Strain identifier

BacDive ID: 7571

Type strain: Yes

Species: Paenarthrobacter ureafaciens

Strain Designation: NC, Murein A11.17

Strain history: CIP <- 2013, DSMZ <- ATCC <- R. Dubos, Corynebacterium creatinivorans: strain Murein A11.17

NCBI tax ID(s): 37931 (species)

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General

@ref: 8551

BacDive-ID: 7571

DSM-Number: 20126

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

description: Paenarthrobacter ureafaciens NC is an obligate aerobe, mesophilic, Gram-negative bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 37931
  • Matching level: species

strain history

@refhistory
8551<- ATCC <- R. Dubos, NC (Corynebacterium creatinovorans)
67770K. Suzuki CNF 023 <-- AJ 1421 <-- ATCC 7562 <-- R. Dubos NC.
123739CIP <- 2013, DSMZ <- ATCC <- R. Dubos, Corynebacterium creatinivorans: strain Murein A11.17

doi: 10.13145/bacdive7571.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Paenarthrobacter
  • species: Paenarthrobacter ureafaciens
  • full scientific name: Paenarthrobacter ureafaciens (Krebs and Eggleston 1939) Busse 2016

  • synonyms

    @refsynonym
    20215Arthrobacter ureafaciens
    20215Corynebacterium ureafaciens

@ref: 8551

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Paenarthrobacter

species: Paenarthrobacter ureafaciens

full scientific name: Paenarthrobacter ureafaciens (Krebs and Eggleston 1939) Busse 2016

strain designation: NC, Murein A11.17

type strain: yes

Morphology

cell morphology

  • @ref: 123739
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
18624Lemon yellow (1012)10-14 daysISP 2
18624Sulfur white (1016)10-14 daysISP 3
18624Colorless10-14 daysISP 4
18624Colorless10-14 daysISP 5
18624Colorless10-14 daysISP 6
18624Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18624noISP 2
18624noISP 3
18624noISP 4
18624noISP 5
18624noISP 6
18624noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18624ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
18624ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
18624ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
18624ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
18624ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
18624ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes
41904MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8551CORYNEBACTERIUM AGAR (DSMZ Medium 53)yesName: CORYNEBACTERIUM AGAR (DSMZ Medium 53) Composition: Agar 15.0 g/l Casein peptone 10.0 g/l NaCl 5.0 g/l Glucose 5.0 g/l Yeast extract 5.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/53
123739CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
123739CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18624positiveoptimum28mesophilic
8551positivegrowth30mesophilic
41904positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123739
  • oxygen tolerance: obligate aerobe

halophily

  • @ref: 18624
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0 %

murein

  • @ref: 8551
  • murein short key: A11.17
  • type: A3alpha L-Lys-L-Ala-L-Thr-L-Ala

observation

  • @ref: 67770
  • observation: quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12373917632nitrate-reduction
12373916301nitrite-reduction
6837917632nitrate+reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose+fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol+fermentation
6837917306maltose+fermentation
6837917716lactose+fermentation
6837917992sucrose+fermentation
6837928087glycogen-fermentation

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideno
12373935581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole-

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+
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)+
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase+3.2.1.23
68379beta-glucuronidase+3.2.1.31
68379alkaline phosphatase-3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase+3.5.1.B15
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23
123739oxidase-
123739catalase+1.11.1.6
123739urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18624+++-+++++++++-++++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18624+++-+++++++++-++++-
123739-++-++++--+++-++++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18624+---+-----+

Isolation, sampling and environmental information

isolation

@refsample type
67770Soil
123739Environment, Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_1504.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_99;97_1005;98_1187;99_1504&stattab=map
  • Last taxonomy: Micrococcaceae
  • 16S sequence: X80744
  • Sequence Identity:
  • Total samples: 451
  • soil counts: 190
  • aquatic counts: 69
  • animal counts: 65
  • plant counts: 127

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
186241Hazard group
85511Risk group (German classification)
1237391Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8551
  • description: A.ureafaciens 16S rDNA
  • accession: X80744
  • length: 1479
  • database: ena
  • NCBI tax ID: 37931

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Paenarthrobacter ureafaciens strain DSM 2012637931.7wgspatric37931
67770Paenarthrobacter ureafaciens DSM 20126GCA_004028095contigncbi37931

GC content

@refGC-contentmethod
855161.7
6777065.7thermal denaturation, midpoint method (Tm)
6777061.7thermal denaturation, midpoint method (Tm)
6777067.6
6777063.6high performance liquid chromatography (HPLC)
6777062.9Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveyes92.149no
anaerobicno99.559no
halophileno93.999no
spore-formingno84.983no
glucose-utilyes83.329no
aerobicyes96.314no
motileyes55.322no
flagellatedno87.759no
thermophileno97.245yes
glucose-fermentno77.181yes

External links

@ref: 8551

culture collection no.: DSM 20126, ATCC 7562, CCM 1644, CIP 67.3, NCIB 7811, JCM 1337, BCRC 10368, CGMCC 1.1897, IAM 1658, IFO 12140, KCCM 40801, KCTC 3387, LMG 3812, MTCC 3454, NBRC 12140, NCIMB 7811, NCTC 7811, NRIC 0157, VKM Ac-1121, VKM Ac-1132, CCUG 577

straininfo link

  • @ref: 77016
  • straininfo: 389307

literature

Pubmed-IDtitleauthorsjournalDOIyeartopicmeshtopic2
12483560The formation and structures of cystites of Arthrobacter ureafaciens NRIC 0157T induced by antibiotics.Tanaka N, Uchimura T, Komagata KJ Gen Appl Microbiol10.2323/jgam.47.852001
12483589Cystite formation of Arthrobacter ureafaciens NRIC 0157(T).Tanaka N, Uchimura T, Komagata KJ Gen Appl Microbiol10.2323/jgam.46.1672000
17141592N-ethylmaleimide-resistant acyl-coenzyme A oxidase from Arthrobacter ureafaciens NBRC 12140: molecular cloning, gene expression and characterization of the recombinant enzyme.Bakke M, Setoyama C, Miura R, Kajiyama NBiochim Biophys Acta10.1016/j.bbapap.2006.10.0082006EnzymologyAcyl-CoA Oxidase/antagonists & inhibitors/*genetics/*isolation & purification, Amino Acid Sequence, Arthrobacter/*enzymology, Cloning, Molecular, Colorimetry, Drug Resistance, Enzyme Stability, Escherichia coli/enzymology, Ethylmaleimide/*pharmacology, Fatty Acids, Nonesterified/analysis, Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, Recombinant Proteins/biosynthesis, Sequence AlignmentGenetics
19540107Isolation and characterization of Arthrobacter sp. HY2 capable of degrading a high concentration of p-nitrophenol.Qiu X, Wu P, Zhang H, Li M, Yan ZBioresour Technol10.1016/j.biortech.2009.05.0562009PathogenicityArthrobacter/drug effects/growth & development/*isolation & purification, Biodegradation, Environmental/drug effects, Carbon/pharmacology, Culture Media, Hydrogen-Ion Concentration/drug effects, Nitrophenols/*metabolism, Temperature, beta-Cyclodextrins/pharmacologyPhylogeny

Reference

@idauthorscataloguedoi/urltitle
8551Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20126)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20126
18624Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20126.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
41904Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/10282
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
68379Automatically annotated from API Coryne
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
77016Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389307.1StrainInfo: A central database for resolving microbial strain identifiers
123739Curators of the CIPCollection of Institut Pasteur (CIP 67.3)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%2067.3