Strain identifier

BacDive ID: 130228

Type strain: Yes

Species: Paraburkholderia diazotrophica

Strain Designation: NKMU-JPY461

Strain history: <- LMG <- W.-M. Chen, Natl. Kaohsiung Marine Univ. Taiwan

NCBI tax ID(s): 667676 (species)

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General

@ref: 21539

BacDive-ID: 130228

DSM-Number: 29787

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

description: Paraburkholderia diazotrophica NKMU-JPY461 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Mimosa candollei, root nodule.

NCBI tax id

  • NCBI tax id: 667676
  • Matching level: species

strain history

  • @ref: 21539
  • history: <- LMG <- W.-M. Chen, Natl. Kaohsiung Marine Univ. Taiwan

doi: 10.13145/bacdive130228.20230509.8.1

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 diazotrophica
  • full scientific name: Paraburkholderia diazotrophica (Sheu et al. 2013) Sawana et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia diazotrophica

@ref: 21539

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia diazotrophica

full scientific name: Paraburkholderia diazotrophica (Sheu et al. 2013) Sawana et al. 2015

strain designation: NKMU-JPY461

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30607negative1.5 µm0.9 µmrod-shapedyes
69480yes92.581
69480negative99.958

colony morphology

  • @ref: 21539
  • incubation period: 2-3 days

pigmentation

  • @ref: 30607
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 21539
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
21539positivegrowth30mesophilic
30607positivegrowth15-40
30607positiveoptimum33.5mesophilic

culture pH

@refabilitytypepHPH range
30607positivegrowth04-08acidophile
30607positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 30607
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30607no
69481no100
69480no99.976

halophily

  • @ref: 30607
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-1 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3060716000ethanolamine+carbon source
3060715963ribitol+carbon source
3060721217L-alaninamide+carbon source
3060716449alanine+carbon source
3060722599arabinose+carbon source
3060718403L-arabitol+carbon source
3060722653asparagine+carbon source
3060735391aspartate+carbon source
3060717126DL-carnitine+carbon source
3060717057cellobiose+carbon source
3060716947citrate+carbon source
3060723652dextrin+carbon source
3060715740formate+carbon source
3060728757fructose+carbon source
3060724148galactonate+carbon source
3060728260galactose+carbon source
3060724265gluconate+carbon source
306075417glucosamine+carbon source
3060717234glucose+carbon source
3060729987glutamate+carbon source
3060717754glycerol+carbon source
3060728087glycogen+carbon source
3060727570histidine+carbon source
3060724996lactate+carbon source
3060715792malonate+carbon source
3060729864mannitol+carbon source
3060737684mannose+carbon source
30607506227N-acetylglucosamine+carbon source
3060728044phenylalanine+carbon source
3060726271proline+carbon source
3060751850methyl pyruvate+carbon source
3060726490quinate+carbon source
3060716634raffinose+carbon source
3060726546rhamnose+carbon source
3060717822serine+carbon source
3060730911sorbitol+carbon source
3060730031succinate+carbon source
3060717992sucrose+carbon source
3060717748thymidine+carbon source
3060727082trehalose+carbon source
3060753423tween 40+carbon source
3060753426tween 80+carbon source
3060717632nitrate+reduction
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

metabolite production

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

metabolite tests

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

enzymes

@refvalueactivityec
21539catalase+1.11.1.6
21539cytochrome-c oxidase+1.9.3.1
30607acid phosphatase+3.1.3.2
30607alkaline phosphatase+3.1.3.1
30607catalase+1.11.1.6
30607cytochrome oxidase+1.9.3.1
30607urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21539+------++++++-+--++/-+/-+

Isolation, sampling and environmental information

isolation

  • @ref: 21539
  • sample type: Mimosa candollei, root nodule
  • host species: Mimosa candollei
  • geographic location: Goias
  • country: Brazil
  • origin.country: BRA
  • continent: Middle and South America

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_17392.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_153;97_10733;98_13169;99_17392&stattab=map
  • Last taxonomy: Paraburkholderia diazotrophica subclade
  • 16S sequence: HM366717
  • Sequence Identity:
  • Total samples: 410
  • soil counts: 301
  • aquatic counts: 29
  • animal counts: 49
  • plant counts: 31

Safety information

risk assessment

  • @ref: 21539
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21539
  • description: Burkholderia diazotrophica strain NKMU-JPY461 16S ribosomal RNA gene, partial sequence
  • accession: HM366717
  • length: 1402
  • database: ena
  • NCBI tax ID: 667676

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia diazotrophica LMG 26031GCA_900108945scaffoldncbi667676
66792Paraburkholderia diazotrophica strain LMG 26031667676.3wgspatric667676
66792Paraburkholderia diazotrophica LMG 260312654588103draftimg667676

GC content

  • @ref: 30607
  • GC-content: 64

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentno90.111no
motileyes83.142no
flagellatedno86.853no
gram-positiveno98.197yes
anaerobicno98.24yes
aerobicyes88.024no
halophileno95.378yes
spore-formingno93.047yes
thermophileno99.589yes
glucose-utilyes90.154yes

External links

@ref: 21539

culture collection no.: DSM 29787, BCRC 80259, JPY 461, KCTC 23308, LMG 26031

straininfo link

  • @ref: 88770
  • straininfo: 371126

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22467155Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp.Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E, Dos Reis Junior FB, Melkonian R, Moulin L, James EK, Sprent JI, Young JPW, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.039859-02012Bacterial Typing Techniques, Base Composition, Brazil, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Mimosa/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNAGenetics
Phylogeny25472981Burkholderia monticola sp. nov., isolated from mountain soil.Baek I, Seo B, Lee I, Yi H, Chun JInt J Syst Evol Microbiol10.1099/ijs.0.066001-02014Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, Cardiolipins/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphatidylethanolamines/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny25575828Burkholderia susongensis sp. nov., a mineral-weathering bacterium isolated from weathered rock surface.Gu JY, Zang SG, Sheng XF, He LY, Huang Z, Wang QInt J Syst Evol Microbiol10.1099/ijs.0.0000592015Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Minerals, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny26031294Burkholderia humisilvae sp. nov., Burkholderia solisilvae sp. nov. and Burkholderia rhizosphaerae sp. nov., isolated from forest soil and rhizosphere soil.Lee JC, Whang KSInt J Syst Evol Microbiol10.1099/ijs.0.0003682015Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Genes, Bacterial, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
21539Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29787Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29787)
30607Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172693828776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88770Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID371126.1