Strain identifier

BacDive ID: 11116

Type strain: Yes

Species: Nocardioides alkalitolerans

Strain Designation: KSL-1

Strain history: <- IG Kim, KRIBB

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6573

BacDive-ID: 11116

DSM-Number: 16699

keywords: Gram-positive, mesophilic, aerobe, Bacteria, 16S sequence, genome sequence, rod-shaped

description: Nocardioides alkalitolerans KSL-1 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil.

NCBI tax id

NCBI tax idMatching level
281714species
1122608strain

strain history

doi: 10.13145/bacdive11116.20220920.7

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides alkalitolerans
  • full scientific name: Nocardioides alkalitolerans Yoon et al. 2005

@ref: 6573

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides alkalitolerans

full scientific name: Nocardioides alkalitolerans Yoon et al. 2005

strain designation: KSL-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31349positive1.75 µm0.9 µmrod-shapedno
67771positive

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6573TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://bacmedia.dsmz.de/medium/92Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water
37632MEDIUM 338 - for Sanguibacter keddieiiyesDistilled water make up to (1000.000 ml);Agar (15.000 g);Yeast extract (3.000 g);Trypto casein soy agar (30.000 g)
6573TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://bacmedia.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
6573GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://bacmedia.dsmz.de/medium/65Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 12.0 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

culture temp

@refgrowthtypetemperaturerange
6573positivegrowth28mesophilic
31349positiveoptimum27.5mesophilic
37632positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31349positivegrowth5.5-12
31349positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31349aerobe
67771aerobe

spore formation

  • @ref: 31349
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31349NaClpositivegrowth<5 %
31349NaClpositiveoptimum2.5 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3134922599arabinose+carbon source
3134917057cellobiose+carbon source
3134916634raffinose+carbon source
3134927082trehalose+carbon source
3134953424tween 20+carbon source
3134953423tween 40+carbon source
3134953425tween 60+carbon source
3134917632nitrate+reduction

enzymes

@refvalueactivityec
31349acid phosphatase+3.1.3.2
31349alkaline phosphatase+3.1.3.1
31349cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6573soilKoreaRepublic of KoreaKORAsia
67770Alkaline serpentinite soilRepublic of KoreaKORAsia
67771From Soil; KoreaRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 6573
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6573
  • description: Nocardioides alkalitolerans strain KSL-1 16S ribosomal RNA gene, partial sequence
  • accession: AY633969
  • length: 1473
  • database: ena
  • NCBI tax ID: 281714

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides alkalitolerans DSM 16699 DSM 16699GCA_000426525scaffoldncbi1122608
66792Nocardioides alkalitolerans DSM 166991122608.3wgspatric1122608
66792Nocardioides alkalitolerans DSM 166992524614663draftimg1122608
67770Nocardioides alkalitolerans DSM 16699, whole genome shotgun sequencing projectAUFN00000000ncbi1122608

GC content

@refGC-contentmethod
3134972.4
6777072.4high performance liquid chromatography (HPLC)

External links

@ref: 6573

culture collection no.: DSM 16699, KCTC 19037, JCM 13365, BCRC 16826, CIP 108736

straininfo link

@refpassport
20218http://www.straininfo.net/strains/386599
20218http://www.straininfo.net/strains/386600

literature

  • topic: Phylogeny
  • Pubmed-ID: 15774667
  • title: Nocardioides alkalitolerans sp. nov., isolated from an alkaline serpentinite soil in Korea.
  • authors: Yoon JH, Kim IG, Lee MH, Lee CH, Oh TK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63374-0
  • year: 2005
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Hydrogen-Ion Concentration, Korea, Molecular Sequence Data, Phenotype, Phylogeny, Propionibacteriaceae/chemistry/*classification/genetics/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6573Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16699)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16699
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
2766310.1099/ijs.0.63374-015774667
31349Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127663
37632Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6398
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc