Strain identifier

BacDive ID: 11232

Type strain: Yes

Species: Nocardiopsis quinghaiensis

Strain history: <- X. Cui, Yunnan Univ., Kunming; YIM 28A4

NCBI tax ID(s): 464995 (species)

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General

@ref: 12053

BacDive-ID: 11232

DSM-Number: 44739

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

description: Nocardiopsis quinghaiensis DSM 44739 is an aerobe, spore-forming, mesophilic bacterium that was isolated from alkaline soil samples.

NCBI tax id

  • NCBI tax id: 464995
  • Matching level: species

strain history

  • @ref: 12053
  • history: <- X. Cui, Yunnan Univ., Kunming; YIM 28A4

doi: 10.13145/bacdive11232.20230509.8.1

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 quinghaiensis
  • full scientific name: Nocardiopsis quinghaiensis Chen et al. 2008

@ref: 12053

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis quinghaiensis

full scientific name: Nocardiopsis quinghaiensis Chen et al. 2008

type strain: yes

Morphology

cell morphology

  • @ref: 32404
  • gram stain: positive
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20108Beige (1001)10-14 daysISP 2
2010810-14 daysISP 3
20108Beige (1001)10-14 daysISP 4
2010810-14 daysISP 5
2010810-14 daysISP 6
2010810-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20108noISP 2
20108noISP 3
20108noISP 4
20108noISP 5
20108noISP 6
20108noISP 7

pigmentation

  • @ref: 32404
  • production: no

multimedia

  • @ref: 12053
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44739.jpg
  • caption: Medium 514 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12053BACTO 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
20108ISP 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
20108ISP 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:
20108ISP 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
20108ISP 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
20108ISP 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
20108ISP 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
12053CZAPEK PEPTONE AGAR (DSMZ Medium 83)yeshttps://mediadive.dsmz.de/medium/83Name: CZAPEK PEPTONE AGAR (DSMZ Medium 83) Composition: Sucrose 30.0 g/l Agar 20.0 g/l Peptone 5.0 g/l NaNO3 3.0 g/l Yeast extract 2.0 g/l K2HPO4 1.0 g/l MgSO4 x 7 H2O 0.5 g/l KCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
12053positivegrowth28mesophilic
20108positiveoptimum28mesophilic
32404positivegrowth10-37
32404positiveoptimum28mesophilic

culture pH

@refabilitytypepH
32404positivegrowth06-08
32404positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 32404
  • oxygen tolerance: aerobe

spore formation

  • @ref: 32404
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
32404NaClpositivegrowth0-10 %
32404NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3240422599arabinose+carbon source
3240417057cellobiose+carbon source
3240416947citrate+carbon source
3240428757fructose+carbon source
3240417234glucose+carbon source
3240417754glycerol+carbon source
3240429864mannitol+carbon source
3240437684mannose+carbon source
3240417268myo-inositol+carbon source
3240416634raffinose+carbon source
3240433942ribose+carbon source
3240417992sucrose+carbon source
3240427082trehalose+carbon source
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
32404catalase+1.11.1.6
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
20108+--------+-+---+-+-

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20108+++------+----+----

Isolation, sampling and environmental information

isolation

  • @ref: 12053
  • sample type: alkaline soil samples
  • geographic location: Qaidam Basin
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Alkaline

taxonmaps

  • @ref: 69479
  • File name: preview.99_4414.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_3317;99_4414&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: EF597511
  • Sequence Identity:
  • Total samples: 22
  • soil counts: 7
  • animal counts: 14
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120531Risk group (German classification)
201081German classification

Sequence information

16S sequences

  • @ref: 12053
  • description: Nocardiopsis quinghaiensis strain YIM 28A4 16S ribosomal RNA gene, partial sequence
  • accession: EF597511
  • length: 1384
  • database: ena
  • NCBI tax ID: 464995

GC content

  • @ref: 12053
  • GC-content: 67.1

External links

@ref: 12053

culture collection no.: DSM 44739, CGMCC 4.3494, YIM 28A4

straininfo link

  • @ref: 80467
  • straininfo: 389430

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18319481Nocardiopsis quinghaiensis sp. nov., isolated from saline soil in China.Chen YG, Cui XL, Kroppenstedt RM, Stackebrandt E, Wen ML, Xu LH, Jiang CLInt J Syst Evol Microbiol10.1099/ijs.0.65441-02008Actinomycetales/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, Soil/*analysis, *Soil Microbiology, Species SpecificityGenetics
Phylogeny20562242Nocardiopsis arvandica sp. nov., isolated from sandy soil.Hamedi J, Mohammadipanah F, Potter G, Sproer C, Schumann P, Goker M, Klenk HPInt J Syst Evol Microbiol10.1099/ijs.0.022756-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12053Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44739)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44739
20108Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44739.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
32404Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2862828776041
68379Automatically annotated from API Coryne
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
80467Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389430.1StrainInfo: A central database for resolving microbial strain identifiers