Pseudomonas marginalis (DSM 18529, CIP 108524, IMSNU 14100)

Name: Pseudomonas marginalis (DSM 18529, CIP 108524, IMSNU 14100)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13140

Type strain

Culture col. no. DSM 18529 CIP 108524 IMSNU 14100 KCTC 12330 CG 20106 1 more

NCBI tax ID(s) 298

Special Collections DSMZ KCTC CIP Literature strains

Links

Pseudomonas marginalis DSM 18529 is an aerobe, mesophilic, Gram-negative plant pathogen that was isolated from rusty root lesions of Korean ginseng.

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

Name and taxonomic classification

SI-ID 232819

KCTC 12330,CIP 108524,DSM 18529,CFBP 7186,LMG 29072,CCM 7510

@ref 20215

Last LPSN update 2025-12-16 09:50:01

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Pseudomonas

Species Pseudomonas marginalis

Full scientific name Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980)

Synonyms (2)

Pseudomonas panacis
"Bacterium marginale"

BacDive ID	Other strains from **Pseudomonas marginalis** (13)	Type strain
12863	P. marginalis CIBP, DSM 13124, ATCC 10844, NCPPB 667, CCUG ... (type strain)
12864	P. marginalis 289, 292, DSM 50275
137648	P. marginalis PP-5, CIP 103779, ATCC 13888, ICMP 8661, ...
141377	P. marginalis CCUG 1318, NCPPB 247
145155	P. marginalis CCUG 27768, IFO 3925, NRRL B-981, NBRC 3925
156505	P. marginalis CCUG 62222
157434	P. marginalis IMI 346520
157435	P. marginalis IMI 347520
157436	P. marginalis IMI 347524
157437	P. marginalis IMI 347528
161361	P. marginalis JCM 13460, ATCC 13889, CFBP 2038, ICMP 5709, ...
161408	P. marginalis JCM 13886, ATCC 13890, ICMP 8660, LMG 5042, ...
161409	P. marginalis JCM 13887, ATCC 13891, ICMP 8662, LMG 5044, ...

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
31450	negative	rod-shaped
67771	negative
121525	negative	rod-shaped
125438			92.917
125438	negative		99
125439	negative		97.7

Pigmentation

@ref	Production	Name
31450
121525		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7580	NUTRIENT AGAR (DSMZ Medium 1)	Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
7580	TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)	Medium recipe at MediaDive	Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
38280	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
121525	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7580	positive	growth	30	mesophilic
31450	positive	growth	04-35
31450	positive	optimum	19.5	psychrophilic
38280	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic
121525	positive	growth	10-30
121525	negative	growth	5
121525	negative	growth	37
121525	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
31450	aerobe
67771	aerobe
121525	obligate aerobe
125438	aerobe	95.011

Spore formation

@ref	Spore formation	Confidence
31450
125439		98.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31450	NaCl	positive	growth	<5 %
31450	NaCl	positive	optimum	2.5 %
121525	NaCl	positive	growth	0-4 %
121525	NaCl		growth	6 %
121525	NaCl		growth	8 %
121525	NaCl		growth	10 %

Observation

31450

Observationaggregates in clumps

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
31450	16449 ChEBI	alanine	+	carbon source
31450	22599 ChEBI	arabinose	+	carbon source
68369	29016 ChEBI	arginine	+	hydrolysis	from API 20NE
31450	22653 ChEBI	asparagine	+	carbon source
31450	35391 ChEBI	aspartate	+	carbon source
31450	16947 ChEBI	citrate	+	carbon source
121525	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
31450	27689 ChEBI	decanoate	+	carbon source
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
31450	17126 ChEBI	DL-carnitine	+	carbon source
31450	4853 ChEBI	esculin	+	hydrolysis
121525	4853 ChEBI	esculin	+	hydrolysis
68369	4853 ChEBI	esculin	+	hydrolysis	from API 20NE
31450	28757 ChEBI	fructose	+	carbon source
31450	28260 ChEBI	galactose	+	carbon source
68369	5291 ChEBI	gelatin	+	hydrolysis	from API 20NE
31450	24265 ChEBI	gluconate	+	carbon source
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
31450	17234 ChEBI	glucose	+	carbon source
31450	29987 ChEBI	glutamate	+	carbon source
31450	17754 ChEBI	glycerol	+	carbon source
31450	27570 ChEBI	histidine	+	carbon source
31450	17596 ChEBI	inosine	+	carbon source
31450	21217 ChEBI	L-alaninamide	+	carbon source
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
31450	18403 ChEBI	L-arabitol	+	carbon source
31450	24996 ChEBI	lactate	+	carbon source
31450	25017 ChEBI	leucine	+	carbon source
31450	25115 ChEBI	malate	+	carbon source
68369	25115 ChEBI	malate	+	assimilation	from API 20NE
31450	15792 ChEBI	malonate	+	carbon source
31450	29864 ChEBI	mannitol	+	carbon source
31450	37684 ChEBI	mannose	+	carbon source
31450	28053 ChEBI	melibiose	+	carbon source
31450	51850 ChEBI	methyl pyruvate	+	carbon source
68369	59640 ChEBI	N-acetylglucosamine	+	assimilation	from API 20NE
31450	17632 ChEBI	nitrate	+	reduction
121525	17632 ChEBI	nitrate	+	reduction
121525	17632 ChEBI	nitrate	-	respiration
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
121525	16301 ChEBI	nitrite	-	reduction
31450	18257 ChEBI	ornithine	+	carbon source
31450	17272 ChEBI	propionate	+	carbon source
31450	17822 ChEBI	serine	+	carbon source
31450	30911 ChEBI	sorbitol	+	carbon source
31450	30031 ChEBI	succinate	+	carbon source
31450	17992 ChEBI	sucrose	+	carbon source
31450	27082 ChEBI	trehalose	+	carbon source
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
31450	16704 ChEBI	uridine	+	carbon source
31450	27248 ChEBI	urocanic acid	+	carbon source

Antibiotic resistance

@ref	Metabolite	Is sensitive	Is resistant
121525	0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
121525	35581 ChEBI	indole

Metabolite tests

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

Enzymes

@ref	Value	Activity	Ec
31450	acid phosphatase	+	3.1.3.2
68382	acid phosphatase	+	3.1.3.2	from API zym
121525	alcohol dehydrogenase	+	1.1.1.1
31450	alkaline phosphatase	+	3.1.3.1
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
121525	amylase	+
68369	arginine dihydrolase	+	3.5.3.6	from API 20NE
121525	beta-galactosidase	-	3.2.1.23
68382	beta-galactosidase	-	3.2.1.23	from API zym
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
121525	caseinase	-	3.4.21.50
31450	catalase	+	1.11.1.6
121525	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31450	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
121525	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
31450	gelatinase	+
121525	gelatinase	+/-
68369	gelatinase	+		from API 20NE
121525	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
121525	lipase	-
68382	lipase (C 14)	-		from API zym
121525	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
121525	ornithine decarboxylase	-	4.1.1.17
121525	oxidase	+
121525	protease	-
68382	trypsin	+	3.4.21.4	from API zym
121525	tryptophan deaminase	-
121525	tween esterase	-
121525	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
121525	-	-	+	+	-	+	-	-	+	-	+	+	-	-	-	-	+	-	-	-

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
7580	+	-	-	+	-	+	+	-	+	+	+	+	+	+/-	+	+	-	+	+	-	+
7580	+	-	-	+	-	+	+	-	+	+	+	+	+	-	+	+	-	+	+	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
121525	not determinedn.d.	+	+	+	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	+	-	-	-	-	+	-	-	-	-	+	+	+	-	-	+	-	-	+	+	-	-	+	+	-	-	-	+	+	+	+	+	+	+	+	+	+	+	+	+	-	+	+	+	-	-	-	-	-	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	-	+	+	+	+	+	+	+	+	+	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent	Isolation date
7580	rusty root lesions of Korean ginseng	Republic of Korea	KOR	Asia
67771	From Ginseng	Republic of Korea	KOR	Asia
121525	Plant, Rusty root of Korea ginseng	Republic of Korea	KOR	Asia	2004

Taxonmaps

69479

Global distribution of 16S sequence AY787208 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	1631
Soil Samples	874
Animal Samples	3216
Plant Samples	2451
Total Samples	8172

Interaction and safety

Risk assessment

@ref	Pathogenicity plant	Biosafety level	Biosafety level comment
7580		1	Risk group (German classification) According to TRBA 466
121525		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	ASM785817v1 assembly for Pseudomonas marginalis DSM 18529	contig	GCA_007858175	307251.4	8117611271	298	69.73

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7580	Pseudomonas panacis strain CG20106 16S ribosomal RNA gene, partial sequence	AY787208	1499		307251
124043	Pseudomonas marginalis CIP 108524 gene for 16S ribosomal RNA, partial sequence.	LC409076	1418		298

GC content

31450

GC-content (mol%)61.4

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Pseudomonas marginalis DSM 18529
NCBI: GCA_007858175

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.70	no
125439	motility	BacteriaNetⓘ	yes	81.90	no
125439	gram_stain	BacteriaNetⓘ	negative	97.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	aerobe	59.10	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas panacis strain DSM 18529
PATRIC: 307251.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	yes
125438	anaerobic	anaerobicⓘ	no	98.86	no
125438	spore-forming	spore-formingⓘ	no	87.19	no
125438	aerobic	aerobicⓘ	yes	95.01	yes
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	92.92	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Genome analysis of Pseudomonas species reveals that Pseudomonas panacis Park et al. 2005 is a later heterotypic synonym of Pseudomonas marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980).	Kujur RRA, Deb S, Das SK	Int J Syst Evol Microbiol	10.1099/ijsem.0.005354	2022
Phylogeny	Pseudomonas panacis sp. nov., isolated from the surface of rusty roots of Korean ginseng.	Park YD, Lee HB, Yi H, Kim Y, Bae KS, Choi JE, Jung HS, Chun J	Int J Syst Evol Microbiol	10.1099/ijs.0.63592-0	2005

References

#7580	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18529
#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 )
#27753	IJSEM 1721 2005 ( DOI 10.1099/ijs.0.63592-0 , PubMed 16014508 )
#31450	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 #27753
#38280	; 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) .
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#121525	Collection of Institut Pasteur ; Curators of the CIP; CIP 108524
#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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Pseudomonas marginalis (DSM 18529, CIP 108524, IMSNU 14100)

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

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_007858175

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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