Name: Rhizobium daejeonense L61
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 13630

Type strain:

Species: Rhizobium daejeonense

Strain Designation: L61

Culture col. no.: DSM 17795, JCM 21505, BCRC 80436, CCBAU 10050, IAM 15042, KCTC 12121, NBRC 102495, NCIMB 14499

Strain history: IAM 15042 <-- Z.-X. Quan L61.

NCBI tax ID(s): 240521 (species)

SI-ID 100321

KCTC 12121, IAM 15042, DSM 17795, JCM 21505, LMG 23367, NBRC 102495, VTT E-072703, LMG 25353

Special Collections

Other strains from Rhizobium daejeonense

Section

When using BacDive for research please cite our paper

Rhizobium daejeonense L61 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from bioreactor for the treatment of nickel-complexed cyanide.

Gram-negative
motile
rod-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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Rhizobiaceae*
	Genus	*Rhizobium*
	Species	**Rhizobium daejeonense**
	Full Scientific Name (LPSN)	Rhizobium daejeonense Quan et al. 2005

	Synonym	"Ciceribacter* daejeonensis"*
	Synonym	"Paenirhizobium* daejeonense"*

Information on morphological and physiological properties Morphology

[Ref.: #31487]	Gram stain	negative
[Ref.: #125439]	Gram stain	negative Confidence in %99.3
[Ref.: #125438]	Gram stain	negative Confidence in %96.8

[Ref.: #31487]	Cell length	1.2 µm

[Ref.: #31487]	Cell width	0.65 µm

[Ref.: #31487]	Cell shape	rod-shaped

[Ref.: #31487]	Motility	yes

[Ref.: #31487]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7190]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #7190]

Culture medium growth

[Ref.: #7190]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7190]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #7190]	growth	28 °C
[Ref.: #31487]	growth	05-41 °C
[Ref.: #31487]	optimum	23 °C
[Ref.: #67770]	growth	28 °C

	pH	Kind of pH		pH
[Ref.: #31487]			optimum	7.5
[Ref.: #31487]			growth	05-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #31487]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %93.1

[Ref.: #31487]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %98.9
[Ref.: #125438]	Ability of spore formation	no Confidence in %94.009

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31487]		NaCl		growth	0-2	%
[Ref.: #31487]		NaCl		optimum	1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #31487]	3-hydroxybenzoate ChEBI	+	carbon source
[Ref.: #31487]	acetate ChEBI	+	carbon source
[Ref.: #31487]	alanine ChEBI	+	carbon source
[Ref.: #31487]	arabinose ChEBI	+	carbon source
[Ref.: #31487]	decanoate ChEBI	+	carbon source
[Ref.: #31487]	fucose ChEBI	+	carbon source
[Ref.: #31487]	glucose ChEBI	+	carbon source
[Ref.: #31487]	histidine ChEBI	+	carbon source
[Ref.: #31487]	lactate ChEBI	+	carbon source
[Ref.: #31487]	malate ChEBI	+	carbon source
[Ref.: #31487]	maltose ChEBI	+	carbon source
[Ref.: #31487]	mannitol ChEBI	+	carbon source
[Ref.: #31487]	mannose ChEBI	+	carbon source
[Ref.: #31487]	proline ChEBI	+	carbon source
[Ref.: #31487]	propionate ChEBI	+	carbon source
[Ref.: #31487]	rhamnose ChEBI	+	carbon source
[Ref.: #31487]	ribose ChEBI	+	carbon source
[Ref.: #31487]	sorbitol ChEBI	+	carbon source
[Ref.: #31487]	valerate ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #31487]	catalase	+	1.11.1.6
[Ref.: #31487]	cytochrome oxidase	+	1.9.3.1
[Ref.: #31487]	urease	+	3.5.1.5

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

[Ref.: #7190]	Sample type/isolated from	bioreactor for the treatment of nickel-complexed cyanide
[Ref.: #7190]	Geographic location (country and/or sea, region)	Daejon
[Ref.: #7190]	Country	Republic of Korea
[Ref.: #7190]	Country ISO 3 Code	KOR
[Ref.: #7190]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Cyanide degrading bioreactor
[Ref.: #67770]	Geographic location (country and/or sea, region)	Daejeon
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Bioreactor

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB681832 (>99% sequence identity) for Rhizobium from Microbeatlas

Aquatic Samples	59
Soil Samples	69
Animal Samples	18
Plant Samples	180
Total Samples	326

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

[Ref.: #7190]

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.: #20218]	Rhizobium daejeonense strain L61T 16S ribosomal RNA gene, partial sequence	AY341343	1421	GenBank ENA	240521 tax ID	*
[Ref.: #20218]	Rhizobium daejeonense gene for 16S rRNA, partial sequence, strain: NBRC 102495	AB681832	1410	GenBank ENA	240521 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Rhizobium daejeonense CCBAU10050	GCA_011045155	contig	GenBank ENA	240521 tax ID
[Ref.: #66792]	Rhizobium daejeonense L61	GCA_014280875	scaffold	GenBank ENA	240521 tax ID	*
[Ref.: #66792]	Rhizobium daejeonense strain CCBAU10050	240521.4	wgs	PATRIC	240521 tax ID	*
[Ref.: #66792]	Rhizobium daejeonense DSM 17795	2738541314	draft	JGI IMG/M	240521 tax ID	*

[Ref.: #31487]	GC-content	60.1 mol%
[Ref.: #67770]	GC-content	60.1 mol%	high performance liquid chromatography (HPLC)

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: Rhizobium daejeonense L61 NCBI: GCA_014280875.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.8	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	94.202	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	82.803	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	94.009	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.462	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	74.027	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhizobium daejeonense L61 NCBI: GCA_014280875
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	76.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.3
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	93.1

Availability in culture collections External links

[Ref.: #7190]

Culture collection no.

DSM 17795, JCM 21505, BCRC 80436, CCBAU 10050, IAM 15042, KCTC 12121, NBRC 102495, NCIMB 14499

[Ref.: #82816]

SI-ID 100321

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhizobium rhizolycopersici sp. nov., Isolated from the Rhizosphere Soil of Tomato Plants in China.	Thin KK, He SW, Wang X, Wang Y, Rong M, Han JG, Zhang X	Curr Microbiol	10.1007/s00284-020-02323-6	2021	*
Phylogeny	Ensifer collicola sp. nov., a bacterium isolated from soil in South Korea.	Jang JH, Lee D, Cha S, Seo T	J Microbiol	10.1007/s12275-017-6608-z	2017	*
Phylogeny	Rhizobium rosettiformans sp. nov., isolated from a hexachlorocyclohexane dump site, and reclassification of Blastobacter aggregatus Hirsch and Muller 1986 as Rhizobium aggregatum comb. nov.	Kaur J, Verma M, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.017491-0	2010	*
Phylogeny	Rhizobium daejeonense sp. nov. isolated from a cyanide treatment bioreactor.	Quan ZX, Bae HS, Baek JH, Chen WF, Im WT, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.63667-0	2005	*

References

#7190

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17795

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#31487

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 #27785 (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 .

#82816

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID100321.1 )

#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 .

#27785

IJSEM 2543 2005 ( DOI 10.1099/ijs.0.63667-0 , PubMed 16280524 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Rhizobium daejeonense in external resources:
SILVA
BRENDA
PANGAEA
GBIF