Strain identifier

BacDive ID: 131849

Type strain: Yes

Species: Nocardiopsis alkaliphila

Strain Designation: WS 2

Strain history: DSM 44657 <-- W. N. Hozzein WS2 (=YIM 80379).

NCBI tax ID(s): 1246461 (strain), 225762 (species)

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General

@ref: 11966

BacDive-ID: 131849

DSM-Number: 44657

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

description: Nocardiopsis alkaliphila WS 2 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
225762species
1246461strain

strain history

@refhistory
11966<- W. N. Hozzein; WS2 <- CCTCC <- YIM <- W. N. Hozzein
67770DSM 44657 <-- W. N. Hozzein WS2 (=YIM 80379).

doi: 10.13145/bacdive131849.20230509.8.1

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 alkaliphila
  • full scientific name: Nocardiopsis alkaliphila Hozzein et al. 2004

@ref: 11966

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis alkaliphila

full scientific name: Nocardiopsis alkaliphila Hozzein et al. 2004 emend. Nouioui et al. 2018

strain designation: WS 2

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
30015positiveno
69480positive100

pigmentation

  • @ref: 30015
  • production: yes

multimedia

  • @ref: 11966
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44657.jpg
  • caption: Medium 215 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
11966CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water
11966BHI MEDIUM (DSMZ Medium 215)yeshttps://mediadive.dsmz.de/medium/215Name: BHI MEDIUM (DSMZ Medium 215) Composition: Brain heart infusion 37.0 g/l Distilled water
11966TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
11966positivegrowth28mesophilic
30015positivegrowth10-45
30015positiveoptimum28-30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
30015positivegrowth7.0-12.0alkaliphile
30015positiveoptimum9.5-10.0

Physiology and metabolism

oxygen tolerance

  • @ref: 30015
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
30015yes
69481yes100
69480yes97.047

halophily

@refsaltgrowthtested relationconcentration
30015NaClpositivegrowth0-10 %
30015NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H6), MK-10(H8), MK-11(H2), MK-9(H6), MK-9(H10), MK-10(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3001522599arabinose+carbon source
3001517057cellobiose+carbon source
3001528260galactose+carbon source
3001517234glucose+carbon source
3001517716lactose+carbon source
3001517306maltose+carbon source
3001516634raffinose+carbon source
3001526546rhamnose+carbon source
3001517822serine+carbon source
3001530911sorbitol+carbon source
3001517992sucrose+carbon source
3001517151xylitol+carbon source
3001518222xylose+carbon source

enzymes

  • @ref: 30015
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
11966soilThe eastern desertEgyptEGYAfrica
67770Soil, the eastern desert of EgyptEgyptEGYAfrica

isolation source categories

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

Safety information

risk assessment

  • @ref: 11966
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 11966
  • description: Nocardiopsis egyptensis 16S ribosomal RNA gene, partial sequence
  • accession: AY230848
  • length: 1516
  • database: ena
  • NCBI tax ID: 225762

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis alkaliphila YIM 803791246461.3wgspatric1246461
66792Nocardiopsis alkaliphila YIM 803792551306677draftimg1246461
67770Nocardiopsis alkaliphila YIM 80379GCA_000341005contigncbi1246461

GC content

@refGC-contentmethod
1196665.8
6777067.5genome sequence analysis
6777065.8thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.332yes
gram-positiveyes92.111yes
anaerobicno99.36yes
aerobicyes94.348no
halophileyes75.979no
spore-formingyes92.371yes
thermophileno95.759yes
glucose-utilyes90.76no
flagellatedno97.979no
glucose-fermentno90.653no

External links

@ref: 11966

culture collection no.: DSM 44657, CCTCC AA 001031, JCM 12678, YIM 80379, NBRC 104163

straininfo link

  • @ref: 90240
  • straininfo: 97671

literature

  • topic: Phylogeny
  • Pubmed-ID: 14742488
  • title: Nocardiopsis alkaliphila sp. nov., a novel alkaliphilic actinomycete isolated from desert soil in Egypt.
  • authors: Hozzein WN, Li WJ, Ali MIA, Hammouda O, Mousa AS, Xu LH, Jiang CL
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.02832-0
  • year: 2004
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/physiology, DNA, Ribosomal/genetics, Desert Climate, Egypt, Microscopy, Electron, Scanning, Molecular Sequence Data, Phospholipids/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
11966Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44657)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44657
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
30015Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2637928776041
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/
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
90240Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97671.1StrainInfo: A central database for resolving microbial strain identifiers