Strain identifier

BacDive ID: 11046

Type strain: Yes

Species: Rhodococcus erythropolis

Strain Designation: djl-6

Strain history: CGMCC 1.6580 <-- J.-L. Xu et al. djl-6.

NCBI tax ID(s): 1303681 (strain), 334542 (species)

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General

@ref: 15685

BacDive-ID: 11046

DSM-Number: 45222

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

description: Rhodococcus erythropolis djl-6 is an aerobe, mesophilic, Gram-positive prokaryote that was isolated from carbendazim-contaminated soil sample from a vegetable field.

NCBI tax id

NCBI tax idMatching level
334542species
1303681strain

strain history

@refhistory
15685<- CGMCC; CGMCC 1.6580
67770CGMCC 1.6580 <-- J.-L. Xu et al. djl-6.

doi: 10.13145/bacdive11046.20230509.8.1

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: 15685

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

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
32188positiveovoid-shapedno
69480positive100

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15685GYM 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
15685TRYPTICASE 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

@refgrowthtypetemperaturerange
15685positivegrowth28mesophilic
32188positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

  • @ref: 32188
  • ability: positive
  • type: optimum
  • pH: 7.75

Physiology and metabolism

oxygen tolerance

  • @ref: 32188
  • oxygen tolerance: aerobe

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 99.999

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3218830089acetate+carbon source
3218821217L-alaninamide+carbon source
3218816449alanine+carbon source
32188286442-oxopentanoate+carbon source
3218823652dextrin+carbon source
3218828757fructose+carbon source
3218824265gluconate+carbon source
3218817234glucose+carbon source
3218817754glycerol+carbon source
3218825115malate+carbon source
3218837684mannose+carbon source
3218833942ribose+carbon source
3218817992sucrose+carbon source
3218853423tween 40+carbon source
3218853426tween 80+carbon source

enzymes

@refvalueactivityec
32188catalase+1.11.1.6
32188urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15685carbendazim-contaminated soil sample from a vegetable fieldJiangsu provinceChinaCHNAsia
67770Carbendazim-contaminated soil from a vegetable fieldJiangsu ProvinceChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Engineered#Contamination
#Environmental#Terrestrial#Soil

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: DQ090961
  • Sequence Identity:
  • Total samples: 28787
  • soil counts: 7777
  • aquatic counts: 6494
  • animal counts: 11681
  • plant counts: 2835

Safety information

risk assessment

  • @ref: 15685
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15685
  • description: Rhodococcus qingshengii strain djl-6 16S ribosomal RNA gene, partial sequence
  • accession: DQ090961
  • length: 1484
  • database: ena
  • NCBI tax ID: 1303681

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Rhodococcus qingshengii JCM 15477GCA_001313445contigncbi1303681
66792Rhodococcus qingshengii JCM 154771303681.3wgspatric1303681
66792Rhodococcus qingshengii strain JCM 15477334542.13wgspatric334542
66792Rhodococcus qingshengii JCM 154772744054616draftimg1303681
66792Rhodococcus qingshengii JCM 154772734481946draftimg1303681
67770Rhodococcus qingshengii JCM 15477GCA_001646745contigncbi334542
66792Rhodococcus qingshengii JCM 15477 djl-6GCA_023221595completencbi1303681

GC content

@refGC-contentmethod
1568559.1
6777062.4genome sequence analysis
6777059.1thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno67no
flagellatedno98.326no
gram-positiveyes83.006no
anaerobicno99.398no
aerobicyes91.829yes
halophileno92.741no
spore-formingno69.963no
motileno93.107yes
glucose-fermentno90.813no
thermophileno99.664no
glucose-utilyes90.613no

External links

@ref: 15685

culture collection no.: DSM 45222, CGMCC 1.6580, KCTC 19205, JCM 15477, CCM 8451

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Metabolism20833408Biodegradation of carbendazim by a novel actinobacterium Rhodococcus jialingiae djl-6-2.Wang Z, Wang Y, Gong F, Zhang J, Hong Q, Li SChemosphere10.1016/j.chemosphere.2010.08.0402010Benzimidazoles/chemistry/*metabolism, Biodegradation, Environmental, Carbamates/chemistry/*metabolism, Fungicides, Industrial/chemistry/*metabolism, Rhodococcus/*metabolism, Soil Pollutants/chemistry/*metabolismBiotechnology
33667802Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome.Chuang S, Yang H, Wang X, Xue C, Jiang J, Hong QJ Hazard Mater10.1016/j.jhazmat.2021.1254962021Benzimidazoles, Biodegradation, Environmental, Carbamates, *Microbiota, Rhodococcus, Soil, Soil Microbiology, *Soil Pollutants/analysis/toxicity
Metabolism35880585Functional analysis, diversity, and distribution of carbendazim hydrolases MheI and CbmA, responsible for the initial step in carbendazim degradation.Zhang M, Bai X, Li Q, Zhang L, Zhu Q, Gao S, Ke Z, Jiang M, Hu J, Qiu J, Hong QEnviron Microbiol10.1111/1462-2920.161392022Amidohydrolases/metabolism, Benzimidazoles, Carbamates/metabolism, *Hydrolases/genetics/metabolism, *Rhodococcus/genetics/metabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15685Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45222)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45222
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
32188Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2843028776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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)