Strain identifier

BacDive ID: 11047

Type strain: No

Species: Rhodococcus erythropolis

Strain Designation: djl-6-2

Strain history: DSM 45257 <-- Z. Wang djl-6-2.

NCBI tax ID(s): 334542 (species)

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General

@ref: 16010

BacDive-ID: 11047

DSM-Number: 45257

keywords: genome sequence, 16S sequence, aerobe, mesophilic, Gram-positive, ovoid-shaped

description: Rhodococcus erythropolis djl-6-2 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from sludge of a carbendazim wastewater treatment facility.

NCBI tax id

  • NCBI tax id: 334542
  • Matching level: species

strain history

@refhistory
16010<- Z. Wang; djl-6-2
67770DSM 45257 <-- Z. Wang djl-6-2.

doi: 10.13145/bacdive11047.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • genus: Rhodococcus
  • species: Rhodococcus erythropolis
  • full scientific name: Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 (Approved Lists 1980)

  • synonyms

    @refsynonym
    20215Mycobacterium erythropolis
    20215Rhodococcus qingshengii
    20215Rhodococcus baikonurensis
    20215Rhodococcus jialingiae
    20215Rhodococcus enclensis
    20215Rhodococcus degradans

@ref: 16010

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiaceae

genus: Rhodococcus

species: Rhodococcus qingshengii

full scientific name: Rhodococcus qingshengii Xu et al. 2007 emend. Nouioui et al. 2018

strain designation: djl-6-2

type strain: no

Morphology

cell morphology

  • @ref: 29442
  • gram stain: positive
  • cell shape: ovoid-shaped
  • motility: no

pigmentation

  • @ref: 29442
  • production: yes

multimedia

  • @ref: 16010
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45257.jpg
  • caption: Medium 535 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16010TRYPTICASE 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
16010GYM 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

culture temp

@refgrowthtypetemperaturerange
16010positivegrowth28mesophilic
29442positivegrowth04-35
67770positivegrowth28mesophilic

culture pH

  • @ref: 29442
  • ability: positive
  • type: growth
  • pH: 04-09
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 29442
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29442
  • spore formation: no

halophily

  • @ref: 29442
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <7 %

observation

  • @ref: 67770
  • observation: quinones: MK-8(H2)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2944218403L-arabitol+carbon source
2944228757fructose+carbon source
2944229864mannitol+carbon source
2944217268myo-inositol+carbon source
6836925115malate+assimilation
6836917128adipate+assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
683695291gelatin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
29442catalase+1.11.1.6
29442urease+3.5.1.5
68369gelatinase-
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
16010-++/-+/-+/-+++/---++---++---

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPAC
16010----++/--++/-+/-+/-+++/-+-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16010sludge of a carbendazim wastewater treatment facilityJiangsu Province, NanjingChinaCHNAsia
67770Sludge of a carbendazim wastewater treatment facilityJiangsu ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Waste#Water treatment plant
#Environmental#Terrestrial#Mud (Sludge)

taxonmaps

  • @ref: 69479
  • File name: preview.99_1118.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_181;97_585;98_672;99_1118&stattab=map
  • Last taxonomy: Nocardiaceae
  • 16S sequence: DQ185597
  • Sequence Identity:
  • Total samples: 28787
  • soil counts: 7777
  • aquatic counts: 6494
  • animal counts: 11681
  • plant counts: 2835

Safety information

risk assessment

  • @ref: 16010
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16010
  • description: Rhodococcus jialingiae strain djl-6-2 16S ribosomal RNA gene, partial sequence
  • accession: DQ185597
  • length: 1489
  • database: ena
  • NCBI tax ID: 334542

Genome sequences

  • @ref: 67770
  • description: Rhodococcus qingshengii djl-6-2
  • accession: GCA_002893965
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 334542

GC content

@refGC-contentmethod
1601060.1thermal denaturation, midpoint method (Tm)
2944260.1

External links

@ref: 16010

culture collection no.: DSM 45257, CCTCC AB 208292, JCM 16906, CCM 8452

literature

  • topic: Metabolism
  • Pubmed-ID: 20833408
  • title: Biodegradation of carbendazim by a novel actinobacterium Rhodococcus jialingiae djl-6-2.
  • authors: Wang Z, Wang Y, Gong F, Zhang J, Hong Q, Li S
  • journal: Chemosphere
  • DOI: 10.1016/j.chemosphere.2010.08.040
  • year: 2010
  • mesh: Benzimidazoles/chemistry/*metabolism, Biodegradation, Environmental, Carbamates/chemistry/*metabolism, Fungicides, Industrial/chemistry/*metabolism, Rhodococcus/*metabolism, Soil Pollutants/chemistry/*metabolism
  • topic2: Biotechnology

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16010Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45257)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45257
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
29442Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2584828776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
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