Strain identifier

BacDive ID: 158267

Type strain: Yes

Species: Amycolatopsis oliviviridis

Strain Designation: SCM_MK2-4

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

NCBI tax ID(s): 1471590 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 64926

BacDive-ID: 158267

DSM-Number: 107509

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

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

NCBI tax id

  • NCBI tax id: 1471590
  • Matching level: species

strain history

@refhistory
64926<- S. Lumyong, Department of Biology, Chiang May University; SCM_MK2-4 <- W. Penkhrue, Department of Biology, Chiang May University; SCM_MK2-4
67770S. Lumyong; Chiang Mai Univ., Thailand; SCM_MK2-4.

doi: 10.13145/bacdive158267.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Pseudonocardiales
  • family: Pseudonocardiaceae
  • genus: Amycolatopsis
  • species: Amycolatopsis oliviviridis
  • full scientific name: Amycolatopsis oliviviridis Penkhrue et al. 2018

@ref: 64926

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis oliviviridis

full scientific name: Amycolatopsis oliviviridis Penkhrue et al. 2018

strain designation: SCM_MK2-4

type strain: yes

Morphology

cell morphology

  • @ref: 65546
  • gram stain: positive
  • cell length: 1.0-2.0 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped

multicellular morphology

@refforms multicellular complexcomplex namecomplex color
65546yesaerial myceliumwhite
65546yesvegetative myceliumlight brown

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
64926ISP2 MEDIUM (DSMZ Medium 987)yeshttps://mediadive.dsmz.de/medium/987Name: 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
64926COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
64926GYM STREPTOMYCES MEDIUM (DSMZ Medium 65)yeshttps://mediadive.dsmz.de/medium/65Name: 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
65546ISP2yes
65546ISP3yes
65546ISP4yes
65546ISP5yes

culture temp

@refgrowthtypetemperaturerange
64926positivegrowth30mesophilic
65546positivegrowth25-37mesophilic
65546nogrowth45thermophilic
65546nogrowth10psychrophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
65546nogrowth4.3
65546positivegrowth10alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 65546
  • oxygen tolerance: aerobe

spore formation

  • @ref: 65546
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
65546NaClpositivegrowth7 %(w/v)
65546NaClpositivegrowth4 %(w/v)

observation

  • @ref: 67770
  • observation: quinones: MK-9(H4), MK-9(H2), MK-8(H4)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6554615963ribitol+carbon source
65546casein+hydrolysis
6554615824D-fructose+carbon source
6554612936D-galactose+builds acid from
6554616899D-mannitol+carbon source
6554616634raffinose+/-carbon source
6554665327D-xylose+builds acid from
6554665327D-xylose+/-carbon source
6554617113erythritol+builds acid from
655465291gelatin+hydrolysis
6554624741hydroxyproline+nitrogen source
6554617368hypoxanthine+hydrolysis
6554630849L-arabinose+/-carbon source
6554617561L-cysteine-nitrogen source
6554616643L-methionine+/-nitrogen source
6554617295L-phenylalanine+nitrogen source
6554662345L-rhamnose-carbon source
6554616857L-threonine+nitrogen source
6554617895L-tyrosine+hydrolysis
6554616414L-valine+nitrogen source
6554617716lactose+carbon source
6554628053melibiose+builds acid from
6554628053melibiose+carbon source
6554617268myo-inositol+carbon source
6554617632nitrate+reduction
6554630623oxalate-carbon source
6554616634raffinose+builds acid from
6554653258sodium citrate+/-carbon source
65546132106sodium propionate-carbon source
6554617992sucrose-carbon source
6554616199urea+hydrolysis
6554615318xanthine-hydrolysis
6837917632nitrate+reduction
6837916199urea-hydrolysis
683795291gelatin+hydrolysis
6837917634D-glucose-fermentation
6837916988D-ribose-fermentation
6837965327D-xylose-fermentation
6837916899D-mannitol-fermentation
6837917306maltose-fermentation
6837917716lactose-fermentation
6837917992sucrose-fermentation
6837928087glycogen-fermentation

metabolite production

  • @ref: 65546
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: no

enzymes

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

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    65546C15:0 iso27
    65546C16:0 iso13.2
    65546C16:1ω7c / C15:0 iso 2OH11
    65546C16:010.2
    65546C17:07.6
    65546C17:0 iso5.9
    65546C17:0 anteiso5.8
    65546C17:1ω8c3.2
    65546C17:1ω6c2.8
    65546C15:0 anteiso2.6
    65546C15:02.6
    65546C14:0 iso1.5
    65546C18:01.4
  • type of FA analysis: whole cell analysis
  • incubation medium: ISP2
  • incubation temperature: 30
  • incubation time: 7
  • library/peak naming table: TSBA40
  • system: MIS MIDI
  • method/protocol: Sasser, 1990

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELControlGLURIBXYLMANMALLACSACGLYG
64926+--+-+/--++/--+---------

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
64926-+-+/--+----+------+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitudeenrichment cultureenrichment culture compositionenrichment culture durationenrichment culture temperature
64926rice field soilSansai City, Chiang Mai (18° 32' 23.9'' N, 99° 2' 24'' E)ThailandTHAAsia18.5499.04
65546paddy soil of rice fieldSansai, Chiang MaiThailandTHAAsia18.999.0666basal agar medium0.1 %(w/v) emulsified PLA4 weeks30
67770Agricultural soil from SansaiChiang MaiThailandTHAAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Agriculture#Field
#Host#Plants#Herbaceous plants (Grass,Crops)
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_4024.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_1734;99_4024&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: AB915815
  • Sequence Identity:
  • Total samples: 1433
  • soil counts: 689
  • aquatic counts: 30
  • animal counts: 79
  • plant counts: 635

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
64926Amycolatopsis oliviviridis gene for 16S rRNA, partial sequenceLC2256371466ena1471590
67770Amycolatopsis sp. SCM_MK2-4 gene for 16S ribosomal RNA, partial sequenceAB9158151388ena1471590

GC content

@refGC-contentmethod
6492668.2
6554668.2high performance liquid chromatography (HPLC)

External links

@ref: 64926

culture collection no.: DSM 107509, JCM 32134, TBRC 7186

straininfo link

  • @ref: 111085
  • straininfo: 399368

literature

  • topic: Phylogeny
  • Pubmed-ID: 29517482
  • title: Amycolatopsis oliviviridis sp. nov., a novel polylactic acid-bioplastic-degrading actinomycete isolated from paddy soil.
  • authors: Penkhrue W, Sujarit K, Kudo T, Ohkuma M, Masaki K, Aizawa T, Pathom-Aree W, Khanongnuch C, Lumyong S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.002682
  • year: 2018
  • mesh: Actinomycetales/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Polyesters/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Thailand, Vitamin K 2/analogs & derivatives/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
64926Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-107509Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 107509)
65546Watsana Penkhrue, Kanaporn Sujarit, Takuji Kudo, Moriya Ohkuma, Kazuo Masaki, Tomoyasu Aizawa, Wasu Pathom-aree, Chartchai Khanongnuch and Saisamorn LumyongAmycolatopsis oliviviridis sp. nov., a novel polylactic acid-bioplastic-degrading actinomycete isolated from paddy soil10.1099/ijsem.0.002682IJSEM 68: 1448-1454 201829517482
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
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/
111085Reimer, 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-ID399368.1