Strain identifier

BacDive ID: 11147

Type strain: Yes

Species: Nocardioides panacisoli

Strain history: <- ST Lee, KAIST

NCBI tax ID(s): 627624 (species)

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General

@ref: 15633

BacDive-ID: 11147

DSM-Number: 21348

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

description: Nocardioides panacisoli DSM 21348 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from soil of a ginseng field.

NCBI tax id

  • NCBI tax id: 627624
  • Matching level: species

strain history

@refhistory
67770KCTC 19470 <-- C. H. Cho et al. Gsoil 346.
67771<- ST Lee, KAIST

doi: 10.13145/bacdive11147.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Propionibacteriales
  • family: Nocardioidaceae
  • genus: Nocardioides
  • species: Nocardioides panacisoli
  • full scientific name: Nocardioides panacisoli Cho et al. 2010

@ref: 15633

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides panacisoli

full scientific name: Nocardioides panacisoli Cho et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29416positive1 µm0.3 µmrod-shapedno
67771positive

colony morphology

@refcolony colorincubation periodmedium used
21353Sand yellow (1002)10-14 daysISP 2
21353Pearl white (1013)10-14 daysISP 3
21353Light ivory (1015) - ochre brown (8001)10-14 daysISP 4
21353Light ivory (1015)10-14 daysISP 5
21353Ivory (1014)10-14 daysISP 7
21353Sand yellow (1002)10-14 dayssuter with tyrosine
21353Ivory (1014)10-14 dayssuter without tyrosine

multicellular morphology

@refforms multicellular complexmedium name
21353noISP 2
21353noISP 3
21353noISP 4
21353noISP 5
21353noISP 7
21353noSuter with tyrosine
21353noSuter without tyrosine

pigmentation

  • @ref: 29416
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15633R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
21353ISP 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
21353ISP 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:
21353ISP 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
21353ISP 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
21353ISP 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
21353suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21353suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
15633positivegrowth28mesophilic
29416positivegrowth10-42
29416positiveoptimum27.5mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29416positivegrowth5.5-8.5alkaliphile
29416positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29416aerobe
67771aerobe

spore formation

  • @ref: 29416
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
21353NaClpositivemaximum5 %
29416NaClpositivegrowth0-2 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2135317234glucose+
2135322599arabinose+
2135317992sucrose+
2135318222xylose-
2135317268myo-inositol-
2135337684mannose+
2135328757fructose+
2135326546rhamnose-
2135316634raffinose-
2135362968cellulose-
29416370543-hydroxybutyrate+carbon source
2941630089acetate+carbon source
2941617128adipate+carbon source
2941616947citrate+carbon source
2941624265gluconate+carbon source
2941617234glucose+carbon source
2941625115malate+carbon source
2941617306maltose+carbon source
2941626271proline+carbon source
2941617272propionate+carbon source
2941617992sucrose+carbon source
2941631011valerate+carbon source
2941617632nitrate+reduction
6837917632nitrate+reduction
683794853esculin+hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose+fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837917306maltose+fermentation
6837917716lactose-fermentation
6837917992sucrose+fermentation
6837928087glycogen+fermentation

metabolite production

  • @ref: 29416
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
29416catalase+1.11.1.6
29416cytochrome oxidase+1.9.3.1
68379gelatinase+
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
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382cystine arylamidase-3.4.11.3
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
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
21353++/-++-+++++/-++--+/-+-++

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
21353+++-++/--+/-+/-+++/-+-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
15633soil of a ginseng fieldPocheon province (37° 58' N 127°15' E)Republic of KoreaKORAsia37.9667127.25
67770Soil of a ginseng fieldPocheon ProvinceRepublic of KoreaKORAsia
67771From soil of ginseng fieldRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)

taxonmaps

  • @ref: 69479
  • File name: preview.99_182993.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_7914;97_9517;98_11686;99_182993&stattab=map
  • Last taxonomy: Nocardioides panacisoli subclade
  • 16S sequence: FJ666101
  • Sequence Identity:
  • Total samples: 239
  • soil counts: 221
  • aquatic counts: 7
  • animal counts: 10
  • plant counts: 1

Safety information

risk assessment

  • @ref: 15633
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15633
  • description: Nocardioides panacisoli strain GSoil 346 16S ribosomal RNA gene, partial sequence
  • accession: FJ666101
  • length: 1449
  • database: ena
  • NCBI tax ID: 627624

GC content

@refGC-contentmethod
1563373.0high performance liquid chromatography (HPLC)
2941673
6777073high performance liquid chromatography (HPLC)

External links

@ref: 15633

culture collection no.: DSM 21348, KCTC 19470, Gsoil 346, JCM 16953

straininfo link

  • @ref: 80396
  • straininfo: 397406

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19651712Nocardioides panacisoli sp. nov., isolated from the soil of a ginseng field.Cho CH, Lee JS, An DS, Whon TW, Kim SGInt J Syst Evol Microbiol10.1099/ijs.0.012690-02009Actinomycetales/*classification/genetics/physiology, Base Composition, Base Sequence, DNA, Bacterial/chemistry, Molecular Sequence Data, Panax/*microbiology, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Homology, Nucleic Acid, *Soil MicrobiologyGenetics
Phylogeny29022545Nocardioides litorisoli sp. nov., isolated from lakeside soil.Wang Y, Xu D, Luo A, Wang G, Zheng SInt J Syst Evol Microbiol10.1099/ijsem.0.0022832017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Lakes/*microbiology, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29683418Nocardioides pelophilus sp. nov., isolated from freshwater mud.Yan ZF, Lin P, Li CT, Kook M, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0027762018Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Fresh Water, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15633Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21348)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21348
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
21353Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM21348.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29416Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2582328776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
80396Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397406.1StrainInfo: A central database for resolving microbial strain identifiers