Variovorax boronicumulans (DSM 21722, KCTC 22010, NBRC 103145)

Name: Variovorax boronicumulans (DSM 21722, KCTC 22010, NBRC 103145)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3017

Type strain

Strain Designation BAM-48

Culture col. no. DSM 21722 KCTC 22010 NBRC 103145 BAM-48 NCIMB 14573 2 more

NCBI tax ID(s) 1321609 436515

Special Collections DSMZ JCM KCTC Literature strains

Links

Variovorax boronicumulans BAM-48 is an aerobe, mesophilic, Gram-negative prokaryote that forms circular colonies and was isolated from soil.

Gram-negative motile rod-shaped colony-forming aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 397257

LMG 31160,KCTC 22010,NBRC 103145,DSM 21722

@ref 20215

Last LPSN update 2025-12-16 09:47:27

Domain Pseudomonadati

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Variovorax

Species Variovorax boronicumulans

Full scientific name Variovorax boronicumulans Miwa et al. 2008

BacDive ID	Other strains from **Variovorax boronicumulans** (3)	Type strain
100653	V. boronicumulans SF002666(FSU),
158134	V. boronicumulans 6cA_C34, DSM 103999
160665	V. boronicumulans ACN3, DSM 105153

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
23100	negative	1.0-2.0 µm	0.5-0.7 µm	rod-shaped
67771	negative
125438	negative				98.175
125439	negative				95.3

Colony morphology

@ref	Colony color	Colony shape	Incubation period	Medium used
23100	yellow	circular	2 days	TSA plates

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15896	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
23100	nutrient agar (Difco)
23100	TSA agar
23100	TSA plates
15896	TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)	Medium recipe at MediaDive	Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15896	positive	growth	28	mesophilic
23100	positive	growth	4.0-37.0
23100	negative	growth	>45.0
23100	positive	optimum	30.0	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	30	mesophilic

Culture pH

@ref	Ability	Type	PH	PH range
23100	positive	optimum	7.0
23100	positive	growth	5.0-9.0	alkaliphile
23100		growth	4.0
23100		growth	10.0

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
67771	aerobe
125438	aerobe	90.838

Spore formation

@ref	Spore formation	Confidence
23100
125438		90.04
125439		96.7

Halophily

@ref	Salt	Growth	Tested relation	Concentration
23100	NaCl	positive	growth	0.0-1.0 %
23100	NaCl		growth	>1.0 %(w/v)

Observation

67771

Observationquinones: Q-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
23100	17128 ChEBI	adipate	-	assimilation
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
23100	28938 ChEBI	ammonium	+	nitrogen source
23100	27613 ChEBI	amygdalin	-	assimilation
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
23100	16947 ChEBI	citrate	+	carbon source
23100	17634 ChEBI	D-glucose	-	assimilation
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
23100	16024 ChEBI	D-mannose	-	assimilation
23100	27689 ChEBI	decanoate	+	assimilation
68369	27689 ChEBI	decanoate	+	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
23100	5291 ChEBI	gelatin	-	hydrolysis
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	+	assimilation	from API 20NE
23100	30849 ChEBI	L-arabinose	+	assimilation
68369	30849 ChEBI	L-arabinose	+	assimilation	from API 20NE
23100	25115 ChEBI	malate	+	assimilation
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
23100	17306 ChEBI	maltose	-	assimilation
68369	17306 ChEBI	maltose	-	assimilation	from API 20NE
23100	29864 ChEBI	mannitol	+	assimilation
23100	28053 ChEBI	melibiose	-	assimilation
23100	17268 ChEBI	myo-inositol	-	assimilation
23100	506227 ChEBI	N-acetylglucosamine	-	assimilation
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
23100	17632 ChEBI	nitrate	-	reduction
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
23100	18401 ChEBI	phenylacetate	-	assimilation
23100	32032 ChEBI	potassium gluconate	-	assimilation
23100	26546 ChEBI	rhamnose	-	assimilation
23100	30911 ChEBI	sorbitol	-	assimilation
23100	17992 ChEBI	sucrose	-	assimilation
23100	27897 ChEBI	tryptophan	-	assimilation
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	+	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite
23100	15688 ChEBI	acetoin
23100	16136 ChEBI	hydrogen sulfide
68369	35581 ChEBI	indole	from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test	Voges-proskauer-test	Citrate test
23100	15688 ChEBI	acetoin		+
23100	16947 ChEBI	citrate			+
68369	35581 ChEBI	indole	-			from API 20NE

Enzymes

@ref	Value	Activity	Ec
23100	acid phosphatase	+	3.1.3.2
23100	alkaline phosphatase	+	3.1.3.1
23100	alpha-chymotrypsin	-	3.4.21.1
23100	alpha-fucosidase	-	3.2.1.51
23100	alpha-galactosidase	-	3.2.1.22
23100	alpha-glucosidase	-	3.2.1.20
23100	alpha-mannosidase	-	3.2.1.24
23100	arginine dihydrolase	-	3.5.3.6
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
23100	beta-galactosidase	-	3.2.1.23
23100	beta-glucosidase	-	3.2.1.21
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
23100	beta-glucuronidase	-	3.2.1.31
23100	catalase	+	1.11.1.6
23100	cystine arylamidase	-	3.4.11.3
23100	cytochrome oxidase	+	1.9.3.1
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
23100	esterase (C 4)	-
23100	esterase lipase (C 8)	+
68369	gelatinase	-		from API 20NE
23100	leucine arylamidase	+	3.4.11.1
23100	lipase (C 14)	-
23100	lysine decarboxylase	-	4.1.1.18
23100	N-acetyl-beta-glucosaminidase	-	3.2.1.52
23100	naphthol-AS-BI-phosphohydrolase	-
23100	ornithine decarboxylase	-	4.1.1.17
23100	trypsin	-	3.4.21.4
23100	tryptophan deaminase	-	4.1.99.1
23100	urease	-	3.5.1.5
68369	urease	+	3.5.1.5	from API 20NE
23100	valine arylamidase	-

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
15896	-	-	-	-	+	-	-	-	+	+	+/-	+	-	-	+	+	-	-	-	+	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Built environment	-
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Enrichment culture	Enrichment culture temperature
15896	soil	Univ. of Tokyo (Yayoi campus)	Japan	JPN	Asia
23100	soil collected in the experimental area of the University of Tokyo					tryptic soya agar (TSA;Difco)	25.0
67770	Soil in the University of Tokyo	Tokyo	Japan	JPN	Asia
67771	From soil	Tokyo	Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB300597 (>99% sequence identity) for Variovorax from Microbeatlas

Aquatic Samples	2157
Soil Samples	3106
Animal Samples	2122
Plant Samples	2332
Total Samples	9717

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15896	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
67770	ASM159134v1 assembly for Variovorax boronicumulans NBRC 103145	contig	GCA_001591345	1321609.3	2731957647	1321609	20.13

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
20218	Variovorax boronicumulans gene for 16S rRNA, partial sequence, strain: NBRC 103145	AB681954	1460		1321609
15896	Variovorax boronicumulans gene for 16S ribosomal RNA, partial sequence	AB300597	1475		1321609

GC content

@ref	GC-content (mol%)	Method
23100	71.2	high performance liquid chromatography (HPLC)
67771	71.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Variovorax boronicumulans NBRC 103145
NCBI: GCA_001591345

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	96.70	no
125439	motility	BacteriaNetⓘ	yes	85.90	no
125439	gram_stain	BacteriaNetⓘ	negative	95.30	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.90	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Variovorax boronicumulans NBRC 103145
PATRIC: 1321609.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.18	yes
125438	anaerobic	anaerobicⓘ	no	98.82	yes
125438	spore-forming	spore-formingⓘ	no	90.04	yes
125438	aerobic	aerobicⓘ	yes	90.84	yes
125438	thermophilic	thermophileⓘ	no	98.50	no
125438	flagellated	motile2+ⓘ	yes	82.54	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660.	Ghimire N, Kim B, Lee CM, Oh TJ.	BMC Genomics	10.1186/s12864-022-08589-3	2022
	Prevalence and Correlates of Phenazine Resistance in Culturable Bacteria from a Dryland Wheat Field.	Perry EK, Newman DK.	Appl Environ Microbiol	10.1128/aem.02320-21	2022
	New variochelins from soil-isolated Variovorax sp. H002.	Haedar JR, Yoshimura A, Wakimoto T.	Beilstein J Org Chem	10.3762/bjoc.20.63	2024
Phylogeny	Diversity of Culturable Bacteria Isolated from Highland Barley Cultivation Soil in Qamdo, Tibet Autonomous Region.	Pan HU, Zhou J, Dawa Z, Dai Y, Zhang Y, Yang H, Wang C, Liu H, Zhou H, Lu X, Tian Y.	Pol J Microbiol	10.33073/pjm-2021-008	2021
	Lesson from Ecotoxicity: Revisiting the Microbial Lipopeptides for the Management of Emerging Diseases for Crop Protection.	Malviya D, Sahu PK, Singh UB, Paul S, Gupta A, Gupta AR, Singh S, Kumar M, Paul D, Rai JP, Singh HV, Brahmaprakash GP.	Int J Environ Res Public Health	10.3390/ijerph17041434	2020
	Promotion of arsenic phytoextraction efficiency in the fern Pteris vittata by the inoculation of As-resistant bacteria: a soil bioremediation perspective.	Lampis S, Santi C, Ciurli A, Andreolli M, Vallini G.	Front Plant Sci	10.3389/fpls.2015.00080	2015
Metabolism	Functions and Unique Diversity of Genes and Microorganisms Involved in Arsenite Oxidation from the Tailings of a Realgar Mine.	Zeng XC, E G, Wang J, Wang N, Chen X, Mu Y, Li H, Yang Y, Liu Y, Wang Y.	Appl Environ Microbiol	10.1128/aem.02190-16	2016
Phylogeny	Variovorax guangxiensis sp. nov., an aerobic, 1-aminocyclopropane-1-carboxylate deaminase producing bacterium isolated from banana rhizosphere.	Gao JL, Yuan M, Wang XM, Qiu TL, Li JW, Liu HC, Li XA, Chen J, Sun JG	Antonie Van Leeuwenhoek	10.1007/s10482-014-0304-3	2014
Phylogeny	Variovorax defluvii sp. nov., isolated from sewage.	Jin L, Kim KK, Ahn CY, Oh HM	Int J Syst Evol Microbiol	10.1099/ijs.0.035295-0	2011
Phylogeny	Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil.	Miwa H, Ahmed I, Yoon J, Yokota A, Fujiwara T	Int J Syst Evol Microbiol	10.1099/ijs.0.65315-0	2008

References

#15896	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21722
#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 )
#23100	Hiroki Miwa,Iftikhar Ahmed,Jaewoo Yoon,Akira Yokota,Toru Fujiwara: Variovorax boronicumulans sp. nov., a boron-accumulating bacterium isolated from soil. IJSEM 58: 286 - 289 2008 ( DOI 10.1099/ijs.0.65315-0 , PubMed 18175723 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771	Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;
#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 .
#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 )

Rate our new design

Content

About us

Variovorax boronicumulans (DSM 21722, KCTC 22010, NBRC 103145)

Name and taxonomic classification

Morphology

Cell morphology

Colony morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001591345

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

Help

Social Media