Strain identifier

BacDive ID: 11220

Type strain: No

Species: Nocardiopsis halophila

Strain history: CIP <- 2006, DSMZ <- YIM

NCBI tax ID(s): 280240 (species)

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General

@ref: 12026

BacDive-ID: 11220

DSM-Number: 44845

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

description: Nocardiopsis halophila DSM 44845 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from hypersaline soil.

NCBI tax id

  • NCBI tax id: 280240
  • Matching level: species

strain history

@refhistory
12026<- W.-J. Li, YIM
67770KCTC 19009 <-- W.-J. Li YIM 90130.
67771<- WJ Li, Yunnan Univ.
116710CIP <- 2006, DSMZ <- YIM

doi: 10.13145/bacdive11220.20240916.9.1

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 halophila
  • full scientific name: Nocardiopsis halophila Al-Tai and Ruan 1994

  • synonyms

    • @ref: 20215
    • synonym: Nocardiopsis baichengensis

@ref: 12026

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis halophila

full scientific name: Nocardiopsis halophila Al-Tai and Ruan 1994 emend. Nouioui et al. 2018

type strain: no

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31676positiverod-shapedno
67771positive
116710positiverod-shapedyes
69480no91.5

colony morphology

@refcolony colorincubation periodmedium used
19881Beige10-14 daysISP 2
19881Beige10-14 daysISP 3
19881Beige10-14 daysISP 4
19881Beige10-14 daysISP 5
19881Beige10-14 daysISP 6
19881Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19881noISP 2
19881noISP 3
19881noISP 4
19881noISP 5
19881noISP 6
19881noISP 7

pigmentation

  • @ref: 31676
  • production: yes

multimedia

  • @ref: 12026
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44845.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12026GYM 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
12026GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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 water
19881ISP 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
19881ISP 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:
19881ISP 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
19881ISP 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
19881ISP 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
19881ISP 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
116710CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
19881positiveoptimum28
12026positivegrowth28
31676positivegrowth20-50
31676positiveoptimum37-40
67770positivegrowth28
67771positivegrowth37

culture pH

@refabilitytypepHPH range
31676positivegrowth06-09alkaliphile
31676positiveoptimum7.2

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31676aerobe
67771aerobe
69480aerobe93.641

spore formation

@refspore formationconfidence
31676yes
69481yes100

halophily

@refsaltgrowthtested relationconcentration
31676NaClpositivegrowth0-18 %
31676NaClpositiveoptimum05-08 %

observation

@refobservation
31676aggregates in chains
67770quinones: MK-10(H2), MK-10(H4), MK-10(H6)
67771quinones: MK-10(H2), MK-10(H4), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3167622599arabinose+carbon source
3167617057cellobiose+carbon source
3167628757fructose+carbon source
3167628260galactose+carbon source
3167617234glucose+carbon source
3167617754glycerol+carbon source
3167617306maltose+carbon source
3167629864mannitol+carbon source
3167637684mannose+carbon source
3167626546rhamnose+carbon source
3167633942ribose+carbon source
3167617992sucrose+carbon source

enzymes

@refvalueactivityec
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

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
19881+++-++--+++++-++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12026hypersaline soilXin Jiang ProvinceChinaCHNAsia
67770Saline soilChinaCHNAsia
67771hypersaline soils in Xinjiang provinceChinaCHNAsia
116710Environment, Hypersaline soilChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_5741.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_2754;97_3390;98_4275;99_5741&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: AY619716
  • Sequence Identity:
  • Total samples: 59
  • soil counts: 28
  • aquatic counts: 3
  • animal counts: 25
  • plant counts: 3

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120261Risk group (German classification)
198811Risk group (German classification)
1167101Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12026
  • description: Nocardiopsis baichengensis 16S ribosomal RNA gene, partial sequence
  • accession: AY619716
  • length: 1487
  • database: nuccore
  • NCBI tax ID: 280240

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis baichengensis YIM 901301236902.3wgspatric1236902
66792Nocardiopsis baichengensis YIM 901302551306672draftimg1236902
67770Nocardiopsis baichengensis YIM 90130GCA_000341205contigncbi1236902

GC content

@refGC-contentmethod
1202673.2
6777073.6genome sequence analysis
6777173.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesyes100no
69480gram-positivegram-positivePositive reaction to Gram-stainingyes89.836yes
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no97.136yes
69480spore-formingspore-formingAbility to form endo- or exosporesyes84.568yes
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)yes93.641yes
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno94.25yes
69480flagellatedmotile2+Ability to perform flagellated movementno91.5yes

External links

@ref: 12026

culture collection no.: DSM 44845, CCTCC AA 2040016, CIP 109298, KCTC 19009, NBRC 104399, YIM 90130, JCM 15310

straininfo link

  • @ref: 80463
  • straininfo: 134265

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16627660Five novel species of the genus Nocardiopsis isolated from hypersaline soils and emended description of Nocardiopsis salina Li et al. 2004.Li WJ, Kroppenstedt RM, Wang D, Tang SK, Lee JC, Park DJ, Kim CJ, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.64033-02006Actinomycetales/chemistry/*classification/cytology/genetics/*isolation & purification, Amino Acids/analysis, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Growth Inhibitors/pharmacology, Lipids/analysis/isolation & purification, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sodium Chloride/pharmacology, *Soil Microbiology, Vitamin K 2/analysis/isolation & purificationEnzymology
Phylogeny31535965Genome analysis reveals that Nocardiopsis baichengensis Li et al. 2006 is a later heterotypic synonym of Nocardiopsis halophila Al-Tai and Ruan 1994.Zhang XT, Salam N, Xiao M, Asem MD, Li WJInt J Syst Evol Microbiol10.1099/ijsem.0.0037212020Actinobacteria/*classification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Genes, Bacterial, Nocardiopsis, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12026Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44845)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44845
19881Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44845.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
31676Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2795428776041
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
80463Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134265.1StrainInfo: A central database for resolving microbial strain identifiers
116710Curators of the CIPCollection of Institut Pasteur (CIP 109298)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109298