Strain identifier

BacDive ID: 11116

Type strain: Yes

Species: Nocardioides alkalitolerans

Strain Designation: KSL-1

Strain history: CIP <- 2005, KCTC <- J. H. Yoon, KRIBB: strain KSL-1

NCBI tax ID(s): 1122608 (strain), 281714 (species)

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General

@ref: 6573

BacDive-ID: 11116

DSM-Number: 16699

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-positive, 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
1122608strain
281714species

strain history

@refhistory
6573<- J.-H. Yoon; KSL-1
67770KCTC 19037 <-- I.-G. Kim KSL-1.
67771<- IG Kim, KRIBB
116253CIP <- 2005, KCTC <- J. H. Yoon, KRIBB: strain KSL-1

doi: 10.13145/bacdive11116.20230509.8.1

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
116253negativerod-shapedno

colony morphology

  • @ref: 116253

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
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)yesName: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled waterhttps://mediadive.dsmz.de/medium/535
6573GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yesName: 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 waterhttps://mediadive.dsmz.de/medium/65
116253CIP Medium 338yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=338

culture temp

@refgrowthtypetemperaturerange
31349positiveoptimum27.5mesophilic
37632positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic
6573positivegrowth28mesophilic
116253positivegrowth10-37
116253nogrowth41thermophilic
116253nogrowth45thermophilic

culture pH

@refabilitytypepHPH range
31349positivegrowth5.5-12alkaliphile
31349positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31349aerobe
67771aerobe
116253obligate aerobe

spore formation

  • @ref: 31349
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31349NaClpositivegrowth<5 %
31349NaClpositiveoptimum2.5 %
116253NaClpositivegrowth0-10 %

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
11625316947citrate-carbon source
1162534853esculin-hydrolysis
116253606565hippurate+hydrolysis
11625317632nitrate-reduction
11625316301nitrite-reduction
11625317632nitrate-respiration

metabolite production

  • @ref: 116253
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11625315688acetoin-
11625317234glucose-

enzymes

@refvalueactivityec
31349acid phosphatase+3.1.3.2
31349alkaline phosphatase+3.1.3.1
31349cytochrome oxidase+1.9.3.1
116253oxidase+
116253beta-galactosidase-3.2.1.23
116253alcohol dehydrogenase-1.1.1.1
116253gelatinase+
116253amylase+
116253DNase+
116253caseinase+3.4.21.50
116253catalase+1.11.1.6
116253tween esterase+
116253gamma-glutamyltransferase+2.3.2.2
116253lecithinase-
116253lipase-
116253lysine decarboxylase-4.1.1.18
116253ornithine decarboxylase-4.1.1.17
116253phenylalanine ammonia-lyase-4.3.1.24
116253protease+
116253tryptophan deaminase-
116253urease-3.5.1.5
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116253-+++++--+-+----+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116253++-+---+--+---------+---+------+--++--+-------+-++------+---+-+++---------++--+++-------++++++-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6573soilKoreaRepublic of KoreaKORAsia
67770Alkaline serpentinite soilRepublic of KoreaKORAsia
67771From Soil; KoreaRepublic of KoreaKORAsia
116253Environment, An alkaline serpentinite soilRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_5919.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_2830;97_3478;98_4398;99_5919&stattab=map
  • Last taxonomy: Nocardioides alkalitolerans subclade
  • 16S sequence: AY633969
  • Sequence Identity:
  • Total samples: 9883
  • soil counts: 5957
  • aquatic counts: 1003
  • animal counts: 1271
  • plant counts: 1652

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
65731Risk group (German classification)
1162531Risk group (French 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 166991122608.3wgspatric1122608
66792Nocardioides alkalitolerans DSM 166992524614663draftimg1122608
67770Nocardioides alkalitolerans DSM 16699GCA_000426525scaffoldncbi1122608

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno95.441yes
flagellatedno98.414yes
gram-positiveyes92.378no
anaerobicno99.17no
aerobicyes95.296yes
halophileno88.093no
spore-formingno84.493yes
glucose-utilyes93.115no
thermophileno99.055no
glucose-fermentno92.554no

External links

@ref: 6573

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

straininfo link

  • @ref: 80365
  • straininfo: 138039

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/urltitleID_cross_referencepubmed
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
31349Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2766328776041
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
68382Automatically annotated from API zym
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
80365Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID138039.1StrainInfo: A central database for resolving microbial strain identifiers
116253Curators of the CIPCollection of Institut Pasteur (CIP 108736)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108736