Strain identifier

BacDive ID: 132166

Type strain: Yes

Species: Paraburkholderia caballeronis

Strain Designation: TNe-841

Strain history: CIP <- 2011, P. Estrada de los Santos, UNAM, Cuernavaca, Morelos, Mexico: strain TNe-841

NCBI tax ID(s): 416943 (species)

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General

@ref: 23955

BacDive-ID: 132166

DSM-Number: 104148

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

description: Paraburkholderia caballeronis TNe-841 is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizosphere of tomato .

NCBI tax id

  • NCBI tax id: 416943
  • Matching level: species

strain history

@refhistory
23955<- CIP; CIP 110324 <- P. Estrada-de los Santos; TNe-841
117083CIP <- 2011, P. Estrada de los Santos, UNAM, Cuernavaca, Morelos, Mexico: strain TNe-841

doi: 10.13145/bacdive132166.20230509.8.1

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 caballeronis
  • full scientific name: Paraburkholderia caballeronis (Martínez-Aguilar et al. 2014) Sawana et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia caballeronis

@ref: 23955

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia caballeronis

full scientific name: Paraburkholderia caballeronis (Martínez-Aguilar et al. 2014) Sawana et al. 2017

strain designation: TNe-841

type strain: yes

Morphology

cell morphology

  • @ref: 117083
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42113MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
23955R2A MEDIUM (DSMZ Medium 830)yesName: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled waterhttps://mediadive.dsmz.de/medium/830
117083CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
23955positivegrowth30mesophilic
42113positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 117083
  • oxygen tolerance: obligate aerobe

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
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction
11708317632nitrate-reduction
11708316301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11708335581indoleno

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
68369arginine dihydrolase-3.5.3.6
117083oxidase-
117083catalase+1.11.1.6
117083urease+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
117083--+--+----++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
23955----+/----+++++-++-+-+-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
23955rhizosphere of tomato (Lycopersicon esculentum)Lycopersicon esculentumNepantlaMexicoMEXNorth America
117083Tomato rhizoplaneNepantla, MexicoMexicoMEXNorth America2007

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
239551Risk group (German classification)
1170831Risk group (French classification)

Sequence information

16S sequences

  • @ref: 23955
  • description: Burkholderia caballeronis strain TNe-841 16S ribosomal RNA gene, partial sequence
  • accession: EF139186
  • length: 1532
  • database: ena
  • NCBI tax ID: 416943

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia caballeronis TNe-841GCA_900104845contigncbi416943
66792Paraburkholderia caballeronis LMG 26416GCA_900109675scaffoldncbi416943
66792Paraburkholderia caballeronis strain LMG 26416416943.14wgspatric416943
66792Paraburkholderia caballeronis LMG 264162651870119draftimg416943

GC content

  • @ref: 23955
  • GC-content: 66.0
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
glucose-fermentno89.687no
motileyes89.883no
flagellatedno81.465no
gram-positiveno98.223no
anaerobicno98.707no
aerobicyes89.786no
halophileno94.593no
spore-formingno94.426no
thermophileno99.357yes
glucose-utilyes89.116yes

External links

@ref: 23955

culture collection no.: DSM 104148, CIP 110324, LMG 26416

straininfo link

  • @ref: 90521
  • straininfo: 377368

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24057982Burkholderia caballeronis sp. nov., a nitrogen fixing species isolated from tomato (Lycopersicon esculentum) with the ability to effectively nodulate Phaseolus vulgaris.Martinez-Aguilar L, Salazar-Salazar C, Mendez RD, Caballero-Mellado J, Hirsch AM, Vasquez-Murrieta MS, Estrada-de los Santos PAntonie Van Leeuwenhoek10.1007/s10482-013-0028-92013Bacterial Typing Techniques, Burkholderia/*classification/genetics/isolation & purification/*physiology, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Lycopersicon esculentum/*microbiology, Mexico, Molecular Sequence Data, *Nitrogen Fixation, Phaseolus/*microbiology, Phylogeny, *Plant Root Nodulation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
29255574Draft genome of Paraburkholderia caballeronis TNe-841(T), a free-living, nitrogen-fixing, tomato plant-associated bacterium.Rojas-Rojas FU, Tapia-Garcia EY, Maymon M, Humm E, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy TBK, Markowitz V, Ivanova N, Kyrpides N, Woyke T, Shapiro N, Hirsch AM, Estrada-de Los Santos PStand Genomic Sci10.1186/s40793-017-0294-72017

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
23955Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-104148Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 104148)
42113Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/8171
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
90521Reimer, 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-ID377368.1
117083Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110324Collection of Institut Pasteur (CIP 110324)