Strain identifier

BacDive ID: 11185

Type strain: Yes

Species: Nocardiopsis prasina

Strain Designation: 208

Strain history: K. Miyashita 208.

NCBI tax ID(s): 1245475 (strain), 2015 (species)

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General

@ref: 11327

BacDive-ID: 11185

DSM-Number: 43845

keywords: genome sequence, 16S sequence, Bacteria, spore-forming, Gram-positive

description: Nocardiopsis prasina 208 is a spore-forming, Gram-positive bacterium that builds an aerial mycelium and was isolated from soil.

NCBI tax id

NCBI tax idMatching level
2015species
1245475strain

strain history

@refhistory
11327<- JCM (Nocardiopsis dassonvillei subsp. prasina) <- K. Miyashita, 208
67770K. Miyashita 208.

doi: 10.13145/bacdive11185.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis prasina
  • full scientific name: Nocardiopsis prasina (Miyashita et al. 1984) Yassin et al. 1997

  • synonyms

    @refsynonym
    20215Nocardiopsis albus subsp. prasina
    20215Nocardiopsis dassonvillei subsp. prasina
    20215Nocardiopsis alba subsp. prasina

@ref: 11327

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis prasina

full scientific name: Nocardiopsis prasina (Miyashita et al. 1984) Yassin et al. 1997 emend. Nouioui et al. 2018

strain designation: 208

type strain: yes

Morphology

cell morphology

@refgram stainconfidencemotility
69480positive90.715
6948095no

colony morphology

@refcolony colorincubation periodmedium used
19966Colourless10-14 daysISP 2
19966Colourless10-14 daysISP 3
19966Colourless10-14 daysISP 4
19966Colourless10-14 daysISP 5
19966Golden yellow (1004)10-14 daysISP 6
19966Golden yellow (1004)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19966yesAerial MyceliumWhiteISP 2
19966noISP 3
19966yesAerial MyceliumCreme (9001)ISP 4
19966noISP 5
19966yesAerial MyceliumCreme (9001)ISP 6
19966noISP 7

multimedia

  • @ref: 11327
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_43845.jpg
  • caption: Medium 65 28°C pH9
  • intellectual property rights: Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11327GYM 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
19966ISP 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
19966ISP 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:
19966ISP 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
19966ISP 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
19966ISP 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
19966ISP 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
11327GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf

culture temp

@refgrowthtypetemperature
19966positiveoptimum28
11327positivegrowth28
67770positivegrowth28

Physiology and metabolism

oxygen tolerance

  • @ref: 69480
  • oxygen tolerance: aerobe
  • confidence: 91.753

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 100

halophily

  • @ref: 19966
  • salt: NaCl
  • growth: positive
  • tested relation: maximum
  • concentration: 10 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H6), MK-10(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1996662968cellulose-
1996616634raffinose+/-
1996626546rhamnose+/-
1996628757fructose+/-
1996629864mannitol+/-
1996617268myo-inositol+/-
1996618222xylose+/-
1996617992sucrose+/-
1996622599arabinose+/-
1996617234glucose+
683685291gelatin+hydrolysis
6836827897tryptophan-energy source
6836816199urea-hydrolysis
6836816947citrate+assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinyes
6836835581indoleno
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin+
6836835581indole-

enzymes

@refvalueactivityec
68368gelatinase+
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase-3.5.3.6
68368beta-galactosidase+3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGEL
19966+---+----++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
11327soilJapanJPNAsia
67770SoilJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_8027.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_1213;99_8027&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: X97884
  • Sequence Identity:
  • Total samples: 65
  • soil counts: 3
  • aquatic counts: 2
  • animal counts: 58
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
113271Risk group (German classification)
199661German classification

Sequence information

16S sequences

  • @ref: 20218
  • description: Nocardiopsis prasina 16S rRNA gene, strain DSM 43845T
  • accession: X97884
  • length: 1461
  • database: nuccore
  • NCBI tax ID: 2015

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis prasina DSM 438451245475.3wgspatric1245475
66792Nocardiopsis prasina DSM 438452554235032draftimg1245475
67770Nocardiopsis prasina DSM 43845GCA_000341265contigncbi1245475

GC content

  • @ref: 67770
  • GC-content: 70.8
  • method: genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.715no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.591no
69480spore-formingspore-formingAbility to form endo- or exosporesyes83.771no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes91.753no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.056yes
69480flagellatedmotile2+Ability to perform flagellated movementno95no

External links

@ref: 11327

culture collection no.: DSM 43845, ATCC 35940, JCM 3336, KCC A-0336, BCRC 16257, CGMCC 4.2085, IFM 0264, IFO 14423, IMSNU 21500, IMSNU 22173, KCTC 9130, MAFF 304004, NBRC 14423, NRRL B-16235, PCM 2493, VKM Ac-1880, VTT E-022153

straininfo link

  • @ref: 80434
  • straininfo: 46019

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9336896Description of Nocardiopsis synnemataformans sp. nov., elevation of Nocardiopsis alba subsp. prasina to Nocardiopsis prasina comb. nov., and designation of Nocardiopsis antarctica and Nocardiopsis alborubida as later subjective synonyms of Nocardiopsis dassonvillei.Yassin AF, Rainey FA, Burghardt J, Gierth D, Ungerechts J, Lux I, Seifert P, Bal C, Schaal KPInt J Syst Bacteriol10.1099/00207713-47-4-9831997Base Composition, Culture Media, Conditioned/metabolism, DNA, Bacterial/*analysis, Humans, Microscopy, Electron, Molecular Sequence Data, Propionibacteriaceae/chemistry/*classification/genetics/growth & development/metabolism/ultrastructure, RNA, Ribosomal, 16S/*analysisCultivation
Phylogeny10808490[Teichoic acids from the cell wall of Nocardiopsis prasina BKM Ac-1880T].Tul'skaia EM, Shashkov AS, Evtushenko LI, Naumova IBMikrobiologiia2000Actinomycetales/*chemistry, Cell Wall/*chemistry, Magnetic Resonance Spectroscopy, Species Specificity, Teichoic Acids/*chemistry

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
11327Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 43845)https://www.dsmz.de/collection/catalogue/details/culture/DSM-43845
19966Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM43845.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
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/
68368Automatically annotated from API 20E
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
80434Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46019.1StrainInfo: A central database for resolving microbial strain identifiers