Name: Acidovorax radicis N35
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 2905

Type strain:

Species: Acidovorax radicis

Strain Designation: N35

Culture col. no.: DSM 23535, LMG 25767

Strain history: <- A. Hartmann, Helmholtz-Zentrum München, Dept. Microbe-Plant Interactions; N35 <- I. Klein

NCBI tax ID(s): 758826 (species)

SI-ID 406929

DSM 23535

Special Collections

Section

When using BacDive for research please cite our paper

Acidovorax radicis N35 is an aerobe, Gram-negative, motile bacterium that was isolated from surface sterilized wheat root (Triticum aestivum var. Naxos.

Gram-negative
motile
rod-shaped
aerobe
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	*Comamonadaceae*
	Genus	*Acidovorax*
	Species	**Acidovorax radicis**
	Full Scientific Name (LPSN)	Acidovorax radicis Li et al. 2011

Information on morphological and physiological properties Morphology

[Ref.: #23078]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98
[Ref.: #125439]	Gram stain	negative Confidence in %96.7

[Ref.: #23078]	Cell length	1.5-2.0 µm

[Ref.: #23078]	Cell width	0.3-0.5 µm

[Ref.: #23078]	Cell shape	rod-shaped

[Ref.: #23078]	Motility	yes

[Ref.: #23078]	Incubation period	2 days
[Ref.: #23078]	Cultivation medium used	NB agar

Multimedia content

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

R2A MEDIUM (DSMZ Medium 830)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

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Culture medium

NB agar

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Culture medium growth

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Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #17264]	growth	28 °C
[Ref.: #23078]	growth	10.0-35.0 °C
[Ref.: #23078]	optimum	30.0 °C

	pH	Kind of pH		pH
[Ref.: #23078]			optimum	7.0
[Ref.: #23078]			growth	5.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #23078]	Oxygen tolerance	aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %91.3

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Ability of spore formation

no Confidence in %98.5

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #23078]		NaCl		optimum	0.0	%
[Ref.: #23078]		NaCl		growth	0.0-2.0	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #23078]	(-)-quinic acid ChEBI	+	carbon source
[Ref.: #23078]	2,3-butanediol ChEBI	-	carbon source
[Ref.: #23078]	2-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #23078]	2-oxobutanoate ChEBI	+	carbon source
[Ref.: #23078]	2-oxoglutarate ChEBI	-	carbon source
[Ref.: #23078]	2-oxopentanoate ChEBI	-	carbon source
[Ref.: #23078]	3-hydroxybutyrate ChEBI	+	carbon source
[Ref.: #23078]	4-hydroxy-L-proline ChEBI	+	carbon source
[Ref.: #23078]	4-hydroxybutyrate ChEBI	-	carbon source
[Ref.: #23078]	4-hydroxyphenylacetic acid ChEBI	+	carbon source
[Ref.: #23078]	acetate ChEBI	+	carbon source
[Ref.: #23078]	alpha-cyclodextrin ChEBI	-	carbon source
[Ref.: #23078]	alpha-D-glucose ChEBI	+	carbon source
[Ref.: #23078]	bromosuccinate ChEBI	+	carbon source
[Ref.: #23078]	casein	-	hydrolysis
[Ref.: #23078]	cellobiose ChEBI	-	carbon source
[Ref.: #23078]	cis-aconitate ChEBI	-	carbon source
[Ref.: #23078]	citrate ChEBI	-	carbon source
[Ref.: #23078]	D-alanine ChEBI	+	carbon source
[Ref.: #23078]	D-arabitol ChEBI	+	carbon source
[Ref.: #23078]	D-fructose ChEBI	+	carbon source
[Ref.: #23078]	D-galactonic acid lactone ChEBI	-	carbon source
[Ref.: #23078]	D-galactose ChEBI	+	carbon source
[Ref.: #23078]	D-galacturonic acid ChEBI	-	carbon source
[Ref.: #23078]	D-glucarate ChEBI	-	carbon source
[Ref.: #23078]	D-gluconate ChEBI	+	carbon source
[Ref.: #23078]	D-glucosaminic acid ChEBI	-	carbon source
[Ref.: #23078]	D-glucose 6-phosphate ChEBI	-	carbon source
[Ref.: #23078]	D-glucuronate ChEBI	-	carbon source
[Ref.: #23078]	D-mannitol ChEBI	+	carbon source
[Ref.: #23078]	D-mannose ChEBI	+	carbon source
[Ref.: #23078]	D-psicose ChEBI	+	carbon source
[Ref.: #23078]	D-serine ChEBI	-	carbon source
[Ref.: #23078]	D-sorbitol ChEBI	+	carbon source
[Ref.: #23078]	dextrin ChEBI	-	carbon source
[Ref.: #23078]	DL-carnitine ChEBI	-	carbon source
[Ref.: #23078]	erythritol ChEBI	-	carbon source
[Ref.: #23078]	ethanolamine ChEBI	-	carbon source
[Ref.: #23078]	formate ChEBI	+	carbon source
[Ref.: #23078]	gamma-aminobutyric acid ChEBI	+	carbon source
[Ref.: #23078]	gentiobiose ChEBI	-	carbon source
[Ref.: #23078]	glucose 1-phosphate ChEBI	-	carbon source
[Ref.: #23078]	glucuronamide ChEBI	-	carbon source
[Ref.: #23078]	glycerol ChEBI	+	carbon source
[Ref.: #23078]	glycerol 1-phosphate ChEBI	-	carbon source
[Ref.: #23078]	glycogen ChEBI	-	carbon source
[Ref.: #23078]	glycyl L-aspartic acid ChEBI	-	carbon source
[Ref.: #23078]	glycyl-l-glutamate ChEBI	+	carbon source
[Ref.: #23078]	inosine ChEBI	-	carbon source
[Ref.: #23078]	itaconate ChEBI	-	carbon source
[Ref.: #23078]	L-alaninamide ChEBI	-	carbon source
[Ref.: #23078]	L-alanine ChEBI	+	carbon source
[Ref.: #23078]	L-alanylglycine ChEBI	+	carbon source
[Ref.: #23078]	L-arabinose ChEBI	+	carbon source
[Ref.: #23078]	L-asparagine ChEBI	+	carbon source
[Ref.: #23078]	L-aspartate ChEBI	+	carbon source
[Ref.: #23078]	L-fucose ChEBI		carbon source
[Ref.: #23078]	L-glutamate ChEBI	+	carbon source
[Ref.: #23078]	L-histidine ChEBI	+	carbon source
[Ref.: #23078]	L-leucine ChEBI	+	carbon source
[Ref.: #23078]	L-ornithine ChEBI	-	carbon source
[Ref.: #23078]	L-phenylalanine ChEBI	+	carbon source
[Ref.: #23078]	L-proline ChEBI	+	carbon source
[Ref.: #23078]	L-pyroglutamic acid ChEBI	-	carbon source
[Ref.: #23078]	L-rhamnose ChEBI	-	carbon source
[Ref.: #23078]	L-serine ChEBI	-	carbon source
[Ref.: #23078]	L-threonine ChEBI	+	carbon source
[Ref.: #23078]	lactate ChEBI	+	carbon source
[Ref.: #23078]	lactose ChEBI	-	carbon source
[Ref.: #23078]	lactulose ChEBI	-	carbon source
[Ref.: #23078]	malonate ChEBI	-	carbon source
[Ref.: #23078]	maltose ChEBI	-	carbon source
[Ref.: #23078]	melibiose ChEBI	-	carbon source
[Ref.: #23078]	methyl beta-D-glucopyranoside ChEBI	-	carbon source
[Ref.: #23078]	methyl pyruvate ChEBI	+	carbon source
[Ref.: #23078]	monomethyl succinate ChEBI	+	carbon source
[Ref.: #23078]	myo-inositol ChEBI	-	carbon source
[Ref.: #23078]	N-acetylgalactosamine ChEBI	-	carbon source
[Ref.: #23078]	N-acetylglucosamine ChEBI	-	carbon source
[Ref.: #23078]	phenylethylamine ChEBI	-	carbon source
[Ref.: #23078]	propionate ChEBI	+	carbon source
[Ref.: #23078]	putrescine ChEBI	-	carbon source
[Ref.: #23078]	raffinose ChEBI	-	carbon source
[Ref.: #23078]	ribitol ChEBI	-	carbon source
[Ref.: #23078]	sebacic acid ChEBI	+	carbon source
[Ref.: #23078]	succinamate ChEBI	+	carbon source
[Ref.: #23078]	succinate ChEBI	+	carbon source
[Ref.: #23078]	sucrose ChEBI	-	carbon source
[Ref.: #23078]	thymidine ChEBI	-	carbon source
[Ref.: #23078]	trehalose ChEBI	-	carbon source
[Ref.: #23078]	tributyrin ChEBI	+	hydrolysis
[Ref.: #23078]	turanose ChEBI	-	carbon source
[Ref.: #23078]	tween 40 ChEBI	+	carbon source
[Ref.: #23078]	tween 80 ChEBI	+	carbon source
[Ref.: #23078]	uridine ChEBI	-	carbon source
[Ref.: #23078]	urocanic acid ChEBI	+	carbon source
[Ref.: #23078]	xylitol ChEBI	-	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #23078]		siderophore ChEBI	yes

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #23078]		catalase	-	1.11.1.6
[Ref.: #23078]		cytochrome oxidase	+	1.9.3.1

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

[Ref.: #17264]	Sample type/isolated from	surface sterilized wheat root (Triticum aestivum var. Naxos
[Ref.: #17264]	Host species	Triticum aestivum var. Naxos
[Ref.: #17264]	Geographic location (country and/or sea, region)	Neumarkt near Munich
[Ref.: #17264]	Country	Germany
[Ref.: #17264]	Country ISO 3 Code	DEU
[Ref.: #17264]	Continent	Europe

[Ref.: #23078]	Sample type/isolated from	surface-sterilized wheat roots (4-week-old wheat plants Triticum aestivum)
[Ref.: #23078]	Enrichment culture	NB (nutrient broth no. 4; Fluka) agar
* 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?

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Global distribution of 16S sequence HM027578 (>99% sequence identity) for Acidovorax from Microbeatlas

Aquatic Samples	28
Soil Samples	3
Animal Samples	4
Plant Samples	4
Total Samples	39

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

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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.: #17264]	Acidovorax radicis strain N35 16S ribosomal RNA gene, partial sequence	HM027578	1492	GenBank ENA	999386 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Acidovorax radicis N35	GCA_000204195	contig	GenBank ENA	999386 tax ID	*
[Ref.: #66792]	Acidovorax radicis N35	999386.3	wgs	PATRIC	999386 tax ID	*
[Ref.: #66792]	Acidovorax radicis N35	2547132374	draft	JGI IMG/M	999386 tax ID	*

[Ref.: #17264]	GC-content	64.9 mol%	sequence analysis
[Ref.: #23078]	GC-content	64.9 mol%	genome sequence analysis

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: Acidovorax radicis N35 PATRIC: 999386.3
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98	no
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.463	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	87.48	no
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	88.315	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	99.497	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	yes	85.445	no

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidovorax radicis N35 NCBI: GCA_000204195
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	98.5
[Ref.: #125439]	BacteriaNet	motilityⓘ	yes	88.4
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	96.7
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	91.3

Availability in culture collections External links

[Ref.: #17264]

Culture collection no.

DSM 23535, LMG 25767

[Ref.: #72428]

SI-ID 406929

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Acidovorax radicis sp. nov., a wheat-root-colonizing bacterium.	Li D, Rothballer M, Schmid M, Esperschutz J, Hartmann A	Int J Syst Evol Microbiol	10.1099/ijs.0.025296-0	2010	*

References

#17264

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 23535

#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 )

#23078

Dan Li,Michael Rothballer,Michael Schmid,Jürgen Esperschütz,Anton Hartmann: Acidovorax radicis sp. nov., a wheat-root-colonizing bacterium. IJSEM 61: 2589 - 2594 2011 ( DOI 10.1099/ijs.0.025296-0 , PubMed 21131505 )

#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) .

#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 .

#72428

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-ID406929.1 )

#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 .

* These data were automatically processed and therefore are not curated

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