Strain identifier

BacDive ID: 11128

Type strain: Yes

Species: Nocardioides maradonensis

Strain Designation: RP-B30

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 598611 (species)

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General

@ref: 8306

BacDive-ID: 11128

DSM-Number: 19769

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

description: Nocardioides maradonensis RP-B30 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from rhizosphere soil of Peucedanum japonicum Thunb..

NCBI tax id

  • NCBI tax id: 598611
  • Matching level: species

strain history

@refhistory
8306<- S. D. Lee, Jeju National Univ., Rep. of Korea; RP-B30
67770DSM 19769 <-- S. D. Lee; Jeju Natl. Univ., South Korea; RP-B30.
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive11128.20230509.8.1

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 maradonensis
  • full scientific name: Nocardioides maradonensis Lee et al. 2011

@ref: 8306

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardioidaceae

genus: Nocardioides

species: Nocardioides maradonensis

full scientific name: Nocardioides maradonensis Lee et al. 2011

strain designation: RP-B30

type strain: yes

Morphology

cell morphology

  • @ref: 67771
  • gram stain: positive

colony morphology

@refcolony colormedium used
69219Dahlia yellow (1033)suter without tyrosine
69219Ivory (1014)ISP 2
69219Light ivory (1015)ISP 5
69219Light ivory (1015)suter with tyrosine
69219Oyster white (1013)ISP 4
69219Oyster white (1013)ISP 7

multicellular morphology

@refforms multicellular complexcomplex namemedium name
69219noAerial myceliumISP 2
69219noAerial myceliumISP 3
69219noAerial myceliumISP 4
69219noAerial myceliumISP 5
69219noAerial myceliumISP 6
69219noAerial myceliumISP 7
69219noAerial myceliumsuter with tyrosine
69219noAerial myceliumsuter without tyrosine

pigmentation

@refproductionname
69219noMelanin
69219nosoluble pigment

multimedia

@refmultimedia contentcaptionintellectual property rights
69219DSM_19769_image3.jpegPlates (GYM, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH
69219DSM_19769_image4.jpegPlates (GYM, ISP2, ISP3, ISP4, ISP5, ISP7)Helmholtz-Zentrum für Infektionsforschung GmbH

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8306GYM 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
8306R2A 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

culture temp

@refgrowthtypetemperaturerange
8306positivegrowth28mesophilic
67770positivegrowth28mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

  • @ref: 69219
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6921922599arabinose-growth
6921962968cellulose-growth
6921928757fructose+growth
6921917234glucose+growth
6921917268inositol-growth
6921937684mannose-growth
6921916634raffinose-growth
6921926546rhamnose-growth
6921917992sucrose+growth
6921918222xylose-growth
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
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 lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382trypsin-3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase+3.2.1.20
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
69219------+------------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
69219-+/-+-++/-+/---+/-+/----++/----

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
8306rhizosphere soil of Peucedanum japonicum Thunb.Peucedanum japonicumJeju, Mara IslandRepublic of KoreaKORAsia
67770Rhizosphere soil of a cliff-associated plant (_n(Peucedanum japonicum) Thunb.) on Mara IslandJejuRepublic of KoreaKORAsia
67771From rhizosphere of plantMara island, JejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_9638.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_142;96_4676;97_5668;98_7122;99_9638&stattab=map
  • Last taxonomy: Nocardioides maradonensis
  • 16S sequence: FM998000
  • Sequence Identity:
  • Total samples: 37
  • soil counts: 14
  • aquatic counts: 1
  • animal counts: 9
  • plant counts: 13

Safety information

risk assessment

  • @ref: 8306
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8306
  • description: Nocardioides sp. RP-B30 partial 16S rRNA gene, strain RP-B30
  • accession: FM998000
  • length: 1399
  • database: ena
  • NCBI tax ID: 598611

GC content

  • @ref: 8306
  • GC-content: 71.7
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 8306

culture collection no.: DSM 19769, JCM 31980, KCTC 19384

straininfo link

  • @ref: 80377
  • straininfo: 408096

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20833879Nocardioides ultimimeridianus sp. nov. and Nocardioides maradonensis sp. nov., isolated from rhizosphere soil.Lee DW, Lee SY, Yoon JH, Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.022715-02010Actinomycetales/*classification/genetics/*isolation & purification/metabolism, Apiaceae/*microbiology, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, *Rhizosphere, *Soil MicrobiologyMetabolism
Phylogeny25249564Nocardioides daecheongensis sp. nov., isolated from soil.Lim JM, Kim SJ, Hamada M, Ahn JH, Weon HY, Suzuki KI, Ahn TY, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.063610-02014Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Forests, Molecular Sequence Data, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics
Phylogeny28875902Nocardioides agrisoli sp. nov., isolated from farmland soil.Wang X, Jiang WK, Cui MD, Yang ZG, Yu X, Hu G, Zhang H, Hong QInt J Syst Evol Microbiol10.1099/ijsem.0.0021582017Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Nucleic Acid Hybridization, Peptidoglycan/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
8306Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19769)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19769
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
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
69219Wink, J.https://cdn.dsmz.de/wink/DSM%2019769.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
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
80377Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408096.1StrainInfo: A central database for resolving microbial strain identifiers