Strain identifier

BacDive ID: 17458

Type strain: Yes

Species: Dyella terrae

Strain Designation: JS14-6

Strain history: S.-W. Kwon JS14-6.

NCBI tax ID(s): 522259 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 16736

BacDive-ID: 17458

DSM-Number: 23153

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

description: Dyella terrae JS14-6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil cultivated with Citrus species.

NCBI tax id

  • NCBI tax id: 522259
  • Matching level: species

strain history

@refhistory
16736<- KACC <- H.-Y. Weon, Rural Development Administration (RDA), Suwon, Republic of Korea; JS14-6
67770S.-W. Kwon JS14-6.

doi: 10.13145/bacdive17458.20230509.8.1

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 terrae
  • full scientific name: Dyella terrae Weon et al. 2009

@ref: 16736

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Xanthomonadales

family: Rhodanobacteraceae

genus: Dyella

species: Dyella terrae

full scientific name: Dyella terrae Weon et al. 2009

strain designation: JS14-6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29047negative3 µm0.45 µmrod-shapedyes
69480yes94.369
69480negative99.979

pigmentation

  • @ref: 29047
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16736
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16736positivegrowth28mesophilic
29047positivegrowth10-35
29047positiveoptimum29mesophilic
67770positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29047positivegrowth04-09alkaliphile
29047positiveoptimum6.5

Physiology and metabolism

oxygen tolerance

  • @ref: 29047
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
29047no
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
29047NaClpositivegrowth0-3 %
29047NaClpositiveoptimum0.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2904717306maltose+carbon source
2904737684mannose+carbon source
2904717822serine+carbon source
2904753426tween 80+carbon source

enzymes

  • @ref: 29047
  • value: acid phosphatase
  • activity: +
  • ec: 3.1.3.2

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16736soil cultivated with Citrus speciesCitrusJeju islandRepublic of KoreaKORAsia
67770Soil cultivated with Citrus speciesCitrus sp.Jeju IslandRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Plants#Shrub (Scrub)
#Host#Plants#Tree

taxonmaps

  • @ref: 69479
  • File name: preview.99_5367.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_114;96_316;97_3161;98_3972;99_5367&stattab=map
  • Last taxonomy: Dyella
  • 16S sequence: EU604273
  • Sequence Identity:
  • Total samples: 1439
  • soil counts: 980
  • aquatic counts: 133
  • animal counts: 188
  • plant counts: 138

Safety information

risk assessment

  • @ref: 16736
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16736
  • description: Dyella terrae strain JS14-6 16S ribosomal RNA gene, partial sequence
  • accession: EU604273
  • length: 1423
  • database: ena
  • NCBI tax ID: 522259

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Dyella terrae strain KACC 12748522259.3wgspatric522259
66792Dyella terrae KACC 127482894703127draftimg522259
67770Dyella terrae KACC 12748GCA_004322705contigncbi522259

GC content

@refGC-contentmethod
1673664.0high performance liquid chromatography (HPLC)
2904764
6777064high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.747no
anaerobicno98.627yes
halophileno95.055no
spore-formingno94.311no
glucose-utilyes88.818no
aerobicyes90.47yes
thermophileno99.428no
motileyes91.125no
flagellatedno67.646no
glucose-fermentno90.652no

External links

@ref: 16736

culture collection no.: DSM 23153, JCM 15424, KACC 12748

straininfo link

  • @ref: 86454
  • straininfo: 403342

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19542132Dyella soli sp. nov. and Dyella terrae sp. nov., isolated from soil.Weon HY, Anandham R, Kim BY, Hong SB, Jeon YA, Kwon SWInt J Syst Evol Microbiol10.1099/ijs.0.004838-02009Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xanthomonadaceae/*classification/genetics/isolation & purification/physiologyGenetics
Phylogeny23435246Dyella jiangningensis sp. nov., a gamma-proteobacterium isolated from the surface of potassium-bearing rock.Zhao F, Guo XQ, Wang P, He LY, Huang Z, Sheng XFInt J Syst Evol Microbiol10.1099/ijs.0.048470-02013Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, *Potassium, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone, 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
Phylogeny30608226Dyella solisilvae sp. nov., isolated from mixed pine and broad-leaved forest soil.Gao ZH, Yang Z, Chen MH, Huang ZJ, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0032182019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, Pinus, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/isolation & purificationTranscriptome
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
Phylogeny31454308Dyella amyloliquefaciens sp. nov., isolated from forest soil.Fu JC, Gao ZH, Wu TT, Chen MH, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0036602019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Nucleic Acid Hybridization, Phospholipids/chemistry, Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/isolation & purificationTranscriptome
Phylogeny34491893Dyella telluris sp. nov. and Dyella acidiphila sp. nov., isolated from forest soil of Dinghushan Biosphere Reserve, China.Huang T, Fu JC, Dong SH, Zhang QM, Wu TT, Qiu LHInt J Syst Evol Microbiol10.1099/ijsem.0.0049852021Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Gammaproteobacteria/*classification/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil MicrobiologyTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
16736Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23153)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23153
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
29047Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2547728776041
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)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86454Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403342.1StrainInfo: A central database for resolving microbial strain identifiers