Strain identifier

BacDive ID: 1967

Type strain: Yes

Species: Paraburkholderia phenoliruptrix

Strain Designation: AC1100

Strain history: CIP <- 2004, CCUG <- 2003, LMG <- 2003, T. Coenye, Ghent Univ., Ghent, Belgium <- 1999, D. Henry, British Columbia Univ., Vancouver, Canada: strain AC1100

NCBI tax ID(s): 252970 (species)

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General

@ref: 7177

BacDive-ID: 1967

DSM-Number: 17773

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

description: Paraburkholderia phenoliruptrix AC1100 is an aerobe, mesophilic, motile bacterium that was isolated from chemostat with 2,4,5-trichlorophenoxyacetic acid.

NCBI tax id

  • NCBI tax id: 252970
  • Matching level: species

strain history

@refhistory
7177<- CCUG <- LMG <- T. Coenye, Gent <- D. Henry, Univ. British Columbia, Vancouver, Canada
121796CIP <- 2004, CCUG <- 2003, LMG <- 2003, T. Coenye, Ghent Univ., Ghent, Belgium <- 1999, D. Henry, British Columbia Univ., Vancouver, Canada: strain AC1100

doi: 10.13145/bacdive1967.20230509.8.1

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 phenoliruptrix
  • full scientific name: Paraburkholderia phenoliruptrix (Coenye et al. 2005) Sawana et al. 2015

  • synonyms

    • @ref: 20215
    • synonym: Burkholderia phenoliruptrix

@ref: 7177

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Burkholderiaceae

genus: Paraburkholderia

species: Paraburkholderia phenoliruptrix

full scientific name: Paraburkholderia phenoliruptrix (Coenye et al. 2005) Sawana et al. 2015

strain designation: AC1100

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes95.781
6948099.965negative
121796nonegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7177NUTRIENT 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
7177MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)yeshttps://mediadive.dsmz.de/medium/457Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
41977MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121796CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7177positivegrowth28mesophilic
41977positivegrowth30mesophilic
58230positivegrowth30mesophilic
121796positivegrowth25-37mesophilic
121796nogrowth5psychrophilic
121796nogrowth10psychrophilic
121796nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
58230aerobe
121796obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.987

halophily

@refsaltgrowthtested relationconcentration
121796NaClpositivegrowth0-2 %
121796NaClnogrowth4 %
121796NaClnogrowth6 %
121796NaClnogrowth8 %
121796NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+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
1217964853esculin-hydrolysis
12179617632nitrate-reduction
12179616301nitrite-reduction
12179617632nitrate-respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12179635581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
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
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
121796oxidase+
121796beta-galactosidase+3.2.1.23
121796alcohol dehydrogenase-1.1.1.1
121796gelatinase-
121796amylase+
121796DNase-
121796caseinase-3.4.21.50
121796catalase+1.11.1.6
121796tween esterase-
121796lecithinase-
121796lipase-
121796lysine decarboxylase-4.1.1.18
121796ornithine decarboxylase-4.1.1.17
121796protease-
121796tryptophan deaminase-
121796urease-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
121796-+++-+----++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7177-------++++++-++/-+/-++++/-

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121796++-+-----------------+--+-++----+---+--+++-+-++--------++-+-----+-----+-++----+--++-------++-+----+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7177chemostat with 2,4,5-trichlorophenoxyacetic acidIllionisUSAUSANorth America
58230Chemostat grown with 2,4,5-trichlorophenoxyaceticVancouverCanadaCANNorth America
121796Chemostat grown with 2 4 5-trichlorophenoxyaceticVancouverCanadaCANNorth America

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Bioreactor

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
71771Risk group (German classification)
1217961Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Burkholderia phenoliruptrix strain LMG 22037 16S ribosomal RNA gene, partial sequenceHQ8490941126ena252970
7177Burkholderia sp. AC1100 16S ribosomal RNA gene, partial sequenceAY4352131485ena252970

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paraburkholderia phenoliruptrix LMG 22037GCA_902833655contigncbi252970
66792Paraburkholderia phenoliruptrix LMG 22037GCA_902859825contigncbi252970
66792Paraburkholderia phenoliruptrix AC1100GCA_000416445contigncbi1337996
66792Paraburkholderia phenoliruptrix strain LMG 22037252970.3wgspatric252970
66792Paraburkholderia phenoliruptrix strain LMG 22037252970.5wgspatric252970
66792Paraburkholderia phenoliruptrix AC11002554235175draftimg1337996

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.86no
gram-positiveno98.098no
anaerobicno98.799no
aerobicyes86.958yes
halophileno95.061no
spore-formingno92.72no
glucose-utilyes89.84yes
flagellatedno85.166no
thermophileno99.425yes
glucose-fermentno89.958yes

External links

@ref: 7177

culture collection no.: DSM 17773, CCUG 48558, CIP 108591, LMG 22037

straininfo link

  • @ref: 71612
  • straininfo: 43466

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15612618Burkholderia phenoliruptrix sp. nov., to accommodate the 2,4,5-trichlorophenoxyacetic acid and halophenol-degrading strain AC1100.Coenye T, Henry D, Speert DP, Vandamme PSyst Appl Microbiol10.1078/072320204236999220042,4,5-Trichlorophenoxyacetic Acid/*metabolism, Bacterial Typing Techniques, Base Composition, Biodegradation, Environmental, Burkholderia/*classification/metabolism, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenols/*metabolism, Phylogeny, Proteome/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Xenobiotics/metabolismMetabolism
Genetics23929488Genome Sequence of the 2,4,5-Trichlorophenoxyacetate-Degrading Bacterium Burkholderia phenoliruptrix Strain AC1100.Xu P, Yu H, Chakrabarty AM, Xun LGenome Announc10.1128/genomeA.00600-132013
Metabolism23955343Catalytic mechanism of 5-chlorohydroxyhydroquinone dehydrochlorinase from the YCII superfamily of largely unknown function.Hayes RP, Lewis KM, Xun L, Kang CJ Biol Chem10.1074/jbc.M113.4993682013Amino Acid Sequence, *Biocatalysis, Burkholderia/*enzymology, Catalytic Domain, Circular Dichroism, Crystallography, X-Ray, Hydroquinones/chemistry/*metabolism, Ligands, Lyases/chemistry/*metabolism, Models, Molecular, Molecular Sequence Data, *Multigene Family, Mutant Proteins/chemistry/metabolism, Mutation/genetics, Protein Structure, Quaternary, Quantum Theory, Sequence Alignment, Solutions, Substrate SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7177Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17773)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17773
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
41977Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6236
58230Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48558)https://www.ccug.se/strain?id=48558
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
71612Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43466.1StrainInfo: A central database for resolving microbial strain identifiers
121796Curators of the CIPCollection of Institut Pasteur (CIP 108591)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108591