Amycolatopsis oliviviridis (DSM 107509, JCM 32134, TBRC 7186)

Name: Amycolatopsis oliviviridis (DSM 107509, JCM 32134, TBRC 7186)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 158267

Type strain

Strain Designation SCM_MK2-4

Culture col. no. DSM 107509 JCM 32134 TBRC 7186 SCM_MK2-4

NCBI tax ID(s) 1471590

Special Collections DSMZ JCM Literature strains

History DSMZ <- S. Lumyong, Department of Biology, Chiang May University; SCM_MK2-4 <- W. Penkhrue, Department of Biology, Chiang May University; SCM_MK2-4 JCM <-- S. Lumyong; Chiang Mai Univ., Thailand; SCM_MK2-4.

Links

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

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

Name and taxonomic classification

SI-ID 399368

TBRC 7186,JCM 32134,DSM 107509

@ref 20215

Last LPSN update 2026-05-29 08:43:55

Domain Bacteria

Phylum Actinomycetota

Class Actinomycetes

Order Pseudonocardiales

Family Pseudonocardiaceae

Genus Amycolatopsis

Species Amycolatopsis oliviviridis

Full scientific name Amycolatopsis oliviviridis Penkhrue et al. 2018

Morphology

Cell morphology

@ref	Gram stain	Cell length	Cell width	Cell shape
65546	positive	1.0-2.0 µm	0.5 µm	rod-shaped

Multicellular morphology

@ref	Forms multicellular complex	Complex name	Complex color
65546		aerial mycelium	white
65546		vegetative mycelium	light brown

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
64926	ISP2 MEDIUM (DSMZ Medium 987)	Medium recipe at MediaDive	Name: ISP 2 MEDIUM (DSMZ Medium 987) Composition: Agar 20.0 g/l Malt extract 10.0 g/l Dextrose 4.0 g/l Yeast extract 4.0 g/l Distilled water
64926	COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)	Medium recipe at MediaDive	Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
64926	GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)	Medium recipe at MediaDive	Name: GYM STREPTOMYCES MEDIUM (DSMZ Medium 65) Composition: Agar 18.0 g/l Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l CaCO3 2.0 g/l Distilled water
65546	ISP2
65546	ISP3
65546	ISP4
65546	ISP5

Culture temp

@ref	Growth	Type	Temperature (°C)
64926	positive	growth	30
65546	positive	growth	25-37
65546	negative	growth	45
65546	negative	growth	10
67770	positive	growth	28

Culture pH

@ref	Ability	Type	PH	PH range
65546		growth	4.3
65546	positive	growth	10	alkaliphile

Physiology and metabolism

Oxygen tolerance

65546

Oxygen toleranceaerobe

Spore formation

65546

Spore formationyes

Halophily

@ref	Salt	Growth	Tested relation	Concentration
65546	NaCl	positive	growth	7 %(w/v)
65546	NaCl	positive	growth	4 %(w/v)

Observation

67770

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

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
65546		casein	+	hydrolysis
65546	15824 ChEBI	D-fructose	+	carbon source
65546	12936 ChEBI	D-galactose	+	builds acid from
68379	17634 ChEBI	D-glucose	-	fermentation	from API Coryne
65546	16899 ChEBI	D-mannitol	+	carbon source
68379	16899 ChEBI	D-mannitol	-	fermentation	from API Coryne
68379	16988 ChEBI	D-ribose	-	fermentation	from API Coryne
65546	65327 ChEBI	D-xylose	+	builds acid from
65546	65327 ChEBI	D-xylose	+/-	carbon source
68379	65327 ChEBI	D-xylose	-	fermentation	from API Coryne
65546	17113 ChEBI	erythritol	+	builds acid from
65546	5291 ChEBI	gelatin	+	hydrolysis
68379	5291 ChEBI	gelatin	+	hydrolysis	from API Coryne
68379	28087 ChEBI	glycogen	-	fermentation	from API Coryne
65546	24741 ChEBI	hydroxyproline	+	nitrogen source
65546	17368 ChEBI	hypoxanthine	+	hydrolysis
65546	30849 ChEBI	L-arabinose	+/-	carbon source
65546	17561 ChEBI	L-cysteine	-	nitrogen source
65546	16643 ChEBI	L-methionine	+/-	nitrogen source
65546	17295 ChEBI	L-phenylalanine	+	nitrogen source
65546	62345 ChEBI	L-rhamnose	-	carbon source
65546	16857 ChEBI	L-threonine	+	nitrogen source
65546	17895 ChEBI	L-tyrosine	+	hydrolysis
65546	16414 ChEBI	L-valine	+	nitrogen source
65546	17716 ChEBI	lactose	+	carbon source
68379	17716 ChEBI	lactose	-	fermentation	from API Coryne
68379	17306 ChEBI	maltose	-	fermentation	from API Coryne
65546	28053 ChEBI	melibiose	+	builds acid from
65546	28053 ChEBI	melibiose	+	carbon source
65546	17268 ChEBI	myo-inositol	+	carbon source
65546	17632 ChEBI	nitrate	+	reduction
68379	17632 ChEBI	nitrate	+	reduction	from API Coryne
65546	30623 ChEBI	oxalate	-	carbon source
65546	16634 ChEBI	raffinose	+/-	carbon source
65546	16634 ChEBI	raffinose	+	builds acid from
65546	15963 ChEBI	ribitol	+	carbon source
65546	53258 ChEBI	sodium citrate	+/-	carbon source
65546	132106 ChEBI	sodium propionate	-	carbon source
65546	17992 ChEBI	sucrose	-	carbon source
68379	17992 ChEBI	sucrose	-	fermentation	from API Coryne
65546	16199 ChEBI	urea	+	hydrolysis
68379	16199 ChEBI	urea	-	hydrolysis	from API Coryne
65546	15318 ChEBI	xanthine	-	hydrolysis

Metabolite production

@ref	Chebi-ID	Metabolite	Production
65546	16136 ChEBI	hydrogen sulfide

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68379	alkaline phosphatase	+	3.1.3.1	from API Coryne
68382	alpha-chymotrypsin	-	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	-	3.2.1.20	from API zym
68379	alpha-glucosidase	-	3.2.1.20	from API Coryne
68382	alpha-mannosidase	-	3.2.1.24	from API zym
68382	beta-galactosidase	-	3.2.1.23	from API zym
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
68379	beta-glucuronidase	-	3.2.1.31	from API Coryne
65546	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
68382	esterase (C 4)	-		from API zym
68379	gelatinase	+		from API Coryne
68382	leucine arylamidase	+	3.4.11.1	from API zym
68382	lipase (C 14)	-		from API zym
68382	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API zym
68379	N-acetyl-beta-glucosaminidase	+	3.2.1.52	from API Coryne
68382	naphthol-AS-BI-phosphohydrolase	-		from API zym
68379	pyrazinamidase	-	3.5.1.B15	from API Coryne
68379	pyrrolidonyl arylamidase	-	3.4.19.3	from API Coryne
68382	trypsin	-	3.4.21.4	from API zym
68379	urease	-	3.5.1.5	from API Coryne
68382	valine arylamidase	-		from API zym

Fatty acid profile

Metadata FA analysis

@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

@ref	Reduction of nitrateNIT	PYZ	PYRA	PAL	beta GUR	beta GAL	alpha GLU	beta NAG	ESC	URE	GEL	Control fermentationControl	GLU	RIB	XYL	MAN	MAL	LAC	SAC	GLYG	CAT
64926	+	-	-	+	-	+/-	-	+	+/-	-	+	-	-	-	-	-	-	-	-	-	not determinedn.d.

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
64926	-	+	-	+/-	-	+	-	-	-	-	+	-	-	-	-	-	-	+	-	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent	Latitude	Longitude	Enrichment culture	Enrichment culture composition	Enrichment culture duration	Enrichment culture temperature
64926	rice field soil	Sansai City, Chiang Mai (18° 32' 23.9'' N, 99° 2' 24'' E)	Thailand	THA	Asia	18.54	99.04 18.54/99.04
65546	paddy soil of rice field	Sansai, Chiang Mai	Thailand	THA	Asia	18.9	99.0666 18.9/99.0666	basal agar medium	0.1 %(w/v) emulsified PLA	4 weeks	30
67770	Agricultural soil from Sansai	Chiang Mai	Thailand	THA	Asia

Taxonmaps

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

Interaction and safety

Sequence information

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
64926	Amycolatopsis oliviviridis gene for 16S rRNA, partial sequence	LC225637	1466		1471590
67770	Amycolatopsis sp. SCM_MK2-4 gene for 16S ribosomal RNA, partial sequence	AB915815	1388		1471590

GC content

@ref	GC-content (mol%)	Method
64926	68.2
65546	68.2	high performance liquid chromatography (HPLC)

Genome-based predictions

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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

Content

About us

Amycolatopsis oliviviridis (DSM 107509, JCM 32134, TBRC 7186)

Name and taxonomic classification

Morphology

Cell morphology

Multicellular morphology

Culture and growth conditions

Culture medium

Culture temp

Culture pH

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

Fatty acid profile

API coryne

API zym

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Sequence information

16S sequences

GC content

Genome-based predictions

Literature

Literature

References

BacDive

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