Strain identifier

BacDive ID: 11221

Type strain: Yes

Species: Nocardiopsis rhodophaea

Strain history: <- WJ Li, Yunnan Univ.

NCBI tax ID(s): 280238 (species)

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General

@ref: 12024

BacDive-ID: 11221

DSM-Number: 44843

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

description: Nocardiopsis rhodophaea DSM 44843 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from hypersaline soil.

NCBI tax id

  • NCBI tax id: 280238
  • Matching level: species

strain history

@refhistory
12024<- W.-J. Li, YIM
67770KCTC 19049 <-- W.-J. Li YIM 90096.
67771<- WJ Li, Yunnan Univ.

doi: 10.13145/bacdive11221.20240510.9

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

@ref: 12024

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis rhodophaea

full scientific name: Nocardiopsis rhodophaea Li et al. 2006

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
31676positiverod-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
20131Rapeseed yellow (1021)10-14 daysISP 2
20131Zinc yellow (1018)10-14 daysISP 3
20131Cream (9001)10-14 daysISP 4
20131Cream (9001)10-14 daysISP 5
20131Pastel orange (2003)10-14 daysISP 6
20131Cream (9001)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20131noISP 2
20131noISP 3
20131noISP 4
20131noISP 5
20131noISP 6
20131noISP 7

pigmentation

  • @ref: 31676
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12024TCG 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
12024GPHF-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
20131ISP 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
20131ISP 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:
20131ISP 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
20131ISP 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
20131ISP 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
20131ISP 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
12024TRYPTICASE 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

culture temp

@refgrowthtypetemperature
12024positivegrowth28
20131positiveoptimum28
31676positivegrowth20-60
31676positiveoptimum37-40
67770positivegrowth28
67771positivegrowth37

culture pH

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

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31676aerobe
67771aerobe

spore formation

  • @ref: 31676
  • spore formation: yes

halophily

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

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3167622599arabinose+carbon source
3167617234glucose+carbon source
3167617754glycerol+carbon source
3167633942ribose+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
20131++--+----++---+-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12024hypersaline soilXin Jiang ProvinceChinaCHNAsia
67770Saline soilChinaCHNAsia
67771hypersaline soils in Xinjiang provinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_24631.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_2754;97_14972;98_18527;99_24631&stattab=map
  • Last taxonomy: Nocardiopsis rhodophaea subclade
  • 16S sequence: AY619714
  • Sequence Identity:
  • Total samples: 2
  • soil counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120241Risk group (German classification)
201311German classification

Sequence information

16S sequences

  • @ref: 12024
  • description: Nocardiopsis rhodophaea 16S ribosomal RNA gene, partial sequence
  • accession: AY619714
  • length: 1490
  • database: nuccore
  • NCBI tax ID: 280238

GC content

@refGC-contentmethod
1202469.0
3167669
6777069thermal denaturation, midpoint method (Tm)
6777169.0thermal denaturation, midpoint method (Tm)

External links

@ref: 12024

culture collection no.: DSM 44843, CCTCC AA 2040014, CIP 109295, KCTC 19049, YIM 90096, JCM 15313

straininfo link

  • @ref: 80464
  • straininfo: 134263

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
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

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12024Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44843)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44843
20131Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44843.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
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
80464Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID134263.1StrainInfo: A central database for resolving microbial strain identifiers