Strain identifier
BacDive ID: 4260
Type strain:
Species: Dietzia cercidiphylli
Strain history: DSM 45140 <-- S.-K. Tang YIM 65002 <-- J. Li.
NCBI tax ID(s): 498199 (species)
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
@ref | history |
---|---|
12384 | <- S.-K. Tang; YIM 65002 <- J. Li |
67770 | DSM 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
@ref | colony color | incubation period | medium used |
---|---|---|---|
19716 | Pure orange | 10-14 days | ISP 2 |
19716 | 10-14 days | ISP 3 | |
19716 | 10-14 days | ISP 4 | |
19716 | 10-14 days | ISP 5 | |
19716 | 10-14 days | ISP 6 | |
19716 | Pure orange | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | medium name |
---|---|---|
19716 | no | ISP 2 |
19716 | no | ISP 3 |
19716 | no | ISP 4 |
19716 | no | ISP 5 |
19716 | no | ISP 6 |
19716 | no | ISP 7 |
pigmentation
- @ref: 31198
- production: yes
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
12384 | TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) | yes | https://mediadive.dsmz.de/medium/535 | Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water |
19716 | ISP 2 | yes | Name: 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 | |
19716 | ISP 3 | yes | Name: 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: | |
19716 | ISP 4 | yes | Name: 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 | |
19716 | ISP 5 | yes | Name: 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 | |
19716 | ISP 6 | yes | Name: 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 | |
19716 | ISP 7 | yes | Name: 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
@ref | growth | type | temperature | range |
---|---|---|---|---|
12384 | positive | growth | 28 | mesophilic |
19716 | positive | optimum | 28 | mesophilic |
31198 | positive | growth | 10-37 | |
31198 | positive | optimum | 28 | mesophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31198 | positive | growth | 06-09 | alkaliphile |
31198 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31198
- oxygen tolerance: aerobe
spore formation
- @ref: 31198
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31198 | NaCl | positive | growth | 0-10 % |
31198 | NaCl | positive | optimum | 0-10 % |
observation
@ref | observation |
---|---|
31198 | aggregates in chains |
67770 | quinones: MK-8(H2) |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31198 | 22599 | arabinose | + | carbon source |
31198 | 28757 | fructose | + | carbon source |
31198 | 17234 | glucose | + | carbon source |
31198 | 17716 | lactose | + | carbon source |
31198 | 17306 | maltose | + | carbon source |
31198 | 37684 | mannose | + | carbon source |
31198 | 17992 | sucrose | + | carbon source |
68379 | 17632 | nitrate | - | reduction |
68379 | 4853 | esculin | - | hydrolysis |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | - | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | + | fermentation |
68379 | 28087 | glycogen | - | fermentation |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31198 | catalase | + | 1.11.1.6 |
31198 | urease | + | 3.5.1.5 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68379 | gelatinase | - | |
68379 | urease | - | 3.5.1.5 |
68379 | beta-glucosidase | - | 3.2.1.21 |
68379 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68379 | alpha-glucosidase | + | 3.2.1.20 |
68379 | beta-galactosidase | - | 3.2.1.23 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
API coryne
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19716 | - | - | - | + | - | - | + | - | - | - | - | - | - | - | - | - | - | + | - |
API zym
@ref | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19716 | + | + | + | - | + | - | - | - | - | + | - | - | - | - | + | + | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
12384 | surface sterilized root sample of Cercidiphyllum japonicum | Cercidiphyllum japonicum | Yunnan Province | China | CHN | Asia |
67770 | Surface-sterilized root of Cercidiphyllum japonicum from Yunnan Province | Cercidiphyllum japonicum | China | CHN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Dietzia cercidiphylli culture-collection DSM:45140 16S ribosomal RNA gene, partial sequence | HQ259255 | 1439 | ena | 498199 |
12384 | Dietzia cercidiphylli strain YIM 65002 16S ribosomal RNA gene, partial sequence | EU375846 | 1456 | ena | 498199 |
GC content
@ref | GC-content | method |
---|---|---|
12384 | 72.6 | |
67770 | 72.6 | high 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
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
12384 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45140) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45140 | ||||
19716 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM45140.pdf | Compendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
31198 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 27525 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68379 | Automatically annotated from API Coryne | ||||||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 | ||||
73755 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID407580.1 | StrainInfo: A central database for resolving microbial strain identifiers |