Dyella thiooxydans (DSM 25733, KACC 12756, LMG 24673)

Name: Dyella thiooxydans (DSM 25733, KACC 12756, LMG 24673)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 17459

Type strain

Strain Designation ATSB10

Culture col. no. DSM 25733 KACC 12756 LMG 24673 ATSB10

NCBI tax ID(s) 445710

Special Collections DSMZ Literature strains

History <- KACC <- R. Anandham, Organic Agriculture Division, Natl. Academy of Agricultural Science, Suwon, Republic of Korea; ATSB10

Links

Dyella thiooxydans ATSB10 is an aerobe, Gram-negative, motile bacterium that was isolated from rhizosphere soil of field-cultivated sunflower.

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

Name and taxonomic classification

SI-ID 356288

LMG 24673,KACC 12756,DSM 25733

@ref 20215

Last LPSN update 2026-02-09 11:22:13

Domain Bacteria

Phylum Pseudomonadota

Class Gammaproteobacteria

Order Lysobacterales

Family Rhodanobacteraceae

Genus Dyella

Species Dyella thiooxydans

Full scientific name Dyella thiooxydans Anandham et al. 2011

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape	Confidence
29831	negative	1.25 µm	0.25 µm	rod-shaped
125438	negative				98.494
125439	negative				98.8

Pigmentation

29831

Productionno

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
18102	MST-MEDIUM (DSMZ Medium 1416)		Medium recipe at MediaDive	Name: MST-MEDIUM, AUTOTROPHIC GROWTH (DSMZ Medium 1416) Composition: Na2S2O3 x 5 H2O 5.0 g/l K2HPO4 4.0 g/l KH2PO4 1.5 g/l NH4Cl 1.0 g/l MgSO4 x 7 H2O 0.5 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l H3BO3 6e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Distilled water
18102	R2A MEDIUM (DSMZ Medium 830)		Medium recipe at MediaDive	Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)
18102	positive	growth	28
29831	positive	optimum	30

Culture pH

@ref	Ability	Type	PH
29831	positive	optimum	7
29831	positive	growth	4.5-7

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
29831	aerobe
125439	obligate aerobe	99.3

Spore formation

@ref	Spore formation	Confidence
125438		91.135
125439		97.1

Halophily

@ref	Salt	Growth	Tested relation	Concentration
29831	NaCl	positive	growth	<3 %
29831	NaCl	positive	optimum	1.5 %

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
29831	37054 ChEBI	3-hydroxybutyrate	+	carbon source
29831	30089 ChEBI	acetate	+	carbon source
29831	4853 ChEBI	esculin	+	hydrolysis
29831	17234 ChEBI	glucose	+	carbon source
29831	28087 ChEBI	glycogen	+	carbon source
29831	17306 ChEBI	maltose	+	carbon source
29831	37684 ChEBI	mannose	+	carbon source
29831	506227 ChEBI	N-acetylglucosamine	+	carbon source
29831	26271 ChEBI	proline	+	carbon source
29831	17272 ChEBI	propionate	+	carbon source
29831	33942 ChEBI	ribose	+	carbon source
29831	17822 ChEBI	serine	+	carbon source
29831	17992 ChEBI	sucrose	+	carbon source
29831	31011 ChEBI	valerate	+	carbon source

Enzymes

@ref	Value	Activity	Ec
29831	acid phosphatase	+	3.1.3.2
29831	alkaline phosphatase	+	3.1.3.1
29831	cytochrome oxidase	+	1.9.3.1
29831	urease	+	3.5.1.5

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	quinate degradation	100	2 of 2
66794	methylglyoxal degradation	100	5 of 5
66794	formaldehyde oxidation	100	3 of 3
66794	ppGpp biosynthesis	100	4 of 4
66794	cis-vaccenate biosynthesis	100	2 of 2
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	adipate degradation	100	2 of 2
66794	denitrification	100	2 of 2
66794	sulfopterin metabolism	100	4 of 4
66794	butanoate fermentation	100	4 of 4
66794	coenzyme A metabolism	100	4 of 4
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	palmitate biosynthesis	100	22 of 22
66794	octane oxidation	100	3 of 3
66794	biotin biosynthesis	100	4 of 4
66794	anapleurotic synthesis of oxalacetate	100	1 of 1
66794	acetate fermentation	100	4 of 4
66794	threonine metabolism	100	10 of 10
66794	suberin monomers biosynthesis	100	2 of 2
66794	folate polyglutamylation	100	1 of 1
66794	tetrahydrofolate metabolism	92.86	13 of 14
66794	glutathione metabolism	92.86	13 of 14
66794	phenylalanine metabolism	92.31	12 of 13
66794	starch degradation	90	9 of 10
66794	Entner Doudoroff pathway	90	9 of 10
66794	propionate fermentation	90	9 of 10
66794	lipid A biosynthesis	88.89	8 of 9
66794	chorismate metabolism	88.89	8 of 9
66794	serine metabolism	88.89	8 of 9
66794	valine metabolism	88.89	8 of 9
66794	gluconeogenesis	87.5	7 of 8
66794	isoleucine metabolism	87.5	7 of 8
66794	heme metabolism	85.71	12 of 14
66794	photosynthesis	85.71	12 of 14
66794	propanol degradation	85.71	6 of 7
66794	glutamate and glutamine metabolism	85.71	24 of 28
66794	ubiquinone biosynthesis	85.71	6 of 7
66794	reductive acetyl coenzyme A pathway	85.71	6 of 7
66794	leucine metabolism	84.62	11 of 13
66794	purine metabolism	84.04	79 of 94
66794	NAD metabolism	83.33	15 of 18
66794	pentose phosphate pathway	81.82	9 of 11
66794	glycogen metabolism	80	4 of 5
66794	peptidoglycan biosynthesis	80	12 of 15
66794	flavin biosynthesis	80	12 of 15
66794	citric acid cycle	78.57	11 of 14
66794	tyrosine metabolism	78.57	11 of 14
66794	CO2 fixation in Crenarchaeota	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	molybdenum cofactor biosynthesis	77.78	7 of 9
66794	aspartate and asparagine metabolism	77.78	7 of 9
66794	pyrimidine metabolism	77.78	35 of 45
66794	glycolysis	76.47	13 of 17
66794	alanine metabolism	75.86	22 of 29
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	75	6 of 8
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	methionine metabolism	73.08	19 of 26
66794	d-xylose degradation	72.73	8 of 11
66794	histidine metabolism	72.41	21 of 29
66794	cardiolipin biosynthesis	71.43	5 of 7
66794	lipid metabolism	70.97	22 of 31
66794	cyanate degradation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	L-lactaldehyde degradation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	tryptophan metabolism	65.79	25 of 38
66794	lysine metabolism	64.29	27 of 42
66794	proline metabolism	63.64	7 of 11
66794	non-pathway related	63.16	24 of 38
66794	ketogluconate metabolism	62.5	5 of 8
66794	isoprenoid biosynthesis	61.54	16 of 26
66794	urea cycle	61.54	8 of 13
66794	cysteine metabolism	61.11	11 of 18
66794	lipoate biosynthesis	60	3 of 5
66794	arginine metabolism	58.33	14 of 24
66794	vitamin B6 metabolism	54.55	6 of 11
66794	metabolism of disaccharids	54.55	6 of 11
66794	vitamin B1 metabolism	53.85	7 of 13
66794	pantothenate biosynthesis	50	3 of 6
66794	degradation of aromatic, nitrogen containing compounds	50	6 of 12
66794	catecholamine biosynthesis	50	2 of 4
66794	phenylmercury acetate degradation	50	1 of 2
66794	dTDPLrhamnose biosynthesis	50	4 of 8
66794	glycine metabolism	50	5 of 10
66794	glycolate and glyoxylate degradation	50	3 of 6
66794	kanosamine biosynthesis II	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	degradation of pentoses	46.43	13 of 28
66794	sulfate reduction	46.15	6 of 13
66794	phosphatidylethanolamine bioynthesis	46.15	6 of 13
66794	degradation of sugar alcohols	43.75	7 of 16
66794	polyamine pathway	43.48	10 of 23
66794	ascorbate metabolism	40.91	9 of 22
66794	oxidative phosphorylation	40.66	37 of 91
66794	vitamin K metabolism	40	2 of 5
66794	metabolism of amino sugars and derivatives	40	2 of 5
66794	hydrogen production	40	2 of 5
66794	factor 420 biosynthesis	40	2 of 5
66794	cellulose degradation	40	2 of 5
66794	3-phenylpropionate degradation	40	6 of 15
66794	glycine betaine biosynthesis	40	2 of 5
66794	D-cycloserine biosynthesis	40	2 of 5
66794	arachidonate biosynthesis	40	2 of 5
66794	3-chlorocatechol degradation	40	2 of 5
66794	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
66794	enterobactin biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	nitrate assimilation	33.33	3 of 9
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	sphingosine metabolism	33.33	2 of 6
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	IAA biosynthesis	33.33	1 of 3
66794	degradation of hexoses	33.33	6 of 18
66794	arachidonic acid metabolism	33.33	6 of 18
66794	phenylpropanoid biosynthesis	30.77	4 of 13
66794	phenol degradation	30	6 of 20
66794	benzoyl-CoA degradation	28.57	2 of 7
66794	degradation of sugar acids	28	7 of 25
66794	carotenoid biosynthesis	27.27	6 of 22
66794	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
66794	toluene degradation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	cyclohexanol degradation	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	vitamin E metabolism	25	1 of 4
66794	chlorophyll metabolism	22.22	4 of 18

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	Latitude	Longitude
18102	rhizosphere soil of field-cultivated sunflower	Jung ha-dong	Republic of Korea	KOR	Asia	35.1714	128.832 35.1714/128.832

Taxonmaps

69479

Global distribution of 16S sequence EF397574 (>99% sequence identity) for Dyella from Microbeatlas

Aquatic Samples	425
Soil Samples	658
Animal Samples	77
Plant Samples	463
Total Samples	1623

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
18102	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
66792	ASM164128v1 assembly for Dyella thiooxydans ATSB10	complete	GCA_001641285	445710.3	2687453130	445710	99.01

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
18102	Dyella thiooxydans strain ATSB10 16S ribosomal RNA gene, partial sequence	EF397574	1422		445710

GC content

@ref	GC-content (mol%)
18102	66.0
29831	66

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Dyella thiooxydans strain ATSB10
PATRIC: 445710.3

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	97.10	no
125439	motility	BacteriaNetⓘ	yes	86.30	no
125439	gram_stain	BacteriaNetⓘ	negative	98.80	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	99.30	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Dyella thiooxydans ATSB10
NCBI: GCA_001641285.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	no	98.49	yes
125438	anaerobic	anaerobicⓘ	no	98.90	yes
125438	aerobic	aerobicⓘ	yes	86.66	yes
125438	spore-forming	spore-formingⓘ	no	91.14	no
125438	thermophilic	thermophileⓘ	no	95.53	yes
125438	flagellated	motile2+ⓘ	yes	67.19	no

Literature

Topic	Title	Authors	Journal	DOI	Year
Genetics	Complete Genome Sequence of Dyella thiooxydans ATSB10, a Thiosulfate-Oxidizing Bacterium Isolated from Sunflower Fields in South Korea.	Hwangbo K, Um Y, Chung H, Yoo J, Kim KY, Madhaiyan M, Sa TM, Lee Y	Genome Announc	10.1128/genomeA.00573-16	2016
Phylogeny	Frateuria flava sp. nov., isolated from soil.	Akter S, Lee SY, Huq MA	Int J Syst Evol Microbiol	10.1099/ijsem.0.005171	2021
Phylogeny	Frateuria defendens sp. nov., bacterium isolated from the yellows grapevine's disease vector Hyalesthes obsoletus.	Lidor O, Santos-Garcia D, Mozes-Daube N, Naor V, Cohen E, Iasur-Kruh L, Bahar O, Zchori-Fein E	Int J Syst Evol Microbiol	10.1099/ijsem.0.003305	2019
Phylogeny	Fulvimonas yonginensis sp. nov., isolated from greenhouse soil, and emended description of the genus Fulvimonas.	Ahn JH, Kim SJ, Weon HY, Hong SB, Seok SJ, Kwon SW	Int J Syst Evol Microbiol	10.1099/ijs.0.064642-0	2014
Phylogeny	Dyella kyungheensis sp. nov., isolated from soil of a cornus fruit field.	Son HM, Yang JE, Yi EJ, Park Y, Won KH, Kim JH, Han CK, Kook M, Yi TH	Int J Syst Evol Microbiol	10.1099/ijs.0.051185-0	2013
Phylogeny	Dyella thiooxydans sp. nov., a facultatively chemolithotrophic, thiosulfate-oxidizing bacterium isolated from rhizosphere soil of sunflower (Helianthus annuus L.).	Anandham R, Kwon SW, Indira Gandhi P, Kim SJ, Weon HY, Kim YS, Sa TM, Kim YK, Jee HJ	Int J Syst Evol Microbiol	10.1099/ijs.0.022012-0	2010

References

#18102	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 25733
#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 )
#26207	IJSEM 392 2011 ( DOI 10.1099/ijs.0.022012-0 , PubMed 20305058 )
#29831	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 #26207
#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 )
#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 .
#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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Dyella thiooxydans (DSM 25733, KACC 12756, LMG 24673)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Metabolite utilization

Enzymes

Pathway annotation

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001641285

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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