Paraburkholderia phytofirmans (DSM 17436, CCUG 49060, LMG 22146)

Name: Paraburkholderia phytofirmans (DSM 17436, CCUG 49060, LMG 22146)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 1966

Type strain

Strain Designation PsJN

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

NCBI tax ID(s) 261302

Special Collections DSMZ CCUG CIP Literature strains

History <- A. Sessitsch, ARC Seibersdorf Research, Austria; PsJN <- J. Nowak CIP <- 2005, CCUG <- 2004, A. Sessitsch, Seibersdorf, Austria: strain PsJN

Links

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

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

Name and taxonomic classification

SI-ID 128227

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

@ref 20215

Last LPSN update 2026-02-09 11:18:13

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Burkholderiaceae

Genus Paraburkholderia

Species Paraburkholderia phytofirmans

Full scientific name Paraburkholderia phytofirmans (Sessitsch et al. 2005) Sawana et al. 2015

Synonyms (1)

Burkholderia phytofirmans

BacDive ID	Other strains from **Paraburkholderia phytofirmans** (1)	Type strain
158058	P. phytofirmans BS 115, DSM 103130

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
31259	negative	1.3 µm	0.65 µm	rod-shaped
121818	negative			oval-shaped
125438	negative				96.969

Colony morphology

@ref	Incubation period
6984	2-3 days
58457	2 days
121818

Pigmentation

31259

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6984	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
41979	MEDIUM 6 - Columbia agar with 10 % horse blood		Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
121818	CIP Medium 45	Medium recipe at CIP
121818	CIP Medium 6	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
6984	positive	growth	30
31259	positive	growth	30-36
31259	positive	optimum	30
41979	positive	growth	30
58457	positive	growth	30

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
58457	aerobe
121818	obligate aerobe
125438	aerobe	91.622
125439	obligate aerobe	99.2

Halophily

@ref	Salt	Growth	Tested relation	Concentration
31259	NaCl	positive	optimum	0.5 %

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
31259	28757 ChEBI	fructose	+	carbon source
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
31259	17234 ChEBI	glucose	+	carbon source
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
121818	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
121818	16301 ChEBI	nitrite	-	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE
31259	18222 ChEBI	xylose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

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
121818	alcohol dehydrogenase	-	1.1.1.1
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
68382	beta-glucuronidase	-	3.2.1.31	from API zym
6984	catalase	+	1.11.1.6
121818	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
31259	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
6984	cytochrome-c oxidase	-	1.9.3.1
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
121818	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
121818	ornithine decarboxylase	-	4.1.1.17
121818	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
121818	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
121818	-	+	+	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-

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
6984	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+	+	+	-	+	+
6984	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+	+	+	+	+	+
6984	-	-	-	-	-	+/-	-	+	+	+	+	+	+	-	+	-	+	+	-	-	+
6984	-	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+/-	+/-	+	-	+	not determinedn.d.

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Root (Rhizome)
#Host Body-Site	#Plant	#Sterilized plant part

Isolation

@ref	Sample type	Country	Country ISO 3 Code	Continent
6984	surface-sterilized onion roots	Canada	CAN	North America
58457	Onion roots,surface-sterilized
121818	Plant, Onion roots, surface-sterilized

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6984	1	Risk group (German classification) According to TRBA 466
121818	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	ASM2012v1 assembly for Paraburkholderia phytofirmans PsJN	complete	GCA_000020125	398527.4	642555113	398527	98.38

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6984	Burkholderia phytofirmans strain PsJN 16S ribosomal RNA gene, partial sequence	AY497470	1488		398527
124043	Paraburkholderia phytofirmans strain CIP 108762 16S ribosomal RNA gene, partial sequence.	PP724044	1361		261302

GC content

6984

GC-content (mol%)61

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Paraburkholderia phytofirmans PsJN
IMG: 642555113

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	78.80	no
125439	motility	BacteriaNetⓘ	yes	52.70	no
125439	gram_stain	BacteriaNetⓘ	negative	66.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.20	no

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	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	96.97	no
125438	anaerobic	anaerobicⓘ	no	97.36	yes
125438	aerobic	aerobicⓘ	yes	91.62	no
125438	spore-forming	spore-formingⓘ	no	85.30	no
125438	thermophilic	thermophileⓘ	no	97.99	no
125438	flagellated	motile2+ⓘ	yes	85.30	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Enantiomer discrimination in beta-phenylalanine degradation by a newly isolated Paraburkholderia strain BS115 and type strain PsJN.	Buss O, Dold SM, Obermeier P, Litty D, Muller D, Gruninger J, Rudat J.	AMB Express	10.1186/s13568-018-0676-2	2018
	Conversion and assimilation of furfural and 5-(hydroxymethyl)furfural by Pseudomonas putida KT2440.	Guarnieri MT, Ann Franden M, Johnson CW, Beckham GT.	Metab Eng Commun	10.1016/j.meteno.2017.02.001	2017
	Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics.	Price MN, Zane GM, Kuehl JV, Melnyk RA, Wall JD, Deutschbauer AM, Arkin AP.	PLoS Genet	10.1371/journal.pgen.1007147	2018
Metabolism	A distinct pathway for tetrahymanol synthesis in bacteria.	Banta AB, Wei JH, Welander PV.	Proc Natl Acad Sci U S A	10.1073/pnas.1511482112	2015
	Transcriptome Profiling of the Endophyte Burkholderia phytofirmans PsJN Indicates Sensing of the Plant Environment and Drought Stress.	Sheibani-Tezerji R, Rattei T, Sessitsch A, Trognitz F, Mitter B.	mBio	10.1128/mbio.00621-15	2015
	Molecular signatures and phylogenomic analysis of the genus Burkholderia: proposal for division of this genus into the emended genus Burkholderia containing pathogenic organisms and a new genus Paraburkholderia gen. nov. harboring environmental species.	Sawana A, Adeolu M, Gupta RS.	Front Genet	10.3389/fgene.2014.00429	2014
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 )
#27581	IJSEM 1187 2005 ( DOI 10.1099/ijs.0.63149-0 , PubMed 15879253 )
#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
#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 .
#121818	Collection of Institut Pasteur ; Curators of the CIP; CIP 108762
#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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Paraburkholderia phytofirmans (DSM 17436, CCUG 49060, LMG 22146)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Halophily

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_000020125

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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