Name: Ancylobacter sonchi Osot
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 157183

Type strain:

Species: Ancylobacter sonchi

Strain Designation: Osot

Culture col. no.: CCUG 70237, JCM 32039, DSM 106440, VKM B-3145

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

NCBI tax ID(s): 1937790 (species)

SI-ID 408086

DSM 106440

Section

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

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

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Hyphomicrobiales*
	Family	*Xanthobacteraceae*
	Genus	*Ancylobacter*
	Species	**Ancylobacter sonchi**
	Full Scientific Name (LPSN)	Ancylobacter sonchi Agafonova et al. 2017

Information on morphological and physiological properties Morphology

[Ref.: #65261]	Gram stain	negative

[Ref.: #65261]	Cell length	0.6-1 µm

[Ref.: #65261]	Cell width	0.4-0.5 µm

[Ref.: #65261]	Cell shape	rod-shaped

[Ref.: #65261]	Motility	yes

[Ref.: #65261]	Colony size	2 mm
[Ref.: #65261]	Colony color	white
[Ref.: #65261]	Colony shape	circular
[Ref.: #65261]	Incubation period	3-5 days
[Ref.: #65261]	Cultivation medium used	mineral salts/methanol agar

[Ref.: #65261]	Colony size	1 mm
[Ref.: #65261]	Colony color	yellow
[Ref.: #65261]	Colony shape	circular
[Ref.: #65261]	Incubation period	3 days
[Ref.: #65261]	Cultivation medium used	R2A agar

[Ref.: #63708]	Incubation period	2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #64914]

Culture medium

R2A MEDIUM (DSMZ Medium 830)

[Ref.: #64914]

Culture medium growth

[Ref.: #64914]

Culture medium link

Medium recipe at MediaDive

[Ref.: #64914]

Culture medium composition

expand / minimize

[Ref.: #65261]

Culture medium

mineral salts/methanol agar

[Ref.: #65261]

Culture medium growth

[Ref.: #65261]

Culture medium

Reasoner's 2A agar (R2A)

[Ref.: #65261]

Culture medium growth

		Temperature
[Ref.: #63708]	growth	30 °C
[Ref.: #64914]	growth	28 °C
[Ref.: #65261]	growth	10-30 °C
[Ref.: #65261]	optimum	22-29 °C
[Ref.: #67770]	growth	25 °C

[Ref.: #63708]	Temperature range	mesophilic
[Ref.: #64914]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #65261]			optimum	7.5-8
[Ref.: #65261]			growth	6-9

Information on physiology and metabolism Physiology and metabolism

[Ref.: #63708]	Oxygen tolerance	aerobe
[Ref.: #65261]	Oxygen tolerance	aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65261]		NaCl		optimum	0.05	%(w/v)
[Ref.: #65261]		NaCl	no	growth	0.5	%(w/v)

[Ref.: #67770]

Observation

quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65261]	ammonia ChEBI	+	assimilation
[Ref.: #65261]	ammonium ChEBI	+	nitrogen source
[Ref.: #65261]	gelatin ChEBI	-	hydrolysis
[Ref.: #65261]	methanol ChEBI	+	assimilation
[Ref.: #65261]	nitrate ChEBI	-	reduction
[Ref.: #65261]	nitrate ChEBI	+	nitrogen source

	Metabolite	Antibiotic sensitivity	Concentration		Antibiotic resistance	Concentration
[Ref.: #65261]	ampicillin ChEBI	yes	10	µg (disc)
[Ref.: #65261]	chloramphenicol ChEBI				yes	30	µg (disc)
[Ref.: #65261]	erythromycin ChEBI	yes	15	µg (disc)
[Ref.: #65261]	gentamicin ChEBI	yes	10	µg (disc)
[Ref.: #65261]	kanamycin ChEBI	yes	30	µg (disc)
[Ref.: #65261]	lincomycin ChEBI				yes	2	µg (disc)
[Ref.: #65261]	nalidixic acid ChEBI				yes	30	µg (disc)
[Ref.: #65261]	neomycin ChEBI				yes	30	µg (disc)
[Ref.: #65261]	novobiocin ChEBI	yes	5	µg (disc)
[Ref.: #65261]	oxacillin ChEBI				yes	5	µg (disc)
[Ref.: #65261]	penicillin ChEBI				yes	10	µg (disc)
[Ref.: #65261]	streptomycin ChEBI	yes	10	µg (disc)
[Ref.: #65261]	tetracycline ChEBI	yes	30	µg (disc)
	Only first 10 entries are displayed. Click here to see all.

	Metabolite	Production
[Ref.: #65261]	acetoin ChEBI	yes
[Ref.: #65261]	hydrogen sulfide ChEBI	no
[Ref.: #65261]	indole ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #65261]	catalase	+	1.11.1.6
[Ref.: #65261]	cytochrome oxidase	+	1.9.3.1
[Ref.: #65261]	glutamate dehydrogenase	+	1.4.1.4
[Ref.: #65261]	urease	+	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #63708]	Sample type/isolated from	Roots of Sonchus arvensis
[Ref.: #63708]	Sampling date	2009
[Ref.: #63708]	Geographic location (country and/or sea, region)	Pushchino,Moscow region
[Ref.: #63708]	Country	Russia
[Ref.: #63708]	Country ISO 3 Code	RUS
[Ref.: #63708]	Continent	Europe

[Ref.: #64914]	Sample type/isolated from	root of field sow thistle (Sonchus arvensis L.)
[Ref.: #64914]	Geographic location (country and/or sea, region)	Pushchino, Moscow region
[Ref.: #64914]	Country	Russia
[Ref.: #64914]	Country ISO 3 Code	RUS
[Ref.: #64914]	Continent	Europe

[Ref.: #65261]	Sample type/isolated from	root of field sow thistle (Sonchus arvensis L.), which was dug out of the soil
[Ref.: #65261]	Geographic location (country and/or sea, region)	Pushchino, Moscow region
[Ref.: #65261]	Country	Russia
[Ref.: #65261]	Country ISO 3 Code	RUS
[Ref.: #65261]	Continent	Europe
[Ref.: #65261]	Enrichment culture	K medium
[Ref.: #65261]	Enrichment culture composition	g 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.
[Ref.: #65261]	Enrichment culture duration	1 week
[Ref.: #65261]	Enrichment culture temperature	28 ̊C
[Ref.: #65261]	Isolation/enrichment procedure	The 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.

[Ref.: #67770]	Sample type/isolated from	Roots of field sow thistle (Sonchus arvensis L.) which was dug out of the soil in the vicinity of Pushchino
[Ref.: #67770]	Host species	Sonchus arvensis L.
[Ref.: #67770]	Geographic location (country and/or sea, region)	Moscow region
[Ref.: #67770]	Country	Russia
[Ref.: #67770]	Country ISO 3 Code	RUS
* marker position based on {}

Isolation sources categories

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

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KY492736 (>99% sequence identity) for Ancylobacter from Microbeatlas

Aquatic Samples	63
Soil Samples	31
Animal Samples	24
Plant Samples	10
Total Samples	128

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

[Ref.: #64914]

Biosafety level

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #64914]	Ancylobacter sonchi strain Osot 16S ribosomal RNA gene, partial sequence	KY492736	1392	ENA	1937790 tax ID

[Ref.: #64914]

GC-content

66.1 mol%

thermal denaturation, midpoint method (Tm)

Availability in culture collections External links

[Ref.: #64914]

Culture collection no.

CCUG 70237, JCM 32039, DSM 106440, VKM B-3145

[Ref.: #110287]	SI-ID 408086	*
[Ref.: #110288]	SI-ID 410666	*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Ancylobacter sonchi sp. nov., a novel methylotrophic bacterium frsmall o, Cyrillicm roots of Sonchus arvensis L.	Agafonova NV, Kaparullina EN, Trotsenko YA, Doronina NV	Int J Syst Evol Microbiol	10.1099/ijsem.0.002330	2017	*

References

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#63708 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 70237

#64914

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 106440

#65261

Nadezhda V. Agafonova, Elena N. Kaparullina, Yuri A. Trotsenko, Nina V. Doronina: Ancylobacter sonchi sp. nov., a novel methylotrophic bacterium from roots of Sonchus arvensis L.. IJSEM 67: 4552 - 4558 2017 ( DOI 10.1099/ijsem.0.002330 , PubMed 28984222 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#69479

João 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 beta .

#110287

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID408086.1 )

#110288

* These data were automatically processed and therefore are not curated

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