Strain identifier

BacDive ID: 16387

Type strain: Yes

Species: Streptomyces turgidiscabies

Strain Designation: SY9113, Sy 9113

Strain history: CIP <- 1998, K. Miyajima, Tokachi Agricultural Experiment Station, Hokkaido, Japan: strain Sy 9113 <- F. Tanaka

NCBI tax ID(s): 85558 (species)

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General

@ref: 10621

BacDive-ID: 16387

DSM-Number: 41838

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

description: Streptomyces turgidiscabies SY9113 is an obligate aerobe, mesophilic, Gram-positive plant pathogen that was isolated from potato.

NCBI tax id

  • NCBI tax id: 85558
  • Matching level: species

strain history

@refhistory
10621<- NBRC <- K. Miyajima; SY9113
67770IFO 16080 <-- K. Miyajima SY9113.
123693CIP <- 1998, K. Miyajima, Tokachi Agricultural Experiment Station, Hokkaido, Japan: strain Sy 9113 <- F. Tanaka

doi: 10.13145/bacdive16387.20230509.8.1

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 turgidiscabies
  • full scientific name: Streptomyces turgidiscabies Miyajima et al. 1998

@ref: 10621

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces turgidiscabies

full scientific name: Streptomyces turgidiscabies Miyajima et al. 1998

strain designation: SY9113, Sy 9113

type strain: yes

Morphology

cell morphology

  • @ref: 123693
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

  • @ref: 123693

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
10621GYM 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
39320MEDIUM 3 - Columbia agaryesColumbia agar (39.000 g);distilled water (1000.000 ml)
10621ROLLED 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
10621STARCH - 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
10621N-Z-AMINE-MEDIUM (DSMZ Medium 554)yeshttps://mediadive.dsmz.de/medium/554Name: N-Z-AMINE-MEDIUM (DSMZ Medium 554) Composition: Starch 20.0 g/l Agar 20.0 g/l Glucose 10.0 g/l N-Z amine 5.0 g/l Yeast extract 5.0 g/l CaCO3 1.0 g/l Distilled water
123693CIP Medium 236yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=236
123693CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57
123693CIP Medium 3yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=3

culture temp

@refgrowthtypetemperaturerange
10621positivegrowth28mesophilic
39320positivegrowth30mesophilic
67770positivegrowth28mesophilic
123693positivegrowth25-30mesophilic
123693nogrowth10psychrophilic
123693nogrowth37mesophilic
123693nogrowth41thermophilic
123693nogrowth45thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 123693
  • oxygen tolerance: obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
123693NaClpositivegrowth0-2 %
123693NaClnogrowth4 %
123693NaClnogrowth6 %
123693NaClnogrowth8 %
123693NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1236934853esculin-hydrolysis
123693606565hippurate+hydrolysis
12369317632nitrate-reduction
12369316301nitrite-reduction
12369317632nitrate-respiration

metabolite production

  • @ref: 123693
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12369315688acetoin-
12369317234glucose-

enzymes

@refvalueactivityec
123693oxidase-
123693beta-galactosidase+3.2.1.23
123693alcohol dehydrogenase-1.1.1.1
123693gelatinase+/-
123693amylase+
123693DNase-
123693caseinase+3.4.21.50
123693catalase+1.11.1.6
123693tween esterase+
123693gamma-glutamyltransferase+2.3.2.2
123693lecithinase-
123693lipase-
123693lysine decarboxylase-4.1.1.18
123693ornithine decarboxylase-4.1.1.17
123693phenylalanine ammonia-lyase-4.3.1.24
123693protease-
123693tryptophan deaminase-
123693urease+3.5.1.5
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123693--+--+----++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
10621potatoHokkaidoJapanJPNAsia
67770Potato tubers with erumpent scab lesionsSyari-cho, HokkaidoJapanJPNAsia
123693Potato tuberHokkaidoJapanJPNAsia1991

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_4214.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15;96_102;97_135;98_3178;99_4214&stattab=map
  • Last taxonomy: Streptomyces turgidiscabies
  • 16S sequence: D63866
  • Sequence Identity:
  • Total samples: 1335
  • soil counts: 1131
  • aquatic counts: 82
  • animal counts: 69
  • plant counts: 53

Safety information

risk assessment

@refpathogenicity plantbiosafety levelbiosafety level comment
10621yes1Risk group (German classification)
1236931Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces sp. 16S ribosomal RNA, complete sequenceD638661530ena1931
20218Streptomyces turgidiscabies gene for 16S ribosomal RNA, 23S ribosomal RNA, complete and partial sequence, strain:ATCC 700248AB0262211865ena85558
20218Streptomyces turgidiscabies gene for 16S rRNA, 16S-23S intergenic spacer, 23S rRNA, partial and complete sequence, isolate:ATCC 700248, clone:T3AB041138340ena85558
20218Streptomyces turgidiscabies strain ATCC 700248 clone ITS1 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296927286ena85558
20218Streptomyces turgidiscabies strain ATCC 700248 clone ITS10 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296928282ena85558
20218Streptomyces turgidiscabies strain ATCC 700248 clone ITS20 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296929282ena85558
20218Streptomyces turgidiscabies strain ATCC 700248 clone ITS24 16S-23S ribosomal RNA intergenic spacer, partial sequenceAY296930281ena85558
20218Streptomyces turgidiscabies gene for 16S rRNA, partial sequence, strain: NBRC 16080AB2499241452ena85558

GC content

@refGC-contentmethod
1062170.9
6777072.5high performance liquid chromatography (HPLC)

External links

@ref: 10621

culture collection no.: DSM 41838, ATCC 700248, IFO 16080, JCM 10429, NBRC 16080, CIP 105577, KACC 20121, NRRL B-24078

straininfo link

  • @ref: 85437
  • straininfo: 43843

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9731290Streptomyces turgidiscabies sp. nov.Miyajima K, Tanaka F, Takeuchi T, Kuninaga SInt J Syst Bacteriol10.1099/00207713-48-2-4951998DNA, Bacterial, Nucleic Acid Hybridization, Pigments, Biological, Solanum tuberosum/*microbiology, Streptomyces/*classification/genetics/physiology/ultrastructure
Enzymology23752895Structure and biosynthesis of scabichelin, a novel tris-hydroxamate siderophore produced by the plant pathogen Streptomyces scabies 87.22.Kodani S, Bicz J, Song L, Deeth RJ, Ohnishi-Kameyama M, Yoshida M, Ochi K, Challis GLOrg Biomol Chem10.1039/c3ob40536b2013Hydroxamic Acids/*chemistry/isolation & purification, Iron Chelating Agents/*chemistry/isolation & purification/*metabolism, Models, Molecular, Molecular Conformation, Multigene Family/genetics, Oligopeptides/*biosynthesis/*chemistry/isolation & purification, Peptide Synthases/genetics/metabolism, Plants/*microbiology, Siderophores/*biosynthesis/*chemistry/isolation & purification, Stereoisomerism, Streptomyces/enzymology/genetics/*metabolismPhylogeny
Phylogeny24123200Streptomyces graminilatus sp. nov., isolated from bamboo litter.Lee HJ, Whang KSInt J Syst Evol Microbiol10.1099/ijs.0.049528-02013Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sasa/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny27476065Streptomyces castaneus sp. nov., a novel actinomycete isolated from the rhizosphere of Peucedanum praeruptorum Dunn.Zhou S, Li Z, Bai L, Yan K, Zhao J, Lu C, Liu C, Wang X, Xiang WArch Microbiol10.1007/s00203-016-1274-92016Apiaceae/*microbiology, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhizosphere, *Soil Microbiology, Streptomyces/classification/genetics/*isolation & purification/metabolismMetabolism
Phylogeny27601150Streptomyces lacrimifluminis sp. nov., a novel actinobacterium that produces antibacterial compounds, isolated from soil.Zhang B, Tang S, Chen X, Zhang L, Zhang G, Zhang W, Liu G, Chen T, Li S, Dyson PInt J Syst Evol Microbiol10.1099/ijsem.0.0014562016Anti-Bacterial Agents/*biosynthesis, Antibiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29944094Streptomyces geranii sp. nov., a novel endophytic actinobacterium isolated from root of Geranium carolinianum L.Li X, Lai X, Gan L, Long X, Hou Y, Zhang Y, Tian YInt J Syst Evol Microbiol10.1099/ijsem.0.0028762018Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Geranium/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Streptomyces/*classification/genetics/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
30764453First Report of Potato Scab Caused by Streptomyces turgidiscabies in China.Zhao WQ, Liu DQ, Yu XMPlant Dis10.1094/PDIS-92-11-1587C2008

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
10621Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 41838)https://www.dsmz.de/collection/catalogue/details/culture/DSM-41838
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
39320Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17612
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
85437Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID43843.1StrainInfo: A central database for resolving microbial strain identifiers
123693Curators of the CIPCollection of Institut Pasteur (CIP 105577)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105577