Strain identifier
BacDive ID: 158267
Type strain:
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)
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
@ref | history |
---|---|
64926 | <- S. Lumyong, Department of Biology, Chiang May University; SCM_MK2-4 <- W. Penkhrue, Department of Biology, Chiang May University; SCM_MK2-4 |
67770 | S. 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
@ref | forms multicellular complex | complex name | complex color |
---|---|---|---|
65546 | yes | aerial mycelium | white |
65546 | yes | vegetative mycelium | light brown |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
64926 | ISP2 MEDIUM (DSMZ Medium 987) | yes | https://mediadive.dsmz.de/medium/987 | 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) | yes | https://mediadive.dsmz.de/medium/693 | 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) | yes | https://mediadive.dsmz.de/medium/65 | 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 | yes | ||
65546 | ISP3 | yes | ||
65546 | ISP4 | yes | ||
65546 | ISP5 | yes |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
64926 | positive | growth | 30 | mesophilic |
65546 | positive | growth | 25-37 | mesophilic |
65546 | no | growth | 45 | thermophilic |
65546 | no | growth | 10 | psychrophilic |
67770 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
65546 | no | growth | 4.3 | |
65546 | positive | growth | 10 | alkaliphile |
Physiology and metabolism
oxygen tolerance
- @ref: 65546
- oxygen tolerance: aerobe
spore formation
- @ref: 65546
- spore formation: yes
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
65546 | NaCl | positive | growth | 7 %(w/v) |
65546 | NaCl | positive | growth | 4 %(w/v) |
observation
- @ref: 67770
- observation: quinones: MK-9(H4), MK-9(H2), MK-8(H4)
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
65546 | 15963 | ribitol | + | carbon source |
65546 | casein | + | hydrolysis | |
65546 | 15824 | D-fructose | + | carbon source |
65546 | 12936 | D-galactose | + | builds acid from |
65546 | 16899 | D-mannitol | + | carbon source |
65546 | 16634 | raffinose | +/- | carbon source |
65546 | 65327 | D-xylose | + | builds acid from |
65546 | 65327 | D-xylose | +/- | carbon source |
65546 | 17113 | erythritol | + | builds acid from |
65546 | 5291 | gelatin | + | hydrolysis |
65546 | 24741 | hydroxyproline | + | nitrogen source |
65546 | 17368 | hypoxanthine | + | hydrolysis |
65546 | 30849 | L-arabinose | +/- | carbon source |
65546 | 17561 | L-cysteine | - | nitrogen source |
65546 | 16643 | L-methionine | +/- | nitrogen source |
65546 | 17295 | L-phenylalanine | + | nitrogen source |
65546 | 62345 | L-rhamnose | - | carbon source |
65546 | 16857 | L-threonine | + | nitrogen source |
65546 | 17895 | L-tyrosine | + | hydrolysis |
65546 | 16414 | L-valine | + | nitrogen source |
65546 | 17716 | lactose | + | carbon source |
65546 | 28053 | melibiose | + | builds acid from |
65546 | 28053 | melibiose | + | carbon source |
65546 | 17268 | myo-inositol | + | carbon source |
65546 | 17632 | nitrate | + | reduction |
65546 | 30623 | oxalate | - | carbon source |
65546 | 16634 | raffinose | + | builds acid from |
65546 | 53258 | sodium citrate | +/- | carbon source |
65546 | 132106 | sodium propionate | - | carbon source |
65546 | 17992 | sucrose | - | carbon source |
65546 | 16199 | urea | + | hydrolysis |
65546 | 15318 | xanthine | - | hydrolysis |
68379 | 17632 | nitrate | + | reduction |
68379 | 16199 | urea | - | hydrolysis |
68379 | 5291 | gelatin | + | hydrolysis |
68379 | 17634 | D-glucose | - | fermentation |
68379 | 16988 | D-ribose | - | fermentation |
68379 | 65327 | D-xylose | - | fermentation |
68379 | 16899 | D-mannitol | - | fermentation |
68379 | 17306 | maltose | - | fermentation |
68379 | 17716 | lactose | - | fermentation |
68379 | 17992 | sucrose | - | fermentation |
68379 | 28087 | glycogen | - | fermentation |
metabolite production
- @ref: 65546
- Chebi-ID: 16136
- metabolite: hydrogen sulfide
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
65546 | catalase | + | 1.11.1.6 |
68379 | gelatinase | + | |
68379 | urease | - | 3.5.1.5 |
68379 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68379 | alpha-glucosidase | - | 3.2.1.20 |
68379 | beta-glucuronidase | - | 3.2.1.31 |
68379 | alkaline phosphatase | + | 3.1.3.1 |
68379 | pyrrolidonyl arylamidase | - | 3.4.19.3 |
68379 | pyrazinamidase | - | 3.5.1.B15 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | - | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | + | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
fatty acid profile
fatty acids
@ref fatty acid percentage 65546 C15:0 iso 27 65546 C16:0 iso 13.2 65546 C16:1ω7c / C15:0 iso 2OH 11 65546 C16:0 10.2 65546 C17:0 7.6 65546 C17:0 iso 5.9 65546 C17:0 anteiso 5.8 65546 C17:1ω8c 3.2 65546 C17:1ω6c 2.8 65546 C15:0 anteiso 2.6 65546 C15:0 2.6 65546 C14:0 iso 1.5 65546 C18:0 1.4 - 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
@ref | NIT | PYZ | PYRA | PAL | beta GUR | beta GAL | alpha GLU | beta NAG | ESC | URE | GEL | Control | GLU | RIB | XYL | MAN | MAL | LAC | SAC | GLYG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
64926 | + | - | - | + | - | +/- | - | + | +/- | - | + | - | - | - | - | - | - | - | - | - |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-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
@ref | sample type | geographic location | country | origin.country | 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 | ||||
65546 | paddy soil of rice field | Sansai, Chiang Mai | Thailand | THA | Asia | 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 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
64926 | Amycolatopsis oliviviridis gene for 16S rRNA, partial sequence | LC225637 | 1466 | ena | 1471590 |
67770 | Amycolatopsis sp. SCM_MK2-4 gene for 16S ribosomal RNA, partial sequence | AB915815 | 1388 | ena | 1471590 |
GC content
@ref | GC-content | method |
---|---|---|
64926 | 68.2 | |
65546 | 68.2 | high 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
@id | authors | title | doi/url | catalogue | journal | pubmed |
---|---|---|---|---|---|---|
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 | 10.1099/ijsem.0.004332 | |||
64926 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-107509 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (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 | 10.1099/ijsem.0.002682 | IJSEM 68: 1448-1454 2018 | 29517482 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | https://microbeatlas.org/ | |||
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 | 10.60712/SI-ID399368.1 |