Strain identifier

BacDive ID: 11135

Type strain: Yes

Species: Nocardioides salarius

Strain Designation: CL-Z59

Strain history: <- Byung C. Cho; CL-Z59

NCBI tax ID(s): 374513 (species)

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General

@ref: 7450

BacDive-ID: 11135

DSM-Number: 18239

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

description: Nocardioides salarius CL-Z59 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from seawater enriched with zooplankton.

NCBI tax id

  • NCBI tax id: 374513
  • Matching level: species

strain history

  • @ref: 7450
  • history: <- Byung C. Cho; CL-Z59

doi: 10.13145/bacdive11135.20230509.8.1

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 salarius
  • full scientific name: Nocardioides salarius Kim et al. 2008

  • synonyms

    • @ref: 20215
    • synonym: Nocardioides basaltis

@ref: 7450

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides salarius

full scientific name: Nocardioides salarius Kim et al. 2008 emend. Hwang et al. 2012

strain designation: CL-Z59

type strain: yes

Morphology

cell morphology

  • @ref: 32486
  • gram stain: positive
  • cell length: 0.6-1.6 µm
  • cell width: 0.3-0.6 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19760Ivory (1014)10-14 daysISP 2
19760Ivory (1014)10-14 daysISP 3
19760Ivory (1014)10-14 daysISP 4
19760Ivory (1014)10-14 daysISP 5
19760Ivory (1014)10-14 daysISP 6
19760Ivory (1014)10-14 daysISP 7

multicellular morphology

@refmedium name
19760ISP 2
19760ISP 3
19760ISP 4
19760ISP 5
19760ISP 6
19760ISP 7

pigmentation

  • @ref: 32486
  • production: yes

multimedia

  • @ref: 7450
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_18239.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7450BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
7450GPHF-MEDIUM (DSMZ Medium 553)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium553.pdf
19760ISP 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
19760ISP 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:
19760ISP 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
19760ISP 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
19760ISP 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
19760ISP 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

culture temp

@refgrowthtypetemperaturerange
7450positivegrowth28mesophilic
19760positiveoptimum28mesophilic
32486positivegrowth10-35
32486positiveoptimum25-30mesophilic

culture pH

@refabilitytypepHPH range
32486positivegrowth06-10alkaliphile
32486positiveoptimum06-07

Physiology and metabolism

oxygen tolerance

  • @ref: 32486
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
32486NaClpositivegrowth01-10 %
32486NaClpositiveoptimum3 %

observation

  • @ref: 32486
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3248629016arginine+carbon source
3248617057cellobiose+carbon source
3248617234glucose+carbon source
3248629864mannitol+carbon source
3248618257ornithine+carbon source
3248633942ribose+carbon source
3248617992sucrose+carbon source
324864853esculin+hydrolysis
6837917632nitrate-reduction
683794853esculin+hydrolysis
6837916199urea+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

enzymes

@refvalueactivityec
32486acid phosphatase+3.1.3.2
32486alkaline phosphatase+3.1.3.1
32486catalase+1.11.1.6
32486gelatinase+
68379gelatinase+
68379urease+3.5.1.5
68379beta-glucosidase+3.2.1.21
68379N-acetyl-beta-glucosaminidase-3.2.1.52
68379alpha-glucosidase+3.2.1.20
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68379pyrazinamidase-3.5.1.B15
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 coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYG
19760--++--+-+++--------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19760+++-+--+-++---++---

Isolation, sampling and environmental information

isolation

  • @ref: 7450
  • sample type: seawater enriched with zooplankton
  • geographic location: South Sea
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Environmental#Aquatic#Marine
#Host#Microbial#Zooplankton

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74501Risk group (German classification)
197601Risk group (German classification)

Sequence information

16S sequences

  • @ref: 7450
  • description: Nocardioides salarius strain CL-Z59 16S ribosomal RNA gene, partial sequence
  • accession: DQ401092
  • length: 1446
  • database: ena
  • NCBI tax ID: 374513

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardioides salarius DSM 18239GCA_016907435contigncbi374513
66792Nocardioides salarius DSM 18239GCA_015070765contigncbi374513
66792Nocardioides salarius DSM 18239GCA_015339545scaffoldncbi374513
66792Nocardioides salarius strain DSM 18239374513.5wgspatric374513
66792Nocardioides salarius strain DSM 18239374513.4wgspatric374513
66792Nocardioides salarius strain DSM 18239374513.3wgspatric374513
66792Nocardioides salarius DSM 182392893566641draftimg374513

GC content

@refGC-contentmethod
745073.3high performance liquid chromatography (HPLC)
3248673.3

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno96.76yes
flagellatedno98.704yes
gram-positiveyes91.546no
anaerobicno98.849yes
aerobicyes90.114yes
halophileno77.782no
spore-formingno86.682no
glucose-utilyes89.506yes
thermophileno99.075yes
glucose-fermentno91.187yes

External links

@ref: 7450

culture collection no.: DSM 18239, KCCM 42320

straininfo link

  • @ref: 80384
  • straininfo: 403005

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18768604Nocardioides salarius sp. nov., isolated from seawater enriched with zooplankton.Kim HM, Choi DH, Hwang CY, Cho BCInt J Syst Evol Microbiol10.1099/ijs.0.65569-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, Temperature, Zooplankton/*microbiologyGenetics
Phylogeny18984703Nocardioides dokdonensis sp. nov., an actinomycete isolated from sand sediment.Park SC, Baik KS, Kim MS, Chun J, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.65835-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Silicon Dioxide, Species SpecificityGenetics
Phylogeny22228655Nocardioides lianchengensis sp. nov., an actinomycete isolated from soil.Zhang J, Ma Y, Yu HInt J Syst Evol Microbiol10.1099/ijs.0.036723-02012Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analysisGenetics
Phylogeny22772977Reclassification of Nocardioides basaltis Kim et al. 2009 as a later synonym of Nocardioides salarius Kim et al. 2008, and emendation of the species description.Hwang CY, Kim HM, Lee YKAntonie Van Leeuwenhoek10.1007/s10482-012-9768-12012Actinomycetales/*classification/genetics, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome
Phylogeny25716951Nocardioides deserti sp. nov., an actinobacterium isolated from desert soil.Tuo L, Dong YP, Habden X, Liu JM, Guo L, Liu XF, Chen L, Jiang ZK, Liu SW, Zhang YB, Zhang YQ, Sun CHInt J Syst Evol Microbiol10.1099/ijs.0.0001472015Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, *Desert Climate, Diaminopimelic Acid/chemistry, Fabaceae/*microbiology, Fatty Acids/chemistry, Molecular Sequence Data, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7450Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18239)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18239
19760Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM18239.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
32486Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2870628776041
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)
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
80384Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403005.1StrainInfo: A central database for resolving microbial strain identifiers