Strain identifier

BacDive ID: 6171

Type strain: Yes

Species: Devosia yakushimensis

Strain Designation: Yak96B

Strain history: <- V Bautista, Tokyo Univ., Japan

NCBI tax ID(s): 470028 (species)

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General

@ref: 15600

BacDive-ID: 6171

DSM-Number: 21277

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

description: Devosia yakushimensis Yak96B is an aerobe, mesophilic, Gram-negative bacterium that was isolated from root nodule of kudzu plant Pueraria lobata Ohwi.

NCBI tax id

  • NCBI tax id: 470028
  • Matching level: species

strain history

@refhistory
15600<- V. V. Bautista, Inst. Molecular and Cellular Biosci., Univ. Tokyo, Japan; Yak96B
67771<- V Bautista, Tokyo Univ., Japan

doi: 10.13145/bacdive6171.20230509.8.1

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 yakushimensis
  • full scientific name: Devosia yakushimensis Bautista et al. 2010

@ref: 15600

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Devosiaceae

genus: Devosia

species: Devosia yakushimensis

full scientific name: Devosia yakushimensis Bautista et al. 2010

strain designation: Yak96B

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29343negative1.6 µm0.5 µmrod-shapedyes
67771negative

pigmentation

  • @ref: 29343
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 15600
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
15600positivegrowth28mesophilic
29343positivegrowth28mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
29343positivegrowth5.5-7
29343positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29343aerobe
67771aerobe

spore formation

  • @ref: 29343
  • spore formation: no

halophily

  • @ref: 29343
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <2.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2934322599arabinose+carbon source
2934317057cellobiose+carbon source
2934328757fructose+carbon source
2934333984fucose+carbon source
2934328260galactose+carbon source
2934324265gluconate+carbon source
2934317234glucose+carbon source
2934317716lactose+carbon source
2934317306maltose+carbon source
2934337684mannose+carbon source
2934328053melibiose+carbon source
2934317268myo-inositol+carbon source
2934316634raffinose+carbon source
2934326546rhamnose+carbon source
2934333942ribose+carbon source
2934317814salicin+carbon source
2934330911sorbitol+carbon source
2934327082trehalose+carbon source
2934318222xylose+carbon source

enzymes

@refvalueactivityec
29343acid phosphatase+3.1.3.2
29343alkaline phosphatase+3.1.3.1
29343alpha-galactosidase+3.2.1.22
29343catalase+1.11.1.6
29343cytochrome oxidase+1.9.3.1
29343urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
15600root nodule of kudzu plant Pueraria lobata (Willd.) OhwiPueraria lobataKagoshima Prefecture, Sea coast of Yakushima IslandJapanJPNAsia
67771From Root nodule of kudzu plant, `Pueraria lobata`Sea Coast of Yakushima IslandJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root nodule

Safety information

risk assessment

  • @ref: 15600
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Devosia yakushimensis gene for 16S rRNA, partial sequence, strain: NBRC 103855AB6821411407ena470028
15600Devosia yakushimensis gene for 16S ribosomal RNA, partial sequenceAB3610681379ena470028

GC content

@refGC-contentmethod
1560065.3high performance liquid chromatography (HPLC)
2934365.3

External links

@ref: 15600

culture collection no.: DSM 21277, KCTC 22147, LMG 24299, NBRC 103855

straininfo link

  • @ref: 75654
  • straininfo: 310296

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19654342Devosia yakushimensis sp. nov., isolated from root nodules of Pueraria lobata (Willd.) Ohwi.Bautista VV, Monsalud RG, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.011254-02009DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/chemistry/metabolism, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/metabolism, Molecular Sequence Data, Phylogeny, Pueraria/*microbiology, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiologyMetabolism
Phylogeny26514816Devosia humi sp. nov., isolated from soil of a Korean pine (Pinus koraiensis) garden.Du J, Kook M, Akter S, Singh H, Won K, Ngo HTT, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0007242015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pinus/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics
Phylogeny32228770Devosia ginsengisoli sp. nov., isolated from ginseng cultivation soil.Quan XT, Siddiqi MZ, Liu QZ, Lee SM, Im WTInt J Syst Evol Microbiol10.1099/ijsem.0.0038432020Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/isolation & purification, Nucleic Acid Hybridization, Panax/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome
Phylogeny33963447Devosia aurantiaca sp. nov., Isolated from Mountain Soil and Proposal of Albitalea gen. nov. to Replace the Illegitimate Prokaryotic Genus Name Geomonas Khan et al. 2020.Khan SA, Kim HM, Chun BH, Jeon COCurr Microbiol10.1007/s00284-021-02515-82021Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Hyphomicrobiaceae, *Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil, UbiquinoneTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
15600Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21277)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21277
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
29343Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604125755
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
75654Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID310296.1StrainInfo: A central database for resolving microbial strain identifiers