Strain identifier

BacDive ID: 16434

Type strain: Yes

Species: Streptomyces radiopugnans

Strain Designation: R97

Strain history: CGMCC 4.3519 <-- J. Mao et al. R97.

NCBI tax ID(s): 403935 (species)

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General

@ref: 10656

BacDive-ID: 16434

DSM-Number: 41901

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive, spiral-shaped

description: Streptomyces radiopugnans R97 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil of radiation area.

NCBI tax id

  • NCBI tax id: 403935
  • Matching level: species

strain history

@refhistory
10656<- Y. Huang, CGMCC <- Q. Tang
67770CGMCC 4.3519 <-- J. Mao et al. R97.

doi: 10.13145/bacdive16434.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Kitasatosporales
  • family: Streptomycetaceae
  • genus: Streptomyces
  • species: Streptomyces radiopugnans
  • full scientific name: Streptomyces radiopugnans Mao et al. 2007

@ref: 10656

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces radiopugnans

full scientific name: Streptomyces radiopugnans Mao et al. 2007

strain designation: R97

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32139positivespiral-shaped
69480no95.333
69480positive100

colony morphology

@refcolony colorincubation periodmedium used
18728Cream (9001)10-14 daysISP 2
18728Cream (9001)10-14 daysISP 3
18728Cream (9001)10-14 daysISP 4
18728Beige (1001)10-14 daysISP 5
18728Beige (1001)10-14 daysISP 6
18728Beige (1001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
18728yesAerial MyceliumCream (9001)ISP 2
18728yesAerial MyceliumCream (9001)ISP 3
18728yesAerial MyceliumCream (9001)ISP 4
18728noISP 5
18728noISP 6
18728noISP 7

pigmentation

  • @ref: 32139
  • production: yes

multimedia

  • @ref: 10656
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_41901.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10656GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
18728ISP 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
18728ISP 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:
18728ISP 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
18728ISP 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
18728ISP 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
18728ISP 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
10656ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
10656STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252)yeshttps://mediadive.dsmz.de/medium/252Name: STARCH - MINERAL SALT - AGAR (STMS) (DSMZ Medium 252) Composition: Agar 14.985 g/l Starch 9.99001 g/l (NH4)2SO4 1.998 g/l CaCO3 1.998 g/l K2HPO4 0.999001 g/l MgSO4 x 7 H2O 0.999001 g/l NaCl 0.999001 g/l FeSO4 x 7 H2O 0.000999001 g/l MnCl2 x 4 H2O 0.000999001 g/l ZnSO4 x 7 H2O 0.000999001 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
10656positivegrowth28mesophilic
32139positivegrowth20-50
32139positiveoptimum35mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32139positivegrowth05-11alkaliphile
32139positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 32139
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32139yes
69481yes100
69480yes100

halophily

  • @ref: 32139
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <7 %

observation

@refobservation
32139aggregates in chains
67770quinones: MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3213922599arabinose+carbon source
3213915428glycine+carbon source
3213929864mannitol+carbon source
3213926546rhamnose+carbon source
3213933942ribose+carbon source
3213917992sucrose+carbon source
3213953425tween 60+carbon source
3213917151xylitol+carbon source
3213918222xylose+carbon source

enzymes

@refvalueactivityec
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)+
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase+3.2.1.22
68382beta-galactosidase+3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
18728++++++---++++-++---

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
10656soil of radiation areaXinjiangChinaCHNAsia
67770Radiation-contaminated soilXinjiang Uigur Autonomous Region of north-west ChinaChinaCHNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_15420.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_2143;97_2583;98_10732;99_15420&stattab=map
  • Last taxonomy: Streptomyces
  • 16S sequence: DQ912930
  • Sequence Identity:
  • Total samples: 67
  • soil counts: 39
  • aquatic counts: 4
  • animal counts: 14
  • plant counts: 10

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
187281German classification
106561Risk group (German classification)

Sequence information

16S sequences

  • @ref: 10656
  • description: Streptomyces radiopugnans strain R97 16S ribosomal RNA gene, partial sequence
  • accession: DQ912930
  • length: 1442
  • database: ena
  • NCBI tax ID: 403935

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Streptomyces radiopugnans strain CGMCC 4.3519403935.4wgspatric403935
66792Streptomyces radiopugnans CGMCC 4.35192663762755draftimg403935
67770Streptomyces radiopugnans CGMCC 4.3519GCA_900110735scaffoldncbi403935

GC content

@refGC-contentmethod
1065672.7
6777072.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
gram-positiveyes89.463no
anaerobicno98.359yes
halophileno78.439yes
spore-formingyes95.139yes
glucose-utilyes87.534no
aerobicyes88.941yes
flagellatedno98.319no
motileno94.385no
thermophileno93.328no
glucose-fermentno88.161no

External links

@ref: 10656

culture collection no.: DSM 41901, CGMCC 4.3519, JCM 15480

straininfo link

  • @ref: 85475
  • straininfo: 397154

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17978221Streptomyces radiopugnans sp. nov., a radiation-resistant actinomycete isolated from radiation-polluted soil in China.Mao J, Tang Q, Zhang Z, Wang W, Wei D, Huang Y, Liu Z, Shi Y, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.65027-02007Bacterial Typing Techniques, China, Cobalt Radioisotopes, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Gamma Rays, Genes, rRNA, Molecular Sequence Data, Phenotype, RNA, Ribosomal, 16S/genetics, *Radiation Tolerance, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Radioactive, Species Specificity, Streptomyces/*classification/genetics/isolation & purification/physiology/*radiation effectsGenetics
Phylogeny21216916Streptomyces fenghuangensis sp. nov., isolated from seawater.Zhu H, Jiang S, Yao Q, Wang Y, Chen M, Chen Y, Guo JInt J Syst Evol Microbiol10.1099/ijs.0.029280-02011DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Streptomyces/*classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny21622834Streptomyces nanhaiensis sp. nov., a marine streptomycete isolated from a deep-sea sediment.Tian XP, Long LJ, Wang FZ, Xu Y, Li J, Zhang J, Zhang CS, Zhang S, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.031591-02011Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny24436069Streptomyces barkulensis sp. nov., isolated from an estuarine lake.Ray L, Mishra SR, Panda AN, Rastogi G, Pattanaik AK, Adhya TK, Suar M, Raina VInt J Syst Evol Microbiol10.1099/ijs.0.056614-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Estuaries, Fatty Acids/chemistry, Geologic Sediments/microbiology, India, Lakes/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
10656Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41901)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41901
18728Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM41901.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
32139Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2838328776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
85475Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397154.1StrainInfo: A central database for resolving microbial strain identifiers