Strain identifier

BacDive ID: 1966

Type strain: Yes

Species: Paraburkholderia phytofirmans

Strain Designation: PsJN

Strain history: CIP <- 2005, CCUG <- 2004, A. Sessitsch, Seibersdorf, Austria: strain PsJN

NCBI tax ID(s): 261302 (species)

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General

@ref: 6984

BacDive-ID: 1966

DSM-Number: 17436

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

description: Paraburkholderia phytofirmans PsJN is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface-sterilized onion roots.

NCBI tax id

  • NCBI tax id: 261302
  • Matching level: species

strain history

@refhistory
6984<- A. Sessitsch, ARC Seibersdorf Research, Austria; PsJN <- J. Nowak
121818CIP <- 2005, CCUG <- 2004, A. Sessitsch, Seibersdorf, Austria: strain PsJN

doi: 10.13145/bacdive1966.20250331.9.3

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Paraburkholderia
  • species: Paraburkholderia phytofirmans
  • full scientific name: Paraburkholderia phytofirmans (Sessitsch et al. 2005) Sawana et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia phytofirmans

@ref: 6984

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia phytofirmans

full scientific name: Paraburkholderia phytofirmans (Sessitsch et al. 2005) Sawana et al. 2015

strain designation: PsJN

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31259negative1.3 µm0.65 µmrod-shapedyes
121818negativeoval-shapedyes
125438negative96.969

colony morphology

@refincubation period
69842-3 days
584572 days
121818

pigmentation

  • @ref: 31259
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6984TRYPTICASE 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
41979MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121818CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45
121818CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperature
6984positivegrowth30
31259positivegrowth30-36
31259positiveoptimum30
41979positivegrowth30
58457positivegrowth30

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
58457aerobe
121818obligate aerobe
125438aerobe91.622
125439obligate aerobe99.2

halophily

  • @ref: 31259
  • salt: NaCl
  • growth: positive
  • tested relation: optimum
  • concentration: 0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3125928757fructose+carbon source
3125917234glucose+carbon source
3125918222xylose+carbon source
12181817632nitrate-reduction
12181816301nitrite-reduction
6836925115malate+assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
6984catalase+1.11.1.6
6984cytochrome-c oxidase-1.9.3.1
31259cytochrome oxidase+1.9.3.1
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
121818oxidase+
121818alcohol dehydrogenase-1.1.1.1
121818catalase+1.11.1.6
121818lysine decarboxylase-4.1.1.18
121818ornithine decarboxylase-4.1.1.17
121818urease-3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121818-+++-+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6984-------++++++-++++-++
6984-------++++++-+++++++
6984-----+/--++++++-+-++--+
6984-------++++++-++/-+/-+-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
6984surface-sterilized onion rootsCanadaCANNorth America
58457Onion roots,surface-sterilized
121818Plant, Onion roots, surface-sterilized

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_1471.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_173;97_187;98_381;99_1471&stattab=map
  • Last taxonomy: Paraburkholderia
  • 16S sequence: AY497470
  • Sequence Identity:
  • Total samples: 722
  • soil counts: 579
  • aquatic counts: 44
  • animal counts: 56
  • plant counts: 43

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
69841Risk group (German classification)
1218181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6984
  • description: Burkholderia phytofirmans strain PsJN 16S ribosomal RNA gene, partial sequence
  • accession: AY497470
  • length: 1488
  • database: nuccore
  • NCBI tax ID: 398527

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia phytofirmans PsJNGCA_000020125completencbi398527
66792Paraburkholderia phytofirmans PsJN398527.31plasmidpatric398527
66792Paraburkholderia phytofirmans PsJN642555113completeimg398527

GC content

  • @ref: 6984
  • GC-content: 61

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno96.969no
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.361yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.622no
125438spore-formingspore-formingAbility to form endo- or exosporesno85.296no
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.986no
125438motile2+flagellatedAbility to perform flagellated movementyes85.301no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno78.8
125439BacteriaNetmotilityAbility to perform movementyes52.7
125439BacteriaNetgram_stainReaction to gram-stainingnegative66.8
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe99.2

External links

@ref: 6984

culture collection no.: DSM 17436, CCUG 49060, LMG 22146, CIP 108762

straininfo link

  • @ref: 71611
  • straininfo: 128227

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879253Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties.Sessitsch A, Coenye T, Sturz AV, Vandamme P, Barka EA, Salles JF, Van Elsas JD, Faure D, Reiter B, Glick BR, Wang-Pruski G, Nowak JInt J Syst Evol Microbiol10.1099/ijs.0.63149-020054-Butyrolactone/analogs & derivatives/analysis/isolation & purification, Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/cytology/*isolation & purification/physiology, Carbon-Carbon Lyases/analysis, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Flagella/physiology, Genes, rRNA, Gentian Violet, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Onions/*microbiology, Phenazines, Phylogeny, Plant Roots/*microbiology, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAEnzymology
Phylogeny17082385Burkholderia ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.Kim HB, Park MJ, Yang HC, An DS, Jin HZ, Yang DCInt J Syst Evol Microbiol10.1099/ijs.0.64387-02006Bacterial Typing Techniques, Burkholderia/*classification/cytology/*isolation & purification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Flagella, Genes, rRNA, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, *Panax, Phylogeny, Quinones/analysis/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil Microbiology, beta-Glucosidase/*biosynthesisGenetics
Enzymology26205522Imidase catalyzing desymmetric imide hydrolysis forming optically active 3-substituted glutaric acid monoamides for the synthesis of gamma-aminobutyric acid (GABA) analogs.Nojiri M, Hibi M, Shizawa H, Horinouchi N, Yasohara Y, Takahashi S, Ogawa JAppl Microbiol Biotechnol10.1007/s00253-015-6812-x2015Alcaligenes faecalis/*enzymology, Amidohydrolases/chemistry/genetics/isolation & purification/*metabolism, Burkholderiaceae/*enzymology, Enzyme Stability, Glutarates/*metabolism, Hydrogen-Ion Concentration, Hydrolysis, Imides/*metabolism, Recombinant Proteins/chemistry/genetics/isolation & purification/*metabolism, Sequence Homology, Amino Acid, Temperature, gamma-Aminobutyric Acid/metabolismMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6984Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17436)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17436
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
31259Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2758128776041
41979Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6426
58457Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 49060)https://www.ccug.se/strain?id=49060
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
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
71611Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID128227.1StrainInfo: A central database for resolving microbial strain identifiers
121818Curators of the CIPCollection of Institut Pasteur (CIP 108762)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108762
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1