Name: Pseudomonas taeanensis MS-3
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 24433

Type strain:

Species: Pseudomonas taeanensis

Strain Designation: MS-3

Culture col. no.: DSM 25633, JCM 16046, KACC 14032, KCTC 22612, NBRL 105641, CCUG 69583

Strain history: H.-Y. Kahng MS-3.

NCBI tax ID(s): 1395571 (strain), 574962 (species)

SI-ID 374142

JCM 16046, KACC 14032, KCTC 22612

Special Collections

Section

Pseudomonas taeanensis MS-3 is an aerobe, Gram-negative, motile bacterium that was isolated from crude oil-contaminated seawater near the shore.

Gram-negative
motile
rod-shaped
aerobe
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 taeanensis**
	Full Scientific Name (LPSN)	Pseudomonas taeanensis Lee et al. 2010

Information on morphological and physiological properties Morphology

[Ref.: #29659]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.5

[Ref.: #29659]	Cell length	1.8-2.5 µm

[Ref.: #29659]	Cell width	0.8-1 µm

[Ref.: #29659]	Cell shape	rod-shaped

[Ref.: #29659]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %91.57

[Ref.: #29659]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21136]

Culture medium

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

[Ref.: #21136]

Culture medium growth

[Ref.: #21136]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21136]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21136]	growth	28 °C
[Ref.: #29659]	growth	04-30 °C
[Ref.: #29659]	optimum	25-28 °C
[Ref.: #63628]	growth	30 °C
[Ref.: #67770]	growth	30 °C

	pH	Kind of pH		pH
[Ref.: #29659]			optimum	6.5-8
[Ref.: #29659]			growth	6-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29659]	Oxygen tolerance	aerobe
[Ref.: #63628]	Oxygen tolerance	aerobe
[Ref.: #69480]	Oxygen tolerance	aerobe Confidence in %90.994

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #29659]		NaCl		growth	0-5	%
[Ref.: #29659]		NaCl		optimum	0-5	%

[Ref.: #29659]	Observation	aggregates in chains
[Ref.: #67770]	Observation	quinones: Q-9

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #29659]	citrate ChEBI	+	carbon source
[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.: #29659]	gluconate ChEBI	+	carbon source
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #29659]	glucose ChEBI	+	carbon source
[Ref.: #29659]	glycerol ChEBI	+	carbon source
[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.: #29659]	mannitol ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #29659]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[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.: #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.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #29659]	catalase	+	1.11.1.6
[Ref.: #29659]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

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.: #21136]	23029	+	-	-	-	-	-	-	-	+	-	-	+	-	-	+	+	-	+	+	-	+

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	alginate biosynthesis	100	4 of 4
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	threonine metabolism	100	10 of 10
[Ref.: #66794]	octane oxidation	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	butanoate fermentation	100	4 of 4
[Ref.: #66794]	propanol degradation	100	7 of 7
[Ref.: #66794]	L-lactaldehyde degradation	100	3 of 3
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	ubiquinone biosynthesis	100	7 of 7
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	glutamate and glutamine metabolism	92.86	26 of 28
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	4-hydroxymandelate degradation	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	molybdenum cofactor biosynthesis	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	alanine metabolism	86.21	25 of 29
[Ref.: #66794]	citric acid cycle	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	heme metabolism	85.71	12 of 14
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	phenol degradation	85	17 of 20
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	phenylalanine metabolism	84.62	11 of 13
[Ref.: #66794]	NAD metabolism	83.33	15 of 18
[Ref.: #66794]	arginine metabolism	83.33	20 of 24
[Ref.: #66794]	vitamin B6 metabolism	81.82	9 of 11
[Ref.: #66794]	proline metabolism	81.82	9 of 11
[Ref.: #66794]	3-chlorocatechol degradation	80	4 of 5
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	phenylacetate degradation (aerobic)	80	4 of 5
[Ref.: #66794]	polyamine pathway	78.26	18 of 23
[Ref.: #66794]	lipid A biosynthesis	77.78	7 of 9
[Ref.: #66794]	sulfate reduction	76.92	10 of 13
[Ref.: #66794]	methionine metabolism	76.92	20 of 26
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	histidine metabolism	75.86	22 of 29
[Ref.: #66794]	carnitine metabolism	75	6 of 8
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	ketogluconate metabolism	75	6 of 8
[Ref.: #66794]	lipid metabolism	74.19	23 of 31
[Ref.: #66794]	lysine metabolism	73.81	31 of 42
[Ref.: #66794]	tryptophan metabolism	73.68	28 of 38
[Ref.: #66794]	purine metabolism	73.4	69 of 94
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	urea cycle	69.23	9 of 13
[Ref.: #66794]	androgen and estrogen metabolism	68.75	11 of 16
[Ref.: #66794]	non-pathway related	68.42	26 of 38
[Ref.: #66794]	glycolate and glyoxylate degradation	66.67	4 of 6
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	3-phenylpropionate degradation	66.67	10 of 15
[Ref.: #66794]	d-mannose degradation	66.67	6 of 9
[Ref.: #66794]	nitrate assimilation	66.67	6 of 9
[Ref.: #66794]	cysteine metabolism	66.67	12 of 18
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	methane metabolism	66.67	2 of 3
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	pyrimidine metabolism	64.44	29 of 45
[Ref.: #66794]	tyrosine metabolism	64.29	9 of 14
[Ref.: #66794]	glutathione metabolism	64.29	9 of 14
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	oxidative phosphorylation	62.64	57 of 91
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	hydrogen production	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	gallate degradation	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
[Ref.: #66794]	isoprenoid biosynthesis	57.69	15 of 26
[Ref.: #66794]	metabolism of disaccharids	54.55	6 of 11
[Ref.: #66794]	phenylpropanoid biosynthesis	53.85	7 of 13
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	lactate fermentation	50	2 of 4
[Ref.: #66794]	cyclohexanol degradation	50	2 of 4
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	aminopropanol phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	pantothenate biosynthesis	50	3 of 6
[Ref.: #66794]	catecholamine biosynthesis	50	2 of 4
[Ref.: #66794]	selenocysteine biosynthesis	50	3 of 6
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	resorcinol degradation	50	1 of 2
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	glycine metabolism	50	5 of 10
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	allantoin degradation	44.44	4 of 9
[Ref.: #66794]	degradation of pentoses	42.86	12 of 28
[Ref.: #66794]	vitamin B12 metabolism	41.18	14 of 34
[Ref.: #66794]	creatinine degradation	40	2 of 5
[Ref.: #66794]	arachidonate biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	factor 420 biosynthesis	40	2 of 5
[Ref.: #66794]	glycogen metabolism	40	2 of 5
[Ref.: #66794]	4-hydroxyphenylacetate degradation	40	4 of 10
[Ref.: #66794]	degradation of sugar acids	40	10 of 25
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	degradation of hexoses	38.89	7 of 18
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	38.46	5 of 13
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	sulfoquinovose degradation	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	bile acid biosynthesis, neutral pathway	29.41	5 of 17
[Ref.: #66794]	benzoyl-CoA degradation	28.57	2 of 7
[Ref.: #66794]	chlorophyll metabolism	27.78	5 of 18
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	carotenoid biosynthesis	22.73	5 of 22
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #21136]	Sample type/isolated from	crude oil-contaminated seawater near the shore
[Ref.: #21136]	Geographic location (country and/or sea, region)	Taean area
[Ref.: #21136]	Country	Republic of Korea
[Ref.: #21136]	Country ISO 3 Code	KOR
[Ref.: #21136]	Continent	Asia

[Ref.: #63628]	Sample type/isolated from	Seashore,oil-contaminated
[Ref.: #63628]	Geographic location (country and/or sea, region)	Taean
[Ref.: #63628]	Country	Republic of Korea
[Ref.: #63628]	Country ISO 3 Code	KOR
[Ref.: #63628]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Crude oil-contaminated seawater in the Taean area of Korea
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	#Oil (Fuel)
#Engineered	#Industrial	#Oil reservoir
#Environmental	#Aquatic	#Marine
#Environmental	#Terrestrial	#Geologic

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence FJ424813 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	66
Soil Samples	79
Animal Samples	64
Plant Samples	42
Total Samples	251

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

[Ref.: #21136]

Biosafety level

Risk group (German classification)
According to TRBA 466

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.: #21136]	Pseudomonas taeanensis MS-3 16S ribosomal RNA gene, partial sequence	FJ424813	1528	GenBank ENA	1395571 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Pseudomonas taeanensis MS-3	GCA_000498575	contig	GenBank ENA	1395571 tax ID
[Ref.: #66792]	Pseudomonas taeanensis MS-3	1395571.3	wgs	PATRIC	1395571 tax ID	*

[Ref.: #21136]	GC-content	57.6 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29659]	GC-content	57.6 mol%

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

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Pseudomonas taeanensis MS-3 PATRIC: 1395571.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	99.5	no
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	98.923	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.099	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	90.994	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	99.49	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	91.57	no

Availability in culture collections External links

[Ref.: #21136]

Culture collection no.

DSM 25633, JCM 16046, KACC 14032, KCTC 22612, NBRL 105641, CCUG 69583

[Ref.: #88312]

SI-ID 374142

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudomonas tumuqii sp. nov., isolated from greenhouse soil.	Kong D, Li Q, Zhou Y, Wang Y, Jiang X, Wang Z, Ruan Z	Arch Microbiol	10.1007/s00203-022-02869-y	2022	*
Phylogeny	Pseudomonas taeanensis sp. nov., isolated from a crude oil-contaminated seashore.	Lee DH, Moon SR, Park YH, Kim JH, Kim H, Parales RE, Kahng HY	Int J Syst Evol Microbiol	10.1099/ijs.0.018093-0	2010	*
Genetics	Draft Genome Sequence of Petroleum Oil-Degrading Marine Bacterium Pseudomonas taeanensis Strain MS-3, Isolated from a Crude Oil-Contaminated Seashore.	Lee SY, Kim SH, Lee DG, Shin S, Yun SH, Choi CW, Chung YH, Choi JS, Kahng HY, Kim SI	Genome Announc	10.1128/genomeA.00818-13	2014	*

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 )

#21136

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25633

#29659

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 #26047 (see below)

#63628 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 69583

#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) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#68369

Automatically annotated from API 20NE .

#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) .

#88312

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-ID374142.1 )

#26047

IJSEM 2719 2015 ( DOI 10.1099/ijs.0.018093-0 , PubMed 20061499 )

* These data were automatically processed and therefore are not curated

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