Strain identifier

BacDive ID: 17459

Type strain: Yes

Species: Dyella thiooxydans

Strain Designation: ATSB10

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

NCBI tax ID(s): 445710 (species)

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General

@ref: 18102

BacDive-ID: 17459

DSM-Number: 25733

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

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

NCBI tax id

  • NCBI tax id: 445710
  • Matching level: species

strain history

  • @ref: 18102
  • history: <- KACC <- R. Anandham, Organic Agriculture Division, Natl. Academy of Agricultural Science, Suwon, Republic of Korea; ATSB10

doi: 10.13145/bacdive17459.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Lysobacterales
  • family: Rhodanobacteraceae
  • genus: Dyella
  • species: Dyella thiooxydans
  • full scientific name: Dyella thiooxydans Anandham et al. 2011

@ref: 18102

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Rhodanobacteraceae

genus: Dyella

species: Dyella thiooxydans

full scientific name: Dyella thiooxydans Anandham et al. 2011

strain designation: ATSB10

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29831negative1.25 µm0.25 µmrod-shapedyes
69480yes90.061
69480negative99.991

pigmentation

  • @ref: 29831
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
18102MST-MEDIUM (DSMZ Medium 1416)yeshttps://mediadive.dsmz.de/medium/1416Name: 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
18102R2A MEDIUM (DSMZ Medium 830)yeshttps://mediadive.dsmz.de/medium/830Name: 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

@refgrowthtypetemperaturerange
18102positivegrowth28mesophilic
29831positiveoptimum30mesophilic

culture pH

@refabilitytypepH
29831positivegrowth4.5-7
29831positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 29831
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.996

halophily

@refsaltgrowthtested relationconcentration
29831NaClpositivegrowth<3 %
29831NaClpositiveoptimum1.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
29831370543-hydroxybutyrate+carbon source
2983130089acetate+carbon source
2983117234glucose+carbon source
2983128087glycogen+carbon source
2983117306maltose+carbon source
2983137684mannose+carbon source
29831506227N-acetylglucosamine+carbon source
2983126271proline+carbon source
2983117272propionate+carbon source
2983133942ribose+carbon source
2983117822serine+carbon source
2983117992sucrose+carbon source
2983131011valerate+carbon source
298314853esculin+hydrolysis

enzymes

@refvalueactivityec
29831acid phosphatase+3.1.3.2
29831alkaline phosphatase+3.1.3.1
29831cytochrome oxidase+1.9.3.1
29831urease+3.5.1.5

Isolation, sampling and environmental information

isolation

  • @ref: 18102
  • sample type: rhizosphere soil of field-cultivated sunflower
  • geographic location: Jung ha-dong
  • country: Republic of Korea
  • origin.country: KOR
  • continent: Asia
  • latitude: 35.1714
  • longitude: 128.832

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

taxonmaps

  • @ref: 69479
  • File name: preview.99_7346.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_114;96_316;97_3477;98_5389;99_7346&stattab=map
  • Last taxonomy: Dyella
  • 16S sequence: EF397574
  • Sequence Identity:
  • Total samples: 1623
  • soil counts: 658
  • aquatic counts: 425
  • animal counts: 77
  • plant counts: 463

Safety information

risk assessment

  • @ref: 18102
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18102
  • description: Dyella thiooxydans strain ATSB10 16S ribosomal RNA gene, partial sequence
  • accession: EF397574
  • length: 1422
  • database: ena
  • NCBI tax ID: 445710

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyella thiooxydans ATSB10GCA_001641285completencbi445710
66792Dyella thiooxydans strain ATSB10445710.3completepatric445710
66792Dyella thiooxydans ATSB102687453130completeimg445710

GC content

@refGC-content
1810266.0
2983166

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno83.466no
gram-positiveno98.161yes
anaerobicno99.036yes
aerobicyes92.305no
halophileno95.971yes
spore-formingno96.639no
glucose-utilyes88.722yes
motileyes86.067yes
thermophileno98.596yes
glucose-fermentno88.792no

External links

@ref: 18102

culture collection no.: DSM 25733, KACC 12756, LMG 24673

straininfo link

  • @ref: 86455
  • straininfo: 356288

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20305058Dyella 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 HJInt J Syst Evol Microbiol10.1099/ijs.0.022012-02010Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids, Helianthus/*microbiology, Molecular Sequence Data, Phenotype, Phospholipids, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/isolation & purificationGenetics
Phylogeny23667147Dyella 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 THInt J Syst Evol Microbiol10.1099/ijs.0.051185-02013Bacterial Typing Techniques, Base Composition, *Cornus, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Xanthomonadaceae/*classification/genetics/isolation & purificationGenetics
Phylogeny24860108Fulvimonas 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 SWInt J Syst Evol Microbiol10.1099/ijs.0.064642-02014Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purificationGenetics
Genetics27340060Complete 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 YGenome Announc10.1128/genomeA.00573-162016Phylogeny
Phylogeny30785390Frateuria 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 EInt J Syst Evol Microbiol10.1099/ijsem.0.0033052019Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Disease Vectors, Fatty Acids/chemistry, Hemiptera/*microbiology, Israel, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, Pseudomonadaceae/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome
Phylogeny34919040Frateuria flava sp. nov., isolated from soil.Akter S, Lee SY, Huq MAInt J Syst Evol Microbiol10.1099/ijsem.0.0051712021Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
18102Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25733)https://www.dsmz.de/collection/catalogue/details/culture/DSM-25733
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29831Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2620728776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
69479João 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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86455Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID356288.1StrainInfo: A central database for resolving microbial strain identifiers