Rhizobium daejeonense (DSM 17795, L61, NCIMB 14499)

Name: Rhizobium daejeonense (DSM 17795, L61, NCIMB 14499)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13630

Type strain

Strain Designation L61

Culture col. no. DSM 17795 L61 NCIMB 14499 NBRC 102495 KCTC 12121 4 more

NCBI tax ID(s) 240521

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- S. T. Lee; L61 <- Z.-X. Quan JCM <-- IAM 15042 <-- Z.-X. Quan L61.

Links

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

Gram-negative motile rod-shaped aerobe genome sequence 16S sequence Bacteria

Name and taxonomic classification

SI-ID 100321

NCIMB 14499,KCTC 12121,IAM 15042,DSM 17795,JCM 21505,LMG 23367,NBRC 102495,VTT E-072703,LMG 25353

@ref 20215

Last LPSN update 2026-05-29 08:28:05

Domain Bacteria

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Hyphomicrobiales

Family Rhizobiaceae

Genus Rhizobium

Species Rhizobium daejeonense

Full scientific name Rhizobium daejeonense Quan et al. 2005

Synonyms (2)

Paenirhizobium daejeonense
"Ciceribacter daejeonensis"

BacDive ID	Other strains from **Rhizobium daejeonense** (1)	Type strain
163211	R. daejeonense JCM 21504, IAM 15041, KCTC 12120, NBRC 102494

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31487	negative	1.2 µm	0.65 µm	rod-shaped
125439	negative				97.779
125438	negative				96.8

Pigmentation

31487

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7190	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: 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

@ref	Growth	Type	Temperature (°C)
7190	positive	growth	28
31487	positive	growth	05-41
31487	positive	optimum	23
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
31487	positive	optimum	7.5
31487	positive	growth	05-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31487	aerobe
125439	obligate aerobe	93.136

Spore formation

@ref	Spore formation	Confidence
31487
125438		94.009
125439		99.728

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31487	NaCl	positive	growth	0-2 %
31487	NaCl	positive	optimum	1 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
31487	16193 ChEBI	3-hydroxybenzoate	+	carbon source
31487	30089 ChEBI	acetate	+	carbon source
31487	16449 ChEBI	alanine	+	carbon source
31487	22599 ChEBI	arabinose	+	carbon source
31487	27689 ChEBI	decanoate	+	carbon source
31487	33984 ChEBI	fucose	+	carbon source
31487	17234 ChEBI	glucose	+	carbon source
31487	27570 ChEBI	histidine	+	carbon source
31487	24996 ChEBI	lactate	+	carbon source
31487	25115 ChEBI	malate	+	carbon source
31487	17306 ChEBI	maltose	+	carbon source
31487	29864 ChEBI	mannitol	+	carbon source
31487	37684 ChEBI	mannose	+	carbon source
31487	26271 ChEBI	proline	+	carbon source
31487	17272 ChEBI	propionate	+	carbon source
31487	26546 ChEBI	rhamnose	+	carbon source
31487	33942 ChEBI	ribose	+	carbon source
31487	30911 ChEBI	sorbitol	+	carbon source
31487	31011 ChEBI	valerate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
31487	catalase	+	1.11.1.6
31487	cytochrome oxidase	+	1.9.3.1
31487	urease	+	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2
#Engineered	#Bioreactor

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
7190	bioreactor for the treatment of nickel-complexed cyanide	Daejon	Republic of Korea	KOR	Asia
67770	Cyanide degrading bioreactor	Daejeon	Republic of Korea	KOR	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7190	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	Rhizobium daejeonense DSM 17795	complete			2738541314	240521	92.72
66792	ASM1428087v1 assembly for Rhizobium daejeonense L61	scaffold	GCA_014280875	240521.6	8117779089	240521	73.41
67770	ASM1104515v1 assembly for Rhizobium daejeonense CCBAU10050	contig	GCA_011045155	240521.4		240521	72.45

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Rhizobium daejeonense strain L61T 16S ribosomal RNA gene, partial sequence	AY341343	1421		240521
20218	Rhizobium daejeonense gene for 16S rRNA, partial sequence, strain: NBRC 102495	AB681832	1410		240521

GC content

@ref	GC-content (mol%)	Method
31487	60.1
67770	60.1	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM1428087v1 assembly for Rhizobium daejeonense L61
NCBI: GCA_014280875

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	93.14	no
125439	gram_stain	BacteriaNetⓘ	negative	97.78	no
125439	motility	BacteriaNetⓘ	yes	69.13	no
125439	spore_formation	BacteriaNetⓘ	no	99.73	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizobium daejeonense L61
NCBI: GCA_014280875.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.80	yes
125438	anaerobic	anaerobicⓘ	no	94.20	yes
125438	aerobic	aerobicⓘ	yes	82.80	yes
125438	spore-forming	spore-formingⓘ	no	94.01	no
125438	thermophilic	thermophileⓘ	no	98.46	yes
125438	flagellated	motile2+ⓘ	yes	74.03	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Validation list no. 225: valid publication of new names and new combinations effectively published outside the IJSEM.	Oren A, Goker M.	Int J Syst Evol Microbiol	10.1099/ijsem.0.006863	2025
Genetics	Selective enrichment, identification, and isolation of diclofenac, ibuprofen, and carbamazepine degrading bacteria from a groundwater biofilm.	Papai M, Benedek T, Tancsics A, Bornemann TLV, Plewka J, Probst AJ, Hussein D, Maroti G, Menashe O, Kriszt B.	Environ Sci Pollut Res Int	10.1007/s11356-022-24975-6	2023
	Uptake of carbamazepine by rhizomes and endophytic bacteria of Phragmites australis.	Sauvetre A, Schroder P.	Front Plant Sci	10.3389/fpls.2015.00083	2015
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 )
#27785	IJSEM 2543 2005 ( DOI 10.1099/ijs.0.63667-0 , PubMed 16280524 )
#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
#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 .
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

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Rhizobium daejeonense (DSM 17795, L61, NCIMB 14499)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014280875

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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