Acidovorax defluvii (DSM 12644, CIP 106824, CCUG 49021)

Name: Acidovorax defluvii (DSM 12644, CIP 106824, CCUG 49021)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 2898

Type strain

Culture col. no. DSM 12644 CIP 106824 CCUG 49021 BSB 411

NCBI tax ID(s) 86669

Special Collections DSMZ CCUG CIP

History <- S. Spring; BSB411 CIP <- 2000, DSMZ <- S. Spring: strain BSB411

Links

Acidovorax defluvii DSM 12644 is an aerobe, Gram-negative, motile bacterium that was isolated from activated sludge of the municipal wastewater treatment plant München I.

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

Name and taxonomic classification

SI-ID 49332

DSM 12644,CIP 106824,CCUG 49021

@ref 20215

Last LPSN update 2026-02-09 11:18:22

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Comamonadaceae

Genus Acidovorax

Species Acidovorax defluvii

Full scientific name Acidovorax defluvii Schulze et al. 1999

BacDive ID	Other strains from **Acidovorax defluvii** (3)	Type strain
2897	A. defluvii G8B1, DSM 12578
150386	A. defluvii CCUG 39798
154119	A. defluvii CCUG 52432

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
118864	negative	rod-shaped
125439	negative		99.1
125438	negative		99

Pigmentation

@ref	Production	Name
118864		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
4777	REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)	Medium recipe at MediaDive	Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
39593	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118864	CIP Medium 72	Medium recipe at CIP
118864	CIP Medium 228	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)
4777	positive	growth	30
39593	positive	growth	30
58444	positive	growth	30
118864	positive	growth	5-30
118864	negative	growth	37
118864	negative	growth	41

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
58444	aerobe
118864	facultative anaerobe

Spore formation

@ref	Spore formation	Confidence
125439		99

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118864	NaCl	positive	growth	0 %
118864	NaCl		growth	2 %
118864	NaCl		growth	4 %
118864	NaCl		growth	6 %
118864	NaCl		growth	8 %
118864	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	+	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
118864	16947 ChEBI	citrate	-	carbon source
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
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
118864	4853 ChEBI	esculin	-	hydrolysis
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
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
118864	17632 ChEBI	nitrate	+	reduction
118864	17632 ChEBI	nitrate	+	respiration
68369	17632 ChEBI	nitrate	+	reduction	from API 20NE
118864	16301 ChEBI	nitrite	+	reduction
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE
118864	35581 ChEBI	indole

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
118864	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
118864	amylase	-
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68382	beta-galactosidase	-	3.2.1.23	from API zym
118864	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118864	caseinase	-	3.4.21.50
118864	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
118864	DNase	-
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118864	gelatinase	+/-
68369	gelatinase	-		from API 20NE
118864	lecithinase	+
68382	leucine arylamidase	+	3.4.11.1	from API zym
118864	lipase	-
68382	lipase (C 14)	-		from API zym
118864	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
118864	ornithine decarboxylase	-	4.1.1.17
118864	oxidase	+
118864	protease	-
68382	trypsin	-	3.4.21.4	from API zym
118864	tryptophan deaminase	-
118864	tween esterase	+
118864	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
118864	-	+	+	+	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-

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
4777	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+

API biotype100

@ref	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
118864	not determinedn.d.	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	+	-	+	-	-	-	-	-	-	+	-	+	+	-	+	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Waste	#Activated sludge
#Engineered	#Waste	#Water treatment plant

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent	Isolation date
4777	activated sludge of the municipal wastewater treatment plant München I		Großlappen near Munich	Germany	DEU	Europe
58444	Activated sludge	1995	München	Germany	DEU	Europe
118864	Environment, Activated sludge		München	Germany	DEU	Europe	1995

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4777	1	Risk group (German classification) According to TRBA 466
118864	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
124043	ASM326890v1 assembly for Acidovorax defluvii DSM 12644	scaffold	GCA_003268905	86669.4	2756170235	86669	36.6

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4777	Acidovorax defluvii 16S rRNA gene	Y18616	1526		86669

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Acidovorax defluvii DSM 12644
IMG: 2756170235

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	99.00	no
125439	motility	BacteriaNetⓘ	yes	83.70	no
125439	gram_stain	BacteriaNetⓘ	negative	99.10	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	81.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Acidovorax defluvii strain DSM 12644
PATRIC: 86669.4

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	99.00	no
125438	anaerobic	anaerobicⓘ	no	95.75	no
125438	aerobic	aerobicⓘ	yes	79.95	no
125438	spore-forming	spore-formingⓘ	no	88.47	no
125438	thermophilic	thermophileⓘ	no	97.47	yes
125438	flagellated	motile2+ⓘ	yes	54.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	A Novel and Advanced Diagnostic Approach toward Paracidovorax citrulli Causing Bacterial Fruit Blotch in Watermelon by Direct SYBR Green Real-Time PCR Assay.	Ham H, Lee BW, Kim K, Lee W, Lee YH, Park DS.	Plant Pathol J	10.5423/ppj.oa.08.2024.0125	2024
Phylogeny	Simplicispira suum sp. nov., isolated from a dust collector at a pig farm.	Cho HY, Heo J, Hong SB, Kim JS, Kwon SW, Kim SJ	Int J Syst Evol Microbiol	10.1099/ijsem.0.002874	2018
Phylogeny	Genotypic diversity of Acidovorax strains isolated from activated sludge and description of Acidovorax defluvii sp. nov.	Schulze R, Spring S, Amann R, Huber I, Ludwig W, Schleifer KH, Kampfer P	Syst Appl Microbiol	10.1016/S0723-2020(99)80067-8	1999

References

#4777	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12644
#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 )
#39593	; Curators of the CIP;
#58444	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 49021
#68369	Automatically annotated from API 20NE .
#68382	Automatically annotated from API zym .
#118864	Collection of Institut Pasteur ; Curators of the CIP; CIP 106824
#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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Acidovorax defluvii (DSM 12644, CIP 106824, CCUG 49021)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API zym

API 20NE

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_003268905

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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