Name: Micromonospora sonchi NEAU-QY3
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132025

Type strain:

Species: Micromonospora sonchi

Strain Designation: NEAU-QY3

Culture col. no.: DSM 101530, CGMCC 4.7312, JCM 32497

Strain history: CGMCC 4.7312 <-- C. Liu; Northeast Agric. Univ., China; NEAU-QY3.

NCBI tax ID(s): 1763543 (species)

SI-ID 404944

DSM 101530

Section

Micromonospora sonchi NEAU-QY3 is an aerobe, spore-forming, Gram-positive bacterium that was isolated from leaves of Sonchus oleraceus.

Gram-positive
spore-forming
aerobe
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Micromonosporales*
	Family	*Micromonosporaceae*
	Genus	*Micromonospora*
	Species	**Micromonospora sonchi**
	Full Scientific Name (LPSN)	Micromonospora sonchi (Ma et al. 2016) Carro and Oren 2022

Synonym

Verrucosispora sonchi

Information on morphological and physiological properties Morphology

[Ref.: #25066]	Gram stain	positive
[Ref.: #69480]	Gram stain	positive Confidence in %100

[Ref.: #25066]	Motility	no

[Ref.: #25066]	Colony color	moderate orange yellow
[Ref.: #25066]	Cultivation medium used	Oatmeal agar (ISP3)

[Ref.: #25066]	Colony color	Strong orange
[Ref.: #25066]	Cultivation medium used	NA (Nutrient Agar)

Multimedia content

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Caption:

Medium 65 28°C

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Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

GPHF-MEDIUM (DSMZ Medium 553)

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Culture medium growth

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Culture medium link

Medium recipe provided by DSMZ

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Culture medium

Oatmeal agar (ISP3)

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Culture medium growth

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Culture medium

NA (Nutrient Agar)

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Culture medium growth

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Culture medium

GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)

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Culture medium growth

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Culture medium link

Medium recipe at MediaDive

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Culture medium composition

expand / minimize

		Temperature
[Ref.: #23816]	growth	28 °C
[Ref.: #25066]	growth	10.0-40.0 °C
[Ref.: #25066]	optimum	28 °C
[Ref.: #67770]	growth	28 °C

[Ref.: #23816]	Temperature range	mesophilic
[Ref.: #25066]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic

	pH	Kind of pH		pH
[Ref.: #25066]			optimum	7.0-8.0
[Ref.: #25066]			growth	7.0-9.0

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

[Ref.: #25066]	Spore description	non-motile, single smooth, on substrate hyphae
[Ref.: #25066]	Type of spore	spore
[Ref.: #25066]	Ability of spore formation	yes
[Ref.: #69481]	Ability of spore formation	yes Confidence in %100
[Ref.: #69480]	Ability of spore formation	yes Confidence in %99.588

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #25066]		NaCl		growth	0.0-1.0	%(w/v)

[Ref.: #25066]	Murein short key	A31
[Ref.: #25066]	Murein types	A1gamma m-Dpm-direct

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Observation

quinones: MK-9(H₄), MK-9(H₂)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #25066]	6-deoxy-d-galactose ChEBI	+	carbon source
[Ref.: #25066]	cellulose ChEBI	+	hydrolysis
[Ref.: #25066]	creatine ChEBI	+	nitrogen source
[Ref.: #25066]	D-arabinose ChEBI	-	carbon source
[Ref.: #25066]	D-fructose ChEBI	+	carbon source
[Ref.: #25066]	D-glucose ChEBI	+	carbon source
[Ref.: #25066]	D-mannitol ChEBI	-	carbon source
[Ref.: #25066]	D-mannose ChEBI	+	carbon source
[Ref.: #25066]	D-ribose ChEBI	-	carbon source
[Ref.: #25066]	D-sorbitol ChEBI	+	carbon source
[Ref.: #25066]	D-xylose ChEBI	+	carbon source
[Ref.: #25066]	esculin ChEBI	+	hydrolysis
[Ref.: #25066]	galactitol ChEBI	-	carbon source
[Ref.: #25066]	glycine ChEBI	-	nitrogen source
[Ref.: #25066]	L-alanine ChEBI	-	nitrogen source
[Ref.: #25066]	L-arginine ChEBI	-	nitrogen source
[Ref.: #25066]	L-asparagine ChEBI	+	nitrogen source
[Ref.: #25066]	L-aspartate ChEBI	+	nitrogen source
[Ref.: #25066]	L-glutamate ChEBI	+	nitrogen source
[Ref.: #25066]	L-glutamine ChEBI	-	nitrogen source
[Ref.: #25066]	L-proline ChEBI	-	nitrogen source
[Ref.: #25066]	L-rhamnose ChEBI	-	carbon source
[Ref.: #25066]	L-serine ChEBI	-	nitrogen source
[Ref.: #25066]	L-threonine ChEBI	-	nitrogen source
[Ref.: #25066]	L-tyrosine ChEBI	-	nitrogen source
[Ref.: #25066]	lactose ChEBI	-	carbon source
[Ref.: #25066]	maltose ChEBI	+	carbon source
[Ref.: #25066]	myo-inositol ChEBI	-	carbon source
[Ref.: #25066]	nitrate ChEBI	-	reduction
[Ref.: #25066]	raffinose ChEBI	+	carbon source
[Ref.: #25066]	starch ChEBI	+	hydrolysis
[Ref.: #25066]	sucrose ChEBI	+	carbon source
[Ref.: #25066]	tween 20 ChEBI	-	hydrolysis
[Ref.: #25066]	tween 40 ChEBI	+	hydrolysis
[Ref.: #25066]	tween 80 ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #25066]		hydrogen sulfide ChEBI	no

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #25066]		catalase	-	1.11.1.6
[Ref.: #25066]		urease	-	3.5.1.5

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

[Ref.: #23816]	Sample type/isolated from	leaves of Sonchus oleraceus
[Ref.: #23816]	Host species	Sonchus oleraceus
[Ref.: #23816]	Geographic location (country and/or sea, region)	Heilongjiang province, Fenghuang Mountain in Wuchang (Harbin)
[Ref.: #23816]	Country	China
[Ref.: #23816]	Country ISO 3 Code	CHN
[Ref.: #23816]	Continent	Asia
[Ref.: #23816]	Geographic location	44.2060°/128.0560°

[Ref.: #25066]	Sample type/isolated from	leaves of S. oleraceus L.
[Ref.: #25066]	Enrichment culture duration	21 days
[Ref.: #25066]	Enrichment culture temperature	28 ̊C

[Ref.: #67770]	Sample type/isolated from	Leaves of Sonchus oleraceus from Fenghuang Mountain in Wuchang
[Ref.: #67770]	Host species	Sonchus oleraceus
[Ref.: #67770]	Geographic location (country and/or sea, region)	Heilongjiang Province, north China
[Ref.: #67770]	Country	China
[Ref.: #67770]	Country ISO 3 Code	CHN
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Host Body-Site	#Plant	#Leaf (Phyllosphere)

What are isolation sources categories?

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

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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.: #23816]	Verrucosispora sonchi strain NEAU-QY3 16S ribosomal RNA gene, partial sequence	KT633950	1509	ENA	1763543 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Micromonospora sonchi CGMCC 4.7312	GCA_014646235	scaffold	GenBank	1763543 tax ID	*
[Ref.: #66792]	Verrucosispora sonchi strain CGMCC 4.7312	1763543.3	wgs	PATRIC	1763543 tax ID	*

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GC-content

71.5 mol%

thermal denaturation, midpoint method (Tm)

Data predicted using genome information as a basis Genome-based predictions

	Trait	Prediction	Confidence in %	In training data
	Predictions from GenomeNet Sporulation v. 1 based on: Verrucosispora sonchi CGMCC 4.7312 NCBI: GCA_014646235.1
[Ref.: #69481]	spore-forming	yes	100	no

	Trait	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Verrucosispora sonchi CGMCC 4.7312 NCBI: GCA_014646235.1
[Ref.: #69480]	flagellated	no	97.316	no
[Ref.: #69480]	gram-positive	yes	92.038	yes
[Ref.: #69480]	anaerobic	no	99.174	yes
[Ref.: #69480]	aerobic	yes	91.523	no
[Ref.: #69480]	halophile	no	94.001	yes
[Ref.: #69480]	spore-forming	yes	93.213	no
[Ref.: #69480]	thermophile	no	95.681	no
[Ref.: #69480]	glucose-util	yes	86.023	yes
[Ref.: #69480]	motile	no	93.87	no
[Ref.: #69480]	glucose-ferment	no	91.331	no

Availability in culture collections External links

[Ref.: #23816]

Culture collection no.

DSM 101530, CGMCC 4.7312, JCM 32497

[Ref.: #90398]

SI-ID 404944

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.).	Ma Z, Zhao S, Cao T, Liu C, Huang Y, Gao Y, Yan K, Xiang W, Wang X	Int J Syst Evol Microbiol	10.1099/ijsem.0.001537	2016	*

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 )

#23816

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 101530

#25066

Z. Z. Ma, S.,Cao, T.,Liu, C.,Huang, Y.,Gao, Y.,Yan, K.,Xiang, W.,Wang, X.: Verrucosispora sonchi sp. nov., a novel endophytic actinobacterium isolated from the leaves of common sowthistle (Sonchus oleraceus L.). IJSEM 66: 5430 - 5436 2016 ( DOI 10.1099/ijsem.0.001537 , PubMed 27707427 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

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

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#69481

Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch: Predictions based on the model GenomeNet Sporulation v. 1 . ( DOI 10.21203/rs.3.rs-2527258/v1 )

#90398

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-ID404944.1 )

* These data were automatically processed and therefore are not curated

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Verrucosispora sonchi CGMCC 4.7312

Verrucosispora sonchi CGMCC 4.7312

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