Strain identifier

BacDive ID: 16446

Type strain: Yes

Species: Streptomyces nigrescens

Strain history: KCC S-0401 <-- IFO 12894 <-- SAJ <-- ISP 5276 <-- INA 1800/54.

NCBI tax ID(s): 1920 (species)

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General

@ref: 9427

BacDive-ID: 16446

DSM-Number: 40276

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, mesophilic

description: Streptomyces nigrescens DSM 40276 is a spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

  • NCBI tax id: 1920
  • Matching level: species

strain history

@refhistory
9427<- E.B. Shirling, ISP <- G.F. Gauze, INA
67770KCC S-0401 <-- IFO 12894 <-- SAJ <-- ISP 5276 <-- INA 1800/54.

doi: 10.13145/bacdive16446.20230509.8.1

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 nigrescens
  • full scientific name: Streptomyces nigrescens (Sveshnikova 1957) Pridham et al. 1958 (Approved Lists 1980)
  • synonyms

    @refsynonym
    20215Actinomyces nigrescens
    20215Streptomyces ruanii

@ref: 9427

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Streptomycetaceae

genus: Streptomyces

species: Streptomyces nigrescens

full scientific name: Streptomyces nigrescens (Sveshnikova 1957) Pridham et al. 1958

type strain: yes

Morphology

colony morphology

@refcolony colorincubation periodmedium used
19809Traffic yellow10-14 daysISP 2
19809Traffic yellow10-14 daysISP 3
19809Beige10-14 daysISP 4
19809Beige10-14 daysISP 5
19809Beige10-14 daysISP 6
19809Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19809yesAerial MyceliumDusty greyISP 2
19809yesAerial MyceliumDusty grey to BlackISP 3
19809yesAerial MyceliumDusty greyISP 4
19809yesAerial MyceliumCreamISP 5
19809yesAerial MyceliumCreamISP 6
19809yesAerial MyceliumCreamISP 7

pigmentation

  • @ref: 32383
  • production: no

multimedia

  • @ref: 9427
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_40276.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
9427GYM 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
9427ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf
19809ISP 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
19809ISP 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:
19809ISP 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
19809ISP 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
19809ISP 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
19809ISP 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
9427positivegrowth28mesophilic
19809positiveoptimum28mesophilic
32383positivegrowth10-37
67770positivegrowth28mesophilic

culture pH

  • @ref: 32383
  • ability: positive
  • type: growth
  • pH: 06-10
  • PH range: alkaliphile

Physiology and metabolism

spore formation

  • @ref: 32383
  • spore formation: yes

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3238322599arabinose+carbon source
3238318403L-arabitol+carbon source
3238317057cellobiose+carbon source
3238328757fructose+carbon source
3238328260galactose+carbon source
3238328087glycogen+carbon source
3238317306maltose+carbon source
3238337684mannose+carbon source
3238326546rhamnose+carbon source
3238333942ribose+carbon source
3238317992sucrose+carbon source
3238327082trehalose+carbon source
3238318222xylose+carbon source
323834853esculin+hydrolysis

enzymes

@refvalueactivityec
32383gelatinase+
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
19809+++-++++++++++++++-

Isolation, sampling and environmental information

isolation

  • @ref: 9427
  • sample type: soil

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
94271Risk group (German classification)
198091Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Streptomyces nigrescens gene for 16S rRNA, partial sequence, strain: NBRC 12894AB1842251476ena1920
32383Streptomyces ruanii strain ISP 5276 16S ribosomal RNA gene, partial sequenceEF4087371450nuccore1226759
9427Streptomyces nigrescens partial 16S rRNA gene, type strain DSM 40276THG7944171518ena1920
67770Streptomyces nigrescens strain NRRL B-12176T 16S ribosomal RNA gene, partial sequenceDQ4425301519ena1920

Genome sequences

  • @ref: 66792
  • description: Streptomyces nigrescens DSM 40276
  • accession: GCA_027626975
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 1920

GC content

  • @ref: 9427
  • GC-content: 70.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno98.061no
gram-positiveyes89.157no
anaerobicno99.028no
aerobicyes89.552no
halophileno89.588no
spore-formingyes83.094no
glucose-fermentno90.145no
thermophileno95.848no
glucose-utilyes89.533no
motileno88.623no

External links

@ref: 9427

culture collection no.: DSM 40276, ATCC 23941, CBS 925.68, IFO 12894, INA 1800/54, ISP 5276, NBRC 12894, RIA 1194, JCM 4401, BCRC 15127, CBS 103.61, CGMCC 4.1410, LMG 19332, NCIMB 14461, NCIMB 9856, NRRL B-12176, VKM Ac-1705

straininfo link

  • @ref: 85483
  • straininfo: 13344

literature

  • topic: Phylogeny
  • Pubmed-ID: 18523180
  • title: Five new members of the Streptomyces violaceusniger 16S rRNA gene clade: Streptomyces castelarensis sp. nov., comb. nov., Streptomyces himastatinicus sp. nov., Streptomyces mordarskii sp. nov., Streptomyces rapamycinicus sp. nov. and Streptomyces ruanii sp. nov.
  • authors: Kumar Y, Goodfellow M
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65408-0
  • year: 2008
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, *Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, DNA, Species Specificity, Streptomyces/*classification/genetics/physiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
9427Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40276)https://www.dsmz.de/collection/catalogue/details/culture/DSM-40276
19809Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM40276.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
32383Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128609
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
85483Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID13344.1StrainInfo: A central database for resolving microbial strain identifiers