Rhizorhapis suberifaciens (DSM 7465, ATCC 49355, CIP 105429)

Name: Rhizorhapis suberifaciens (DSM 7465, ATCC 49355, CIP 105429)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14222

Type strain

Strain Designation CA1, EY 2404, Ca 1

Culture col. no. DSM 7465 ATCC 49355 CIP 105429 ICMP 12535 JCM 8521 11 more

NCBI tax ID(s) 1219056 13656

Special Collections DSMZ JCM CIP

Links

Rhizorhapis suberifaciens CA1 is a mesophilic, Gram-negative, motile plant pathogen that was isolated from Lactuca sativa, corky roots.

Gram-negative motile rod-shaped mesophilic plant pathogen genome sequence 16S sequence

Name and taxonomic classification

SI-ID 4820

LMG 11026,ATCC 49355,LMG 15574,LMG 15591,LMG 9830,NCPPB 3629,DSM 7465,LMG 17323,IFO 15211,JCM 8521,CIP 105429,KCTC 2841,NBRC 15211,ICMP 12535

@ref 20215

Last LPSN update 2025-12-16 09:50:18

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Rhizorhapis

Species Rhizorhapis suberifaciens

Full scientific name Rhizorhapis suberifaciens (van Bruggen et al. 1990) Francis et al. 2014

Synonyms (3)

Sphingomonas suberifaciens
Sphingobium suberifaciens
Rhizomonas suberifaciens

BacDive ID	Other strains from **Rhizorhapis suberifaciens** (3)	Type strain
165803	R. suberifaciens JCM 8522, ATCC 49356, LMG 11117, NCPPB 3628
165804	R. suberifaciens JCM 8523, ATCC 49381, KCTC 2842, LMG 9837, ...
165805	R. suberifaciens JCM 8524, ATCC 49382, IFO 15212, KCTC 2842, ...

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
123343	negative	rod-shaped
125439	negative		96.9
125438	negative		94.608

Pigmentation

@ref	Production	Name
123343		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
3170	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
3170	RHIZOMONAS SUBERIFACIENS MEDIUM (DSMZ Medium 726)	Medium recipe at MediaDive	Name: RHIZOMONAS SUBERIFACIENS MEDIUM (DSMZ Medium 726) Composition: Agar 11.0 g/l Enzymatic digest of casein 5.0 g/l Glucose 2.5 g/l K2HPO4 x 3 H2O 1.3 g/l MgSO4 x 7 H2O 0.5 g/l KNO3 0.5 g/l Ca(NO3)2 x 4 H2O 0.06 g/l Distilled water
36403	MEDIUM 254 - for Rhizomonas suberifaciens		Distilled water make up to (1000.000 ml);Magnesium sulphate heptahydrate (0.500 g);Glucose (2.500 g);Potassium nitrate (0.500 g);Calcium nitrate tetrahydrate (0.060g);Di Potassium monohydrogenophosphate (1.000 g);Casein hydrolysate acid hydrolysed vitamin
123343	CIP Medium 254	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
3170	positive	growth	28	mesophilic
36403	positive	growth	30	mesophilic
67770	positive	growth	26	mesophilic
123343	positive	growth	25-30	mesophilic
123343	negative	growth	5
123343	negative	growth	10
123343	negative	growth	37
123343	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
125439	obligate aerobe	97.9

Spore formation

@ref	Spore formation	Confidence
125439		95.9

Halophily

@ref	Salt	Growth	Tested relation	Concentration
123343	NaCl	positive	growth	0 %
123343	NaCl		growth	2 %
123343	NaCl		growth	4 %
123343	NaCl		growth	6 %
123343	NaCl		growth	8 %
123343	NaCl		growth	10 %

Observation

67770

Observationquinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
123343	16947 ChEBI	citrate	-	carbon source
68369	17634 ChEBI	D-glucose	-	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
123343	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
123343	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
123343	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
123343	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
123343	35581 ChEBI	indole

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
123343	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	+	3.2.1.23	from API zym
123343	beta-galactosidase	+	3.2.1.23
68382	beta-glucosidase	+	3.2.1.21	from API zym
68369	beta-glucosidase	+	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
123343	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
123343	gelatinase	-
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
123343	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
123343	ornithine decarboxylase	-	4.1.1.17
123343	oxidase	+
123343	phenylalanine ammonia-lyase	-	4.3.1.24
68382	trypsin	+	3.4.21.4	from API zym
123343	tryptophan deaminase	-
123343	urease	-	3.5.1.5
68369	urease	-	3.5.1.5	from API 20NE
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
123343	-	+	+	+	-	+	+	-	+	-	+	-	-	+	-	+	+	-	-	-

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
3170	+	-	-	-	-	+	-	+	-	+	-	-	-	-	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent
3170	Lactuca sativa, corky roots	Lactuca sativa	California	USA	USA	North America
67770	Lettuce roots		CA	USA	USA	North America
123343	Plant, Corked lettuce roots		California	United States of America	USA	North America

Taxonmaps

69479

Global distribution of 16S sequence KF437561 (>99% sequence identity) for Rhizorhapis suberifaciens subclade from Microbeatlas

Aquatic Samples	5886
Soil Samples	12941
Animal Samples	2084
Plant Samples	3457
Total Samples	24368

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
3170		1	Risk group (German classification) According to TRBA 466
123343		1	Risk group (French 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	ASM1420004v1 assembly for Rhizorhapis suberifaciens DSM 7465	scaffold	GCA_014200045	13656.4	2829787817	13656	72.47

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
3170	Sphingomonas suberifaciens gene for 16S rRNA, partial sequence	D13737	1415	1219056
3170	Rhizorhapis suberifaciens NBRC 15211 16S ribosomal RNA gene, partial sequence	KF437561	1453	1219056
67770	Sphingomonas suberifaciens gene for 16S rRNA, partial sequence, strain: NBRC 15211	AB680813	1414	1219056
124043	Rhizorhapis suberifaciens NBRC 15211 strain MDA087 16S ribosomal RNA gene, partial sequence.	OR461859	1340	1219056
124043	Rhizorhapis suberifaciens NBRC 15211 strain MDA264 16S ribosomal RNA gene, partial sequence.	OR461957	1309	1219056

GC content

@ref	GC-content (mol%)	Method
3170	59
67770	58.6-59.2	Buoyant density centrifugation (BD)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Rhizorhapis suberifaciens DSM 7465
NCBI: GCA_014200045

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	95.90	no
125439	motility	BacteriaNetⓘ	yes	58.70	no
125439	gram_stain	BacteriaNetⓘ	negative	96.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Rhizorhapis suberifaciens DSM 7465
NCBI: GCA_014200045.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	94.61	no
125438	anaerobic	anaerobicⓘ	no	89.94	no
125438	aerobic	aerobicⓘ	yes	88.63	no
125438	spore-forming	spore-formingⓘ	no	89.16	no
125438	thermophilic	thermophileⓘ	no	96.33	yes
125438	flagellated	motile2+ⓘ	yes	70.36	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Novel primers and PCR protocols for the specific detection and quantification of Sphingobium suberifaciens in situ.	Bull CT, Goldman PH, Martin KJ	Mol Cell Probes	10.1016/j.mcp.2014.03.001	2014
Phylogeny	Proposal of Sphingomonas suberifaciens (van Bruggen, Jochimsen and Brown 1990) comb. nov., sphingomonas natatoria (Sly 1985) comb. nov., Sphingomonas ursincola (Yurkov et al. 1997) comb. nov., and emendation of the genus Sphingomonas.	Yabuuchi E, Kosako Y, Naka T, Suzuki S, Yano I	Microbiol Immunol	10.1111/j.1348-0421.1999.tb02414.x	1999
Phylogeny	Phylogenetic evidence for Sphingomonas and Rhizomonas as nonphotosynthetic members of the alpha-4 subclass of the Proteobacteria.	Takeuchi M, Sawada H, Oyaizu H, Yokota A	Int J Syst Bacteriol	10.1099/00207713-44-2-308	1994
Phylogeny	Sphingobium subterraneum sp. nov., isolated from ground water.	Lee JC, Kim SG, Whang KS	Int J Syst Evol Microbiol	10.1099/ijs.0.069708-0	2014
Phylogeny	Reclassification of rhizosphere bacteria including strains causing corky root of lettuce and proposal of Rhizorhapis suberifaciens gen. nov., comb. nov., Sphingobium mellinum sp. nov., Sphingobium xanthum sp. nov. and Rhizorhabdus argentea gen. nov., sp. nov.	Francis IM, Jochimsen KN, De Vos P, van Bruggen AHC	Int J Syst Evol Microbiol	10.1099/ijs.0.058909-0	2014
Phylogeny	Sphingobium limneticum sp. nov. and Sphingobium boeckii sp. nov., two freshwater planktonic members of the family Sphingomonadaceae, and reclassification of Sphingomonas suberifaciens as Sphingobium suberifaciens comb. nov.	Chen H, Jogler M, Rohde M, Klenk HP, Busse HJ, Tindall BJ, Sproer C, Overmann J	Int J Syst Evol Microbiol	10.1099/ijs.0.040105-0	2012

References

#3170	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 7465
#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 )
#36403	; Curators of the CIP;
#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;
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#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 .
#123343	Collection of Institut Pasteur ; Curators of the CIP; CIP 105429
#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 .
#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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Rhizorhapis suberifaciens (DSM 7465, ATCC 49355, CIP 105429)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Antibiotic resistance

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_014200045

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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