Deinococcus aerius (DSM 21212, CIP 110035, JCM 11750)

Name: Deinococcus aerius (DSM 21212, CIP 110035, JCM 11750)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 3894

Type strain

Strain Designation TR0125

Culture col. no. DSM 21212 CIP 110035 JCM 11750 TR0125

NCBI tax ID(s) 200253

Special Collections DSMZ JCM CIP Literature strains

Links

Deinococcus aerius TR0125 is an aerobe, mesophilic, coccus-shaped prokaryote that was isolated from air dust collected in the high atmosphere.

coccus-shaped aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 364125

DSM 21212,JCM 11750,CIP 110035

@ref 20215

Last LPSN update 2025-12-16 09:47:40

Domain Thermotogati

Phylum Deinococcota

Class Deinococci

Order Deinococcales

Family Deinococcaceae

Genus Deinococcus

Species Deinococcus aerius

Full scientific name Deinococcus aerius Yang et al. 2009

Morphology

Cell morphology

@ref	Cell length	Cell width	Cell shape	Motility	Gram stain
29176	1.25 µm	1.25 µm	coccus-shaped
116061			coccus-shaped		positive

Pigmentation

29176

Productionyes

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
15498	TGE MEDIUM (DSMZ Medium 1207)	Medium recipe at MediaDive	Name: TGE (DSMZ Medium 1207) Composition: Agar 15.0 g/l Tryptone 10.0 g/l Beef extract 6.0 g/l Glucose 2.0 g/l Distilled water
15498	GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484)	Medium recipe at MediaDive	Name: Glycerol-Yeast extract-Peptone Medium (DSMZ Medium 1484) Composition: Agar 15.0 g/l Yeast extract 5.0 g/l Bacto peptone 3.0 g/l Betaine 1.25 g/l Sodium pyruvate 1.25 g/l MgSO4 x 7 H2O 0.03 g/l Nitrilotriacetic acid 0.015 g/l NaCl 0.01 g/l MnSO4 x H2O 0.005 g/l ZnSO4 x 7 H2O 0.0018 g/l CoSO4 x 7 H2O 0.0018 g/l FeSO4 x 7 H2O 0.001 g/l CaCl2 x 2 H2O 0.001 g/l NiCl2 x 6 H2O 0.0003 g/l AlK(SO4)2 x 12 H2O 0.0002 g/l Pyridoxine hydrochloride 0.0001 g/l Na2MoO4 x 2 H2O 0.0001 g/l H3BO3 0.0001 g/l CuSO4 x 5 H2O 0.0001 g/l (DL)-alpha-Lipoic acid 5e-05 g/l p-Aminobenzoic acid 5e-05 g/l Calcium D-(+)-pantothenate 5e-05 g/l Nicotinic acid 5e-05 g/l Riboflavin 5e-05 g/l Thiamine HCl 5e-05 g/l Folic acid 2e-05 g/l Biotin 2e-05 g/l Na2WO4 x 2 H2O 4e-06 g/l Na2SeO3 x 5 H2O 3e-06 g/l Vitamin B12 1e-06 g/l Glycerol Distilled water
37913	MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati		Distilled water make up to (1000.000 ml);R2A agar (18.200 g)
116061	CIP Medium 566	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
15498	positive	growth	28	mesophilic
29176	positive	optimum	27.5	mesophilic
37913	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
29176	aerobe
116061	facultative anaerobe

Spore formation

29176

Spore formationno

Murein

@ref	Murein short key	Type
15498	A21.01	A3ß L-Orn-Gly₂_-₃

Observation

@ref	Observation
29176	aggregates in clumps
67770	quinones: MK-8

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29176	16449 ChEBI	alanine	+	carbon source
29176	22599 ChEBI	arabinose	+	carbon source
29176	4853 ChEBI	esculin	+	hydrolysis
29176	5417 ChEBI	glucosamine	+	carbon source
29176	29987 ChEBI	glutamate	+	carbon source
29176	15428 ChEBI	glycine	+	carbon source
29176	17306 ChEBI	maltose	+	carbon source
116061	17632 ChEBI	nitrate	-	reduction
116061	16301 ChEBI	nitrite	-	reduction
29176	18257 ChEBI	ornithine	+	carbon source
29176	26271 ChEBI	proline	+	carbon source
29176	16634 ChEBI	raffinose	+	carbon source
29176	17992 ChEBI	sucrose	+	carbon source

Metabolite production

@ref	Chebi-ID	Metabolite	Production
116061	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	-	3.1.3.2	from API zym
29176	alkaline phosphatase	+	3.1.3.1
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
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
29176	catalase	+	1.11.1.6
116061	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
29176	cytochrome oxidase	+	1.9.3.1
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
116061	oxidase	+
68382	trypsin	-	3.4.21.4	from API zym
116061	urease	-	3.5.1.5
68382	valine arylamidase	-		from API zym

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	coenzyme A metabolism	100	4 of 4
66794	starch degradation	100	10 of 10
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
66794	gluconeogenesis	100	8 of 8
66794	butanoate fermentation	100	4 of 4
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	denitrification	100	2 of 2
66794	glycogen metabolism	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	adipate degradation	100	2 of 2
66794	threonine metabolism	100	10 of 10
66794	molybdenum cofactor biosynthesis	100	9 of 9
66794	folate polyglutamylation	100	1 of 1
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	valine metabolism	100	9 of 9
66794	suberin monomers biosynthesis	100	2 of 2
66794	ethanol fermentation	100	2 of 2
66794	phenylacetate degradation (aerobic)	100	5 of 5
66794	palmitate biosynthesis	95.45	21 of 22
66794	pentose phosphate pathway	90.91	10 of 11
66794	Entner Doudoroff pathway	90	9 of 10
66794	chorismate metabolism	88.89	8 of 9
66794	d-mannose degradation	88.89	8 of 9
66794	C4 and CAM-carbon fixation	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	purine metabolism	86.17	81 of 94
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	photosynthesis	85.71	12 of 14
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	phenylalanine metabolism	84.62	11 of 13
66794	glycolate and glyoxylate degradation	83.33	5 of 6
66794	metabolism of disaccharids	81.82	9 of 11
66794	flavin biosynthesis	80	12 of 15
66794	metabolism of amino sugars and derivatives	80	4 of 5
66794	ethylmalonyl-CoA pathway	80	4 of 5
66794	myo-inositol biosynthesis	80	8 of 10
66794	peptidoglycan biosynthesis	80	12 of 15
66794	propionate fermentation	80	8 of 10
66794	methylglyoxal degradation	80	4 of 5
66794	4-hydroxyphenylacetate degradation	80	8 of 10
66794	pyrimidine metabolism	80	36 of 45
66794	alanine metabolism	79.31	23 of 29
66794	tryptophan metabolism	78.95	30 of 38
66794	citric acid cycle	78.57	11 of 14
66794	4-hydroxymandelate degradation	77.78	7 of 9
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	allantoin degradation	77.78	7 of 9
66794	leucine metabolism	76.92	10 of 13
66794	glycolysis	76.47	13 of 17
66794	acetate fermentation	75	3 of 4
66794	ppGpp biosynthesis	75	3 of 4
66794	degradation of sugar alcohols	75	12 of 16
66794	glycogen biosynthesis	75	3 of 4
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	sulfopterin metabolism	75	3 of 4
66794	NAD metabolism	72.22	13 of 18
66794	heme metabolism	71.43	10 of 14
66794	isoprenoid biosynthesis	69.23	18 of 26
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetyl CoA biosynthesis	66.67	2 of 3
66794	aspartate and asparagine metabolism	66.67	6 of 9
66794	acetoin degradation	66.67	2 of 3
66794	serine metabolism	66.67	6 of 9
66794	histidine metabolism	65.52	19 of 29
66794	oxidative phosphorylation	64.84	59 of 91
66794	tetrahydrofolate metabolism	64.29	9 of 14
66794	glutathione metabolism	64.29	9 of 14
66794	degradation of pentoses	64.29	18 of 28
66794	d-xylose degradation	63.64	7 of 11
66794	proline metabolism	63.64	7 of 11
66794	dTDPLrhamnose biosynthesis	62.5	5 of 8
66794	ketogluconate metabolism	62.5	5 of 8
66794	arginine metabolism	62.5	15 of 24
66794	urea cycle	61.54	8 of 13
66794	lipid metabolism	61.29	19 of 31
66794	degradation of hexoses	61.11	11 of 18
66794	cysteine metabolism	61.11	11 of 18
66794	non-pathway related	60.53	23 of 38
66794	glycine betaine biosynthesis	60	3 of 5
66794	lipoate biosynthesis	60	3 of 5
66794	phenol degradation	60	12 of 20
66794	coenzyme M biosynthesis	60	6 of 10
66794	gallate degradation	60	3 of 5
66794	propanol degradation	57.14	4 of 7
66794	cardiolipin biosynthesis	57.14	4 of 7
66794	nitrate assimilation	55.56	5 of 9
66794	lysine metabolism	54.76	23 of 42
66794	methionine metabolism	53.85	14 of 26
66794	3-phenylpropionate degradation	53.33	8 of 15
66794	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	glycine metabolism	50	5 of 10
66794	kanosamine biosynthesis II	50	1 of 2
66794	cyclohexanol degradation	50	2 of 4
66794	carotenoid biosynthesis	50	11 of 22
66794	ribulose monophosphate pathway	50	1 of 2
66794	resorcinol degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	phenylmercury acetate degradation	50	1 of 2
66794	polyamine pathway	47.83	11 of 23
66794	vitamin B1 metabolism	46.15	6 of 13
66794	sulfate reduction	46.15	6 of 13
66794	lipid A biosynthesis	44.44	4 of 9
66794	degradation of sugar acids	44	11 of 25
66794	cellulose degradation	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	vitamin K metabolism	40	2 of 5
66794	phosphatidylethanolamine bioynthesis	38.46	5 of 13
66794	androgen and estrogen metabolism	37.5	6 of 16
66794	carnitine metabolism	37.5	3 of 8
66794	vitamin B6 metabolism	36.36	4 of 11
66794	tyrosine metabolism	35.71	5 of 14
66794	bile acid biosynthesis, neutral pathway	35.29	6 of 17
66794	IAA biosynthesis	33.33	1 of 3
66794	cyanate degradation	33.33	1 of 3
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	pantothenate biosynthesis	33.33	2 of 6
66794	sphingosine metabolism	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	octane oxidation	33.33	1 of 3
66794	ascorbate metabolism	31.82	7 of 22
66794	chlorophyll metabolism	27.78	5 of 18
66794	vitamin B12 metabolism	26.47	9 of 34
66794	biotin biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	CMP-KDO biosynthesis	25	1 of 4
66794	toluene degradation	25	1 of 4
66794	daunorubicin biosynthesis	22.22	2 of 9
66794	arachidonic acid metabolism	22.22	4 of 18

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
116061	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Environmental	#Air	#Outdoor Air
#Environmental	#Terrestrial	#Dust

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
15498	air dust collected in the high atmosphere	Main Island	Japan	JPN	Asia
67770	Air sample collected from the high atmosphere		Japan	JPN	Asia
116061	Environment, Dust samples, high atmosphere		Japan	JPN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AB087288 (>99% sequence identity) for Deinococcus aerius subclade from Microbeatlas

Aquatic Samples	2
Soil Samples	4
Animal Samples	22
Plant Samples
Total Samples	28

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
15498	1	Risk group (German classification) According to TRBA 466
116061	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
67770	ASM289737v1 assembly for Deinococcus aerius TR0125	contig	GCA_002897375	200253.7	2895784119	200253	69.44

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
15498	Deinococcus aerius gene for 16S ribosomal RNA, partial sequence	AB087288	1468		200253

GC content

@ref	GC-content (mol%)	Method
15498	70.5	high performance liquid chromatography (HPLC)
29176	70.5

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Deinococcus aerius TR0125
NCBI: GCA_002897375

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	87.90	no
125439	motility	BacteriaNetⓘ	yes	56.30	no
125439	gram_stain	BacteriaNetⓘ	negative	88.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	facultative anaerobe	81.40	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	DNA Damage and Survival Time Course of Deinococcal Cell Pellets During 3 Years of Exposure to Outer Space.	Kawaguchi Y, Shibuya M, Kinoshita I, Yatabe J, Narumi I, Shibata H, Hayashi R, Fujiwara D, Murano Y, Hashimoto H, Imai E, Kodaira S, Uchihori Y, Nakagawa K, Mita H, Yokobori SI, Yamagishi A.	Front Microbiol	10.3389/fmicb.2020.02050	2020
Genetics	Draft Genome Sequence of the Radioresistant Bacterium Deinococcus aerius TR0125, Isolated from the High Atmosphere above Japan.	Satoh K, Arai H, Sanzen T, Kawaguchi Y, Hayashi H, Yokobori SI, Yamagishi A, Oono Y, Narumi I	Genome Announc	10.1128/genomeA.00080-18	2018
Phylogeny	Deinococcus aerius sp. nov., isolated from the high atmosphere.	Yang Y, Itoh T, Yokobori S, Itahashi S, Shimada H, Satoh K, Ohba H, Narumi I, Yamagishi A	Int J Syst Evol Microbiol	10.1099/ijs.0.007963-0	2009

References

#15498	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 21212
#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 )
#29176	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 #25600 (see below)
#37913	; Curators of the CIP;
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#67770	Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#68382	Automatically annotated from API zym .
#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 .
#116061	Collection of Institut Pasteur ; Curators of the CIP; CIP 110035
#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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Deinococcus aerius (DSM 21212, CIP 110035, JCM 11750)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Murein

Observation

Metabolite utilization

Metabolite production

Enzymes

Pathway annotation

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_002897375

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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