Strain identifier

BacDive ID: 157183

Type strain: Yes

Species: Ancylobacter sonchi

Strain Designation: Osot

Strain history: N. V. Doronina; G. K. Skryabin Inst. of Biochem. & Physiol. of Microorg., RAS, Russia; Osot.

NCBI tax ID(s): 1937790 (species)

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General

@ref: 64914

BacDive-ID: 157183

DSM-Number: 106440

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

description: Ancylobacter sonchi Osot is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Roots of Sonchus arvensis.

NCBI tax id

  • NCBI tax id: 1937790
  • Matching level: species

strain history

@refhistory
64914<- N. V. Doronina, Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Science, Pushchino, Russia; Osot
67770N. V. Doronina; G. K. Skryabin Inst. of Biochem. & Physiol. of Microorg., RAS, Russia; Osot.

doi: 10.13145/bacdive157183.20241212.9.2

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Xanthobacteraceae
  • genus: Ancylobacter
  • species: Ancylobacter sonchi
  • full scientific name: Ancylobacter sonchi Agafonova et al. 2017

@ref: 64914

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Xanthobacteraceae

genus: Ancylobacter

species: Ancylobacter sonchi

full scientific name: Ancylobacter sonchi Agafonova et al. 2017

strain designation: Osot

type strain: yes

Morphology

cell morphology

  • @ref: 65261
  • gram stain: negative
  • cell length: 0.6-1 µm
  • cell width: 0.4-0.5 µm
  • cell shape: rod-shaped
  • motility: yes

colony morphology

@refincubation periodcolony sizecolony colorcolony shapemedium used
637082 days
652613-5 days2 mmwhitecircularmineral salts/methanol agar
652613 days1 mmyellowcircularR2A agar

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64914R2A 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
65261mineral salts/methanol agaryes
65261Reasoner's 2A agar (R2A)yes

culture temp

@refgrowthtypetemperature
63708positivegrowth30
64914positivegrowth28
65261positivegrowth10-30
65261positiveoptimum22-29
67770positivegrowth25

culture pH

@refabilitytypepHPH range
65261positivegrowth6-9alkaliphile
65261positiveoptimum7.5-8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
63708aerobe
65261aerobe

halophily

@refsaltgrowthtested relationconcentration
65261NaClpositiveoptimum0.05 %(w/v)
65261NaClnogrowth0.5 %(w/v)

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6526116134ammonia+assimilation
6526128938ammonium+nitrogen source
652615291gelatin-hydrolysis
6526117790methanol+assimilation
6526117632nitrate-reduction
6526117632nitrate+nitrogen source

antibiotic resistance

@refChEBImetaboliteis antibioticis sensitivesensitivity conc.is resistantresistance conc.
6526128368novobiocinyesyes5 µg (disc)
6526117833gentamicinyesyes10 µg (disc)
6526117076streptomycinyesyes10 µg (disc)
6526128971ampicillinyesyes10 µg (disc)
6526148923erythromycinyesyes15 µg (disc)
6526127902tetracyclineyesyes30 µg (disc)
652616104kanamycinyesyes30 µg (disc)
652616472lincomycinyesyes2 µg (disc)
652617809oxacillinyesyes5 µg (disc)
6526117334penicillinyesyes10 µg (disc)
652617507neomycinyesyes30 µg (disc)
65261100147nalidixic acidyesyes30 µg (disc)
6526117698chloramphenicolyesyes30 µg (disc)

metabolite production

@refChebi-IDmetaboliteproduction
6526115688acetoinyes
6526116136hydrogen sulfideno
6526135581indoleyes

enzymes

@refvalueactivityec
65261catalase+1.11.1.6
65261cytochrome oxidase+1.9.3.1
65261urease+3.5.1.5
65261glutamate dehydrogenase+1.4.1.4

Isolation, sampling and environmental information

isolation

@refsample typesampling dategeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperatureisolation procedurehost species
63708Roots of Sonchus arvensis2009Pushchino,Moscow regionRussiaRUSEurope
64914root of field sow thistle (Sonchus arvensis L.)Pushchino, Moscow regionRussiaRUSEurope
65261root of field sow thistle (Sonchus arvensis L.), which was dug out of the soilPushchino, Moscow regionRussiaRUSEuropeK mediumg l-1: H2PO4, 2.0; (NH4)2SO4, 2.0; MgSO4 x 7H2O, 0.025; NaCl, 0.5; FeSO4 x 7H2O, 0.002; pH 7.5.1 week28The root (1 g) was washed three times with sterile distilled water and placed into an Erlenmeyer flask (750 ml) with 200 ml of sterile medium K' and 0.5 % (v/v) methanol. The K' medium .The flask was incubated for 1 week at 28°C with shaking (180 r.p.m.). In subsequent enrichments, 20 ml of the previous enrichment culture was diluted 1 : 10 (until the total volume reached 200 ml) with the same medium and was incubated at 28°C with shaking for 3 days.
67770Roots of field sow thistle (Sonchus arvensis L.) which was dug out of the soil in the vicinity of PushchinoMoscow regionRussiaRUSSonchus arvensis L.

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Shrub (Scrub)
#Host Body-Site#Plant#Root (Rhizome)

taxonmaps

  • @ref: 69479
  • File name: preview.99_57345.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_355;96_2984;97_3669;98_40879;99_57345&stattab=map
  • Last taxonomy: Ancylobacter
  • 16S sequence: KY492736
  • Sequence Identity:
  • Total samples: 128
  • soil counts: 31
  • aquatic counts: 63
  • animal counts: 24
  • plant counts: 10

Safety information

risk assessment

  • @ref: 64914
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 64914
  • description: Ancylobacter sonchi strain Osot 16S ribosomal RNA gene, partial sequence
  • accession: KY492736
  • length: 1392
  • database: nuccore
  • NCBI tax ID: 1937790

GC content

  • @ref: 64914
  • GC-content: 66.1
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 64914

culture collection no.: CCUG 70237, JCM 32039, DSM 106440, VKM B-3145

straininfo link

@refstraininfo
110287408086
110288410666

literature

  • topic: Phylogeny
  • Pubmed-ID: 28984222
  • title: Ancylobacter sonchi sp. nov., a novel methylotrophic bacterium frsmall o, Cyrillicm roots of Sonchus arvensis L.
  • authors: Agafonova NV, Kaparullina EN, Trotsenko YA, Doronina NV
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002330
  • year: 2017
  • mesh: Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Plant Roots/*microbiology, RNA, Ribosomal, 16S/genetics, Russia, Sequence Analysis, DNA, Sonchus/*microbiology, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
63708Curators of the CCUGhttps://www.ccug.se/strain?id=70237Culture Collection University of Gothenburg (CCUG) (CCUG 70237)
64914Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-106440Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 106440)
65261Nadezhda V. Agafonova, Elena N. Kaparullina, Yuri A. Trotsenko, Nina V. DoroninaAncylobacter sonchi sp. nov., a novel methylotrophic bacterium from roots of Sonchus arvensis L.10.1099/ijsem.0.002330IJSEM 67: 4552-4558 201728984222
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
110287Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID408086.1
110288Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID410666.1