Strain identifier

BacDive ID: 7581

Type strain: Yes

Species: Pseudarthrobacter chlorophenolicus

Strain Designation: A6

Strain history: CIP <- 2001, J.K. Jansson, Södertörn Univ. College, Sweden: strain A6

NCBI tax ID(s): 85085 (species)

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General

@ref: 4844

BacDive-ID: 7581

DSM-Number: 12829

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

description: Pseudarthrobacter chlorophenolicus A6 is an obligate aerobe, Gram-positive bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 85085
  • Matching level: species

strain history

@refhistory
4844<- J.K. Jansson; A6
419062001, J.K. Jansson, Södertörn Univ. College, Sweden: strain A6
67770KCTC 9906 <-- DSM 12829 <-- J. K. Jansson A6.
118243CIP <- 2001, J.K. Jansson, Södertörn Univ. College, Sweden: strain A6

doi: 10.13145/bacdive7581.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Pseudarthrobacter
  • species: Pseudarthrobacter chlorophenolicus
  • full scientific name: Pseudarthrobacter chlorophenolicus (Westerberg et al. 2000) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter chlorophenolicus

@ref: 4844

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Pseudarthrobacter

species: Pseudarthrobacter chlorophenolicus

full scientific name: Pseudarthrobacter chlorophenolicus (Westerberg et al. 2000) Busse 2016

strain designation: A6

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
118243positiverod-shapedno
69480positive90.062

colony morphology

@refcolony colorincubation periodmedium used
18371Light ivory (1015)10-14 daysISP 2
18371Light ivory (1015)10-14 daysISP 3
18371Light ivory (1015)10-14 daysISP 4
18371Colorless10-14 daysISP 5
18371Colorless10-14 daysISP 6
18371Colorless10-14 daysISP 7
118243

multicellular morphology

@refforms multicellular complexmedium name
18371noISP 2
18371noISP 3
18371noISP 4
18371noISP 5
18371noISP 6
18371noISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4844TRYPTICASE 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
18371ISP 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
18371ISP 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:
18371ISP 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
18371ISP 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
18371ISP 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
18371ISP 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
41906MEDIUM 368 - for Luria bertaniyesDistilled water make up to (1000.000 ml);Sodium chloride (10.000 g);Agar(15.000 g);Yeast extract (5.000 g);Tryptone (10.000 g)
118243CIP Medium 368yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=368

culture temp

@refgrowthtypetemperature
18371positiveoptimum28
4844positivegrowth28
41906positivegrowth30
67770positivegrowth28
118243positivegrowth10-37
118243nogrowth41
118243nogrowth45

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
118243obligate aerobe
69480aerobe91.708

halophily

@refsaltgrowthtested relationconcentration
118243NaClpositivegrowth0-8 %
118243NaClnogrowth10 %

murein

  • @ref: 4844
  • murein short key: A11.23
  • type: A3alpha L-Lys-L-Ser-L-Thr-L-Ala

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11824316947citrate-carbon source
1182434853esculin+hydrolysis
118243606565hippurate-hydrolysis
11824317632nitrate-reduction
11824316301nitrite-reduction
11824317632nitrate-respiration
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

antibiotic resistance

  • @ref: 118243
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

  • @ref: 118243
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11824315688acetoin-
11824317234glucose-

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase+3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382naphthol-AS-BI-phosphohydrolase-
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 (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
118243oxidase-
118243beta-galactosidase+3.2.1.23
118243alcohol dehydrogenase-1.1.1.1
118243gelatinase+
118243amylase-
118243DNase+
118243caseinase+3.4.21.50
118243catalase+1.11.1.6
118243tween esterase+
118243gamma-glutamyltransferase+2.3.2.2
118243lecithinase-
118243lipase-
118243lysine decarboxylase-4.1.1.18
118243ornithine decarboxylase-4.1.1.17
118243phenylalanine ammonia-lyase-4.3.1.24
118243tryptophan deaminase-
118243urease+3.5.1.5

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
18371----+++-+++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
18371--+-+--+-+-++-++-+-
118243----+--+------+--+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
118243+++++-++++++++++++--+++--+--+--++++++------+-+--++++-++++---+++++++---++++-----++-----+-++++++++-+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
4844soilUSA, Colorado, Fort CollinsUSAUSANorth America
67770SoilFort Collins, COUSAUSANorth America
118243Environment, SoilColoradoUnited States of AmericaUSANorth America1984

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1761.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_99;97_106;98_115;99_1761&stattab=map
  • Last taxonomy: Pseudarthrobacter
  • 16S sequence: AF102267
  • Sequence Identity:
  • Total samples: 723
  • soil counts: 366
  • aquatic counts: 56
  • animal counts: 202
  • plant counts: 99

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183711
48441Risk group (German classification)
1182431Risk group (French classification)

Sequence information

16S sequences

  • @ref: 4844
  • description: Arthrobacter chlorophenolicus 16S ribosomal RNA gene, partial sequence
  • accession: AF102267
  • length: 1446
  • database: nuccore
  • NCBI tax ID: 85085

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudarthrobacter chlorophenolicus A6GCA_000022025completencbi452863
66792Arthrobacter chlorophenolicus A6452863.6completepatric452863
66792Pseudarthrobacter chlorophenolicus A6452863.41plasmidpatric452863
66792Pseudarthrobacter chlorophenolicus A6452863.40plasmidpatric452863
66792Pseudarthrobacter chlorophenolicus strain A685085.8wgspatric85085
66792Pseudarthrobacter chlorophenolicus A6643348509completeimg452863
66792Pseudarthrobacter chlorophenolicus DSM 128292634166551draftimg452863
67770Pseudarthrobacter chlorophenolicus A6GCA_900104315contigncbi85085

GC content

  • @ref: 4844
  • GC-content: 65.1
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno89no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.062no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no98.413yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.708yes
69480spore-formingspore-formingAbility to form endo- or exosporesno57.136no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno99yes
69480flagellatedmotile2+Ability to perform flagellated movementno73no

External links

@ref: 4844

culture collection no.: DSM 12829, ATCC 700700, CIP 107037, JCM 12360, KCTC 9906, NCIMB 13794, MTCC 3706

straininfo link

  • @ref: 77025
  • straininfo: 44090

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11155983Arthrobacter chlorophenolicus sp. nov., a new species capable of degrading high concentrations of 4-chlorophenol.Westerberg K, Elvang AM, Stackebrandt E, Jansson JKInt J Syst Evol Microbiol10.1099/00207713-50-6-20832000Arthrobacter/chemistry/*classification/genetics/growth & development/metabolism, Bacterial Typing Techniques, Biodegradation, Environmental, Chlorophenols/*metabolism, Culture Media, DNA, Ribosomal/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phenols/metabolism, Phylogeny, Pigments, Biological/biosynthesis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/metabolismMetabolism
Phylogeny18676480Arthrobacter defluvii sp. nov., 4-chlorophenol-degrading bacteria isolated from sewage.Kim KK, Lee KC, Oh HM, Kim MJ, Eom MK, Lee JSInt J Syst Evol Microbiol10.1099/ijs.0.65550-02008Arthrobacter/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Chlorophenols/*metabolism, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species SpecificityGenetics
Phylogeny25052022Arthrobacter enclensis sp. nov., isolated from sediment sample.Dastager SG, Liu Q, Tang SK, Krishnamurthi S, Lee JC, Li WJArch Microbiol10.1007/s00203-014-1016-92014Arthrobacter/chemistry/*classification/genetics, Base Composition, Fatty Acids/analysis, Geologic Sediments/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitle
4844Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12829)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12829
18371Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM12829.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
41906Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/19234
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
77025Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID44090.1StrainInfo: A central database for resolving microbial strain identifiers
118243Curators of the CIPCollection of Institut Pasteur (CIP 107037)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107037