Stutzerimonas xanthomarina (NRIC 0617, DSM 18231, CCUG 46543)

Name: Stutzerimonas xanthomarina (NRIC 0617, DSM 18231, CCUG 46543)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 13135

Type strain

Culture col. no. NRIC 0617 DSM 18231 CCUG 46543 JCM 12468 KMM 1447 2 more

NCBI tax ID(s) 271420

Special Collections DSMZ CCUG JCM CIP

History <- JCM <- M. Uchino <- KMM 2006, KMM M. Uchino <-- KMM 1447. CIP <- 2006, KMM

Links

Stutzerimonas xanthomarina NRIC 0617 is an aerobe, mesophilic, Gram-negative prokaryote that was isolated from ascidian Halocynthia aurantium.

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

Name and taxonomic classification

SI-ID 131488

CCUG 46543,JCM 12468,DSM 18231,LMG 23572,CIP 109222

@ref 20215

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

Domain Pseudomonadati

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Pseudomonadales

Family Pseudomonadaceae

Genus Stutzerimonas

Species Stutzerimonas xanthomarina

Full scientific name Stutzerimonas xanthomarina (Romanenko et al. 2005) Lalucat et al. 2022

Synonyms (1)

Pseudomonas xanthomarina

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
123968	negative	rod-shaped
125438	negative		100
125439	negative		99.9
125439			90.4

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
7444	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
7444	BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)	Medium recipe at MediaDive	Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water
37485	Marine agar (MA)		Distilled water make up to (1000.000 ml);Marine agar (55.100 g)
123968	CIP Medium 13	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7444	positive	growth	28	mesophilic
37485	positive	growth	25	mesophilic
57257	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
57257	aerobe
123968	obligate aerobe
125438	aerobe	90.875
125439	obligate aerobe	97.4

Spore formation

@ref	Spore formation	Confidence
125439		99.6

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
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
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
123968	17632 ChEBI	nitrate	+	reduction
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
123968	16301 ChEBI	nitrite	+	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
123968	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
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
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
123968	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
68369	gelatinase	-		from API 20NE
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
123968	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
123968	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
123968	-	+	+	+	-	+	-	-	-	-	-	+	+	-	-	-	-	-	-	+

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
7444	+	-	-	-	-	-	-	-	+	-	-	+	-	+	+	-	+	+	+	-	+
7444	+	-	-	-	-	-	-	-	+	-	-	+	-	+	+	-	-	+	+	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Tunicata

Isolation

@ref	Sample type	Host species	Geographic location	Country	Country ISO 3 Code	Continent	Sampling date	Isolation date
7444	ascidian Halocynthia aurantium	Halocynthia aurantium	Sea of Japan, Peter the Great Bay	Russia	RUS	Asia
57257	Ascidian (Halocynthia aurantium)		The Sea of Japan,Troitsa Bay	Russia	RUS	Asia	1992-11-01
67770	Seawater
123968	Ascidian Halocynthia aurantium		Troitsa bay, Peter the Great bay, The Sea of Japan	Russian Federation	RUS	Europe		1992

Taxonmaps

69479

Global distribution of 16S sequence AB176954 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	64
Soil Samples	62
Animal Samples	92
Plant Samples	25
Total Samples	243

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7444	1	Risk group (German classification) According to TRBA 466
123968	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	IMG-taxon 2675902960 annotated assembly for Stutzerimonas xanthomarina LMG 23572	chromosome	GCA_900108535	271420.6	2675902960	271420	89.13
67770	IMG-taxon 2687453778 annotated assembly for Stutzerimonas xanthomarina DSM 18231	contig	GCA_900129835	1403346.6	2687453778	1403346	75.91
66792	ASM2432833v1 assembly for Stutzerimonas xanthomarina DSM 18231	contig	GCA_024328335	271420.21	8119110453	271420	70.79

16S sequences

@ref	Description	Accession	Length	NCBI tax ID
7444	Pseudomonas xanthomarina gene for 16S rRNA, partial sequence	AB176954	1464	271420
124043	Pseudomonas xanthomarina strain DSM 18231 16S ribosomal RNA gene, partial sequence.	MN901207	612	271420
124043	Stutzerimonas xanthomarina strain DSM 18231 16S ribosomal RNA gene, partial sequence.	PQ524550	599	271420

GC content

@ref	GC-content (mol%)	Method
7444	59.1	thermal denaturation, midpoint method (Tm)
67770	59.1	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: Stutzerimonas xanthomarina DSM 18231
NCBI: GCA_900129835

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.60	no
125439	motility	BacteriaNetⓘ	yes	90.40	no
125439	gram_stain	BacteriaNetⓘ	negative	99.90	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	97.40	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Pseudomonas xanthomarina strain LMG 23572
PATRIC: 271420.6

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	100.00	no
125438	anaerobic	anaerobicⓘ	no	98.89	no
125438	spore-forming	spore-formingⓘ	no	84.62	no
125438	aerobic	aerobicⓘ	yes	90.88	no
125438	thermophilic	thermophileⓘ	no	98.50	yes
125438	flagellated	motile2+ⓘ	yes	89.44	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative Genomic Analysis of Three Pseudomonas Species Isolated from the Eastern Oyster (Crassostrea virginica) Tissues, Mantle Fluid, and the Overlying Estuarine Water Column.	Pathak A, Stothard P, Chauhan A.	Microorganisms	10.3390/microorganisms9030490	2021
Metabolism	The genome of Alcaligenes aquatilis strain BU33N: Insights into hydrocarbon degradation capacity.	Mahjoubi M, Aliyu H, Cappello S, Naifer M, Souissi Y, Cowan DA, Cherif A.	PLoS One	10.1371/journal.pone.0221574	2019
	Isolation, characterization, and genetic manipulation of cold-tolerant, manganese-oxidizing Pseudomonas sp. strains.	Jones I, Vermillion D, Tracy C, Denton R, Davis R, Geszvain K.	Appl Environ Microbiol	10.1128/aem.00510-24	2024
Metabolism	Structure of polysaccharide moiety of Pseudomonas xanthomarina KMM 1447(T) lipopolysaccharide.	Kokoulin MS, Tomshich SV, Kalinovsky AI, Romanenko LA, Komandrova NA	Carbohydr Res	10.1016/j.carres.2016.07.020	2016
Phylogeny	Monitoring of oil pollution at Gemsa Bay and bioremediation capacity of bacterial isolates with biosurfactants and nanoparticles.	El-Sheshtawy HS, Khalil NM, Ahmed W, Abdallah RI	Mar Pollut Bull	10.1016/j.marpolbul.2014.07.059	2014
Phylogeny	Pseudomonas lopnurensis sp. nov., an endophytic bacterium isolated from Populus euphratica at the ancient Ugan river.	Mamtimin T, Anwar N, Abdurahman M, Kurban M, Rozahon M, Mamtimin H, Hamood B, Rahman E, Wu M	Antonie Van Leeuwenhoek	10.1007/s10482-021-01524-8	2021
Phylogeny	Pseudomonas nitrititolerans sp. nov., a nitrite-tolerant denitrifying bacterium isolated from a nitrification/denitrification bioreactor.	Peng JS, Liu Y, Yan L, Hou TT, Liu HC, Zhou YG, Liu ZP	Int J Syst Evol Microbiol	10.1099/ijsem.0.003516	2019
Phylogeny	Pseudomonas zhaodongensis sp. nov., isolated from saline and alkaline soils.	Zhang L, Pan Y, Wang K, Zhang X, Zhang C, Zhang S, Fu X, Jiang J	Int J Syst Evol Microbiol	10.1099/ijs.0.000057	2015
Phylogeny	Pseudomonas kunmingensis sp. nov., an exopolysaccharide-producing bacterium isolated from a phosphate mine.	Xie F, Ma H, Quan S, Liu D, Chen G, Chao Y, Qian S	Int J Syst Evol Microbiol	10.1099/ijs.0.055632-0	2013
Phylogeny	Pseudomonas xanthomarina sp. nov., a novel bacterium isolated from marine ascidian.	Romanenko LA, Uchino M, Falsen E, Lysenko AM, Zhukova NV, Mikhailov VV	J Gen Appl Microbiol	10.2323/jgam.51.65	2005
Phylogeny	Pseudomonas marianensis sp. nov., a marine bacterium isolated from deep-sea sediments of the Mariana Trench.	Yang Y, Gao Y, Liu Y, Liu B, Wang D, Xu Y, Wei Y	Arch Microbiol	10.1007/s00203-022-03250-9	2022

References

#7444	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18231
#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 )
#37485	; Curators of the CIP;
#57257	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 46543
#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 .
#123968	Collection of Institut Pasteur ; Curators of the CIP; CIP 109222
#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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Stutzerimonas xanthomarina (NRIC 0617, DSM 18231, CCUG 46543)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Metabolite utilization

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_900108535

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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