Ideonella dechloratans (CIP 104251, CCUG 30977, CCUG 30898)

Name: Ideonella dechloratans (CIP 104251, CCUG 30977, CCUG 30898)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 137263

Type strain

Culture col. no. CIP 104251 CCUG 30977 CCUG 30898 ATCC 51718

NCBI tax ID(s) 36863

Special Collections CCUG CIP

History CIP <- 1994, CCUG <- 1993, A. Malmqvist, ANOX, Lund, Sweden

Links

Ideonella dechloratans CIP 104251 is an aerobe, mesophilic, Gram-negative prokaryote of the family Sphaerotilaceae.

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

Name and taxonomic classification

SI-ID 43141

ATCC 51718,CCUG 30977,CCUG 30898,CIP 104251

@ref 20215

Last LPSN update 2026-02-09 11:32:51

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Sphaerotilaceae

Genus Ideonella

Species Ideonella dechloratans

Full scientific name Ideonella dechloratans Malmqvist et al. 1994

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
125439	negative		98.7
125438	negative		98
37168	negative	rod-shaped

Culture and growth conditions

Culture medium

@ref	Name	Growth	Composition	Medium link
37168	MEDIUM 3 - Columbia agar		Columbia agar (39.000 g);distilled water (1000.000 ml)
37168	CIP Medium 3			Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
37168	positive	growth	30	mesophilic
37168	negative	growth	5
37168	negative	growth	10
37168	negative	growth	41
50345	positive	growth	37-42

Physiology and metabolism

Oxygen tolerance

50345

Oxygen toleranceaerobe

Spore formation

@ref	Spore formation	Confidence
125439		98.2
125438		91.888

Halophily

@ref	Salt	Growth	Tested relation	Concentration
37168	NaCl	positive	growth	0 %
37168	NaCl		growth	2 %
37168	NaCl		growth	4 %
37168	NaCl		growth	6 %
37168	NaCl		growth	8 %
37168	NaCl		growth	10 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
37168	4853 ChEBI	esculin	-	hydrolysis
37168	17632 ChEBI	nitrate	-	reduction
37168	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
37168	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
37168	alcohol dehydrogenase	-	1.1.1.1
37168	amylase	+
37168	beta-galactosidase	-	3.2.1.23
37168	caseinase	+	3.4.21.50
37168	catalase	+	1.11.1.6
37168	DNase	-
37168	gelatinase	-
37168	lecithinase	+
37168	lipase	+
37168	lysine decarboxylase	-	4.1.1.18
37168	ornithine decarboxylase	-	4.1.1.17
37168	oxidase	+
37168	urease	-	3.5.1.5

Isolation, sampling and environmental information

Isolation source categories

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

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
37168		Lund	Sweden	SWE	Europe
50345	Activated sludge,wastewater treatment plant	Malmö,Sjölunda	Sweden	SWE	Europe

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
37168	1	Risk group (French classification)

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM2104930v1 assembly for Ideonella dechloratans CCUG 30977	complete	GCA_021049305	36863.8	8046849519	36863	98.66
66792	ASM880184v1 assembly for Ideonella dechloratans CCUG 30977	contig	GCA_008801845	36863.4		36863	47.16
66792	Ideonella dechloratans Anox B, ATCC 51718	complete			2510461017	36863

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
124043	Ideonella dechloratans partial 16S rRNA gene, strain CCUG 30977T	X72724	1500		36863

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ideonella dechloratans CCUG 30977
NCBI: GCA_021049305

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	98.20	no
125439	motility	BacteriaNetⓘ	yes	87.00	no
125439	gram_stain	BacteriaNetⓘ	negative	98.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	89.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ideonella dechloratans CCUG 30977
NCBI: GCA_021049305.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.00	no
125438	anaerobic	anaerobicⓘ	no	95.58	no
125438	aerobic	aerobicⓘ	yes	77.59	no
125438	spore-forming	spore-formingⓘ	no	91.89	no
125438	thermophilic	thermophileⓘ	no	95.57	yes
125438	flagellated	motile2+ⓘ	yes	84.84	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Heterologous expression of the gene for chlorite dismutase from Ideonella dechloratans is induced by an FNR-type transcription factor.	Rova M, Hellberg Lindqvist M, Goetelen T, Blomqvist S, Nilsson T.	Microbiologyopen	10.1002/mbo3.1049	2020
Metabolism	Expression of chlorite dismutase and chlorate reductase in the presence of oxygen and/or chlorate as the terminal electron acceptor in Ideonella dechloratans.	Lindqvist MH, Johansson N, Nilsson T, Rova M.	Appl Environ Microbiol	10.1128/aem.07303-11	2012
	An Isolated Arthrobacter sp. Enhances Rice (Oryza sativa L.) Plant Growth.	Chhetri G, Kim I, Kang M, So Y, Kim J, Seo T.	Microorganisms	10.3390/microorganisms10061187	2022
Metabolism	Metabolic primers for detection of (Per)chlorate-reducing bacteria in the environment and phylogenetic analysis of cld gene sequences.	Bender KS, Rice MR, Fugate WH, Coates JD, Achenbach LA.	Appl Environ Microbiol	10.1128/aem.70.9.5651-5658.2004	2004
Metabolism	Quantitative detection of perchlorate-reducing bacteria by real-time PCR targeting the perchlorate reductase gene.	Nozawa-Inoue M, Jien M, Hamilton NS, Stewart V, Scow KM, Hristova KR.	Appl Environ Microbiol	10.1128/aem.01658-07	2008
Enzymology	Sequencing and transcriptional analysis of the chlorite dismutase gene of Dechloromonas agitata and its use as a metabolic probe.	Bender KS, O'Connor SM, Chakraborty R, Coates JD, Achenbach LA.	Appl Environ Microbiol	10.1128/aem.68.10.4820-4826.2002	2002
Phylogeny	Aquincola rivuli sp. nov., isolated from a freshwater stream.	Sheu SY, Hsieh TY, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.003429	2019
Phylogeny	Ideonella livida sp. nov., isolated from a freshwater lake.	Chen WM, Chen LC, Sheu DS, Tsai JM, Sheu SY	Int J Syst Evol Microbiol	10.1099/ijsem.0.004363	2020
Phylogeny	Ideonella paludis sp. nov., isolated from a marsh.	Sheu SY, Chen ZH, Young CC, Chen WM	Int J Syst Evol Microbiol	10.1099/ijsem.0.000832	2015
Phylogeny	Microaerobic enrichment of benzene-degrading bacteria and description of Ideonella benzenivorans sp. nov., capable of degrading benzene, toluene and ethylbenzene under microaerobic conditions.	Bedics A, Tancsics A, Toth E, Banerjee S, Harkai P, Kovacs B, Boka K, Kriszt B	Antonie Van Leeuwenhoek	10.1007/s10482-022-01759-z	2022

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 )
#37168	Collection of Institut Pasteur ; Curators of the CIP; CIP 104251
#50345	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 30977
#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) .
#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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Ideonella dechloratans (CIP 104251, CCUG 30977, CCUG 30898)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Metabolite production

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_021049305

16S sequences

Genome-based predictions

Predictions

Literature

Literature

References

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