Name: Deinococcus aerius TR0125
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 3894

Type strain:

Species: Deinococcus aerius

Strain Designation: TR0125

Culture col. no.: DSM 21212, CIP 110035, JCM 11750

Strain history: CIP <- 2009, DSMZ <- A. Yamagishi, Tokyo Univ., Tokyo, Japan: strain TR0125

NCBI tax ID(s): 200253 (species)

SI-ID 364125

DSM 21212, JCM 11750, CIP 110035

Special Collections

Section

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

coccus-shaped
aerobe
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	*Deinococcota*
	Class	*Deinococci*
	Order	*Deinococcales*
	Family	*Deinococcaceae*
	Genus	*Deinococcus*
	Species	**Deinococcus aerius**
	Full Scientific Name (LPSN)	Deinococcus aerius Yang et al. 2009

Information on morphological and physiological properties Morphology

[Ref.: #116061]	Gram stain	positive

[Ref.: #116061]	Cell shape	coccus-shaped
[Ref.: #29176]	Cell shape	coccus-shaped

[Ref.: #116061]	Motility	no
[Ref.: #29176]	Motility	no

[Ref.: #29176]	Cell length	1.25 µm

[Ref.: #29176]	Cell width	1.25 µm

[Ref.: #29176]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #15498]

Culture medium

TGE MEDIUM (DSMZ Medium 1207)

[Ref.: #15498]

Culture medium growth

[Ref.: #15498]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15498]

Culture medium composition

expand / minimize

[Ref.: #15498]

Culture medium

GLYCEROL-YEAST EXTRACT-PEPTONE MEDIUM (DSMZ Medium 1484)

[Ref.: #15498]

Culture medium growth

[Ref.: #15498]

Culture medium link

Medium recipe at MediaDive

[Ref.: #15498]

Culture medium composition

expand / minimize

[Ref.: #37913]

Culture medium

MEDIUM 566- Reasoner's 2A agar for Flavobacterium micromati

[Ref.: #37913]

Culture medium growth

[Ref.: #37913]

Culture medium composition

expand / minimize

[Ref.: #116061]

Culture medium

CIP Medium 566

[Ref.: #116061]

Culture medium growth

[Ref.: #116061]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #15498]	growth	28 °C
[Ref.: #29176]	optimum	27.5 °C
[Ref.: #37913]	growth	30 °C
[Ref.: #67770]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #29176]	Oxygen tolerance	aerobe
[Ref.: #116061]	Oxygen tolerance	facultative anaerobe

[Ref.: #29176]

Ability of spore formation

[Ref.: #15498]	Murein short key	A21.01
[Ref.: #15498]	Murein types	A3ß L-Orn-Gly₂_-₃

[Ref.: #29176]	Observation	aggregates in clumps
[Ref.: #67770]	Observation	quinones: MK-8

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #29176]	alanine ChEBI	+	carbon source
[Ref.: #29176]	arabinose ChEBI	+	carbon source
[Ref.: #29176]	esculin ChEBI	+	hydrolysis
[Ref.: #29176]	glucosamine ChEBI	+	carbon source
[Ref.: #29176]	glutamate ChEBI	+	carbon source
[Ref.: #29176]	glycine ChEBI	+	carbon source
[Ref.: #29176]	maltose ChEBI	+	carbon source
[Ref.: #116061]	nitrate ChEBI	-	reduction
[Ref.: #116061]	nitrite ChEBI	-	reduction
[Ref.: #29176]	ornithine ChEBI	+	carbon source
[Ref.: #29176]	proline ChEBI	+	carbon source
[Ref.: #29176]	raffinose ChEBI	+	carbon source
[Ref.: #29176]	sucrose ChEBI	+	carbon source
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #116061]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	-	3.1.3.2	* from API zym
[Ref.: #29176]	alkaline phosphatase	+	3.1.3.1
[Ref.: #68382]	alkaline phosphatase	-	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	-	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #29176]	catalase	+	1.11.1.6
[Ref.: #116061]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #29176]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #116061]	oxidase	+
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #116061]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #116061]	12309	-	-	+	+	-	+	-	-	-	-	-	+	-	-	-	-	-	-	-	-

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

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

[Ref.: #15498]	Sample type/isolated from	air dust collected in the high atmosphere
[Ref.: #15498]	Geographic location (country and/or sea, region)	Main Island
[Ref.: #15498]	Country	Japan
[Ref.: #15498]	Country ISO 3 Code	JPN
[Ref.: #15498]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Air sample collected from the high atmosphere
[Ref.: #67770]	Country	Japan
[Ref.: #67770]	Country ISO 3 Code	JPN
[Ref.: #67770]	Continent	Asia

[Ref.: #116061]	Sample type/isolated from	Environment, Dust samples, high atmosphere
[Ref.: #116061]	Country	Japan
[Ref.: #116061]	Country ISO 3 Code	JPN
[Ref.: #116061]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Air	#Outdoor Air
#Environmental	#Terrestrial	#Dust

What are isolation sources categories?

[Ref.: #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

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

[Ref.: #15498]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #116061]	Biosafety level	1	Risk group (French classification)

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.: #15498]	Deinococcus aerius gene for 16S ribosomal RNA, partial sequence	AB087288	1468	GenBank ENA	200253 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Deinococcus aerius TR0125	GCA_002897375	contig	GenBank ENA	200253 tax ID
[Ref.: #66792]	Deinococcus aerius TR0125	2895784119	draft	JGI IMG/M	200253 tax ID	*

[Ref.: #15498]	GC-content	70.5 mol%	high performance liquid chromatography (HPLC)
[Ref.: #29176]	GC-content	70.5 mol%

Availability in culture collections External links

[Ref.: #15498]

Culture collection no.

DSM 21212, CIP 110035, JCM 11750

[Ref.: #73404]

SI-ID 364125

Literature:

Topic	Title	Authors	Journal	DOI	Year
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;

#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) .

#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 .

#73404

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-ID364125.1 )

#116061 Collection of Institut Pasteur ; Curators of the CIP; CIP 110035

#25600

IJSEM 1862 2009 ( DOI 10.1099/ijs.0.007963-0 , PubMed 19567578 )

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Deinococcus aerius in external resources:
SILVA
BRENDA
PANGAEA
GBIF