Strain identifier

BacDive ID: 140754

Type strain: Yes

Species: Dyella agri

Strain Designation: DKC-1

Strain history: J. Kim; Kyonggi Univ., South Korea; DKC-1.

NCBI tax ID(s): 1926869 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9 (current version):
version 8.1:
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 9 (current version)

General

@ref: 43532

BacDive-ID: 140754

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

description: Dyella agri DKC-1 is an aerobe, Gram-negative, motile bacterium that forms circular colonies and was isolated from reclaimed grassland soil.

NCBI tax id

  • NCBI tax id: 1926869
  • Matching level: species

strain history

  • @ref: 67770
  • history: J. Kim; Kyonggi Univ., South Korea; DKC-1.

doi: 10.13145/bacdive140754.20240510.9

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 agri
  • full scientific name: Dyella agri Chaudhary and Kim 2017

@ref: 43532

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Lysobacterales

family: Rhodanobacteraceae

genus: Dyella

species: Dyella agri

strain designation: DKC-1

type strain: yes

Morphology

cell morphology

  • @ref: 43532
  • gram stain: negative
  • cell length: 1.5-2 µm
  • cell width: 0.5-0.8 µm
  • cell shape: rod-shaped
  • motility: yes
  • flagellum arrangement: polar

colony morphology

  • @ref: 43532
  • colony size: 1-2 mm
  • colony color: Yellow
  • colony shape: circular
  • incubation period: 5 days
  • medium used: R2A agar

Culture and growth conditions

culture medium

  • @ref: 43532
  • name: Reasoner's 2A agar (R2A)
  • growth: yes

culture temp

@refgrowthtypetemperature
43532positivegrowth20-37
43532positiveoptimum25-35
67770positivegrowth30

culture pH

@refabilitytypepHPH range
43532positivegrowth4.5-9alkaliphile
43532positiveoptimum6-8

Physiology and metabolism

oxygen tolerance

  • @ref: 43532
  • oxygen tolerance: aerobe

spore formation

  • @ref: 43532
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43532NaClpositivegrowth0-3 %(w/v)
43532NaClpositiveoptimum0 %(w/v)non-halophilic

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
43532161933-hydroxybenzoate-assimilation
43532370543-hydroxybutyrate-assimilation
43532178794-hydroxybenzoate-assimilation
4353217128adipate-assimilation
4353227689decanoate-assimilation
4353216899D-mannitol-assimilation
4353216024D-mannose-assimilation
4353216988D-ribose-assimilation
4353217924D-sorbitol-assimilation
435325291gelatin-assimilation
4353228087glycogen-assimilation
4353217268myo-inositol-assimilation
4353217240itaconate-assimilation
4353216977L-alanine-assimilation
4353230849L-arabinose-assimilation
4353216467L-arginine-assimilation
4353262345L-rhamnose-assimilation
4353216828L-tryptophan-assimilation
4353224996lactate-assimilation
4353225115malate-assimilation
4353228053melibiose-assimilation
4353218401phenylacetate-assimilation
43532potassium 2-dehydro-D-gluconate-assimilation
43532potassium 5-dehydro-D-gluconate-assimilation
4353232032potassium gluconate-assimilation
4353217814salicin-assimilation
4353253258sodium citrate-assimilation
4353262983sodium malonate-assimilation
435329300suberic acid-assimilation
4353217992sucrose-assimilation
4353216199urea-assimilation
4353231011valerate-assimilation
4353217234glucose-fermentation
43532casein-hydrolysis
4353217029chitin-hydrolysis
4353216991dna-hydrolysis
435325291gelatin-hydrolysis
4353228017starch-hydrolysis
4353253423tween 40-hydrolysis
4353253426tween 80-hydrolysis
4353217632nitrate-reduction
435323557154-nitrophenyl beta-D-galactopyranoside+assimilation
4353217634D-glucose+assimilation
4353218287L-fucose+assimilation
4353215971L-histidine+assimilation
4353217115L-serine+assimilation
4353217306maltose+assimilation
43532506227N-acetylglucosamine+assimilation
4353217272propionate+assimilation
4353285146carboxymethylcellulose+hydrolysis
4353217203L-proline+/-assimilation
4353232954sodium acetate+/-assimilation
43532esculin ferric citrate+/-fermentation
4353217234glucose+/-fermentation
435324853esculin+/-hydrolysis
4353218186tyrosine+/-hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
4353215688acetoinno
4353216136hydrogen sulfideno
4353235581indoleno

metabolite tests

@refChebi-IDmetabolitemethylred-testvoges-proskauer-test
4353217234glucose-
4353215688acetoin-

enzymes

@refvalueactivityec
43532catalase+1.11.1.6
43532cytochrome oxidase+1.9.3.1
43532alkaline phosphatase+3.1.3.1
43532esterase Lipase (C 8)+
43532leucine arylamidase+3.4.11.1
43532valine arylamidase+
43532cystine arylamidase+3.4.11.3
43532acid phosphatase+3.1.3.2
43532beta-galactosidase+3.2.1.23
43532alpha-mannosidase+3.2.1.24
43532alpha-fucosidase+3.2.1.51
43532alpha-chymotrypsin+/-3.4.21.1
43532naphthol-AS-BI-phosphohydrolase+/-
43532alpha-glucosidase+/-3.2.1.20
43532esterase (C 4)-
43532lipase (C 14)-
43532trypsin-3.4.21.4
43532alpha-galactosidase-3.2.1.22
43532beta-glucuronidase-3.2.1.31
43532beta-glucosidase-3.2.1.21
43532N-acetyl-beta-glucosaminidase-3.2.1.52

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43532C10:0 3OH2.8
    43532C12:0 3OH2.3
    43532C14:01.1
    43532C14:0 3OH / C16:1 iso I1.9
    43532C16:013.5
    43532C16:1ω6c / C16:1ω7c45.5
    43532C18:1ω7c / C18:1ω6c27.2
  • type of FA analysis: whole cell analysis
  • incubation medium: R2A
  • agar/liquid: agar
  • incubation temperature: 28
  • incubation time: 3
  • incubation_oxygen: aerobic
  • software version: Sherlock 6.0B
  • library/peak naming table: TSBA6
  • system: MIS MIDI
  • cutoff value:

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
43532reclaimed grassland soilHwaseongRepublic of KoreaKORAsia
67770Reclaimed grassland soilHwaseongRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Grassland
#Environmental#Terrestrial#Soil

Sequence information

16S sequences

  • @ref: 43532
  • description: Dyella agri 16S ribosomal RNA gene, partial sequence
  • accession: KY313412
  • database: nuccore

GC content

  • @ref: 43532
  • GC-content: 63.1
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 43532

culture collection no.: KEMB 9005-571, KACC 19176, JCM 31925

literature

  • topic: Phylogeny
  • Pubmed-ID: 28920848
  • title: Dyella agri sp. nov., isolated from reclaimed grassland soil.
  • authors: Chaudhary DK, Kim J
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002291
  • year: 2017
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Grassland, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistry, Xanthomonadaceae/*classification/genetics/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
43532Dhiraj Kumar Chaudhary, Jaisoo KimDyella agri sp. nov., isolated from reclaimed grassland soil10.1099/ijsem.0.002291IJSEM 67: 4246-4252 201728920848
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/