Pseudomonas fuscovaginae strain LMG 215850340.51completepatric50340
66792Pseudomonas fuscovaginae LMG 21582667527230draftimg50340

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.232no
anaerobicno98.902yes
halophileno87.451no
spore-formingno95.243no
glucose-utilyes95.009yes
aerobicyes94.444yes
thermophileno99.868yes
motileyes88.89no
flagellatedyes83.11no
glucose-fermentno87.416no

External links

@ref: 3066

culture collection no.: CCUG 32780, LMG 2158, DSM 7231, ICMP 5940, NCPPB 3085, CIP 106695, PDDCC 5940

straininfo link

  • @ref: 82260
  • straininfo: 4080

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17082407Pseudomonas moraviensis sp. nov. and Pseudomonas vranovensis sp. nov., soil bacteria isolated on nitroaromatic compounds, and emended description of Pseudomonas asplenii.Tvrzova L, Schumann P, Sproer C, Sedlacek I, Pacova Z, Sedo O, Zdrahal Z, Steffen M, Lang EInt J Syst Evol Microbiol10.1099/ijs.0.63988-02006Amino Acids/metabolism, Bacterial Typing Techniques, Carbohydrate Metabolism, Czech Republic, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/cytology/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Ribotyping, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyMetabolism
Phylogeny32392123Genome analysis-based reclassification of Pseudomonas fuscovaginae and Pseudomonas shirazica as later heterotypic synonyms of Pseudomonas asplenii and Pseudomonas asiatica, respectively.Tohya M, Watanabe S, Tada T, Tin HH, Kirikae TInt J Syst Evol Microbiol10.1099/ijsem.0.0041992020Bacterial Typing Techniques, DNA, Bacterial/genetics, Genes, Bacterial, Nucleic Acid Hybridization, *Phylogeny, Pseudomonas/*classification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3066Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 7231)https://www.dsmz.de/collection/catalogue/details/culture/DSM-7231
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
39527Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18853
51179Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 32780)https://www.ccug.se/strain?id=32780
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)
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
82260Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID4080.1StrainInfo: A central database for resolving microbial strain identifiers
119500Curators of the CIPCollection of Institut Pasteur (CIP 106695)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106695