Strain identifier

BacDive ID: 7531

Type strain: Yes

Species: Arthrobacter pascens

Strain Designation: B89

Strain history: CIP <- 1986, DSM <- CCM <- A.G. Lochhead: strain B89 Central Exp. Farm, Ottawa, Canada

NCBI tax ID(s): 1677 (species)

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General

@ref: 8774

BacDive-ID: 7531

DSM-Number: 20545

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

description: Arthrobacter pascens B89 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from Soil.

NCBI tax id

  • NCBI tax id: 1677
  • Matching level: species

strain history

@refhistory
8774<- CCM <- MRI <- A.G. Lochhead, B89
67770CCM 1653 <-- MRI <-- A. G. Lochhead B89.
121615CIP <- 1986, DSM <- CCM <- A.G. Lochhead: strain B89 Central Exp. Farm, Ottawa, Canada

doi: 10.13145/bacdive7531.20230509.8.1

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 pascens
  • full scientific name: Arthrobacter pascens Lochhead and Burton 1953 (Approved Lists 1980)

@ref: 8774

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Arthrobacter

species: Arthrobacter pascens

full scientific name: Arthrobacter pascens Lochhead and Burton 1953

strain designation: B89

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480positive100
121615positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
18447Beige (1001)10-14 daysISP 2
18447Light ivory (1015)10-14 daysISP 3
18447Colorless10-14 daysISP 4
18447Colorless10-14 daysISP 5
18447Colorless10-14 daysISP 6
18447Colorless10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18447noISP 2
18447noISP 3
18447noISP 4
18447noISP 5
18447noISP 6
18447noISP 7

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
18447ISP 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
18447ISP 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
18447ISP 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
18447ISP 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
18447ISP 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
18447ISP 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:
37391MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
8774CORYNEBACTERIUM 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
121615CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
121615CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
18447positiveoptimum28mesophilic
8774positivegrowth30mesophilic
37391positivegrowth30mesophilic
47856positivegrowth20-30
67770positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
47856aerobe
121615facultative anaerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.34

compound production

  • @ref: 8774
  • compound: terregens factor

halophily

  • @ref: 18447
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 5 %

murein

  • @ref: 8774
  • murein short key: A11.05
  • type: A3alpha L-Lys-L-Ala2

observation

  • @ref: 67770
  • observation: Production of "Terregens factor"

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1844717234glucose-
1844722599arabinose-
1844717992sucrose-
1844718222xylose-
1844717268myo-inositol-
1844729864mannitol-
1844728757fructose-
1844716634raffinose+
1844762968cellulose-
683685291gelatin-hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
12161517632nitrate+reduction
12161516301nitrite-reduction
6837917632nitrate-reduction
683794853esculin-hydrolysis
6837916199urea-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
12161535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
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
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin-3.4.21.1
68382cystine arylamidase+3.4.11.3
68382valine arylamidase+
68382leucine arylamidase+3.4.11.1
68382esterase lipase (C 8)+
68382esterase (C 4)+
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
121615oxidase-
121615catalase+1.11.1.6
121615urease-3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18447-++-+++---+/--+-+----

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphatasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControlNaphthol-AS-BI-phosphohydrolase
18447-++-+++----+-+----
121615++++++++-+++-+--+--+

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
18447+----------

Isolation, sampling and environmental information

isolation

@refsample type
67770Soil
121615Environment, Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_607.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_99;97_106;98_386;99_607&stattab=map
  • Last taxonomy: Arthrobacter
  • 16S sequence: X80740
  • Sequence Identity:
  • Total samples: 5315
  • soil counts: 1582
  • aquatic counts: 227
  • animal counts: 159
  • plant counts: 3347

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
184471
87741Risk group (German classification)
1216151Risk group (French classification)

Sequence information

16S sequences

  • @ref: 8774
  • description: A.pascens 16S rDNA
  • accession: X80740
  • length: 1474
  • database: ena
  • NCBI tax ID: 1677

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Arthrobacter pascens DSM 20545GCA_017052465contigncbi1677
66792Arthrobacter pascens strain DSM 205451677.4wgspatric1677

GC content

@refGC-contentmethod
877463.7
6777063.7thermal denaturation, midpoint method (Tm)
6777064.9Buoyant density centrifugation (BD)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno80no
motileno89.357no
gram-positiveyes92.865no
anaerobicno99.538yes
aerobicyes96.704yes
halophileno81.474no
spore-formingno86.339no
glucose-utilyes80.634yes
flagellatedno96.469no
thermophileno98.763yes
glucose-fermentno86.358no

External links

@ref: 8774

culture collection no.: DSM 20545, ATCC 13346, CCM 1653, NCIB 8910, CCUG 23843, JCM 11606, BCRC 12112, CDA 858, CIP 102362, HAMBI 1862, IAM 12343, IFO 12139, KCTC 3445, LMG 16255, NBRC 12139, NCIMB 8910, NRRL B-1814, VKM Ac-1116, VKM Ac-1128, IMET 10355

straininfo link

  • @ref: 76976
  • straininfo: 10202

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12508874Citricoccus muralis gen. nov., sp. nov., a novel actinobacterium isolated from a medieval wall painting.Altenburger P, Kampfer P, Schumann P, Steiner R, Lubitz W, Busse HJInt J Syst Evol Microbiol10.1099/00207713-52-6-20952002Austria, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Environmental Microbiology, Lipids/analysis, Micrococcaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Paintings, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Terminology as TopicGenetics
Phylogeny26963092Arthrobacter pokkalii sp nov, a Novel Plant Associated Actinobacterium with Plant Beneficial Properties, Isolated from Saline Tolerant Pokkali Rice, Kerala, India.Krishnan R, Menon RR, Tanaka N, Busse HJ, Krishnamurthi S, Rameshkumar NPLoS One10.1371/journal.pone.01503222016*Arthrobacter/classification/genetics/isolation & purification, India, Oryza/*microbiology, RNA, Bacterial/*genetics, RNA, Ribosomal, 16S/*genetics, *Rhizosphere, *Soil MicrobiologyEnzymology

Reference

@idauthorscataloguedoi/urltitle
8774Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 20545)https://www.dsmz.de/collection/catalogue/details/culture/DSM-20545
18447Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM20545.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
37391Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/14040
47856Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 23843)https://www.ccug.se/strain?id=23843
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
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)
76976Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID10202.1StrainInfo: A central database for resolving microbial strain identifiers
121615Curators of the CIPCollection of Institut Pasteur (CIP 102362)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20102362