Name: Rhodococcus erythropolis djl-6
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 11046

Type strain:

Species: Rhodococcus erythropolis

Strain Designation: djl-6

Culture col. no.: DSM 45222, CGMCC 1.6580, KCTC 19205, JCM 15477, CCM 8451

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

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

Special Collections

Other strains from Rhodococcus erythropolis

Section

When using BacDive for research please cite our paper

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

Gram-positive
ovoid-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Mycobacteriales*
	Family	*Nocardiaceae*
	Genus	*Rhodococcus*
	Species	**Rhodococcus erythropolis**
	Full Scientific Name (LPSN)	Rhodococcus erythropolis (Gray and Thornton 1928) Goodfellow and Alderson 1979 (Approved Lists 1980)

	Synonym	Rhodococcus jialingiae
	Synonym	Rhodococcus enclensis
	Synonym	Rhodococcus degradans
	Synonym	"Mycobacterium* erythropolis"*
	Synonym	Rhodococcus qingshengii
	Synonym	Rhodococcus baikonurensis

Information on morphological and physiological properties Morphology

[Ref.: #32188]	Gram stain	positive
[Ref.: #125439]	Gram stain	positive Confidence in %93.8

[Ref.: #32188]	Cell shape	ovoid-shaped

[Ref.: #32188]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %90.5

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15685]

Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

[Ref.: #15685]

Culture medium growth

[Ref.: #15685]

Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

[Ref.: #15685]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15685]	growth	28 °C
[Ref.: #32188]	optimum	30 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #32188]			optimum	7.75

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32188]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %96.9

[Ref.: #67770]

Observation

quinones: MK-8(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32188]	2-oxopentanoate ChEBI	+	carbon source
[Ref.: #32188]	acetate ChEBI	+	carbon source
[Ref.: #32188]	alanine ChEBI	+	carbon source
[Ref.: #32188]	dextrin ChEBI	+	carbon source
[Ref.: #32188]	fructose ChEBI	+	carbon source
[Ref.: #32188]	gluconate ChEBI	+	carbon source
[Ref.: #32188]	glucose ChEBI	+	carbon source
[Ref.: #32188]	glycerol ChEBI	+	carbon source
[Ref.: #32188]	L-alaninamide ChEBI	+	carbon source
[Ref.: #32188]	malate ChEBI	+	carbon source
[Ref.: #32188]	mannose ChEBI	+	carbon source
[Ref.: #32188]	ribose ChEBI	+	carbon source
[Ref.: #32188]	sucrose ChEBI	+	carbon source
[Ref.: #32188]	tween 40 ChEBI	+	carbon source
[Ref.: #32188]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32188]		catalase	+	1.11.1.6
[Ref.: #32188]		urease	+	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #15685]	Sample type/isolated from	carbendazim-contaminated soil sample from a vegetable field
[Ref.: #15685]	Geographic location (country and/or sea, region)	Jiangsu province
[Ref.: #15685]	Country	China
[Ref.: #15685]	Country ISO 3 Code	CHN
[Ref.: #15685]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Carbendazim-contaminated soil from a vegetable field
[Ref.: #67770]	Geographic location (country and/or sea, region)	Jiangsu Province
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence DQ090961 (>99% sequence identity) for Nocardiaceae from Microbeatlas

Aquatic Samples	6494
Soil Samples	7777
Animal Samples	11681
Plant Samples	2835
Total Samples	28787

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #15685]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #15685]	Rhodococcus qingshengii strain djl-6 16S ribosomal RNA gene, partial sequence	DQ090961	1484	GenBank ENA	1303681 tax ID
[Ref.: #124043]	Rhodococcus qingshengii JCM 15477 strain H44 16S ribosomal RNA gene, partial sequence.	OR122181	1226	GenBank ENA	1303681 tax ID	*

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rhodococcus qingshengii JCM 15477	GCA_001646745	contig	GenBank ENA	334542 tax ID
[Ref.: #66792]	Rhodococcus qingshengii JCM 15477	GCA_001313445	contig	GenBank ENA	1303681 tax ID	*
[Ref.: #66792]	Rhodococcus qingshengii JCM 15477	1303681.3	wgs	PATRIC	1303681 tax ID	*
[Ref.: #66792]	Rhodococcus qingshengii strain JCM 15477	334542.13	wgs	PATRIC	334542 tax ID	*
[Ref.: #66792]	Rhodococcus qingshengii JCM 15477	2744054616	draft	JGI IMG/M	1303681 tax ID	*
[Ref.: #66792]	Rhodococcus qingshengii JCM 15477	2734481946	draft	JGI IMG/M	1303681 tax ID	*

[Ref.: #15685]	GC-content	59.1 mol%
[Ref.: #67770]	GC-content	62.4 mol%	genome sequence analysis
[Ref.: #67770]	GC-content	59.1 mol%	thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhodococcus qingshengii JCM 15477 djl-6 NCBI: GCA_023221595.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	yes	88.338	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.474	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	85.765	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	yes	56.358	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	90.5	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhodococcus qingshengii JCM 15477 djl-6 NCBI: GCA_023221595
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	56.7
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	86.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	positive	93.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	96.9

Availability in culture collections External links

[Ref.: #15685]

Culture collection no.

DSM 45222, CGMCC 1.6580, KCTC 19205, JCM 15477, CCM 8451

Literature:

	Title	Authors	Journal	DOI	Year
Metabolism	Biodegradation of carbendazim by a novel actinobacterium Rhodococcus jialingiae djl-6-2.	Wang Z, Wang Y, Gong F, Zhang J, Hong Q, Li S	Chemosphere	10.1016/j.chemosphere.2010.08.040	2010	*
Metabolism	Functional 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 Q	Environ Microbiol	10.1111/1462-2920.16139	2022	*
	Potential 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 Q	J Hazard Mater	10.1016/j.jhazmat.2021.125496	2021	*

References

#15685

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 45222

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#32188

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28430 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João 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.: MicrobeAtlas 1.0 beta .

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

#28430

IJSEM 2754 2007 ( DOI 10.1099/ijs.0.65095-0 , PubMed 18048720 )

* These data were automatically processed and therefore are not curated

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Rhodococcus qingshengii JCM 15477 djl-6

Rhodococcus qingshengii JCM 15477 djl-6

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