Strain identifier

BacDive ID: 13886

Type strain: Yes

Species: Aromatoleum buckelii

Strain Designation: U120

Strain history: CIP <- 2010, DSMZ <- G. Fuchs and Rudolphi, Univ. Freiburg, Germany <- E. Lang, DSMZ, Braunschweig, Germany: strain U120

NCBI tax ID(s): 200254 (species)

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General

@ref: 5439

BacDive-ID: 13886

DSM-Number: 14744

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, coccus-shaped

description: Aromatoleum buckelii U120 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 200254
  • Matching level: species

strain history

@refhistory
5439<- G. Fuchs; U120
117074CIP <- 2010, DSMZ <- G. Fuchs and Rudolphi, Univ. Freiburg, Germany <- E. Lang, DSMZ, Braunschweig, Germany: strain U120

doi: 10.13145/bacdive13886.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Rhodocyclales
  • family: Zoogloeaceae
  • genus: Aromatoleum
  • species: Aromatoleum buckelii
  • full scientific name: Aromatoleum buckelii (Mechichi et al. 2002) Rabus et al. 2019

  • synonyms

    • @ref: 20215
    • synonym: Azoarcus buckelii

@ref: 5439

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Rhizobiales

family: Zoogloeaceae

genus: Aromatoleum

species: Aromatoleum buckelii

full scientific name: Aromatoleum buckelii (Mechichi et al. 2002) Rabus et al. 2019

strain designation: U120

type strain: yes

Morphology

cell morphology

  • @ref: 117074
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5439R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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 water
5439THAUERA AROMATICA MEDIUM (DSMZ Medium 586)yeshttps://mediadive.dsmz.de/medium/586Name: THAUERA AROMATICA MEDIUM (DSMZ Medium 586) Composition: K2HPO4 5.83251 g/l KNO3 1.97044 g/l KH2PO4 0.803941 g/l Na-benzoate 0.70936 g/l NH4Cl 0.522168 g/l MgSO4 x 7 H2O 0.197044 g/l CaCl2 x 2 H2O 0.0246305 g/l HCl 0.0246305 g/l FeCl2 x 4 H2O 0.0147783 g/l CoCl2 x 6 H2O 0.00187192 g/l MnCl2 x 4 H2O 0.000985222 g/l ZnCl2 0.000689655 g/l Na2MoO4 x 2 H2O 0.00035468 g/l p-Aminobenzoic acid 0.000246305 g/l alpha-lipoic acid 0.000246305 g/l Riboflavin 0.000246305 g/l Pantothenic acid 0.000246305 g/l Vitamin B12 0.000246305 g/l Thiamine-HCl x 2 H2O 0.000246305 g/l NiCl2 x 6 H2O 0.000236453 g/l Nicotine amide 0.000123153 g/l Nicotinic acid 0.000123153 g/l Folic acid 9.85222e-05 g/l Biotin 9.85222e-05 g/l H3BO3 5.91133e-05 g/l Pyridoxamine hydrochloride 4.92611e-05 g/l CuCl2 x 2 H2O 1.97044e-05 g/l Distilled water
117074CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566

culture temp

  • @ref: 5439
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
5439aerobe
5439anaerobe
117074facultative anaerobe

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371melibiose-builds acid from28053
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate-assimilation27689
68369gluconate-assimilation24265
68369maltose-assimilation17306
68369N-acetylglucosamine-assimilation59640
68369D-mannitol-assimilation16899
68369D-mannose-assimilation16024
68369L-arabinose-assimilation30849
68369D-glucose-assimilation17634
68369gelatin-hydrolysis5291
68369esculin+hydrolysis4853
68369urea-hydrolysis16199
68369arginine-hydrolysis29016
68369D-glucose-fermentation17634
68369tryptophan-energy source27897
68369nitrate-reduction17632
117074nitrate+reduction17632
117074nitrite-reduction16301

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
11707435581indoleno

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
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
117074oxidase-
117074catalase+1.11.1.6
117074urease-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
117074-+++-+----++---+----

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
5439-----+-+---------+--+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
117074+/---------+/-+/-+/-+/---------------+/-+/--+/-------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5439soilUlmGermanyDEUEurope
117074Environment, SoilUlmGermanyDEUEurope1991

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_5633.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_129;96_1730;97_3233;98_4199;99_5633&stattab=map
  • Last taxonomy: Aromatoleum
  • 16S sequence: AJ315676
  • Sequence Identity:
  • Total samples: 385
  • soil counts: 181
  • aquatic counts: 141
  • animal counts: 25
  • plant counts: 38

Safety information

risk assessment

  • @ref: 117074
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Azoarcus buckelii 16S rRNA gene, strain U120
  • accession: AJ315676
  • length: 1510
  • database: ena
  • NCBI tax ID: 200254

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aromatoleum buckelii U120GCA_012910785contigncbi200254
66792Aromatoleum buckelii U1202887686508draftimg200254

External links

@ref: 5439

culture collection no.: DSM 14744, LMG 26916, CIP 110165

straininfo link

  • @ref: 83061
  • straininfo: 87975

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5439Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14744)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14744
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
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
68371Automatically annotated from API 50CH acid
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
83061Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID87975.1StrainInfo: A central database for resolving microbial strain identifiers
117074Curators of the CIPCollection of Institut Pasteur (CIP 110165)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110165