Rhodanobacter rhizosphaerae (KACC 18699, NBRC 111845, CR164)

Name: Rhodanobacter rhizosphaerae (KACC 18699, NBRC 111845, CR164)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 140574

Type strain

Strain Designation CR164

Culture col. no. KACC 18699 NBRC 111845 CR164

NCBI tax ID(s) 624397

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Rhodanobacter rhizosphaerae CR164 is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from rhizosphere soil of a ginseng field located at Geumasn.

Gram-negative rod-shaped colony-forming aerobe mesophilic 16S sequence

Name and taxonomic classification

SI-ID 393395

NBRC 111845

@ref 20215

Last LPSN update 2025-12-16 10:03:38

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Rhodanobacteraceae

Genus Rhodanobacter

Species Rhodanobacter rhizosphaerae

Full scientific name Rhodanobacter rhizosphaerae Cho et al. 2017

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility
43209	negative	1.5-1.7 µm	0.5-0.7 µm	rod-shaped

Colony morphology

@ref	Colony size	Colony color	Colony shape	Incubation period	Medium used
43209	0.5-1.0 mm	yellow	circular	3 days	TSA

Culture and growth conditions

Culture medium

@ref	Name	Growth
43209	Trypticase Soy Agar (TSA)
43209	Nutrient agar (NA)
43209	LB (Luria-Bertani) MEDIUM
43209	SCA
43209	PDA

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
43209	positive	optimum	28	mesophilic
43209	positive	growth	15-37

Culture pH

@ref	Ability	Type	PH	PH range
43209	positive	optimum	7
43209	positive	growth	6.0-9.0	alkaliphile

Physiology and metabolism

Oxygen tolerance

43209

Oxygen toleranceaerobe

Spore formation

@ref	Type of spore	Spore formation
43209	spore

Halophily

@ref	Salt	Growth	Tested relation	Concentration
43209	NaCl	positive	growth	0-1.0 %(w/v)
43209	NaCl	positive	optimum	0 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
43209		2-oxogluconate	-	assimilation
43209	30916 ChEBI	2-oxoglutarate	-	builds acid from
43209	58143 ChEBI	5-dehydro-D-gluconate	+	assimilation
43209	58143 ChEBI	5-dehydro-D-gluconate	-	builds acid from
43209	17128 ChEBI	adipate	+	assimilation
43209	27613 ChEBI	amygdalin	-	assimilation
43209	27613 ChEBI	amygdalin	-	builds acid from
43209	18305 ChEBI	arbutin	+	assimilation
43209	18305 ChEBI	arbutin	+	builds acid from
43209	17057 ChEBI	cellobiose	-	assimilation
43209	17057 ChEBI	cellobiose	+	builds acid from
43209	16947 ChEBI	citrate	-	assimilation
43209	17108 ChEBI	D-arabinose	-	assimilation
43209	17108 ChEBI	D-arabinose	-	builds acid from
43209	18333 ChEBI	D-arabitol	-	assimilation
43209	18333 ChEBI	D-arabitol	-	builds acid from
43209	15824 ChEBI	D-fructose	-	assimilation
43209	15824 ChEBI	D-fructose	-	builds acid from
43209	28847 ChEBI	D-fucose	-	assimilation
43209	28847 ChEBI	D-fucose	-	builds acid from
43209	12936 ChEBI	D-galactose	-	assimilation
43209	12936 ChEBI	D-galactose	-	builds acid from
43209	17634 ChEBI	D-glucose	+	assimilation
43209	17634 ChEBI	D-glucose	-	builds acid from
43209	62318 ChEBI	D-lyxose	-	assimilation
43209	62318 ChEBI	D-lyxose	-	builds acid from
43209	16899 ChEBI	D-mannitol	-	builds acid from
43209	16024 ChEBI	D-mannose	+	assimilation
43209	16024 ChEBI	D-mannose	-	assimilation
43209	16024 ChEBI	D-mannose	-	builds acid from
43209	16988 ChEBI	D-ribose	+	assimilation
43209	16988 ChEBI	D-ribose	-	builds acid from
43209	17924 ChEBI	D-sorbitol	-	assimilation
43209	17924 ChEBI	D-sorbitol	-	builds acid from
43209	16443 ChEBI	D-tagatose	-	assimilation
43209	16443 ChEBI	D-tagatose	-	builds acid from
43209	65327 ChEBI	D-xylose	-	assimilation
43209	65327 ChEBI	D-xylose	-	builds acid from
43209	27689 ChEBI	decanoate	-	assimilation
43209	17113 ChEBI	erythritol	-	assimilation
43209	17113 ChEBI	erythritol	-	builds acid from
43209	4853 ChEBI	esculin	-	hydrolysis
43209	4853 ChEBI	esculin	+	assimilation
43209	4853 ChEBI	esculin	-	builds acid from
43209	16813 ChEBI	galactitol	-	assimilation
43209	16813 ChEBI	galactitol	-	builds acid from
43209	5291 ChEBI	gelatin	+	hydrolysis
43209	28066 ChEBI	gentiobiose	-	assimilation
43209	28066 ChEBI	gentiobiose	-	builds acid from
43209	24265 ChEBI	gluconate	+	assimilation
43209	24265 ChEBI	gluconate	-	builds acid from
43209	17754 ChEBI	glycerol	+	assimilation
43209	17754 ChEBI	glycerol	-	builds acid from
43209	28087 ChEBI	glycogen	-	assimilation
43209	28087 ChEBI	glycogen	-	builds acid from
43209	15443 ChEBI	inulin	-	assimilation
43209	15443 ChEBI	inulin	-	builds acid from
43209	30849 ChEBI	L-arabinose	-	assimilation
43209	18403 ChEBI	L-arabitol	-	assimilation
43209	18403 ChEBI	L-arabitol	-	builds acid from
43209	18287 ChEBI	L-fucose	+	assimilation
43209	18287 ChEBI	L-fucose	-	builds acid from
43209	62345 ChEBI	L-rhamnose	-	assimilation
43209	62345 ChEBI	L-rhamnose	-	builds acid from
43209	17266 ChEBI	L-sorbose	-	assimilation
43209	17266 ChEBI	L-sorbose	-	builds acid from
43209	17895 ChEBI	L-tyrosine	-	hydrolysis
43209	65328 ChEBI	L-xylose	-	assimilation
43209	65328 ChEBI	L-xylose	-	builds acid from
43209	17716 ChEBI	lactose	-	assimilation
43209	17716 ChEBI	lactose	-	builds acid from
43209	25115 ChEBI	malate	-	assimilation
43209	17306 ChEBI	maltose	+	assimilation
43209	17306 ChEBI	maltose	-	builds acid from
43209	6731 ChEBI	melezitose	-	assimilation
43209	6731 ChEBI	melezitose	-	builds acid from
43209	28053 ChEBI	melibiose	-	assimilation
43209	28053 ChEBI	melibiose	-	builds acid from
43209	320061 ChEBI	methyl alpha-D-glucopyranoside	-	assimilation
43209	320061 ChEBI	methyl alpha-D-glucopyranoside	+	builds acid from
43209	43943 ChEBI	methyl alpha-D-mannoside	-	assimilation
43209	43943 ChEBI	methyl alpha-D-mannoside	-	builds acid from
43209	74863 ChEBI	methyl beta-D-xylopyranoside	-	assimilation
43209	74863 ChEBI	methyl beta-D-xylopyranoside	-	builds acid from
43209	17268 ChEBI	myo-inositol	-	assimilation
43209	17268 ChEBI	myo-inositol	-	builds acid from
43209	506227 ChEBI	N-acetylglucosamine	+	assimilation
43209	506227 ChEBI	N-acetylglucosamine	-	builds acid from
43209	17632 ChEBI	nitrate	+	reduction
43209	18401 ChEBI	phenylacetate	-	assimilation
43209	16634 ChEBI	raffinose	-	assimilation
43209	16634 ChEBI	raffinose	+	builds acid from
43209	15963 ChEBI	ribitol	-	assimilation
43209	15963 ChEBI	ribitol	-	builds acid from
43209	17814 ChEBI	salicin	-	assimilation
43209	17814 ChEBI	salicin	-	builds acid from
43209	28017 ChEBI	starch	+	hydrolysis
43209	28017 ChEBI	starch	+	assimilation
43209	28017 ChEBI	starch	+	builds acid from
43209	17992 ChEBI	sucrose	-	assimilation
43209	17992 ChEBI	sucrose	+	builds acid from
43209	27082 ChEBI	trehalose	+	assimilation
43209	27082 ChEBI	trehalose	-	builds acid from
43209	32528 ChEBI	turanose	-	assimilation
43209	32528 ChEBI	turanose	-	builds acid from
43209	16199 ChEBI	urea	-	hydrolysis
43209	17151 ChEBI	xylitol	-	assimilation
43209	17151 ChEBI	xylitol	-	builds acid from

Antibiotic resistance

@ref	ChEBI	Metabolite	Sensitivity conc.	Resistance conc.
43209	2637	amikacin	30 µg (disc)
43209	2676	amoxicillin	10 µg (disc)
43209	28971	ampicillin		20 µg (disc)
43209	2790	apramycin	30 µg (disc)
43209	28669	bacitracin	10 Unit
43209	3371	capreomycin		30 µg (disc)
43209	17698	chloramphenicol	30 µg (disc)
43209	27641	cycloheximide		30 µg (disc)
43209	48923	erythromycin	15 µg (disc)
43209	28915	fosfomycin		30 µg (disc)
43209	17833	gentamicin	10 µg (disc)
43209	5530	gramicidin s	30 µg (disc)
43209	24753	hygromycin	30 µg (disc)
43209	6104	kanamycin	30 µg (disc)
43209	6472	lincomycin		15 µg (disc)
43209	100147	nalidixic acid	30 µg (disc)
43209	7507	neomycin		30 µg (disc)
43209	7660	nystatin		50 µg (disc)
43209	16869	oleandomycin	15 µg (disc)
43209	17334	penicillin	10 Unit
43209	8309	polymyxin b		100 Unit
43209	28077	rifampicin		10 µg (disc)
43209	48844	roxithromycin	15 µg (disc)
43209	80025	salinomycin		30 µg (disc)
43209	9169	sisomycin		10 µg (disc)
43209	17636	sphingomyelin		30 µg (disc)
43209	85260	spiramycin	100 µg (disc)
43209	17076	streptomycin	10 µg (disc)
43209	29687	teicoplanin	30 µg (disc)
43209	27902	tetracycline	30 µg (disc)
43209	28001	vancomycin	30 µg (disc)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
43209	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
43209	6-phospho-beta-galactosidase	+	3.2.1.85
43209	acid phosphatase	+	3.1.3.2
43209	alkaline phosphatase	+	3.1.3.1
43209	alpha-chymotrypsin	+	3.4.21.1
43209	alpha-fucosidase	+	3.2.1.51
43209	alpha-galactosidase	+	3.2.1.22
43209	alpha-glucosidase	+	3.2.1.20
43209	alpha-mannosidase	+	3.2.1.24
43209	beta-glucosidase	+	3.2.1.21
43209	beta-glucuronidase	+	3.2.1.31
43209	catalase	+	1.11.1.6
43209	cystine arylamidase	+	3.4.11.3
43209	cytochrome oxidase	+	1.9.3.1
43209	esterase (C 4)	+
43209	esterase Lipase (C 8)	+
43209	leucine arylamidase	+	3.4.11.1
43209	lipase (C 14)	+
43209	N-acetyl-beta-glucosaminidase	+	3.2.1.52
43209	naphthol-AS-BI-phosphohydrolase	+
43209	trypsin	+	3.4.21.4
43209	valine arylamidase	+

Fatty acid profile

Metadata FA analysis

@ref

43209

Fatty acid	Percentage
C17:1 iso ω9c	21.8
C15:0 iso	12.1
C11:0 iso	11.9
C16:0 iso	11.1
C17:0 iso	9.8
C13:0 iso 3OH	5.6
C11:0 iso 3OH	5.2
C16:1ω7c / C15:0 iso 2OH	3.7
C15:0 anteiso	3.2

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude
43209	rhizosphere soil of a ginseng field located at Geumasn	Geumasn, Korea	Republic of Korea	KOR	Asia	36	127 36/127

Taxonmaps

69479

Global distribution of 16S sequence FJ772032 (>99% sequence identity) for Rhodanobacter rhizosphaerae from Microbeatlas

Aquatic Samples	14
Soil Samples	89
Animal Samples	9
Plant Samples	18
Total Samples	130

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
43209	Rhodanobacter rhizosphaerae strain CR164 16S ribosomal RNA gene, partial sequence	FJ772032	1486		624397

GC content

@ref	GC-content (mol%)	Method
43209	62.3	high performance liquid chromatography (HPLC)

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
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

References

#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 )
#43209	Geon-Yeong Cho, Jae-Chan Lee and Kyung-Sook Whang: Rhodanobacter rhizosphaerae sp. nov., isolated from soil of ginseng rhizosphere. IJSEM 67: 1387 - 1392 2017 ( DOI 10.1099/ijsem.0.001825 , PubMed 28126050 )
#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 .
#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 rhizosphaerae (KACC 18699, NBRC 111845, CR164)

Name and taxonomic classification