Name: Ideonella azotifigens 1a22
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 17955

Type strain:

Species: Ideonella azotifigens

Strain Designation: 1a22

Culture col. no.: DSM 21438, JCM 15503

Strain history: D. H. Buckley 1a22.

NCBI tax ID(s): 513160 (species)

SI-ID 401901

DSM 21438

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Ideonella*
	Species	**Ideonella azotifigens**
	Full Scientific Name (LPSN)	Ideonella azotifigens Noar and Buckley 2009

Information on morphological and physiological properties Morphology

[Ref.: #28994]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %99.998

[Ref.: #28994]	Cell length	4 µm

[Ref.: #28994]	Cell width	0.75 µm

[Ref.: #28994]	Cell shape	rod-shaped

[Ref.: #28994]	Motility	yes
[Ref.: #69480]	Motility	yes Confidence in %93.672

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15705]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #15705]

Culture medium growth

[Ref.: #15705]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15705]

Culture medium composition

expand / minimize

		Temperature
[Ref.: #15705]	growth	28 °C
[Ref.: #28994]	growth	04-35 °C
[Ref.: #28994]	optimum	06-08 °C
[Ref.: #67770]	growth	30 °C

[Ref.: #15705]	Temperature range	mesophilic
[Ref.: #28994]	Temperature range	psychrophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #28994]			optimum	6.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #28994]

Oxygen tolerance

aerobe

[Ref.: #69481]	Ability of spore formation	no Confidence in %99
[Ref.: #69480]	Ability of spore formation	no Confidence in %99.992

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #28994]		NaCl		growth	0-0.5	%

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #28994]	acetate ChEBI	+	carbon source
[Ref.: #28994]	cellobiose ChEBI	+	carbon source
[Ref.: #28994]	glucose ChEBI	+	carbon source
[Ref.: #28994]	glutamate ChEBI	+	carbon source
[Ref.: #28994]	malate ChEBI	+	carbon source
[Ref.: #28994]	mannitol ChEBI	+	carbon source
[Ref.: #28994]	mannose ChEBI	+	carbon source
[Ref.: #28994]	N-acetylglucosamine ChEBI	+	carbon source
[Ref.: #28994]	tween 20 ChEBI	+	carbon source
[Ref.: #28994]	tween 40 ChEBI	+	carbon source
[Ref.: #28994]	tween 60 ChEBI	+	carbon source
[Ref.: #28994]	tween 80 ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Enzyme	Enzyme activity	EC number
[Ref.: #28994]	catalase	+	1.11.1.6
[Ref.: #28994]	cytochrome oxidase	+	1.9.3.1
[Ref.: #28994]	gelatinase	+

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

[Ref.: #15705]	Sample type/isolated from	grass rhizosphere soil
[Ref.: #15705]	Geographic location (country and/or sea, region)	Ithaca, NY
[Ref.: #15705]	Country	USA
[Ref.: #15705]	Country ISO 3 Code	USA
[Ref.: #15705]	Continent	North America

[Ref.: #67770]	Sample type/isolated from	Soil in association with the rhizosphere of a perennial grass
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

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

[Ref.: #15705]

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.: #15705]	Ideonella sp. 1a22 16S ribosomal RNA gene, partial sequence	EU542576	1396	ENA	513160 tax ID
[Ref.: #67770]	Ideonella azotifigens JCM 15503 gene for 16S ribosomal RNA, partial sequence	LC508797	1451	ENA	513160 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Ideonella azotifigens DSM 21438	GCA_006519715	contig	GenBank	513160 tax ID	*
[Ref.: #66792]	Ideonella azotifigens strain DSM 21438	513160.3	wgs	PATRIC	513160 tax ID	*

[Ref.: #15705]	GC-content	67.4 mol%
[Ref.: #67770]	GC-content	67.4 mol%	high performance liquid chromatography (HPLC)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Ideonella azotifigens strain DSM 21438 PATRIC: 513160.3
[Ref.: #69481]	spore-forming	no	99	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Ideonella azotifigens strain DSM 21438 PATRIC: 513160.3
[Ref.: #69480]	gram-positive	no	98.052	yes
[Ref.: #69480]	anaerobic	no	98.767	yes
[Ref.: #69480]	halophile	no	96.345	yes
[Ref.: #69480]	spore-forming	no	91.45	no
[Ref.: #69480]	glucose-util	yes	89	yes
[Ref.: #69480]	aerobic	yes	93.565	yes
[Ref.: #69480]	thermophile	no	99.417	yes
[Ref.: #69480]	motile	yes	88.595	yes
[Ref.: #69480]	flagellated	yes	50.916	no
[Ref.: #69480]	glucose-ferment	no	91.467	no

Availability in culture collections External links

[Ref.: #15705]

Culture collection no.

DSM 21438, JCM 15503

[Ref.: #86942]

SI-ID 401901

Literature:

Topic	Title	Authors	Journal	DOI	Year
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 )

#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 (see below)

#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;

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#86942

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-ID401901.1 )

#25427

IJSEM 1940 2009 ( DOI 10.1099/ijs.0.003368-0 , PubMed 19567574 )

* These data were automatically processed and therefore are not curated

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Ideonella azotifigens strain DSM 21438

Ideonella azotifigens strain DSM 21438

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