Strain identifier
BacDive ID: 16446
Type strain:
Species: Streptomyces nigrescens
Strain history: KCC S-0401 <-- IFO 12894 <-- SAJ <-- ISP 5276 <-- INA 1800/54.
NCBI tax ID(s): 1920 (species)
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
@ref | history |
---|---|
9427 | <- E.B. Shirling, ISP <- G.F. Gauze, INA |
67770 | KCC 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
@ref synonym 20215 Actinomyces nigrescens 20215 Streptomyces 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
@ref | colony color | incubation period | medium used |
---|---|---|---|
19809 | Traffic yellow | 10-14 days | ISP 2 |
19809 | Traffic yellow | 10-14 days | ISP 3 |
19809 | Beige | 10-14 days | ISP 4 |
19809 | Beige | 10-14 days | ISP 5 |
19809 | Beige | 10-14 days | ISP 6 |
19809 | Beige | 10-14 days | ISP 7 |
multicellular morphology
@ref | forms multicellular complex | complex name | complex color | medium name |
---|---|---|---|---|
19809 | yes | Aerial Mycelium | Dusty grey | ISP 2 |
19809 | yes | Aerial Mycelium | Dusty grey to Black | ISP 3 |
19809 | yes | Aerial Mycelium | Dusty grey | ISP 4 |
19809 | yes | Aerial Mycelium | Cream | ISP 5 |
19809 | yes | Aerial Mycelium | Cream | ISP 6 |
19809 | yes | Aerial Mycelium | Cream | ISP 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
@ref | name | growth | link | composition |
---|---|---|---|---|
9427 | GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) | yes | https://mediadive.dsmz.de/medium/65 | Name: 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 |
9427 | ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) | yes | https://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium84.pdf | |
19809 | 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 | |
19809 | 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: | |
19809 | 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 | |
19809 | 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 | |
19809 | 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 | |
19809 | 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 |
---|---|---|---|---|
9427 | positive | growth | 28 | mesophilic |
19809 | positive | optimum | 28 | mesophilic |
32383 | positive | growth | 10-37 | |
67770 | positive | growth | 28 | mesophilic |
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
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32383 | 22599 | arabinose | + | carbon source |
32383 | 18403 | L-arabitol | + | carbon source |
32383 | 17057 | cellobiose | + | carbon source |
32383 | 28757 | fructose | + | carbon source |
32383 | 28260 | galactose | + | carbon source |
32383 | 28087 | glycogen | + | carbon source |
32383 | 17306 | maltose | + | carbon source |
32383 | 37684 | mannose | + | carbon source |
32383 | 26546 | rhamnose | + | carbon source |
32383 | 33942 | ribose | + | carbon source |
32383 | 17992 | sucrose | + | carbon source |
32383 | 27082 | trehalose | + | carbon source |
32383 | 18222 | xylose | + | carbon source |
32383 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32383 | gelatinase | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | + | |
68382 | cystine arylamidase | + | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | + | 3.2.1.22 |
68382 | beta-galactosidase | + | 3.2.1.23 |
68382 | beta-glucuronidase | + | 3.2.1.31 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucosidase | + | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | + | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
@ref | biosafety level | biosafety level comment |
---|---|---|
9427 | 1 | Risk group (German classification) |
19809 | 1 | Risk group (German classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Streptomyces nigrescens gene for 16S rRNA, partial sequence, strain: NBRC 12894 | AB184225 | 1476 | ena | 1920 |
32383 | Streptomyces ruanii strain ISP 5276 16S ribosomal RNA gene, partial sequence | EF408737 | 1450 | nuccore | 1226759 |
9427 | Streptomyces nigrescens partial 16S rRNA gene, type strain DSM 40276T | HG794417 | 1518 | ena | 1920 |
67770 | Streptomyces nigrescens strain NRRL B-12176T 16S ribosomal RNA gene, partial sequence | DQ442530 | 1519 | ena | 1920 |
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
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 98.061 | no |
gram-positive | yes | 89.157 | no |
anaerobic | no | 99.028 | no |
aerobic | yes | 89.552 | no |
halophile | no | 89.588 | no |
spore-forming | yes | 83.094 | no |
glucose-ferment | no | 90.145 | no |
thermophile | no | 95.848 | no |
glucose-util | yes | 89.533 | no |
motile | no | 88.623 | no |
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
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
9427 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 40276) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-40276 | ||||
19809 | Wink, J. | http://www.dsmz.de/microorganisms/wink_pdf/DSM40276.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 | ||
32383 | 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 | 28609 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
68382 | Automatically annotated from API zym | ||||||
85483 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID13344.1 | StrainInfo: A central database for resolving microbial strain identifiers |