Name: Paraburkholderia diazotrophica NKMU-JPY461
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 130228

Type strain:

Species: Paraburkholderia diazotrophica

Strain Designation: NKMU-JPY461

Culture col. no.: DSM 29787, BCRC 80259, JPY 461, KCTC 23308, LMG 26031

Strain history: <- LMG <- W.-M. Chen, Natl. Kaohsiung Marine Univ. Taiwan

NCBI tax ID(s): 667676 (species)

SI-ID 371126

LMG 26031, BCRC 80259, KCTC 23308

Section

Paraburkholderia diazotrophica NKMU-JPY461 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Mimosa candollei, root nodule.

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	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Burkholderiaceae*
	Genus	*Paraburkholderia*
	Species	**Paraburkholderia diazotrophica**
	Full Scientific Name (LPSN)	Paraburkholderia diazotrophica (Sheu et al. 2013) Sawana et al. 2015

Synonym

Burkholderia diazotrophica

Information on morphological and physiological properties Morphology

[Ref.: #30607]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.958

[Ref.: #30607]	Cell length	1.5 µm

[Ref.: #30607]	Cell width	0.9 µm

[Ref.: #30607]	Cell shape	rod-shaped

[Ref.: #30607]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %92.581

[Ref.: #21539]

Incubation period

2-3 days

[Ref.: #30607]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #21539]

Culture medium

TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)

[Ref.: #21539]

Culture medium growth

[Ref.: #21539]

Culture medium link

Medium recipe at MediaDive

[Ref.: #21539]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #21539]	growth	30 °C
[Ref.: #30607]	growth	15-40 °C
[Ref.: #30607]	optimum	33.5 °C

[Ref.: #21539]	Temperature range	mesophilic
[Ref.: #30607]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #30607]			optimum	6.5
[Ref.: #30607]			growth	04-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #30607]

Oxygen tolerance

aerobe

[Ref.: #30607]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.976

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #30607]		NaCl		growth	0-1	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #30607]	alanine ChEBI	+	carbon source
[Ref.: #30607]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30607]	asparagine ChEBI	+	carbon source
[Ref.: #30607]	aspartate ChEBI	+	carbon source
[Ref.: #30607]	cellobiose ChEBI	+	carbon source
[Ref.: #30607]	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.: #30607]	dextrin ChEBI	+	carbon source
[Ref.: #30607]	DL-carnitine ChEBI	+	carbon source
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30607]	ethanolamine ChEBI	+	carbon source
[Ref.: #30607]	formate ChEBI	+	carbon source
[Ref.: #30607]	fructose ChEBI	+	carbon source
[Ref.: #30607]	galactonate ChEBI	+	carbon source
[Ref.: #30607]	galactose ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #30607]	gluconate ChEBI	+	carbon source
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30607]	glucosamine ChEBI	+	carbon source
[Ref.: #30607]	glucose ChEBI	+	carbon source
[Ref.: #30607]	glutamate ChEBI	+	carbon source
[Ref.: #30607]	glycerol ChEBI	+	carbon source
[Ref.: #30607]	glycogen ChEBI	+	carbon source
[Ref.: #30607]	histidine ChEBI	+	carbon source
[Ref.: #30607]	L-alaninamide ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #30607]	L-arabitol ChEBI	+	carbon source
[Ref.: #30607]	lactate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #30607]	malonate ChEBI	+	carbon source
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #30607]	mannitol ChEBI	+	carbon source
[Ref.: #30607]	mannose ChEBI	+	carbon source
[Ref.: #30607]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #30607]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #30607]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #30607]	phenylalanine ChEBI	+	carbon source
[Ref.: #30607]	proline ChEBI	+	carbon source
[Ref.: #30607]	quinate ChEBI	+	carbon source
[Ref.: #30607]	raffinose ChEBI	+	carbon source
[Ref.: #30607]	rhamnose ChEBI	+	carbon source
[Ref.: #30607]	ribitol ChEBI	+	carbon source
[Ref.: #30607]	serine ChEBI	+	carbon source
[Ref.: #30607]	sorbitol ChEBI	+	carbon source
[Ref.: #30607]	succinate ChEBI	+	carbon source
[Ref.: #30607]	sucrose ChEBI	+	carbon source
[Ref.: #30607]	thymidine ChEBI	+	carbon source
[Ref.: #30607]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #30607]	tween 40 ChEBI	+	carbon source
[Ref.: #30607]	tween 80 ChEBI	+	carbon source
[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.: #30607]	acid phosphatase	+	3.1.3.2
[Ref.: #30607]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68369]	beta-glucosidase	-	3.2.1.21	* from API 20NE
[Ref.: #21539]	catalase	+	1.11.1.6
[Ref.: #30607]	catalase	+	1.11.1.6
[Ref.: #30607]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #21539]	cytochrome-c oxidase	+	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #30607]	urease	+	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
	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.: #21539]	24073	+	-	-	-	-	-	-	+	+	+	+	+	+	-	+	-	-	+	+/-	+/-	+

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

[Ref.: #21539]	Sample type/isolated from	Mimosa candollei, root nodule
[Ref.: #21539]	Host species	Mimosa candollei
[Ref.: #21539]	Geographic location (country and/or sea, region)	Goias
[Ref.: #21539]	Country	Brazil
[Ref.: #21539]	Country ISO 3 Code	BRA
[Ref.: #21539]	Continent	Middle and South America
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Shrub (Scrub)
#Host Body-Site	#Plant	#Root nodule

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence HM366717 (>99% sequence identity) for Paraburkholderia diazotrophica subclade from Microbeatlas

Aquatic Samples	29
Soil Samples	301
Animal Samples	49
Plant Samples	31
Total Samples	410

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

[Ref.: #21539]

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.: #21539]	Burkholderia diazotrophica strain NKMU-JPY461 16S ribosomal RNA gene, partial sequence	HM366717	1402	ENA	667676 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paraburkholderia diazotrophica LMG 26031	GCA_900108945	scaffold	GenBank	667676 tax ID	*
[Ref.: #66792]	Paraburkholderia diazotrophica strain LMG 26031	667676.3	wgs	PATRIC	667676 tax ID	*
[Ref.: #66792]	Paraburkholderia diazotrophica LMG 26031	2654588103	draft	JGI IMG/M	667676 tax ID	*

[Ref.: #30607]

GC-content

64 mol%

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: Paraburkholderia diazotrophica LMG 26031 NCBI: GCA_900108945.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paraburkholderia diazotrophica LMG 26031 NCBI: GCA_900108945.1
[Ref.: #69480]	glucose-ferment	no	90.111	no
[Ref.: #69480]	motile	yes	83.142	no
[Ref.: #69480]	flagellated	no	86.853	no
[Ref.: #69480]	gram-positive	no	98.197	yes
[Ref.: #69480]	anaerobic	no	98.24	yes
[Ref.: #69480]	aerobic	yes	88.024	no
[Ref.: #69480]	halophile	no	95.378	yes
[Ref.: #69480]	spore-forming	no	93.047	yes
[Ref.: #69480]	thermophile	no	99.589	yes
[Ref.: #69480]	glucose-util	yes	90.154	yes

Availability in culture collections External links

[Ref.: #21539]

Culture collection no.

DSM 29787, BCRC 80259, JPY 461, KCTC 23308, LMG 26031

[Ref.: #88770]

SI-ID 371126

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Burkholderia susongensis sp. nov., a mineral-weathering bacterium isolated from weathered rock surface.	Gu JY, Zang SG, Sheng XF, He LY, Huang Z, Wang Q	Int J Syst Evol Microbiol	10.1099/ijs.0.000059	2015	*
Phylogeny	Burkholderia monticola sp. nov., isolated from mountain soil.	Baek I, Seo B, Lee I, Yi H, Chun J	Int J Syst Evol Microbiol	10.1099/ijs.0.066001-0	2014	*
Phylogeny	Burkholderia diazotrophica sp. nov., isolated from root nodules of Mimosa spp.	Sheu SY, Chou JH, Bontemps C, Elliott GN, Gross E, Dos Reis Junior FB, Melkonian R, Moulin L, James EK, Sprent JI, Young JPW, Chen WM	Int J Syst Evol Microbiol	10.1099/ijs.0.039859-0	2012	*
Phylogeny	Burkholderia humisilvae sp. nov., Burkholderia solisilvae sp. nov. and Burkholderia rhizosphaerae sp. nov., isolated from forest soil and rhizosphere soil.	Lee JC, Whang KS	Int J Syst Evol Microbiol	10.1099/ijs.0.000368	2015	*

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 )

#21539

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 29787

#30607

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 #26938 (see below)

#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 .

#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 )

#88770

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-ID371126.1 )

#26938

IJSEM 435 2013 ( DOI 10.1099/ijs.0.039859-0 , PubMed 22467155 )

* These data were automatically processed and therefore are not curated

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Paraburkholderia diazotrophica LMG 26031

Paraburkholderia diazotrophica LMG 26031

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