Strain identifier

BacDive ID: 7604

Type strain: Yes

Species: Arthrobacter parietis

Strain Designation: R-5303

Strain history: CIP <- 2005, DSMZ

NCBI tax ID(s): 271434 (species)

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General

@ref: 6433

BacDive-ID: 7604

DSM-Number: 16404

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

description: Arthrobacter parietis R-5303 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Biofilm covering the Sevilia tomb, Roman necropolis of Carmona.

NCBI tax id

  • NCBI tax id: 271434
  • Matching level: species

strain history

@refhistory
6433<- J. Heyrman, R-5303
373922005, DSMZ
67770LMG 22281 <-- J. Heyrman R-5303.
121597CIP <- 2005, DSMZ

doi: 10.13145/bacdive7604.20230509.8.1

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 parietis
  • full scientific name: Arthrobacter parietis Heyrman et al. 2005

@ref: 6433

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter parietis

full scientific name: Arthrobacter parietis Heyrman et al. 2005

strain designation: R-5303

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
31342positive0.9 µmcoccus-shapedno
121597positivecoccus-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18610Lemon yellow (1012)10-14 daysISP 2
18610Lemon yellow (1012)10-14 daysISP 3
18610Lemon yellow (1012)10-14 daysISP 4
18610Lemon yellow (1012)10-14 daysISP 5
18610Lemon yellow (1012)10-14 daysISP 6
18610Lemon yellow (1012)10-14 daysISP 7
121597

multicellular morphology

@refforms multicellular complexmedium name
18610noISP 2
18610noISP 3
18610noISP 4
18610noISP 5
18610noISP 6
18610noISP 7

pigmentation

  • @ref: 31342
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6433TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
6433BACTO 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
18610ISP 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
18610ISP 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:
18610ISP 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
18610ISP 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
18610ISP 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
18610ISP 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
37392MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121597CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
18610positiveoptimum28mesophilic
6433positivegrowth28mesophilic
31342positivegrowth04-37
31342positiveoptimum26mesophilic
37392positivegrowth25mesophilic
67770positivegrowth28mesophilic
121597positivegrowth10-37
121597nogrowth41thermophilic
121597nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31342positivegrowth06-09alkaliphile
31342positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31342aerobe
121597obligate aerobe

spore formation

  • @ref: 31342
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31342NaClpositivegrowth05-15 %
31342NaClpositiveoptimum10 %
121597NaClpositivegrowth0-4 %
121597NaClnogrowth6 %
121597NaClnogrowth8 %
121597NaClnogrowth10 %

murein

  • @ref: 6433
  • murein short key: A11.27
  • type: A3alpha L-Lys-L-Thr-L-Ala2

observation

@refobservation
31342aggregates in clumps
67770quinones: MK-9(H2), MK-10(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1861062968cellulose+
1861016634raffinose+
1861026546rhamnose+
1861028757fructose+
1861029864mannitol+
1861017268myo-inositol+
1861018222xylose+
1861017992sucrose+
1861022599arabinose+
1861017234glucose+
313425291gelatin+carbon source
3134217234glucose+carbon source
313424853esculin+hydrolysis
3134217632nitrate+reduction
12159716947citrate-carbon source
1215974853esculin+hydrolysis
121597606565hippurate+hydrolysis
12159717632nitrate+reduction
12159716301nitrite-reduction
12159717632nitrate-respiration
683794853esculin-hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917992sucrose-fermentation

metabolite production

  • @ref: 121597
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12159715688acetoin-
12159717234glucose-

enzymes

@refvalueactivityec
31342alpha-galactosidase+3.2.1.22
31342catalase+1.11.1.6
31342gelatinase+
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
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase+3.2.1.23
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin+3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382lipase (C 14)-
68382esterase lipase (C 8)-
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
121597oxidase-
121597beta-galactosidase+3.2.1.23
121597alcohol dehydrogenase-1.1.1.1
121597gelatinase-
121597amylase-
121597DNase+
121597caseinase+3.4.21.50
121597catalase+1.11.1.6
121597tween esterase-
121597gamma-glutamyltransferase-2.3.2.2
121597lecithinase-
121597lipase-
121597lysine decarboxylase-4.1.1.18
121597ornithine decarboxylase-4.1.1.17
121597phenylalanine ammonia-lyase-4.3.1.24
121597protease-
121597tryptophan deaminase-
121597urease-3.5.1.5

API coryne

@refPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELSAC
18610----+---++-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18610-------+--+-+----+-
121597-+--+--+-++++-+--+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6433Biofilm covering the Sevilia tomb, Roman necropolis of CarmonaCarmonaSpainESPEurope
67770Biofilm overgrowing a mural painting in the Servilia tombRoman necropolis of CarmonaSpainESPEurope
121597Mural paintings sitesServilia tomb, CarmonaSpainESPEurope

isolation source categories

Cat1Cat2
#Environmental#Biofilm
#Environmental#Terrestrial

taxonmaps

  • @ref: 69479
  • File name: preview.99_5961.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_803;97_937;98_1098;99_5961&stattab=map
  • Last taxonomy: Arthrobacter
  • 16S sequence: AJ639830
  • Sequence Identity:
  • Total samples: 5651
  • soil counts: 2709
  • aquatic counts: 534
  • animal counts: 1557
  • plant counts: 851

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
64331Risk group (German classification)
186102Hazard group
1215971Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6433
  • description: Arthrobacter parietes partial 16S rRNA gene, type strain LMG 22281T
  • accession: AJ639830
  • length: 1475
  • database: ena
  • NCBI tax ID: 271434

GC content

@refGC-contentmethod
643363.8
6777063.8high performance liquid chromatography (HPLC)

External links

@ref: 6433

culture collection no.: DSM 16404, LMG 22281, JCM 14917, CIP 108898, VTT E-052087

straininfo link

  • @ref: 77048
  • straininfo: 19456

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
6433Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16404)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16404
18610Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM16404.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
37392Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6579
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
77048Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID19456.1StrainInfo: A central database for resolving microbial strain identifiers
121597Curators of the CIPCollection of Institut Pasteur (CIP 108898)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108898