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, mesophilic, Gram-positive, rod-shaped

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

NCBI tax id

NCBI tax idMatching level
245836species
1246485strain

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/bacdive11217.20230509.8.1

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 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
69480positive100
122380positiverod-shapedno

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

@refgrowthtypetemperaturerange
12020positivegrowth28mesophilic
31248positivegrowth20-40
31248positiveoptimum28mesophilic
33986positivegrowth30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic
122380positivegrowth25-37mesophilic
122380nogrowth10psychrophilic
122380nogrowth41thermophilic
122380nogrowth45thermophilic

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31248aerobe
67771aerobe

spore formation

@refspore formationconfidence
31248yes
69480yes99.322

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

traitpredictionconfidencetraining_data
spore-formingyes74no
motileno93.801yes
gram-positiveyes88.284no
anaerobicno98.609yes
aerobicyes93.759yes
halophileyes82.495yes
spore-formingyes92.404yes
thermophileno96.706yes
glucose-utilyes89.355no
flagellatedno97.301yes
glucose-fermentno90.542no

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)
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