Strain identifier

BacDive ID: 11217

Type strain: Yes

Species: Nocardiopsis salina

Strain history: CIP <- 2004, KCTC

NCBI tax ID(s): 1246485 (strain), 245836 (species)

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General

@ref: 12020

BacDive-ID: 11217

DSM-Number: 44839

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

description: Nocardiopsis salina DSM 44839 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from hypersaline soil.

NCBI tax id

NCBI tax idMatching level
1246485strain
245836species

strain history

@refhistory
12020<- W.-J. Li, YIM
339862004, KCTC
67770KCTC 19003 <-- W.-J. Li YIM 90010.
67771<- WJ Li, Yunnan Univ.
122380CIP <- 2004, KCTC

doi: 10.13145/bacdive11217.20240916.9.1

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 salina
  • full scientific name: Nocardiopsis salina Li et al. 2004

@ref: 12020

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis salina

full scientific name: Nocardiopsis salina Li et al. 2004 emend. Li et al. 2006 emend. Nouioui et al. 2018

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31248positive0.8-1.2 µm0.4-0.6 µmrod-shapedno
67771positive
122380positiverod-shapedno
69480no90
69480positive90.152

colony morphology

  • @ref: 122380

pigmentation

  • @ref: 31248
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12020BACTO 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
33986Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
12020GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159)yeshttps://mediadive.dsmz.de/medium/1159Name: GYM STREPTOMYCES MEDIUM 10% NACL (DSMZ Medium 1159) Composition: NaCl 100.0 g/l Agar 15.0 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
12020SEA WATER AGAR (DSMZ Medium 246)yeshttps://mediadive.dsmz.de/medium/246Name: SEA WATER AGAR (DSMZ Medium 246) Composition: Agar 20.0 g/l Peptone 10.0 g/l Beef extract 10.0 g/l Tap water Sea water
122380CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
122380CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperature
12020positivegrowth28
31248positivegrowth20-40
31248positiveoptimum28
33986positivegrowth30
67770positivegrowth28
67771positivegrowth28
122380positivegrowth25-37
122380nogrowth10
122380nogrowth41
122380nogrowth45

culture pH

@refabilitytypepHPH range
31248positivegrowth6.0-9.0alkaliphile
31248positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31248aerobe
67771aerobe
69480aerobe90.208

spore formation

  • @ref: 31248
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31248NaClpositivegrowth03-20 %
31248NaClpositiveoptimum10 %
122380NaClpositivegrowth6-10 %
122380NaClnogrowth0 %
122380NaClnogrowth2 %
122380NaClnogrowth4 %

observation

@refobservation
31248aggregates in chains
67770quinones: MK-10(H6), MK-10(H8), MK-12
67771quinones: MK-10(H6), MK-10(H8), MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3124828757fructose+carbon source
3124816634raffinose+carbon source
3124833942ribose+carbon source
3124817992sucrose+carbon source
3124817632nitrate+reduction
12238016947citrate-carbon source
1223804853esculin-hydrolysis
122380606565hippurate+hydrolysis
12238017632nitrate-reduction
12238016301nitrite-reduction

metabolite production

  • @ref: 122380
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12238015688acetoin-
12238017234glucose-

enzymes

@refvalueactivityec
31248gelatinase+
122380oxidase-
122380beta-galactosidase+3.2.1.23
122380alcohol dehydrogenase-1.1.1.1
122380gelatinase+
122380amylase-
122380DNase-
122380caseinase+3.4.21.50
122380catalase+1.11.1.6
122380tween esterase+
122380gamma-glutamyltransferase-2.3.2.2
122380lecithinase+
122380lipase+
122380lysine decarboxylase-4.1.1.18
122380ornithine decarboxylase-4.1.1.17
122380phenylalanine ammonia-lyase-4.3.1.24
122380tryptophan deaminase-
122380urease-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
122380-+++-+----++---+----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122380---+-+-----+-----+-----+-----+---------------+--+---------------------+--------++--------+-------+-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12020hypersaline soilXin Jiang provinceChinaCHNAsia
67770Saline soilChinaCHNAsia
67771From a hypersaline habitat in Xinjiang ProvinceChinaCHNAsia
122380Environment, Soil sampleChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_31248.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_1154;98_23237;99_31248&stattab=map
  • Last taxonomy: Nocardiopsis salina
  • 16S sequence: AY373031
  • Sequence Identity:
  • Total samples: 43
  • soil counts: 10
  • animal counts: 31
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120201Risk group (German classification)
1223801Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31248
  • description: Nocardiopsis salina 16S ribosomal RNA gene, partial sequence
  • accession: AY373031
  • length: 1449
  • database: nuccore
  • NCBI tax ID: 1246485

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis salina YIM 900101246485.3wgspatric1246485
66792Nocardiopsis salina YIM 900102551306679draftimg1246485
67770Nocardiopsis salina YIM 90010GCA_000341025contigncbi1246485

GC content

@refGC-contentmethod
1202073.1
6777073.1thermal denaturation, midpoint method (Tm)
6777070.4genome sequence analysis

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes74no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes90.152yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.453yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes82.339no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes90.208no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno93.106yes
69480flagellatedmotile2+Ability to perform flagellated movementno90no

External links

@ref: 12020

culture collection no.: DSM 44839, CCTCC AA 204009, KCTC 19003, YIM 90010, JCM 13364, CIP 108478

straininfo link

  • @ref: 80460
  • straininfo: 133656

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15388747Nocardiopsis salina sp. nov., a novel halophilic actinomycete isolated from saline soil in China.Li WJ, Park DJ, Tang SK, Wang D, Lee JC, Xu LH, Kim CJ, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.63127-02004Actinomycetales/*classification/cytology/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, China, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA, Growth Inhibitors/pharmacology, Hydrogen-Ion Concentration, Microscopy, Electron, Scanning, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic/pharmacology, Sequence Analysis, DNA, *Soil Microbiology, Stearic Acids/analysis, Temperature, Vitamin K 2/analysisEnzymology
Phylogeny19625431Nocardiopsis litoralis sp. nov., a halophilic marine actinomycete isolated from a sea anemone.Chen YG, Wang YX, Zhang YQ, Tang SK, Liu ZX, Xiao HD, Xu LH, Cui XL, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.009704-02009Actinomycetales/classification/genetics/*isolation & purification/metabolism, Animals, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Anemones/*microbiology, Sodium Chloride/*metabolismMetabolism
Phylogeny20118291Nocardiopsis nikkonensis sp. nov., isolated from a compost sample.Yamamura H, Ohkubo SY, Ishida Y, Otoguro M, Tamura T, Hayakawa MInt J Syst Evol Microbiol10.1099/ijs.0.016956-02010Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryGenetics
Phylogeny34128783Nocardiopsis coralli sp. nov. a novel actinobacterium isolated from the coral Galaxea astreata.Li F, Xie Q, Zhou S, Kong F, Xu Y, Ma Q, Wu W, Huang D, Zhao Y, Huang XInt J Syst Evol Microbiol10.1099/ijsem.0.0048172021Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nocardiopsis/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12020Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44839)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44839
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
31248Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2757128776041
33986Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6221
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
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
80460Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID133656.1StrainInfo: A central database for resolving microbial strain identifiers
122380Curators of the CIPCollection of Institut Pasteur (CIP 108478)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108478