Name: Amycolatopsis oliviviridis SCM_MK2-4
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 158267

Type strain:

Species: Amycolatopsis oliviviridis

Strain Designation: SCM_MK2-4

Culture col. no.: DSM 107509, JCM 32134, TBRC 7186

Strain history: S. Lumyong; Chiang Mai Univ., Thailand; SCM_MK2-4.

NCBI tax ID(s): 1471590 (species)

SI-ID 399368

DSM 107509

Special Collections

Section

When using BacDive for research please cite our paper

Amycolatopsis oliviviridis SCM_MK2-4 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from rice field soil.

Gram-positive
rod-shaped
spore-forming
aerobe
mesophilic
16S sequence
Bacteria

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

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Actinomycetota*
	Class	*Actinomycetes*
	Order	*Pseudonocardiales*
	Family	*Pseudonocardiaceae*
	Genus	*Amycolatopsis*
	Species	**Amycolatopsis oliviviridis**
	Full Scientific Name (LPSN)	Amycolatopsis oliviviridis Penkhrue et al. 2018

Information on morphological and physiological properties Morphology

[Ref.: #65546]	Gram stain	positive

[Ref.: #65546]	Cell length	1.0-2.0 µm

[Ref.: #65546]	Cell width	0.5 µm

[Ref.: #65546]	Cell shape	rod-shaped

[Ref.: #65546]	Multicellular complex forming ability	yes
[Ref.: #65546]	Multicellular complex name	aerial mycelium
[Ref.: #65546]	Multicellular complex color	white

[Ref.: #65546]	Multicellular complex forming ability	yes
[Ref.: #65546]	Multicellular complex name	vegetative mycelium
[Ref.: #65546]	Multicellular complex color	light brown

Information on culture and growth conditions Culture and growth conditions

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Culture medium

ISP2 MEDIUM (DSMZ Medium 987)

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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

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Culture medium

COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)

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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

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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

[Ref.: #64926]

Culture medium composition

expand / minimize

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Culture medium

ISP2

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Culture medium growth

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Culture medium

ISP3

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Culture medium growth

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Culture medium

ISP4

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Culture medium growth

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Culture medium

ISP5

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Culture medium growth

	Kind of temperature		Temperature
[Ref.: #64926]		growth	30 °C
[Ref.: #65546]		growth	25-37 °C
[Ref.: #65546]	negative	growth	45 °C
[Ref.: #65546]	negative	growth	10 °C
[Ref.: #67770]		growth	28 °C

	pH	Kind of pH		pH
[Ref.: #65546]		no	growth	4.3
[Ref.: #65546]			growth	10

Information on physiology and metabolism Physiology and metabolism

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Oxygen tolerance

aerobe

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Ability of spore formation

yes

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #65546]		NaCl		growth	7	%(w/v)
[Ref.: #65546]		NaCl		growth	4	%(w/v)

[Ref.: #67770]

Observation

quinones: MK-9(H₄), MK-9(H₂), MK-8(H₄)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #65546]	casein	+	hydrolysis
[Ref.: #65546]	D-fructose ChEBI	+	carbon source
[Ref.: #65546]	D-galactose ChEBI	+	builds acid from
[Ref.: #68379]	D-glucose ChEBI	-	fermentation	* from API Coryne
[Ref.: #65546]	D-mannitol ChEBI	+	carbon source
[Ref.: #68379]	D-mannitol ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	D-ribose ChEBI	-	fermentation	* from API Coryne
[Ref.: #65546]	D-xylose ChEBI	+	builds acid from
[Ref.: #65546]	D-xylose ChEBI	+/-	carbon source
[Ref.: #68379]	D-xylose ChEBI	-	fermentation	* from API Coryne
[Ref.: #65546]	erythritol ChEBI	+	builds acid from
[Ref.: #65546]	gelatin ChEBI	+	hydrolysis
[Ref.: #68379]	gelatin ChEBI	+	hydrolysis	* from API Coryne
[Ref.: #68379]	glycogen ChEBI	-	fermentation	* from API Coryne
[Ref.: #65546]	hydroxyproline ChEBI	+	nitrogen source
[Ref.: #65546]	hypoxanthine ChEBI	+	hydrolysis
[Ref.: #65546]	L-arabinose ChEBI	+/-	carbon source
[Ref.: #65546]	L-cysteine ChEBI	-	nitrogen source
[Ref.: #65546]	L-methionine ChEBI	+/-	nitrogen source
[Ref.: #65546]	L-phenylalanine ChEBI	+	nitrogen source
[Ref.: #65546]	L-rhamnose ChEBI	-	carbon source
[Ref.: #65546]	L-threonine ChEBI	+	nitrogen source
[Ref.: #65546]	L-tyrosine ChEBI	+	hydrolysis
[Ref.: #65546]	L-valine ChEBI	+	nitrogen source
[Ref.: #65546]	lactose ChEBI	+	carbon source
[Ref.: #68379]	lactose ChEBI	-	fermentation	* from API Coryne
[Ref.: #68379]	maltose ChEBI	-	fermentation	* from API Coryne
[Ref.: #65546]	melibiose ChEBI	+	builds acid from
[Ref.: #65546]	melibiose ChEBI	+	carbon source
[Ref.: #65546]	myo-inositol ChEBI	+	carbon source
[Ref.: #65546]	nitrate ChEBI	+	reduction
[Ref.: #68379]	nitrate ChEBI	+	reduction	* from API Coryne
[Ref.: #65546]	oxalate ChEBI	-	carbon source
[Ref.: #65546]	raffinose ChEBI	+/-	carbon source
[Ref.: #65546]	raffinose ChEBI	+	builds acid from
[Ref.: #65546]	ribitol ChEBI	+	carbon source
[Ref.: #65546]	sodium citrate ChEBI	+/-	carbon source
[Ref.: #65546]	sodium propionate ChEBI	-	carbon source
[Ref.: #65546]	sucrose ChEBI	-	carbon source
[Ref.: #68379]	sucrose ChEBI	-	fermentation	* from API Coryne
[Ref.: #65546]	urea ChEBI	+	hydrolysis
[Ref.: #68379]	urea ChEBI	-	hydrolysis	* from API Coryne
[Ref.: #65546]	xanthine ChEBI	-	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #65546]		hydrogen sulfide ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68379]	alkaline phosphatase	+	3.1.3.1	* from API Coryne, API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68379]	alpha-glucosidase	-	3.2.1.20	* from API Coryne, API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68379]	beta-glucuronidase	-	3.2.1.31	* from API Coryne, API zym
[Ref.: #65546]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68379]	gelatinase	+		* from API Coryne
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68379]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API Coryne, API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	-		* from API zym
[Ref.: #68379]	pyrazinamidase	-	3.5.1.B15	* from API Coryne
[Ref.: #68379]	pyrrolidonyl arylamidase	-	3.4.19.3	* from API Coryne
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #68379]	urease	-	3.5.1.5	* from API Coryne
[Ref.: #68382]	valine arylamidase	-		* from API zym
	Only first 10 entries are displayed. Click here to see all.

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #65546]

Fatty acid	Percentage
C15:0 iso	27
C16:0 iso	13.2
C16:1ω7c / C15:0 iso 2OH	11
C16:0	10.2
C17:0	7.6
C17:0 iso	5.9
C17:0 anteiso	5.8
C17:1ω8c	3.2
C17:1ω6c	2.8
C15:0 anteiso	2.6
C15:0	2.6
C14:0 iso	1.5
C18:0	1.4

API® Coryne:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitrateNIT	PyrazinamidasePYZ	Pyrrolidonyl arylamidasePYRA	Alkaline phosphatasePAL	beta-Glucuronidasebeta GUR	beta-Galactosidasebeta GAL	alpha-Glucosidasealpha GLU	N-Acetyl-beta-Glucosidasebeta NAG	Esculin hydrolysis/beta-GlucosidaseESC	Urease/urea hydrolysisURE	Gelatinase/gelatin hydrolysisGEL	Control fermentationControl	Fermentation of D-glucoseGLU	Fermentation of D-riboseRIB	Fermentation of D-xyloseXYL	Fermentation of D-mannitolMAN	Fermentation of maltoseMAL	Fermentation of lactoseLAC	Fermentation of sucroseSAC	Fermentation of glycogenGLYG	CatalaseCAT
[Ref.: #64926]	4363	+	-	-	+	-	+/-	-	+	+/-	-	+	-	-	-	-	-	-	-	-	-	not determinedn.d.

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #64926]	14474	-	+	-	+/-	-	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-

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

[Ref.: #64926]	Sample type/isolated from	rice field soil
[Ref.: #64926]	Geographic location (country and/or sea, region)	Sansai City, Chiang Mai (18° 32' 23.9'' N, 99° 2' 24'' E)
[Ref.: #64926]	Country	Thailand
[Ref.: #64926]	Country ISO 3 Code	THA
[Ref.: #64926]	Continent	Asia
[Ref.: #64926]	Geographic location	18.5400°/99.0400°

[Ref.: #65546]	Sample type/isolated from	paddy soil of rice field
[Ref.: #65546]	Geographic location (country and/or sea, region)	Sansai, Chiang Mai
[Ref.: #65546]	Country	Thailand
[Ref.: #65546]	Country ISO 3 Code	THA
[Ref.: #65546]	Continent	Asia
[Ref.: #65546]	Geographic location	18.9000°/99.0666°
[Ref.: #65546]	Enrichment culture	basal agar medium
[Ref.: #65546]	Enrichment culture composition	0.1 %(w/v) emulsified PLA
[Ref.: #65546]	Enrichment culture duration	4 weeks
[Ref.: #65546]	Enrichment culture temperature	30 ̊C

[Ref.: #67770]	Sample type/isolated from	Agricultural soil from Sansai
[Ref.: #67770]	Geographic location (country and/or sea, region)	Chiang Mai
[Ref.: #67770]	Country	Thailand
[Ref.: #67770]	Country ISO 3 Code	THA
[Ref.: #67770]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AB915815 (>99% sequence identity) for Amycolatopsis from Microbeatlas

Aquatic Samples	30
Soil Samples	689
Animal Samples	79
Plant Samples	635
Total Samples	1433

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.: #67770]	Amycolatopsis sp. SCM_MK2-4 gene for 16S ribosomal RNA, partial sequence	AB915815	1388	GenBank ENA	1471590 tax ID
[Ref.: #64926]	Amycolatopsis oliviviridis gene for 16S rRNA, partial sequence	LC225637	1466	GenBank ENA	1471590 tax ID

[Ref.: #64926]	GC-content	68.2 mol%
[Ref.: #65546]	GC-content	68.2 mol%	high performance liquid chromatography (HPLC)

Availability in culture collections External links

[Ref.: #64926]

Culture collection no.

DSM 107509, JCM 32134, TBRC 7186

[Ref.: #111085]

SI-ID 399368

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Amycolatopsis oliviviridis sp. nov., a novel polylactic acid-bioplastic-degrading actinomycete isolated from paddy soil.	Penkhrue W, Sujarit K, Kudo T, Ohkuma M, Masaki K, Aizawa T, Pathom-Aree W, Khanongnuch C, Lumyong S	Int J Syst Evol Microbiol	10.1099/ijsem.0.002682	2018	*

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 )

#64926

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 107509

#65546

Watsana Penkhrue, Kanaporn Sujarit, Takuji Kudo, Moriya Ohkuma, Kazuo Masaki, Tomoyasu Aizawa, Wasu Pathom-aree, Chartchai Khanongnuch and Saisamorn Lumyong: Amycolatopsis oliviviridis sp. nov., a novel polylactic acid-bioplastic-degrading actinomycete isolated from paddy soil. IJSEM 68: 1448 - 1454 2018 ( DOI 10.1099/ijsem.0.002682 , PubMed 29517482 )

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

#68379

Automatically annotated from API Coryne .

#68382

Automatically annotated from API zym .

#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 .

#111085

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-ID399368.1 )

* These data were automatically processed and therefore are not curated

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