Strain identifier

BacDive ID: 7521

Type strain: Yes

Species: Arthrobacter crystallopoietes

Strain history: CIP <- 1987, NCIB <- 1964, S.C. Rittenberg: strain SC 255

NCBI tax ID(s): 37928 (species)

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General

@ref: 8542

BacDive-ID: 7521

DSM-Number: 20117

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

description: Arthrobacter crystallopoietes DSM 20117 is an obligate aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 37928
  • Matching level: species

strain history

@refhistory
8542<- ATCC <- J.C. Ensign
67770ATCC 15481 <-- J. C. Ensign.
118805CIP <- 1987, NCIB <- 1964, S.C. Rittenberg: strain SC 255

doi: 10.13145/bacdive7521.20230509.8.1

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 crystallopoietes
  • full scientific name: Arthrobacter crystallopoietes Ensign and Rittenberg 1963 (Approved Lists 1980)

@ref: 8542

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter crystallopoietes

full scientific name: Arthrobacter crystallopoietes Ensign and Rittenberg 1963 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
118805positiveoval-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18421Sand yellow (1002)10-14 daysISP 2
18421Light ivory (1015)10-14 daysISP 3
18421Light ivory (1014)10-14 daysISP 6

multicellular morphology

@refforms multicellular complexmedium name
18421noISP 2
18421noISP 3
18421noISP 6

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18421ISP 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
18421ISP 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:
18421ISP 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
37390MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8542CORYNEBACTERIUM 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
118805CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
118805CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18421positiveoptimum28mesophilic
8542positivegrowth30mesophilic
37390positivegrowth30mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 118805
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no98
69480no99.708

halophily

  • @ref: 18421
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 8542
  • murein short key: A11.04
  • type: A3alpha L-Lys-L-Ala

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1842117234glucose+
1842122599arabinose-
1842117992sucrose+
1842118222xylose+
1842117268myo-inositol-
1842129864mannitol-
1842128757fructose+
1842126546rhamnose+
1842116634raffinose-
1842162968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11880517632nitrate+reduction
11880516301nitrite-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
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno
11880535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
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
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
118805oxidase-
118805catalase+1.11.1.6
118805urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18421++--++----+---+--+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18421++--++----+---+--+-
118805+-+-+----++-+-+++---

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18421----+----+-

Isolation, sampling and environmental information

isolation

@refsample type
8542soil
67770Soil
118805Environment, Soil

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1312.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_458;97_886;98_1037;99_1312&stattab=map
  • Last taxonomy: Arthrobacter crystallopoietes subclade
  • 16S sequence: X80738
  • Sequence Identity:
  • Total samples: 1045
  • soil counts: 516
  • aquatic counts: 49
  • animal counts: 227
  • plant counts: 253

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184211
85421Risk group (German classification)
1188051Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: A.crystallopoietes 16S rDNA
  • accession: X80738
  • length: 1472
  • database: ena
  • NCBI tax ID: 37928

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter crystallopoietes DSM 20117GCA_002849715completencbi37928
66792Arthrobacter crystallopoietes strain DSM 2011737928.6patric37928
66792Arthrobacter crystallopoietes strain DSM 2011737928.10wgspatric37928
66792Arthrobacter crystallopoietes DSM 201172806310726completeimg37928
66792Arthrobacter crystallopoietes DSM 201172634166276draftimg37928
67770Arthrobacter crystallopoietes DSM 20117GCA_900100805contigncbi37928

GC content

@refGC-contentmethod
854262.9
6777062.9Buoyant density centrifugation (BD)
6777064.4genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno98no
flagellatedno98.145no
gram-positiveyes93.251no
anaerobicno99.592no
aerobicyes97.026no
halophileno60.161no
spore-formingno85.981no
thermophileno98.703yes
glucose-utilyes83.981yes
motileno92.743no
glucose-fermentno88.585yes

External links

@ref: 8542

culture collection no.: DSM 20117, ATCC 15481, CCM 2386, NCIB 9499, JCM 2522, BCRC 11571, CCUG 23841, CCUG 23886, CGMCC 1.1926, CIP 102717, IAM 14588, IFO 14235, IMET 10362, KCCM 41107, KCTC 3379, LMG 3819, NBRC 14235, NCIMB 9499, VKM Ac-1107, SC 255

straininfo link

  • @ref: 76966
  • straininfo: 999

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23223813Description of Tersicoccus phoenicis gen. nov., sp. nov. isolated from spacecraft assembly clean room environments.Vaishampayan P, Moissl-Eichinger C, Pukall R, Schumann P, Sproer C, Augustus A, Roberts AH, Namba G, Cisneros J, Salmassi T, Venkateswaran KInt J Syst Evol Microbiol10.1099/ijs.0.047134-02012Arthrobacter/classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Environment, Controlled, *Environmental Microbiology, Fatty Acids/analysis, Florida, French Guiana, Micrococcaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Peptidoglycan/analysis, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spacecraft, Vitamin K 2/analogs & derivatives/analysisGenetics
26705241Chemical synthesis and enzymatic, stereoselective hydrolysis of a functionalized dihydropyrimidine for the synthesis of beta-amino acids.Slomka C, Zhong S, Fellinger A, Engel U, Syldatk C, Brase S, Rudat JAMB Express10.1186/s13568-015-0174-82015
Enzymology28605882Toward a cell-free hydantoinase process: screening for expression optimization and one-step purification as well as immobilization of hydantoinase and carbamoylase.Slomka C, Spath GP, Lemke P, Skoupi M, Niemeyer CM, Syldatk C, Rudat JAMB Express10.1186/s13568-017-0420-32017
32704326Antibacterial scalarane from Doriprismatica stellata nudibranchs (Gastropoda, Nudibranchia), egg ribbons, and their dietary sponge Spongia cf. agaricina (Demospongiae, Dictyoceratida).Hertzer C, Kehraus S, Bohringer N, Kaligis F, Bara R, Erpenbeck D, Worheide G, Schaberle TF, Wagele H, Konig GMBeilstein J Org Chem10.3762/bjoc.16.1322020

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8542Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20117)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20117
18421Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20117.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
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
37390Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14435
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
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
76966Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID999.1StrainInfo: A central database for resolving microbial strain identifiers
118805Curators of the CIPCollection of Institut Pasteur (CIP 102717)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102717