Strain identifier

BacDive ID: 1946

Type strain: Yes

Species: Burkholderia ambifaria

Strain history: CIP <- 2001, CCUG <- D. Janssens, LMG, Gent, Belgium <- T. Coenye, Gent, Belgium <- J.L. Parke

NCBI tax ID(s): 152480 (species)

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General

@ref: 6283

BacDive-ID: 1946

DSM-Number: 16087

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

description: Burkholderia ambifaria DSM 16087 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from pea rhizosphere.

NCBI tax id

  • NCBI tax id: 152480
  • Matching level: species

strain history

@refhistory
6283<- CCUG <- LMG <- T. Coenye, Univ. Ghent, Belgium <- J. L. Parke
116324CIP <- 2001, CCUG <- D. Janssens, LMG, Gent, Belgium <- T. Coenye, Gent, Belgium <- J.L. Parke

doi: 10.13145/bacdive1946.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Burkholderiaceae
  • genus: Burkholderia
  • species: Burkholderia ambifaria
  • full scientific name: Burkholderia ambifaria Coenye et al. 2001

@ref: 6283

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Burkholderia

species: Burkholderia ambifaria

full scientific name: Burkholderia ambifaria Coenye et al. 2001

type strain: yes

Morphology

cell morphology

  • @ref: 116324
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 6283
  • type of hemolysis: gamma
  • incubation period: 1-2 days

pigmentation

  • @ref: 116324
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6283CASO AGAR (MERCK 105458) (DSMZ Medium 220)yeshttps://mediadive.dsmz.de/medium/220Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
33102MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116324CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
6283positivegrowth28mesophilic
33102positivegrowth30mesophilic
56273positivegrowth30mesophilic
116324positivegrowth25-37mesophilic
116324nogrowth5psychrophilic
116324nogrowth10psychrophilic
116324nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
56273aerobe
116324obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
116324NaClpositivegrowth0-4 %
116324NaClnogrowth6 %
116324NaClnogrowth8 %
116324NaClnogrowth10 %

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
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction
11632416947citrate+carbon source
1163244853esculin+hydrolysis
11632417632nitrate+reduction
11632416301nitrite-reduction
11632417632nitrate-respiration

antibiotic resistance

  • @ref: 116324
  • 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
11632435581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
6283catalase+1.11.1.6
6283cytochrome-c 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
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
116324oxidase+
116324beta-galactosidase+3.2.1.23
116324alcohol dehydrogenase-1.1.1.1
116324gelatinase+/-
116324amylase-
116324DNase-
116324caseinase+3.4.21.50
116324catalase+1.11.1.6
116324tween esterase+
116324lecithinase+
116324lipase+
116324lysine decarboxylase-4.1.1.18
116324ornithine decarboxylase-4.1.1.17
116324protease+
116324urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116324-+++-+----++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6283+----+-++++++-+++++++
6283+----+-++++++-+++++++
6283+----++++++++-++++++

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116324+++++--++----+----++++--+-++-+++++--++-+---+++++++++-++++--++++++--+---+++++++-++++++++++++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
6283pea rhizosphereWisconsinUSAUSANorth America
56273Pea rhizosphereWIUSAUSANorth America1985
116324Plant, Healthy pea plantsWisconsinUnited States of AmericaUSANorth America1985

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_198.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_18;97_18;98_21;99_198&stattab=map
  • Last taxonomy: Burkholderia
  • 16S sequence: HQ849072
  • Sequence Identity:
  • Total samples: 5054
  • soil counts: 1055
  • aquatic counts: 564
  • animal counts: 1930
  • plant counts: 1505

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
62832Risk group (German classification)
1163241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia ambifaria strain CIP 107266 16S ribosomal RNA gene, partial sequenceEU0241771313ena152480
20218Burkholderia ambifaria strain LMG 19182 16S ribosomal RNA gene, partial sequenceHQ8490721124ena152480

External links

@ref: 6283

culture collection no.: DSM 16087, CCUG 44356, CIP 107266, LMG 19182

straininfo link

  • @ref: 71591
  • straininfo: 84230

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11491349Burkholderia ambifaria sp. nov., a novel member of the Burkholderia cepacia complex including biocontrol and cystic fibrosis-related isolates.Coenye T, Mahenthiralingam E, Henry D, LiPuma JJ, Laevens S, Gillis M, Speert DP, Vandamme PInt J Syst Evol Microbiol10.1099/00207713-51-4-14812001Base Composition, Burkholderia/*classification/genetics/*isolation & purification/metabolism, Burkholderia cepacia/*classification/genetics/*isolation & purification/metabolism, Cystic Fibrosis/*microbiology, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Environmental Microbiology, Fatty Acids/analysis, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Polymorphism, Genetic, Polymorphism, Restriction Fragment Length, Species SpecificityEnzymology
Metabolism31924623Exploiting the Natural Diversity of RhlA Acyltransferases for the Synthesis of the Rhamnolipid Precursor 3-(3-Hydroxyalkanoyloxy)Alkanoic Acid.Germer A, Tiso T, Muller C, Behrens B, Vosse C, Scholz K, Froning M, Hayen H, Blank LMAppl Environ Microbiol10.1128/AEM.02317-192020Acyltransferases/*genetics/metabolism, Bacteria/*genetics/metabolism, Bacterial Proteins/*genetics/metabolism, Carboxylic Acids/*metabolism, Glycolipids/biosynthesis/*metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6283Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16087)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16087
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
33102Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/4682
56273Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 44356)https://www.ccug.se/strain?id=44356
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
71591Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID84230.1StrainInfo: A central database for resolving microbial strain identifiers
116324Curators of the CIPCollection of Institut Pasteur (CIP 107266)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107266