Name: Pseudomonas thivervalensis CCUG 54622
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 13066

Type strain:

Species: Pseudomonas thivervalensis

Culture col. no.: CCUG 54622, DSM 13194, CFBP 11261, JCM 11941, LMG 21626, CIP 109843, CFBP 5754

Strain history: CIP <- 2008, CFBP <- W. Achouak, UMR 163 CNRS-CEA, Saint-Paul-les-Durance, France: strain CFBP 11261

NCBI tax ID(s): 86265 (species)

SI-ID 49436

DSM 13194, CFBP 11261, LMG 21626, JCM 11941, CCUG 54622, CFBP 5754, CIP 109843, NCPPB 4260

Section

Pseudomonas thivervalensis CCUG 54622 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from rhizoplane of Brassica napus.

Gram-negative
motile
rod-shaped
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 thivervalensis**
	Full Scientific Name (LPSN)	Pseudomonas thivervalensis Achouak et al. 2000

Information on morphological and physiological properties Morphology

[Ref.: #123529]	Gram stain	negative

[Ref.: #123529]	Cell shape	rod-shaped

[Ref.: #123529]	Motility	yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #4964]

Culture medium

REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)

[Ref.: #4964]

Culture medium growth

[Ref.: #4964]

Culture medium link

Medium recipe at MediaDive

[Ref.: #4964]

Culture medium composition

expand / minimize

[Ref.: #37857]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37857]

Culture medium growth

[Ref.: #37857]

Culture medium composition

expand / minimize

[Ref.: #123529]

Culture medium

CIP Medium 328

[Ref.: #123529]

Culture medium growth

[Ref.: #123529]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #123529]

Culture medium

CIP Medium 72

[Ref.: #123529]

Culture medium growth

[Ref.: #123529]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #4964]	growth	30 °C
[Ref.: #37857]	growth	25 °C
[Ref.: #60264]	growth	30 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #4964]	Temperature range	mesophilic
[Ref.: #37857]	Temperature range	mesophilic
[Ref.: #60264]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #60264]	Oxygen tolerance	aerobe
[Ref.: #123529]	Oxygen tolerance	obligate aerobe

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[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.: #123529]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #123529]	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.: #123529]		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.: #123529]	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.: #123529]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #123529]	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.: #4964]	22993	+	-	-	-	-	-	+	-	+	+	+	+	+	-	+	+	-	+	+	-	+

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.: #123529]	12153	-	-	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #4964]	Sample type/isolated from	rhizoplane of Brassica napus
[Ref.: #4964]	Host species	Brassica napus
[Ref.: #4964]	Geographic location (country and/or sea, region)	Sexy-les-Bois
[Ref.: #4964]	Country	France
[Ref.: #4964]	Country ISO 3 Code	FRA
[Ref.: #4964]	Continent	Europe

[Ref.: #60264]	Sample type/isolated from	Rhizoplane of Brassica napus
[Ref.: #60264]	Country	France
[Ref.: #60264]	Country ISO 3 Code	FRA
[Ref.: #60264]	Continent	Europe

[Ref.: #67770]	Sample type/isolated from	Rhizoplane of Brassica napus
[Ref.: #67770]	Host species	Brassica napus
[Ref.: #67770]	Country	France
[Ref.: #67770]	Country ISO 3 Code	FRA
[Ref.: #67770]	Continent	Europe

[Ref.: #123529]	Sample type/isolated from	Environment, Brassica napus, rhizosphere
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizoplane

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF100323 (>99% sequence identity) for Pseudomonas from Microbeatlas

Aquatic Samples	8731
Soil Samples	16904
Animal Samples	11521
Plant Samples	5158
Total Samples	42314

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

[Ref.: #4964]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #123529]	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.: #4964]	Pseudomonas thivervalensis 16S ribosomal RNA gene, partial sequence	AF100323	1430	ENA	86265 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]	Pseudomonas thivervalensis DSM 13194	GCA_001269655	contig	GenBank	86265 tax ID
[Ref.: #67770]	Pseudomonas thivervalensis LMG 21626	GCA_001637285	contig	GenBank	86265 tax ID
[Ref.: #66792]	Pseudomonas thivervalensis DSM 13194	GCA_900102295	chromosome	GenBank	86265 tax ID	*
[Ref.: #66792]	Pseudomonas thivervalensis strain LMG 21626	86265.5	wgs	PATRIC	86265 tax ID	*
[Ref.: #66792]	Pseudomonas thivervalensis LMG 21626	2744054620	draft	JGI IMG/M	86265 tax ID	*
[Ref.: #66792]	Pseudomonas thivervalensis DSM 13194	2639762509	draft	JGI IMG/M	86265 tax ID	*

[Ref.: #67770]

GC-content

60.8 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 Diaspora project based on: Pseudomonas thivervalensis DSM 13194 NCBI: GCA_900102295.1
[Ref.: #69480]	motile	yes	91.086	no
[Ref.: #69480]	flagellated	yes	81.996	no
[Ref.: #69480]	gram-positive	no	98.356	no
[Ref.: #69480]	anaerobic	no	98.452	no
[Ref.: #69480]	aerobic	yes	93.55	no
[Ref.: #69480]	halophile	no	91.395	no
[Ref.: #69480]	spore-forming	no	95.742	no
[Ref.: #69480]	glucose-ferment	no	89.163	yes
[Ref.: #69480]	thermophile	no	99.839	no
[Ref.: #69480]	glucose-util	yes	95.317	yes

Availability in culture collections External links

[Ref.: #4964]

Culture collection no.

CCUG 54622, DSM 13194, CFBP 11261, JCM 11941, LMG 21626, CIP 109843, CFBP 5754

[Ref.: #82276]

SI-ID 49436

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Pseudomonas canavaninivorans sp. nov., isolated from bean rhizosphere.	Hauth F, Buck H, Hartig JS	Int J Syst Evol Microbiol	10.1099/ijsem.0.005203	2022	*
Phylogeny	Pseudomonas bijieensis sp. nov., isolated from cornfield soil.	Liang J, Wang S, Yiming A, Fu L, Ahmad I, Chen G, Zhu B	Int J Syst Evol Microbiol	10.1099/ijsem.0.004676	2021	*
Phylogeny	Pseudomonas viciae sp. nov., isolated from rhizosphere of broad bean.	Zhao H, Ma Y, Wu X, Zhang L	Int J Syst Evol Microbiol	10.1099/ijsem.0.004373	2020	*
Metabolism	Pyoverdine and histicorrugatin-mediated iron acquisition in Pseudomonas thivervalensis.	Matthijs S, Brandt N, Ongena M, Achouak W, Meyer JM, Budzikiewicz H	Biometals	10.1007/s10534-016-9929-1	2016	*
Phylogeny	Pseudomonas brassicacearum sp. nov. and Pseudomonas thivervalensis sp. nov., two root-associated bacteria isolated from Brassica napus and Arabidopsis thaliana.	Achouak W, Sutra L, Heulin T, Meyer JM, Fromin N, Degraeve S, Christen R, Gardan L	Int J Syst Evol Microbiol	10.1099/00207713-50-1-9	2000	*

References

#4964

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 13194

#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 )

#37857 ; Curators of the CIP;
#60264 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54622

#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) .

#82276

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-ID49436.1 )

#123529 Collection of Institut Pasteur ; Curators of the CIP; CIP 109843
* These data were automatically processed and therefore are not curated

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Pseudomonas thivervalensis DSM 13194

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