Strain identifier

BacDive ID: 13268

Type strain: Yes

Species: Amycolatopsis ultiminotia

Strain Designation: RP-AC36

Strain history: DSM 45180 <-- S. D. Lee RP-Ac 36.

NCBI tax ID(s): 543629 (species)

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General

@ref: 15643

BacDive-ID: 13268

DSM-Number: 45180

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

description: Amycolatopsis ultiminotia RP-AC36 is an aerobe, mesophilic, Gram-positive bacterium that builds an aerial mycelium and was isolated from rhizosphere of a cliff-associated plant .

NCBI tax id

  • NCBI tax id: 543629
  • Matching level: species

strain history

@refhistory
15643<- S. D. Lee; RP-Ac 36
67770DSM 45180 <-- S. D. Lee RP-Ac 36.

doi: 10.13145/bacdive13268.20230509.8.1

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 ultiminotia
  • full scientific name: Amycolatopsis ultiminotia Lee 2009

@ref: 15643

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis ultiminotia

full scientific name: Amycolatopsis ultiminotia Lee 2009

strain designation: RP-AC36

type strain: yes

Morphology

cell morphology

  • @ref: 29112
  • gram stain: positive
  • cell shape: rod-shaped

colony morphology

@refcolony colorincubation periodmedium used
20176Sand yellow (1002)10-14 daysISP 2
20176Ivory (1014)10-14 daysISP 3
20176Ivory (1014)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
20176yesAerial MyceliumLight ivoryISP 2
20176noISP 3
20176noIPS 7

pigmentation

  • @ref: 29112
  • production: yes

multimedia

  • @ref: 15643
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45180.jpg
  • caption: Medium 553 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15643GPHF-MEDIUM (DSMZ Medium 553)yeshttps://mediadive.dsmz.de/medium/553Name: GPHF-MEDIUM (DSMZ Medium 553) Composition: Agar 20.0 g/l Glucose 10.0 g/l Beef extract 5.0 g/l Yeast extract 5.0 g/l Casein peptone 5.0 g/l CaCl2 x 2 H2O 0.74 g/l Distilled water
15643GYM 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
20176ISP 2yesName: ISP 2 / Yeast Malt Agar (5265); 5265 Composition Malt extract 10.0 g/l Yeast extract 4.0 g/l Glucose 4.0 g/l Agar 15.0 g/l Preparation: Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.0 Usage: Maintenance and Taxonomy Organisms: All Actinomycetes
20176ISP 3yesName: ISP 3; 5315 Composition Dog oat flakes 20.0 g/l Trace element solution (5314) 2.5 ml/l Agar 18.0 g/l Preparation: Oat flakes are cooked for 20 minutes, trace element solution and agar are added (in the case of non rolled oat flakes the suspension has to bee filtrated). Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.8 Usage: Maintenance and taxonomy (e.g. SEM As liquid medium for metabolite production) Organisms: All Actinomycetes Trace element solution 5314 Name: Trace element solution 5314; 5314 Composition CaCl2 x H2O 3.0 g/l Fe-III-citrate 1.0 g/l MnSO4 0.2 g/l ZnCl2 0.1 g/l CuSO4 x 5 H2O 0.025 g/l Sodium tetra borate 0.2 g/l CoCl2 x 6 H2O 0.004 g/l Sodium molybdate 0.01 g/l Preparation: Use double destillated water. Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Trace element solution for different media Organisms:
20176ISP 7yesName: ISP 7 (5322) Composition Glycerol 15.0 g/l L-Tyrosine 0.5 g/l L-Asparagine 1.0 g/l K2HPO4 0.5 g/l NaCl 0.5 g/l FeSO4 x 7 H2O 0.01 g/l Trace element solution 5343 1.0 ml/l Agar 20.0 Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.3 Usage: Production of melanoid pigments Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
15643positivegrowth28mesophilic
20176positiveoptimum28mesophilic
29112positivegrowth10-37
29112positiveoptimum28.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29112positivegrowth5.1-12.1alkaliphile
29112positiveoptimum7.1

Physiology and metabolism

oxygen tolerance

  • @ref: 29112
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
29112NaClpositivegrowth0-5 %
29112NaClpositiveoptimum2.5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2017617234glucose+
2017622599arabinose+/-
2017617992sucrose+/-
2017618222xylose+/-
2017617268myo-inositol+
2017629864mannitol+
2017628757fructose+
2017626546rhamnose+
2017616634raffinose+/-
2017662968cellulose-
2911217057cellobiose+carbon source
2911217234glucose+carbon source
2911217754glycerol+carbon source
2911217716lactose+carbon source
2911217306maltose+carbon source
2911226546rhamnose+carbon source
2911218222xylose+carbon source
291124853esculin+hydrolysis

enzymes

@refvalueactivityec
29112catalase+1.11.1.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
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

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
20176+++++++-+++++---++-

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
15643rhizosphere of a cliff-associated plant (Peucedanum japonicum Thunb.)Peucedanum japonicumJeju, Mara IslandRepublic of KoreaKORAsia
67770Rhizosphere of a cliff-associated plant, Peucedanum japonicum Thunb.Peucedanum japonicumMara Island, JejuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Rhizosphere

Safety information

risk assessment

  • @ref: 15643
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15643
  • description: Amycolatopsis ultiminotia partial 16S rRNA gene, type strain RP-AC36T
  • accession: FM177516
  • length: 1413
  • database: ena
  • NCBI tax ID: 543629

GC content

@refGC-contentmethod
1564367.5high performance liquid chromatography (HPLC)
2911267.5

External links

@ref: 15643

culture collection no.: DSM 45180, JCM 16898, NRRL B-24662

straininfo link

  • @ref: 82472
  • straininfo: 399558

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19502324Amycolatopsis ultiminotia sp. nov., isolated from rhizosphere soil, and emended description of the genus Amycolatopsis.Lee SDInt J Syst Evol Microbiol10.1099/ijs.0.006577-02009Actinomycetales/*classification/genetics/isolation & purification/physiology, Apiaceae/*microbiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genotype, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, Plant Roots/*microbiology, Polymerase Chain Reaction/methods, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
Phylogeny23053697Amycolatopsis jiangsuensis sp. nov., a novel endophytic actinomycete isolated from a coastal plant in Jiangsu, China.Xing K, Liu W, Zhang YJ, Bian GK, Zhang WD, Tamura T, Lee JS, Qin S, Jiang JHAntonie Van Leeuwenhoek10.1007/s10482-012-9823-y2012Actinomycetales/*classification/*isolation & purification, Bacterial Typing Techniques, Carbohydrates/analysis, Cell Wall/chemistry, China, Chrysanthemum/*microbiology, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Endophytes/*classification/*isolation & purification, Fatty Acids/analysis, Microscopy, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vitamin K 2/analysisEnzymology
Phylogeny23645018Amycolatopsis cihanbeyliensis sp. nov., a halotolerant actinomycete isolated from a salt mine.Tatar D, Sazak A, Guven K, Cetin D, Sahin NInt J Syst Evol Microbiol10.1099/ijs.0.050963-02013Actinomycetales/*classification/genetics/isolation & purification, Arabinose/analysis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Galactose/analysis, *Mining, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Sodium Chloride, *Soil Microbiology, Turkey, Vitamin K 2/analogs & derivatives/analysisGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
15643Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45180)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45180
20176Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45180.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
29112Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2553928776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
82472Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399558.1StrainInfo: A central database for resolving microbial strain identifiers