Strain identifier

BacDive ID: 7603

Type strain: Yes

Species: Arthrobacter castelli

Strain Designation: R-5102

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 1121019 (strain), 271431 (species)

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General

@ref: 6431

BacDive-ID: 7603

DSM-Number: 16402

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

description: Arthrobacter castelli R-5102 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Mural painting, biofilm.

NCBI tax id

NCBI tax idMatching level
1121019strain
271431species

strain history

@refhistory
6431<- J. Heyrman, R-5102
364472005, DSMZ
67770IAM 15349 <-- DSM 16402 <-- J. Heyrman R-5102.
117208CIP <- 2005, DSMZ

doi: 10.13145/bacdive7603.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Arthrobacter
  • species: Arthrobacter castelli
  • full scientific name: Arthrobacter castelli Heyrman et al. 2005

@ref: 6431

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter castelli

full scientific name: Arthrobacter castelli Heyrman et al. 2005 emend. Nouioui et al. 2018

strain designation: R-5102

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotilityconfidence
31342positive0.9 µmrod-shapedno
69480positive100
117208positivecoccus-shapedno

colony morphology

@refincubation periodcolony colormedium used
64318-14 days
1829610-14 daysHoney yellow (1005)ISP 2
1829610-14 daysHoney yellow (1005)ISP 3
1829610-14 daysCream (9001)ISP 4
1829610-14 daysHoney yellow (1005)ISP 5
1829610-14 daysLemon yellow (1012)ISP 6
1829610-14 daysLemon yellow (1012)ISP 7

multicellular morphology

@refforms multicellular complexmedium name
18296noISP 2
18296noISP 3
18296noISP 4
18296noISP 5
18296noISP 6
18296noISP 7

pigmentation

  • @ref: 31342
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6431BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
18296ISP 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
18296ISP 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:
18296ISP 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
18296ISP 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
18296ISP 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
18296ISP 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
36447MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromatiyesDistilled water make up to (1000.000 ml);R2A agar (18.200 g)
117208CIP Medium 566yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=566
117208CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328
117208CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18296positiveoptimum28mesophilic
6431positivegrowth28mesophilic
31342positivegrowth15-37
31342positiveoptimum29.5mesophilic
36447positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 31342
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
31342no
69481no99
69480no99.432

observation

@refobservation
31342aggregates in chains
67770quinones: MK-9(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1829662968cellulose-
1829616634raffinose-
1829626546rhamnose-
1829628757fructose+
1829629864mannitol-
1829617268myo-inositol-
1829618222xylose-
1829617992sucrose+
1829622599arabinose-
1829617234glucose+
3134216199urea+carbon source
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
31342acid phosphatase+3.1.3.2
31342alkaline phosphatase+3.1.3.1
31342catalase+1.11.1.6
31342urease+3.5.1.5
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
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

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18296-+++-++---++---+/----

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18296++++++---++-+-+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6431Mural painting, biofilmHerbersteinAustriaAUTEurope
67770Rosy biofilm overgrowing a mural painting in the Saint-Catherine chapelcastle of HerbersteinAustriaAUTEurope
117208Mural paintingHerberstein Castle, HimsdorfAustriaAUTEurope

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Engineered#Other#Painting
#Environmental#Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_1807.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1023;97_1193;98_1429;99_1807&stattab=map
  • Last taxonomy: Arthrobacter castelli
  • 16S sequence: AJ639826
  • Sequence Identity:
  • Total samples: 781
  • soil counts: 114
  • aquatic counts: 253
  • animal counts: 390
  • plant counts: 24

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64311Risk group (German classification)
182962Hazard group
1172081Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6431
  • description: Arthrobacter castelli partial 16S rRNA gene, type strain LMG 22283T
  • accession: AJ639826
  • length: 1509
  • database: ena
  • NCBI tax ID: 271431

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter castelli DSM 164021121019.4wgspatric1121019
66792Arthrobacter castelli DSM 164022524023227draftimg1121019
67770Arthrobacter castelli DSM 16402GCA_000430705scaffoldncbi1121019

GC content

@refGC-contentmethod
643168.1
6777063.6genome sequence analysis
6777068.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno90.342no
flagellatedno97.526no
gram-positiveyes93.348yes
anaerobicno99.557no
aerobicyes95.843no
halophileyes55.718no
spore-formingno84.82yes
thermophileno98.251yes
glucose-utilyes88.055yes
glucose-fermentno86.973no

External links

@ref: 6431

culture collection no.: DSM 16402, LMG 22283, JCM 21794, IAM 15349, CIP 108896, LMG 19502

straininfo link

  • @ref: 77047
  • straininfo: 132113

literature

  • topic: Phylogeny
  • Pubmed-ID: 16014466
  • title: Six novel Arthrobacter species isolated from deteriorated mural paintings.
  • authors: Heyrman J, Verbeeren J, Schumann P, Swings J, De Vos P
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63358-0
  • year: 2005
  • mesh: Arthrobacter/chemistry/*classification/genetics/*isolation & purification, Austria, Bacterial Typing Techniques, Base Composition, Biofilms/*growth & development, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, *Paintings, Polymerase Chain Reaction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
6431Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16402)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16402
18296Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16402.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
31342Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2765628776041
36447Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6577
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/
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
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
77047Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132113.1StrainInfo: A central database for resolving microbial strain identifiers
117208Curators of the CIPCollection of Institut Pasteur (CIP 108896)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108896