Name: Paraburkholderia nodosa DSM 21604
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 1978

Type strain:

Species: Paraburkholderia nodosa

Culture col. no.: DSM 21604, BCRC 17575, LMG 23741, CCUG 54299, BR Br3437, BR 3437

Strain history: <- LMG; Br3437 {2008} <- P. Vandamme, University Ghent Belgium <- W.-M. Chen, NKMU -Nat. Kaohsiung Marine Univ. Taiwan, Dep. of Seafood Science <- S. M. de Faria, EMBRAPA-Agrobiologia Brazil

NCBI tax ID(s): 1121127 (strain), 392320 (species)

SI-ID 307510

BCRC 17575, CCRC 17575, LMG 23741, DSM 21604

Section

Paraburkholderia nodosa DSM 21604 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Mimosa scabrella, root nodules.

Gram-negative
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 nodosa**
	Full Scientific Name (LPSN)	Paraburkholderia nodosa (Chen et al. 2007) Sawana et al. 2015

Synonym

Burkholderia nodosa

Information on morphological and physiological properties Morphology

[Ref.: #32046]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.983

[Ref.: #32046]	Cell length	1.5 µm

[Ref.: #32046]	Cell width	0.65 µm

[Ref.: #32046]	Cell shape	rod-shaped

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15840]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #15840]

Culture medium growth

[Ref.: #15840]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15840]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15840]	growth	28 °C
[Ref.: #32046]	growth	28-37 °C
[Ref.: #32046]	optimum	32.5 °C
[Ref.: #60131]	growth	30 °C

[Ref.: #15840]	Temperature range	mesophilic
[Ref.: #32046]	Temperature range	mesophilic
[Ref.: #60131]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #60131]

Oxygen tolerance

aerobe

[Ref.: #32046]	Ability of spore formation	no
[Ref.: #69481]	Ability of spore formation	no Confidence in %100
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.926

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32046]	acetate ChEBI	+	carbon source
[Ref.: #32046]	adipate ChEBI	+	carbon source
[Ref.: #68369]	adipate ChEBI	+	assimilation	* from API 20NE
[Ref.: #32046]	alanine ChEBI	+	carbon source
[Ref.: #32046]	arabinose ChEBI	+	carbon source
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32046]	asparagine ChEBI	+	carbon source
[Ref.: #32046]	aspartate ChEBI	+	carbon source
[Ref.: #32046]	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.: #32046]	decanoate ChEBI	+	carbon source
[Ref.: #68369]	decanoate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32046]	formate ChEBI	+	carbon source
[Ref.: #32046]	fructose ChEBI	+	carbon source
[Ref.: #32046]	fucose ChEBI	+	carbon source
[Ref.: #32046]	galactose ChEBI	+	carbon source
[Ref.: #32046]	galacturonate ChEBI	+	carbon source
[Ref.: #32046]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #68369]	gelatin ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32046]	gluconate ChEBI	+	carbon source
[Ref.: #68369]	gluconate ChEBI	+	assimilation	* from API 20NE
[Ref.: #32046]	glucose ChEBI	+	carbon source
[Ref.: #32046]	glutamate ChEBI	+	carbon source
[Ref.: #32046]	histidine ChEBI	+	carbon source
[Ref.: #32046]	L-alaninamide ChEBI	+	carbon source
[Ref.: #68369]	L-arabinose ChEBI	+	assimilation	* from API 20NE
[Ref.: #32046]	lactate ChEBI	+	carbon source
[Ref.: #32046]	leucine ChEBI	+	carbon source
[Ref.: #32046]	malate ChEBI	+	carbon source
[Ref.: #68369]	malate ChEBI	+	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #32046]	mannitol ChEBI	+	carbon source
[Ref.: #32046]	mannose ChEBI	+	carbon source
[Ref.: #32046]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #32046]	myo-inositol ChEBI	+	carbon source
[Ref.: #32046]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #68369]	N-acetylglucosamine ChEBI	+	assimilation	* from API 20NE
[Ref.: #32046]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #32046]	phenylalanine ChEBI	+	carbon source
[Ref.: #32046]	proline ChEBI	+	carbon source
[Ref.: #32046]	rhamnose ChEBI	+	carbon source
[Ref.: #32046]	ribitol ChEBI	+	carbon source
[Ref.: #32046]	serine ChEBI	+	carbon source
[Ref.: #32046]	succinate ChEBI	+	carbon source
[Ref.: #32046]	trehalose ChEBI	+	carbon source
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #32046]	tween 40 ChEBI	+	carbon source
[Ref.: #32046]	tween 80 ChEBI	+	carbon source
[Ref.: #32046]	urea ChEBI	+	carbon source
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #32046]	urocanic acid ChEBI	+	carbon source
[Ref.: #32046]	xylitol 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.: #32046]	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.: #32046]	catalase	+	1.11.1.6
[Ref.: #32046]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68369]	cytochrome oxidase	-	1.9.3.1	* from API 20NE
[Ref.: #15840]	cytochrome-c oxidase	-	1.9.3.1
[Ref.: #68369]	gelatinase	-		* from API 20NE
[Ref.: #32046]	urease	+	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #60131]

Fatty acid	Percentage	ECL
C16:0	26	16
C17:0 CYCLO	18.6	16.888
C18:1 ω7c /12t/9t	16.9	17.824
C14:0	6.8	14
C16:1 ω7c	6.1	15.819
C16:1 2OH	5.3	17.047
C14:0 3OH/C16:1 ISO I	4.7	15.485
C19:0 CYCLO ω8c	3.5	18.9
C16:0 3OH	3.2	17.52
C16:0 2OH	2.8	17.233
C18:1 2OH	1.7	19.088
C13:1 at 12-13	1.1	12.931
Unidentified	1	18.136
C16:1 ω5c	1	15.908
C18:2 ω6,9c/C18:0 ANTE	0.6	17.724
C15:0	0.4	15
C12:0 ALDE ?	0.3	10.915

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.: #15840]	25315	+	-	-	-	-	-	-	+	+	+	+	+	+	-	+	+	+	+	+	+	-
[Ref.: #15840]	23827	+	-	-	-	-	-	-	-	+	+	+	+	+	-	+	+	+	+	+	+	-

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

[Ref.: #15840]	Sample type/isolated from	Mimosa scabrella, root nodules
[Ref.: #15840]	Host species	Mimosa scabrella

[Ref.: #60131]	Sample type/isolated from	Nitrogen-fixing nodules on the roots of Mimosa s.
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Tree
#Host Body-Site	#Plant	#Root nodule

What are isolation sources categories?

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

[Ref.: #15840]

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.: #15840]	Burkholderia nodosa strain Br3437 16S ribosomal RNA gene, partial sequence	AY773189	1500	ENA	392320 tax ID
[Ref.: #20218]	Burkholderia nodosa strain LMG 23741 16S ribosomal RNA gene, partial sequence	HQ849091	1124	ENA	392320 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Paraburkholderia nodosa DSM 21604	GCA_000519185	scaffold	GenBank	1121127 tax ID	*
[Ref.: #66792]	Burkholderia nodosa DSM 21604	1121127.3	wgs	PATRIC	1121127 tax ID	*
[Ref.: #66792]	Paraburkholderia nodosa DSM 21604	2515154189	draft	JGI IMG/M	1121127 tax ID	*

[Ref.: #15840]

GC-content

62.8 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 nodosa DSM 21604 DSM 21604 NCBI: GCA_000519185.1
[Ref.: #69481]	spore-forming	no	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Paraburkholderia nodosa DSM 21604 DSM 21604 NCBI: GCA_000519185.1
[Ref.: #69480]	motile	yes	87.877	no
[Ref.: #69480]	flagellated	no	80.825	no
[Ref.: #69480]	gram-positive	no	97.925	yes
[Ref.: #69480]	anaerobic	no	97.42	yes
[Ref.: #69480]	halophile	no	95.201	no
[Ref.: #69480]	spore-forming	no	93.141	yes
[Ref.: #69480]	thermophile	no	99.604	yes
[Ref.: #69480]	glucose-util	yes	91.722	yes
[Ref.: #69480]	aerobic	yes	84.517	yes
[Ref.: #69480]	glucose-ferment	no	89.139	yes

Availability in culture collections External links

[Ref.: #15840]

Culture collection no.

DSM 21604, BCRC 17575, LMG 23741, CCUG 54299, BR Br3437, BR 3437

[Ref.: #71623]	SI-ID 307510	*
[Ref.: #71624]	SI-ID 409827	*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Phylogenetic diversity of rhizobia nodulating native Mimosa gymnas grown in a South Brazilian ecotone.	Paulitsch F, Klepa MS, da Silva AR, do Carmo MRB, Dall'Agnol RF, Delamuta JRM, Hungria M, da Silva Batista JS	Mol Biol Rep	10.1007/s11033-018-4506-z	2018	*
Phylogeny	Burkholderia nodosa sp. nov., isolated from root nodules of the woody Brazilian legumes Mimosa bimucronata and Mimosa scabrella.	Chen WM, de Faria SM, James EK, Elliott GN, Lin KY, Chou JH, Sheu SY, Cnockaert M, Sprent JI, Vandamme P	Int J Syst Evol Microbiol	10.1099/ijs.0.64873-0	2007	*

References

#15840

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21604

#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 )

#20218

Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.: StrainInfo introduces electronic passports for microorganisms.. Syst Appl Microbiol. 37: 42 - 50 2014 ( DOI 10.1016/j.syapm.2013.11.002 , PubMed 24321274 )

#32046

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 #28296 (see below)

#60131 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54299

#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 .

#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 )

#71623

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-ID307510.1 )

#71624

#28296

IJSEM 1055 2007 ( DOI 10.1099/ijs.0.64873-0 , PubMed 17473258 )

* These data were automatically processed and therefore are not curated

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Paraburkholderia nodosa DSM 21604 DSM 21604

Paraburkholderia nodosa DSM 21604 DSM 21604

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