Name: Pseudomonas xanthomarina NRIC 0617
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13135

Type strain:

Species: Pseudomonas xanthomarina

Culture col. no.: NRIC 0617, DSM 18231, CCUG 46543, JCM 12468, KMM 1447, LMG 23572, CIP 109222

Strain history: CIP <- 2006, KMM

NCBI tax ID(s): 1403346 (strain), 271420 (species)

SI-ID 131488

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

Other strains from Pseudomonas xanthomarina

P. xanthomarina KO_13, DSM 30813

Section

Pseudomonas xanthomarina NRIC 0617 is an aerobe, mesophilic, motile bacterium that was isolated from ascidian Halocynthia aurantium.

motile
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Pseudomonadales*
	Family	*Pseudomonadaceae*
	Genus	*Pseudomonas*
	Species	**Pseudomonas xanthomarina**
	Full Scientific Name (LPSN)	Pseudomonas xanthomarina Romanenko et al. 2005

Synonym

Stutzerimonas xanthomarina

Information on morphological and physiological properties Morphology

[Ref.: #123968]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.999

[Ref.: #123968]	Cell shape	rod-shaped

[Ref.: #123968]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %98.258

Information on culture and growth conditions Culture and growth conditions

[Ref.: #7444]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #7444]

Culture medium growth

[Ref.: #7444]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7444]

Culture medium composition

expand / minimize

[Ref.: #7444]

Culture medium

BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)

[Ref.: #7444]

Culture medium growth

[Ref.: #7444]

Culture medium link

Medium recipe at MediaDive

[Ref.: #7444]

Culture medium composition

expand / minimize

[Ref.: #37485]

Culture medium

Marine agar (MA)

[Ref.: #37485]

Culture medium growth

[Ref.: #37485]

Culture medium composition

expand / minimize

[Ref.: #123968]

Culture medium

CIP Medium 13

[Ref.: #123968]

Culture medium growth

[Ref.: #123968]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #7444]	growth	28 °C
[Ref.: #37485]	growth	25 °C
[Ref.: #57257]	growth	30 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #7444]	Temperature range	mesophilic
[Ref.: #37485]	Temperature range	mesophilic
[Ref.: #57257]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #57257]	Oxygen tolerance	aerobe
[Ref.: #123968]	Oxygen tolerance	obligate aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.991

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #123968]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #123968]	nitrite ChEBI	+	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #123968]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	+	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	+	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE, API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #123968]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #123968]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #123968]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #7444]	24683	+	-	-	-	-	-	-	-	+	-	-	+	-	+	+	-	+	+	+	-	+
[Ref.: #7444]	23094	+	-	-	-	-	-	-	-	+	-	-	+	-	+	+	-	-	+	+	-	+

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #123968]	11728	-	+	+	+	-	+	-	-	-	-	-	+	+	-	-	-	-	-	-	+

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7444]	Sample type/isolated from	ascidian Halocynthia aurantium
[Ref.: #7444]	Host species	Halocynthia aurantium
[Ref.: #7444]	Geographic location (country and/or sea, region)	Sea of Japan, Peter the Great Bay
[Ref.: #7444]	Country	Russia
[Ref.: #7444]	Country ISO 3 Code	RUS
[Ref.: #7444]	Continent	Asia

[Ref.: #57257]	Sample type/isolated from	Ascidian (Halocynthia aurantium)
[Ref.: #57257]	Sampling date	1992-11-01
[Ref.: #57257]	Geographic location (country and/or sea, region)	The Sea of Japan,Troitsa Bay
[Ref.: #57257]	Country	Russia
[Ref.: #57257]	Country ISO 3 Code	RUS
[Ref.: #57257]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Seawater

[Ref.: #123968]	Sample type/isolated from	Ascidian Halocynthia aurantium
[Ref.: #123968]	Geographic location (country and/or sea, region)	Troitsa bay, Peter the Great bay, The Sea of Japan
[Ref.: #123968]	Country	Russian Federation
[Ref.: #123968]	Country ISO 3 Code	RUS
[Ref.: #123968]	Continent	Europe
[Ref.: #123968]	Isolation date	1992
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	#Marine
#Host	#Invertebrates (Other)	#Tunicata

What are isolation sources categories?

[Ref.: #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

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #7444]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123968]	Biosafety level	1	Risk group (French classification)

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7444]	Pseudomonas xanthomarina gene for 16S rRNA, partial sequence	AB176954	1464	ENA	271420 tax ID

Genome sequence information:

Only first 5 entries are displayed. Click here to see all.

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Stutzerimonas xanthomarina DSM 18231	GCA_900129835	contig	GenBank	1403346 tax ID
[Ref.: #66792]	Stutzerimonas xanthomarina LMG 23572	GCA_900108535	chromosome	GenBank	271420 tax ID	*
[Ref.: #66792]	Pseudomonas xanthomarina DSM 18231	1403346.6	wgs	PATRIC	1403346 tax ID	*
[Ref.: #66792]	Pseudomonas xanthomarina strain LMG 23572	271420.6	complete	PATRIC	271420 tax ID	*
[Ref.: #66792]	Pseudomonas xanthomarina LMG 23572	2675902960	draft	JGI IMG/M	271420 tax ID	*
[Ref.: #66792]	Pseudomonas xanthomarina DSM 18231	2687453778	draft	JGI IMG/M	1403346 tax ID	*

[Ref.: #7444]	GC-content	59.1 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67770]	GC-content	59.1 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Pseudomonas xanthomarina strain LMG 23572 PATRIC: 271420.6
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudomonas xanthomarina strain LMG 23572 PATRIC: 271420.6
[Ref.: #69480]	motile	yes	91.049	no
[Ref.: #69480]	gram-positive	no	98.799	no
[Ref.: #69480]	anaerobic	no	97.836	yes
[Ref.: #69480]	halophile	no	82.81	no
[Ref.: #69480]	spore-forming	no	95.778	no
[Ref.: #69480]	glucose-util	yes	89.925	yes
[Ref.: #69480]	aerobic	yes	90.848	no
[Ref.: #69480]	flagellated	yes	84.507	no
[Ref.: #69480]	thermophile	no	99.678	yes
[Ref.: #69480]	glucose-ferment	no	92.065	no

Availability in culture collections External links

[Ref.: #7444]

Culture collection no.

NRIC 0617, DSM 18231, CCUG 46543, JCM 12468, KMM 1447, LMG 23572, CIP 109222

[Ref.: #82343]

SI-ID 131488

Literature:

Only first 10 entries are displayed. Click here to see all.

Topic	Title	Authors	Journal	DOI	Year
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	*
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	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	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 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 .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#82343

Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.: StrainInfo: A central database for resolving microbial strain identifiers . ( DOI 10.60712/SI-ID131488.1 )

#123968 Collection of Institut Pasteur ; Curators of the CIP; CIP 109222
* These data were automatically processed and therefore are not curated

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Pseudomonas xanthomarina strain LMG 23572

Pseudomonas xanthomarina strain LMG 23572

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