Strain identifier

BacDive ID: 6168

Type strain: Yes

Species: Devosia soli

Strain Designation: HST3-14

Strain history: <- SD Lee, Cheju Univ.

NCBI tax ID(s): 395930 (species)

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General

@ref: 17215

BacDive-ID: 6168

DSM-Number: 23447

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

description: Devosia soli HST3-14 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment sample from Hwasun Beach.

NCBI tax id

  • NCBI tax id: 395930
  • Matching level: species

strain history

@refhistory
17215<- KCTC <- S. D. Lee; HST3-14
67770S. D. Lee HST3-14.
67771<- SD Lee, Cheju Univ.

doi: 10.13145/bacdive6168.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Devosiaceae
  • genus: Devosia
  • species: Devosia soli
  • full scientific name: Devosia soli Yoo et al. 2006

  • synonyms

    • @ref: 20215
    • synonym: Devosia subaequoris

@ref: 17215

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Devosiaceae

genus: Devosia

species: Devosia subaequoris

full scientific name: Devosia subaequoris Lee 2007

strain designation: HST3-14

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32246negative1.2 µm0.7 µmrod-shapedyes
67771negative
69480yes92.823
69480negative99.949

pigmentation

  • @ref: 32246
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17215
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l NaHCO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
17215positivegrowth28mesophilic
32246positivegrowth20-42
32246positiveoptimum31mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32246positivegrowth5.1-12.1alkaliphile
32246positiveoptimum8.6

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32246aerobe
67771aerobe

spore formation

@refspore formationconfidence
32246no
69481no100
69480no99.991

halophily

@refsaltgrowthtested relationconcentration
32246NaClpositivegrowth0-3 %
32246NaClpositiveoptimum1.5 %

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3224617306maltose+carbon source
3224629864mannitol+carbon source
3224637684mannose+carbon source
322464853esculin+hydrolysis

enzymes

@refvalueactivityec
32246alkaline phosphatase+3.1.3.1
32246catalase+1.11.1.6
32246cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
17215sediment sample from Hwasun BeachJejuRepublic of KoreaKORAsia
67770Sediment from Hwasun BeachJejuRepublic of KoreaKORAsia
67771From beach sedimentJejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Coast

Safety information

risk assessment

  • @ref: 17215
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17215
  • description: Devosia subaequoris partial 16S rRNA gene, strain type strain: HST3-14
  • accession: AM293857
  • length: 1370
  • database: ena
  • NCBI tax ID: 395930

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Devosia subaequoris DSM 23447GCA_014197055contigncbi395930
66792Devosia subaequoris strain DSM 23447395930.6wgspatric395930
66792Devosia subaequoris DSM 234472830079415draftimg395930

GC content

@refGC-contentmethod
3224659.1
6777059.1high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno95.851no
anaerobicno98.84yes
halophileno87.024yes
spore-formingno95.973no
glucose-utilyes90.31no
aerobicyes93.513yes
motileyes84.231no
flagellatedno63.989no
thermophileno97.796yes
glucose-fermentno92.098no

External links

@ref: 17215

culture collection no.: DSM 23447, JCM 14206, KCTC 12772, CGMCC 1.10441

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17911285Devosia subaequoris sp. nov., isolated from beach sediment.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.65185-02007Aerobiosis/physiology, Bacterial Typing Techniques, Base Composition, Catalase/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/physiology, Korea, Locomotion/physiology, Molecular Sequence Data, Oxidoreductases/metabolism, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Temperature, Ubiquinone/analysisMetabolism
Phylogeny27902276Devosia elaeis sp. nov., isolated from oil palm rhizospheric soil.Mohd Nor MN, Sabaratnam V, Tan GYAInt J Syst Evol Microbiol10.1099/ijsem.0.0016832017Arecaceae/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Malaysia, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17215Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23447)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23447
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
32246Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2848728776041
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/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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