Strain identifier

BacDive ID: 4260

Type strain: Yes

Species: Dietzia cercidiphylli

Strain history: DSM 45140 <-- S.-K. Tang YIM 65002 <-- J. Li.

NCBI tax ID(s): 498199 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 12384

BacDive-ID: 4260

DSM-Number: 45140

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

description: Dietzia cercidiphylli DSM 45140 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from surface sterilized root sample of Cercidiphyllum japonicum.

NCBI tax id

  • NCBI tax id: 498199
  • Matching level: species

strain history

@refhistory
12384<- S.-K. Tang; YIM 65002 <- J. Li
67770DSM 45140 <-- S.-K. Tang YIM 65002 <-- J. Li.

doi: 10.13145/bacdive4260.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Mycobacteriales
  • family: Dietziaceae
  • genus: Dietzia
  • species: Dietzia cercidiphylli
  • full scientific name: Dietzia cercidiphylli Li et al. 2008

@ref: 12384

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Dietziaceae

genus: Dietzia

species: Dietzia cercidiphylli

full scientific name: Dietzia cercidiphylli Li et al. 2008

type strain: yes

Morphology

cell morphology

  • @ref: 31198
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19716Pure orange10-14 daysISP 2
1971610-14 daysISP 3
1971610-14 daysISP 4
1971610-14 daysISP 5
1971610-14 daysISP 6
19716Pure orange10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19716noISP 2
19716noISP 3
19716noISP 4
19716noISP 5
19716noISP 6
19716noISP 7

pigmentation

  • @ref: 31198
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12384TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
19716ISP 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
19716ISP 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:
19716ISP 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
19716ISP 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
19716ISP 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
19716ISP 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
12384positivegrowth28mesophilic
19716positiveoptimum28mesophilic
31198positivegrowth10-37
31198positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31198positivegrowth06-09alkaliphile
31198positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31198
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31198
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31198NaClpositivegrowth0-10 %
31198NaClpositiveoptimum0-10 %

observation

@refobservation
31198aggregates in chains
67770quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3119822599arabinose+carbon source
3119828757fructose+carbon source
3119817234glucose+carbon source
3119817716lactose+carbon source
3119817306maltose+carbon source
3119837684mannose+carbon source
3119817992sucrose+carbon source
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
31198catalase+1.11.1.6
31198urease+3.5.1.5
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
19716---+--+----------+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19716+++-+----+----++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
12384surface sterilized root sample of Cercidiphyllum japonicumCercidiphyllum japonicumYunnan ProvinceChinaCHNAsia
67770Surface-sterilized root of Cercidiphyllum japonicum from Yunnan ProvinceCercidiphyllum japonicumChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_35663.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_611;97_2732;98_26309;99_35663&stattab=map
  • Last taxonomy: Dietzia
  • 16S sequence: HQ259255
  • Sequence Identity:
  • Total samples: 5016
  • soil counts: 321
  • aquatic counts: 1379
  • animal counts: 3158
  • plant counts: 158

Safety information

risk assessment

  • @ref: 12384
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Dietzia cercidiphylli culture-collection DSM:45140 16S ribosomal RNA gene, partial sequenceHQ2592551439ena498199
12384Dietzia cercidiphylli strain YIM 65002 16S ribosomal RNA gene, partial sequenceEU3758461456ena498199

GC content

@refGC-contentmethod
1238472.6
6777072.6high performance liquid chromatography (HPLC)

External links

@ref: 12384

culture collection no.: DSM 45140, CCTCC AA 207016, JCM 16002, YIM 65002

straininfo link

  • @ref: 73755
  • straininfo: 407580

literature

  • topic: Phylogeny
  • Pubmed-ID: 18984691
  • title: Dietzia schimae sp. nov. and Dietzia cercidiphylli sp. nov., from surface-sterilized plant tissues.
  • authors: Li J, Zhao GZ, Zhang YQ, Klenk HP, Pukall R, Qin S, Xu LH, Li WJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.2008/000919-0
  • year: 2008
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/microbiology, Plant Stems/microbiology, Plants/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sterilization/methods, Theaceae/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
12384Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45140)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45140
19716Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45140.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
31198Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127525
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
73755Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID407580.1StrainInfo: A central database for resolving microbial strain identifiers