Rhodanobacter soli (DSM 25158, JCM 16126, KCTC 22620)

Name: Rhodanobacter soli (DSM 25158, JCM 16126, KCTC 22620)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17523

Type strain

Culture col. no. DSM 25158 JCM 16126 KCTC 22620 DCY 45

NCBI tax ID(s) 590609

Special Collections DSMZ JCM KCTC Literature strains

History DSMZ <- KCTC <- D.-C. Yang, Kyung Hee Univ., Republic of Korea JCM <-- D.-C. Yang DCY45. KCTC <- DC Yang, Kyunghee Univ.

Links

Rhodanobacter soli DSM 25158 is an aerobe, Gram-negative, motile bacterium that was isolated from ginseng field.

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

Name and taxonomic classification

SI-ID 400041

KCTC 22620,JCM 16126,DSM 25158

@ref 20215

Last LPSN update 2026-05-29 08:29:02

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Rhodanobacteraceae

Genus Rhodanobacter

Species Rhodanobacter soli

Full scientific name Rhodanobacter soli Bui et al. 2010

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29719	negative	2.3 µm	0.5 µm	rod-shaped
67771	negative
125439	negative				98.958

Pigmentation

29719

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
17920	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)
17920	positive	growth	28
29719	positive	growth	30
29719	positive	optimum	30
67770	positive	growth	30
67771	positive	growth	28-30

Culture pH

@ref	Ability	Type	PH	PH range
29719	positive	optimum	7
29719	positive	growth	05-10	alkaliphile

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29719	aerobe
67771	aerobe
125439	obligate aerobe	99.533

Spore formation

@ref	Spore formation	Confidence
29719
125439		99.745

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29719	NaCl	positive	growth	0-3 %
29719	NaCl	positive	optimum	0-3 %

Observation

@ref	Observation
29719	aggregates in chains
67770	quinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29719	37054 ChEBI	3-hydroxybutyrate	+	carbon source
29719	30089 ChEBI	acetate	+	carbon source
29719	17234 ChEBI	glucose	+	carbon source
29719	17306 ChEBI	maltose	+	carbon source
29719	29864 ChEBI	mannitol	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29719	catalase	+	1.11.1.6
29719	cytochrome oxidase	+	1.9.3.1

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
17920	ginseng field	Pocheon Province	Republic of Korea	KOR	Asia
67770	Soil of a ginseng field		Republic of Korea	KOR	Asia
67771	From soil from ginseng field		Republic of Korea	KOR	Asia

Taxonmaps

69479

Global distribution of 16S sequence FJ605268 (>99% sequence identity) for Rhodanobacter from Microbeatlas

Aquatic Samples	61
Soil Samples	613
Animal Samples	52
Plant Samples	43
Total Samples	769

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
17920	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	NCBI tax ID	Score
124043	ASM3952349v1 assembly for Rhodanobacter soli JCM 16126	scaffold	GCA_039523495	590609	55.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
17920	Rhodanobacter soli strain DCY45 16S ribosomal RNA gene, partial sequence	FJ605268	1475		590609

GC content

@ref	GC-content (mol%)	Method
17920	65.4	high performance liquid chromatography (HPLC)
29719	65.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: ASM3952349v1 assembly for Rhodanobacter soli JCM 16126
NCBI: GCA_039523495

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.53	no
125439	motility	BacteriaNetⓘ	yes	78.87	no
125439	gram_stain	BacteriaNetⓘ	negative	98.96	no
125439	spore_formation	BacteriaNetⓘ	no	99.75	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Rhodanobacter ginsengiterrae sp. nov., an antagonistic bacterium against root rot fungal pathogen Fusarium solani, isolated from ginseng rhizospheric soil.	Huo Y, Kang JP, Park JK, Li J, Chen L, Yang DC	Arch Microbiol	10.1007/s00203-018-1560-9	2018
Phylogeny	Rhodanobacter rhizosphaerae sp. nov., isolated from soil of ginseng rhizosphere.	Cho GY, Lee JC, Whang KS	Int J Syst Evol Microbiol	10.1099/ijsem.0.001825	2017
Phylogeny	Rhodanobacter humi sp. nov., an acid-tolerant and alkalitolerant gammaproteobacterium isolated from forest soil.	Dahal RH, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.001786	2017
Phylogeny	Rhodanobacter aciditrophus sp. nov., an acidophilic bacterium isolated from mine wastewater.	Koh HW, Hong H, Min UG, Kang MS, Kim SG, Na JG, Rhee SK, Park SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.000614	2015
Phylogeny	Rhodanobacter koreensis sp. nov., a bacterium isolated from tomato rhizosphere.	Won K, Singh H, Ngo HTT, Son H, Kook M, Kim KY, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.000077	2015
Phylogeny	Rhodanobacter glycinis sp. nov., a yellow-pigmented gammaproteobacterium isolated from the rhizoplane of field-grown soybean.	Madhaiyan M, Poonguzhali S, Saravanan VS, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.055525-0	2014
Phylogeny	Rhodanobacter panaciterrae sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a ginseng field.	Wang L, An DS, Kim SG, Jin FX, Lee ST, Im WT	Int J Syst Evol Microbiol	10.1099/ijs.0.025718-0	2011
Phylogeny	Rhodanobacter soli sp. nov., isolated from soil of a ginseng field.	Bui TPN, Kim YJ, Kim H, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.019422-0	2010

References

#17920	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25158
#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 )
#26102	IJSEM 2935 2010 ( DOI 10.1099/ijs.0.019422-0 , PubMed 20118296 )
#29719	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 #26102
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 )

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Rhodanobacter soli (DSM 25158, JCM 16126, KCTC 22620)

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

Observation

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_039523495

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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