Strain identifier

BacDive ID: 13394

Type strain: Yes

Species: Pseudonocardia oroxyli

Strain Designation: D10

Strain history: Y. Huang D10.

NCBI tax ID(s): 366584 (species)

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General

@ref: 12142

BacDive-ID: 13394

DSM-Number: 44984

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

description: Pseudonocardia oroxyli D10 is a spore-forming, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from surface-sterilized root of Oroxylum indicum.

NCBI tax id

  • NCBI tax id: 366584
  • Matching level: species

strain history

@refhistory
12142<- Y. Huang, CGMCC <- Q. Gu; D10
67770Y. Huang D10.

doi: 10.13145/bacdive13394.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Pseudonocardia
  • species: Pseudonocardia oroxyli
  • full scientific name: Pseudonocardia oroxyli Gu et al. 2006

@ref: 12142

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Pseudonocardia

species: Pseudonocardia oroxyli

full scientific name: Pseudonocardia oroxyli Gu et al. 2006 emend. Nouioui et al. 2018

strain designation: D10

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: positive
  • confidence: 100

colony morphology

@refcolony colorincubation periodmedium used
19898Saffron yellow10-14 daysISP 2
19898Beige10-14 daysISP 3
19898Beige10-14 daysISP 4
19898Beige10-14 daysISP 5
19898Beige10-14 daysISP 6
19898Beige10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
19898yesAerial MyceliumPure whiteISP 2
19898yesAerial MyceliumPure whiteISP 3
19898yesAerial MyceliumPure whiteISP 4
19898noISP 5
19898yesAerial MyceliumPure whiteISP 6
19898yesAerial MyceliumPure whiteISP 7

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12142GYM 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
12142TRYPTICASE 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
19898ISP 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
19898ISP 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:
19898ISP 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
19898ISP 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
19898ISP 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
19898ISP 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

culture temp

@refgrowthtypetemperaturerange
12142positivegrowth28mesophilic
19898positiveoptimum28mesophilic
67770positivegrowth28mesophilic

Physiology and metabolism

spore formation

  • @ref: 69481
  • spore formation: yes
  • confidence: 91

observation

  • @ref: 67770
  • observation: quinones: MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activity
1989817234glucose+
1989822599arabinose-
1989817992sucrose+
1989818222xylose-
1989817268myo-inositol+
1989829864mannitol+
1989828757fructose+
1989826546rhamnose+
1989816634raffinose+
1989862968cellulose+

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
19898+++++++--++---++---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
12142surface-sterilized root of Oroxylum indicumOroxylum indicumYunnan Province, Liushahe riverChinaCHNAsia
67770Surface-sterilized root of Oroxylum indicum in the rainforest around the Liusha RiverOroxylum indicumsouth-west of Jinghong City, Yunnan ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_16013.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_2672;97_3280;98_12070;99_16013&stattab=map
  • Last taxonomy: Pseudonocardia
  • 16S sequence: DQ343154
  • Sequence Identity:
  • Total samples: 206
  • soil counts: 82
  • aquatic counts: 24
  • animal counts: 69
  • plant counts: 31

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121421Risk group (German classification)
198981Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12142
  • description: Pseudonocardia oroxyli strain D10 16S ribosomal RNA gene, partial sequence
  • accession: DQ343154
  • length: 1413
  • database: ena
  • NCBI tax ID: 366584

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudonocardia oroxyli strain CGMCC 4.3143366584.5wgspatric366584
66792Pseudonocardia oroxyli CGMCC 4.31432667527404draftimg366584
67770Pseudonocardia oroxyli CGMCC 4.3143GCA_900102195scaffoldncbi366584

GC content

@refGC-contentmethod
1214270.6
6777073genome sequence analysis
6777070.6thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes91no
gram-positiveyes88.355no
anaerobicno99.104no
halophileno93.05no
spore-formingyes64.029no
glucose-utilyes88.874yes
aerobicyes95.188no
motileno92.397no
flagellatedno98.601no
thermophileno99.391yes
glucose-fermentno92.189no

External links

@ref: 12142

culture collection no.: DSM 44984, CGMCC 4.3143, JCM 13909

straininfo link

  • @ref: 82591
  • straininfo: 297297

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16957120Pseudonocardia oroxyli sp. nov., a novel actinomycete isolated from surface-sterilized Oroxylum indicum root.Gu Q, Luo H, Zheng W, Liu Z, Huang YInt J Syst Evol Microbiol10.1099/ijs.0.64385-02006Actinomycetales/classification/genetics/*isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Molecular Sequence Data, RNA, Ribosomal, 16S/*analysis/geneticsGenetics
Phylogeny18768609Pseudonocardia ailaonensis sp. nov., isolated from soil in China.Qin S, Su YY, Zhang YQ, Wang HB, Jiang CL, Xu LH, Li WJInt J Syst Evol Microbiol10.1099/ijs.0.65721-02008Actinomycetales/*classification/genetics/*isolation & purification/physiology, Aerobiosis, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pigments, Biological/biosynthesis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny33890128Pseudonocardia pini sp. nov., an endophytic actinobacterium isolated from roots of the pine tree Callitris preissii.Kaewkla O, Franco CMMArch Microbiol10.1007/s00203-021-02309-32021*Cupressaceae/microbiology, Fatty Acids/analysis, Nucleic Acid Hybridization, Phylogeny, *Plant Roots/microbiology, *Pseudonocardia/classification/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species SpecificityTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
12142Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44984)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44984
19898Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44984.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
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 updatesNucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
82591Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297297.1StrainInfo: A central database for resolving microbial strain identifiers