Strain identifier

BacDive ID: 7620

Type strain: Yes

Species: Pseudarthrobacter defluvii

Strain Designation: 4C1-a

Strain history: <- KK Kim, KAIST

NCBI tax ID(s): 410837 (species)

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General

@ref: 7694

BacDive-ID: 7620

DSM-Number: 18782

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

description: Pseudarthrobacter defluvii 4C1-a is an aerobe, mesophilic, Gram-positive bacterium that was isolated from sewage.

NCBI tax id

  • NCBI tax id: 410837
  • Matching level: species

strain history

@refhistory
7694<- Kwang Kyu Kim; 4C1-a
67771<- KK Kim, KAIST

doi: 10.13145/bacdive7620.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Micrococcaceae
  • genus: Pseudarthrobacter
  • species: Pseudarthrobacter defluvii
  • full scientific name: Pseudarthrobacter defluvii (Kim et al. 2008) Busse 2016

  • synonyms

    • @ref: 20215
    • synonym: Arthrobacter defluvii

@ref: 7694

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Micrococcaceae

genus: Pseudarthrobacter

species: Pseudarthrobacter defluvii

full scientific name: Pseudarthrobacter defluvii (Kim et al. 2008) Busse 2016

strain designation: 4C1-a

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32477positive01-02 µm0.4-0.6 µmovoid-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
18326Ivory (1014)10-14 daysISP 2
18326Ivory (1014)10-14 daysISP 3
18326Ivory (1014)10-14 daysISP 4
18326Ivory (1014)10-14 daysISP 5
18326Ivory (1014)10-14 daysISP 6
18326Ivory (1014)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
18326noISP 2
18326noISP 3
18326noISP 4
18326noISP 5
18326noISP 6
18326noISP 7

pigmentation

  • @ref: 32477
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7694TRYPTICASE 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
18326ISP 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
18326ISP 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:
18326ISP 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
18326ISP 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
18326ISP 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
18326ISP 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

culture temp

@refgrowthtypetemperaturerange
7694positivegrowth28mesophilic
18326positiveoptimum28mesophilic
32477positivegrowth05-37
32477positiveoptimum25-30mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
32477positivegrowth06-10alkaliphile
32477positiveoptimum07-08

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32477aerobe
67771aerobe

spore formation

  • @ref: 32477
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
32477NaClpositivegrowth0-5 %
32477NaClpositiveoptimum0-5 %

murein

  • @ref: 7694
  • murein short key: A11.23
  • type: A3alpha L-Lys-L-Ser-L-Thr-L-Ala

observation

  • @ref: 32477
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
32477168082-dehydro-D-gluconate+carbon source
32477161933-hydroxybenzoate+carbon source
32477370543-hydroxybutyrate+carbon source
32477581435-dehydro-D-gluconate+carbon source
3247730089acetate+carbon source
3247716449alanine+carbon source
3247722599arabinose+carbon source
3247716947citrate+carbon source
3247733984fucose+carbon source
3247724265gluconate+carbon source
3247717234glucose+carbon source
3247728087glycogen+carbon source
3247727570histidine+carbon source
3247724996lactate+carbon source
3247725115malate+carbon source
3247715792malonate+carbon source
3247717306maltose+carbon source
3247729864mannitol+carbon source
3247737684mannose+carbon source
3247728053melibiose+carbon source
3247718401phenylacetate+carbon source
3247726271proline+carbon source
3247717272propionate+carbon source
3247726546rhamnose+carbon source
3247733942ribose+carbon source
3247717814salicin+carbon source
3247717822serine+carbon source
3247717992sucrose+carbon source
3247731011valerate+carbon source
324774853esculin+hydrolysis
3247717632nitrate+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

enzymes

@refvalueactivityec
32477catalase+1.11.1.6
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
18326--+-+++--+-------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18326-++-+--+---++-++-++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7694sewageGeumho River in DaeguRepublic of KoreaKORAsia
67771From sewageGeumho River, DaeguRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Engineered
  • Cat2: #Waste
  • Cat3: #Wastewater

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
183261German classification
76941Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7694
  • description: Arthrobacter defluvii partial 16S rRNA gene, type strain 4C1-aT
  • accession: AM409361
  • length: 1463
  • database: ena
  • NCBI tax ID: 410837

GC content

@refGC-content
769464.4
3247763.5-64.4

External links

@ref: 7694

culture collection no.: DSM 18782, KCTC 19209

straininfo link

  • @ref: 77064
  • straininfo: 407148

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
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/urltitleID_cross_referencepubmed
7694Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18782)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18782
18326Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18782.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
32477Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2869728776041
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
77064Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407148.1StrainInfo: A central database for resolving microbial strain identifiers