Strain identifier

BacDive ID: 11218

Type strain: Yes

Species: Nocardiopsis gilva

Strain history: CIP <- 2006, DSMZ <- W.J. Li, YIM

NCBI tax ID(s): 1235441 (strain), 280236 (species)

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General

@ref: 12022

BacDive-ID: 11218

DSM-Number: 44841

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

description: Nocardiopsis gilva DSM 44841 is an aerobe, spore-forming, mesophilic bacterium that was isolated from hypersaline soil.

NCBI tax id

NCBI tax idMatching level
1235441strain
280236species

strain history

@refhistory
12022<- W.-J. Li, YIM
67770KCTC 19006 <-- W.-J. Li YIM 90087.
67771<- WJ Li, Yunnan Univ.
119618CIP <- 2006, DSMZ <- W.J. Li, YIM

doi: 10.13145/bacdive11218.20230509.8.1

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 gilva
  • full scientific name: Nocardiopsis gilva Li et al. 2006

@ref: 12022

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis gilva

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

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31676positiverod-shapedno
67771positive
69480no94.256
69480positive100
119618positiverod-shapedno

colony morphology

@refcolony colorincubation periodmedium used
20130Zinc yellow (1018)10-14 daysISP 2
20130Zinc yellow (1018)10-14 daysISP 3
20130Zinc yellow (1018)10-14 daysISP 4
20130Zinc yellow (1018)10-14 daysISP 5
20130Zinc yellow (1018)10-14 daysISP 6
20130Zinc yellow (1018)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20130noISP 2
20130noISP 3
20130noISP 4
20130noISP 5
20130noISP 6
20130noISP 7

pigmentation

  • @ref: 31676
  • production: yes

multimedia

  • @ref: 12022
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44841.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12022TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)yeshttps://mediadive.dsmz.de/medium/535Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
20130ISP 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
20130ISP 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:
20130ISP 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
20130ISP 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
20130ISP 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
20130ISP 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
12022GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
12022TCG MEDIUM (DSMZ Medium 1009)yeshttps://mediadive.dsmz.de/medium/1009Name: TCG MEDIUM (DSMZ Medium 1009) Composition: Casitone 5.0 g/l Glucose 4.0 g/l Tryptone 3.0 g/l Sea water
119618CIP Medium 57yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=57

culture temp

@refgrowthtypetemperaturerange
12022positivegrowth28mesophilic
20130positiveoptimum28mesophilic
31676positivegrowth10-40
31676positiveoptimum28-30mesophilic
67770positivegrowth28mesophilic
67771positivegrowth28mesophilic

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31676aerobe
67771aerobe

spore formation

@refspore formationconfidence
31676yes
69481yes100
69480yes100

halophily

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

observation

@refobservation
31676aggregates in chains
67770quinones: MK-11(H4), MK-11(H6), MK-11(H8)
67771quinones: MK-11(H4), MK-11(H6), MK-11(H8)

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
3167617716lactose+carbon source
3167629864mannitol+carbon source
3167616634raffinose+carbon source
3167630911sorbitol+carbon source
3167617992sucrose+carbon source
3167618222xylose+carbon source
3167617632nitrate+reduction

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
20130+++-++----+---+----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12022hypersaline soilXin Jiang ProvinceChinaCHNAsia
67770Saline soilChinaCHNAsia
67771hypersaline soil in Xinjiang provinceChinaCHNAsia
119618Environment, Hypersaline soilChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120221Risk group (German classification)
201301German classification
1196181Risk group (French classification)

Sequence information

16S sequences

  • @ref: 12022
  • description: Nocardiopsis gilva 16S ribosomal RNA gene, partial sequence
  • accession: AY619712
  • length: 1486
  • database: ena
  • NCBI tax ID: 1235441

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis gilva YIM 90087GCA_002263495completencbi1235441
66792Nocardiopsis gilva YIM 900871235441.3wgspatric1235441
66792Nocardiopsis gilva YIM 900871235441.5completepatric1235441
66792Nocardiopsis gilva YIM 900872773857897completeimg1235441
66792Nocardiopsis gilva YIM 900872554235033draftimg1235441
67770Nocardiopsis gilva YIM 90087GCA_000341165contigncbi1235441

GC content

@refGC-contentmethod
1202268.1
6777069.7genome sequence analysis
6777068.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
flagellatedno98.126yes
gram-positiveyes90.85yes
anaerobicno99.052yes
aerobicyes90.958yes
halophileno60.226no
spore-formingyes90.726no
glucose-utilyes89.913yes
thermophileno97.28yes
motileno91.939yes
glucose-fermentno93.806no

External links

@ref: 12022

culture collection no.: DSM 44841, CCTCC AA 2040012, CIP 109294, KCTC 19006, NBRC 104397, YIM 90087, JCM 15312

straininfo link

  • @ref: 80461
  • straininfo: 134261

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
Pathogenicity23441911Isolation and characterization of new p-Terphenyls with antifungal, antibacterial, and antioxidant activities from halophilic actinomycete Nocardiopsis gilva YIM 90087.Tian SZ, Pu X, Luo G, Zhao LX, Xu LH, Li WJ, Luo YJ Agric Food Chem10.1021/jf400718w2013Actinomycetales/*chemistry, Anti-Bacterial Agents/*pharmacology, Antifungal Agents/*pharmacology, Antioxidants/*pharmacology, Bacillus subtilis/drug effects, Candida albicans/drug effects, Fusarium/drug effects, Molecular Structure, Novobiocin/chemistry/isolation & purification/pharmacology, Staphylococcus aureus/drug effects, Terphenyl Compounds/chemistry/*isolation & purification/*pharmacologyPhylogeny
Phylogeny27565851Nocardiopsis akesuensis sp. nov., an actinomycete isolated from a salt water beach.Gao GB, Luo XX, Xia ZF, Zhang Y, Wan CX, Zhang LLInt J Syst Evol Microbiol10.1099/ijsem.0.0014602016Actinobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/chemistryTranscriptome
Stress29651284Transcriptomic and Ectoine Analysis of Halotolerant Nocardiopsis gilva YIM 90087(T) Under Salt Stress.Han J, Gao QX, Zhang YG, Li L, Mohamad OAA, Rao MPN, Xiao M, Hozzein WN, Alkhalifah DHM, Tao Y, Li WJFront Microbiol10.3389/fmicb.2018.006182018

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12022Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44841)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44841
20130Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44841.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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68382Automatically annotated from API zym
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
80461Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134261.1StrainInfo: A central database for resolving microbial strain identifiers
119618Curators of the CIPCollection of Institut Pasteur (CIP 109294)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109294