Name: Paraburkholderia phytofirmans PsJN
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 1966

Type strain:

Species: Paraburkholderia phytofirmans

Strain Designation: PsJN

Culture col. no.: DSM 17436, CCUG 49060, LMG 22146, CIP 108762

Strain history: CIP <- 2005, CCUG <- 2004, A. Sessitsch, Seibersdorf, Austria: strain PsJN

NCBI tax ID(s): 261302 (species)

SI-ID 128227

LMG 22146, LMG 22487, CCUG 49060, CIP 108762, DSM 17436

Special Collections

Other strains from Paraburkholderia phytofirmans

Section

When using BacDive for research please cite our paper

Paraburkholderia phytofirmans PsJN is an aerobe, mesophilic, Gram-negative bacterium that was isolated from surface-sterilized onion roots.

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	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Burkholderiaceae*
	Genus	*Paraburkholderia*
	Species	**Paraburkholderia phytofirmans**
	Full Scientific Name (LPSN)	Paraburkholderia phytofirmans (Sessitsch et al. 2005) Sawana et al. 2015

Synonym

Burkholderia phytofirmans

Information on morphological and physiological properties Morphology

[Ref.: #31259]	Gram stain	negative
[Ref.: #121818]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %96.969

[Ref.: #31259]	Cell length	1.3 µm

[Ref.: #31259]	Cell width	0.65 µm

[Ref.: #31259]	Cell shape	rod-shaped
[Ref.: #121818]	Cell shape	oval-shaped

[Ref.: #31259]	Motility	yes
[Ref.: #121818]	Motility	yes

[Ref.: #6984]	Incubation period	2-3 days

[Ref.: #58457]	Incubation period	2 days

[Ref.: #31259]

Pigment production

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6984]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #6984]

Culture medium growth

[Ref.: #6984]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6984]

Culture medium composition

expand / minimize

[Ref.: #41979]

Culture medium

MEDIUM 6 - Columbia agar with 10 % horse blood

[Ref.: #41979]

Culture medium growth

[Ref.: #41979]

Culture medium composition

expand / minimize

[Ref.: #121818]

Culture medium

CIP Medium 45

[Ref.: #121818]

Culture medium growth

[Ref.: #121818]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #121818]

Culture medium

CIP Medium 6

[Ref.: #121818]

Culture medium growth

[Ref.: #121818]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #6984]	growth	30 °C
[Ref.: #31259]	growth	30-36 °C
[Ref.: #31259]	optimum	30 °C
[Ref.: #41979]	growth	30 °C
[Ref.: #58457]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #58457]	Oxygen tolerance	aerobe
[Ref.: #121818]	Oxygen tolerance	obligate aerobe
[Ref.: #125438]	Oxygen tolerance	aerobe Confidence in %91.622
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %99.2

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #31259]		NaCl		optimum	0.5	%

	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.: #31259]	fructose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #31259]	glucose 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.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #121818]	nitrate ChEBI	-	reduction
[Ref.: #68369]	nitrate ChEBI	-	reduction	* from API 20NE
[Ref.: #121818]	nitrite ChEBI	-	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #31259]	xylose ChEBI	+	carbon source
	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.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #121818]	alcohol dehydrogenase	-	1.1.1.1
[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.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #6984]	catalase	+	1.11.1.6
[Ref.: #121818]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #31259]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #6984]	cytochrome-c oxidase	-	1.9.3.1
[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.: #121818]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #121818]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #121818]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #121818]	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.: #6984]	27725	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+	+	+	-	+	+
[Ref.: #6984]	27223	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+	+	+	+	+	+
[Ref.: #6984]	26465	-	-	-	-	-	+/-	-	+	+	+	+	+	+	-	+	-	+	+	-	-	+
[Ref.: #6984]	26464	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+/-	+/-	+	-	+	not determinedn.d.

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.: #121818]	11439	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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

[Ref.: #6984]	Sample type/isolated from	surface-sterilized onion roots
[Ref.: #6984]	Country	Canada
[Ref.: #6984]	Country ISO 3 Code	CAN
[Ref.: #6984]	Continent	North America

[Ref.: #58457]	Sample type/isolated from	Onion roots,surface-sterilized

[Ref.: #121818]	Sample type/isolated from	Plant, Onion roots, surface-sterilized
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AY497470 (>99% sequence identity) for Paraburkholderia from Microbeatlas

Aquatic Samples	44
Soil Samples	579
Animal Samples	56
Plant Samples	43
Total Samples	722

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

[Ref.: #6984]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #121818]	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.: #6984]	Burkholderia phytofirmans strain PsJN 16S ribosomal RNA gene, partial sequence	AY497470	1488	GenBank ENA	398527 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paraburkholderia phytofirmans PsJN	GCA_000020125	complete	GenBank ENA	398527 tax ID	*
[Ref.: #66792]	Paraburkholderia phytofirmans PsJN	398527.31	plasmid	PATRIC	398527 tax ID	*
[Ref.: #66792]	Paraburkholderia phytofirmans PsJN	642555113	complete	JGI IMG/M	398527 tax ID	*

[Ref.: #6984]

GC-content

61 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Paraburkholderia phytofirmans PsJN PsJN NCBI: GCA_000020125.1
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.969	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.361	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	91.622	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	85.296	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.986	no
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	85.301	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paraburkholderia phytofirmans PsJN IMG: 642555113
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	78.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	52.7
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	66.8
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	99.2

Availability in culture collections External links

[Ref.: #6984]

Culture collection no.

DSM 17436, CCUG 49060, LMG 22146, CIP 108762

[Ref.: #71611]

SI-ID 128227

Literature:

Topic	Title	Authors	Journal	DOI	Year
Enzymology	Imidase catalyzing desymmetric imide hydrolysis forming optically active 3-substituted glutaric acid monoamides for the synthesis of gamma-aminobutyric acid (GABA) analogs.	Nojiri M, Hibi M, Shizawa H, Horinouchi N, Yasohara Y, Takahashi S, Ogawa J	Appl Microbiol Biotechnol	10.1007/s00253-015-6812-x	2015	*
Phylogeny	Burkholderia ginsengisoli sp. nov., a beta-glucosidase-producing bacterium isolated from soil of a ginseng field.	Kim HB, Park MJ, Yang HC, An DS, Jin HZ, Yang DC	Int J Syst Evol Microbiol	10.1099/ijs.0.64387-0	2006	*
Phylogeny	Burkholderia phytofirmans sp. nov., a novel plant-associated bacterium with plant-beneficial properties.	Sessitsch A, Coenye T, Sturz AV, Vandamme P, Barka EA, Salles JF, Van Elsas JD, Faure D, Reiter B, Glick BR, Wang-Pruski G, Nowak J	Int J Syst Evol Microbiol	10.1099/ijs.0.63149-0	2005	*

References

#6984

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17436

#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 )

#31259

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 #27581 (see below)

#41979 ; Curators of the CIP;
#58457 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 49060

#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) .

#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 .

#71611

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-ID128227.1 )

#121818 Collection of Institut Pasteur ; Curators of the CIP; CIP 108762

#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 .

#27581

IJSEM 1187 2005 ( DOI 10.1099/ijs.0.63149-0 , PubMed 15879253 )

* These data were automatically processed and therefore are not curated

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Paraburkholderia phytofirmans PsJN PsJN

Paraburkholderia phytofirmans PsJN

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