Ideonella azotifigens (DSM 21438, JCM 15503, 1a22)

Name: Ideonella azotifigens (DSM 21438, JCM 15503, 1a22)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17955

Type strain

Strain Designation 1a22

Culture col. no. DSM 21438 JCM 15503 1a22

NCBI tax ID(s) 513160

Special Collections DSMZ JCM Literature strains

History <- D.H. Buckley, Cornell University <- J. D. Noar, Cornell University; 1a22 D. H. Buckley 1a22.

Links

Ideonella azotifigens 1a22 is an aerobe, Gram-negative, motile bacterium that was isolated from grass rhizosphere soil.

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

Name and taxonomic classification

SI-ID 401901

JCM 15503,DSM 21438,CCUG 75669T

@ref 20215

Last LPSN update 2026-02-09 11:22:21

Domain Bacteria

Phylum Pseudomonadota

Class Betaproteobacteria

Order Burkholderiales

Family Sphaerotilaceae

Genus Ideonella

Species Ideonella azotifigens

Full scientific name Ideonella azotifigens Noar and Buckley 2009

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Motility	Confidence
28994	negative	4 µm	0.75 µm	rod-shaped
125438	negative					92

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
15705	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
15705	positive	growth	28
28994	positive	growth	04-35
28994	positive	optimum	06-08
67770	positive	growth	30

Culture pH

@ref	Ability	Type	PH
28994	positive	optimum	6.5

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
28994	aerobe
125439	obligate aerobe	99.5

Halophily

@ref	Salt	Growth	Tested relation	Concentration
28994	NaCl	positive	growth	0-0.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
28994	30089 ChEBI	acetate	+	carbon source
28994	17057 ChEBI	cellobiose	+	carbon source
28994	17234 ChEBI	glucose	+	carbon source
28994	29987 ChEBI	glutamate	+	carbon source
28994	25115 ChEBI	malate	+	carbon source
28994	29864 ChEBI	mannitol	+	carbon source
28994	37684 ChEBI	mannose	+	carbon source
28994	506227 ChEBI	N-acetylglucosamine	+	carbon source
28994	53424 ChEBI	tween 20	+	carbon source
28994	53423 ChEBI	tween 40	+	carbon source
28994	53425 ChEBI	tween 60	+	carbon source
28994	53426 ChEBI	tween 80	+	carbon source

Enzymes

@ref	Value	Activity	Ec
28994	catalase	+	1.11.1.6
28994	cytochrome oxidase	+	1.9.3.1
28994	gelatinase	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Terrestrial	#Soil
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Rhizosphere

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15705	grass rhizosphere soil	Ithaca, NY	USA	USA	North America
67770	Soil in association with the rhizosphere of a perennial grass

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15705	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
124043	ASM3952321v1 assembly for Ideonella azotifigens JCM 15503	scaffold	GCA_039523215			513160	63.95
66792	ASM651971v1 assembly for Ideonella azotifigens DSM 21438	contig	GCA_006519715	513160.3	8065715578	513160

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15705	Ideonella sp. 1a22 16S ribosomal RNA gene, partial sequence	EU542576	1396		513160
67770	Ideonella azotifigens JCM 15503 gene for 16S ribosomal RNA, partial sequence	LC508797	1451		513160

GC content

@ref	GC-content (mol%)	Method
15705	67.4
67770	67.4	high performance liquid chromatography (HPLC)

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Ideonella azotifigens DSM 21438
NCBI: GCA_006519715

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	89.00	no
125439	motility	BacteriaNetⓘ	yes	76.40	no
125439	gram_stain	BacteriaNetⓘ	negative	87.70	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Ideonella azotifigens strain DSM 21438
PATRIC: 513160.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	92.00	no
125438	anaerobic	anaerobicⓘ	no	95.47	yes
125438	spore-forming	spore-formingⓘ	no	82.91	no
125438	aerobic	aerobicⓘ	yes	84.67	yes
125438	thermophilic	thermophileⓘ	no	94.96	yes
125438	flagellated	motile2+ⓘ	yes	80.11	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Biodegradation of different PET variants from food containers by Ideonella sakaiensis.	Walter A, Sopracolle L, Mutschlechner M, Spruck M, Griesbeck C.	Arch Microbiol	10.1007/s00203-022-03306-w	2022
Phylogeny	Ideonella sakaiensis sp. nov., isolated from a microbial consortium that degrades poly(ethylene terephthalate).	Tanasupawat S, Takehana T, Yoshida S, Hiraga K, Oda K	Int J Syst Evol Microbiol	10.1099/ijsem.0.001058	2016
Phylogeny	Ideonella azotifigens sp. nov., an aerobic diazotroph of the Betaproteobacteria isolated from grass rhizosphere soil, and emended description of the genus Ideonella.	Noar JD, Buckley DH	Int J Syst Evol Microbiol	10.1099/ijs.0.003368-0	2009

References

#15705	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21438
#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 )
#25427	IJSEM 1940 2009 ( DOI 10.1099/ijs.0.003368-0 , PubMed 19567574 )
#28994	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 #25427
#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) .
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#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 azotifigens (DSM 21438, JCM 15503, 1a22)

Name and taxonomic classification

Morphology

Cell morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Halophily

Metabolite utilization

Enzymes

Isolation, sampling and environmental information

Isolation source categories

Isolation

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_039523215

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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