Strain identifier

BacDive ID: 13273

Type strain: Yes

Species: Amycolatopsis samaneae

Strain history: BCC 35842 <-- K. Duangmal RM287.

NCBI tax ID(s): 664691 (species)

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General

@ref: 17974

BacDive-ID: 13273

DSM-Number: 45649

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

description: Amycolatopsis samaneae DSM 45649 is an aerobe, spore-forming, mesophilic bacterium that builds an aerial mycelium and was isolated from roots of Samanea saman.

NCBI tax id

  • NCBI tax id: 664691
  • Matching level: species

strain history

@refhistory
17974<- C Suriyachadkun, BCC; BCC 35842 <- R. Mingma
67770BCC 35842 <-- K. Duangmal RM287.

doi: 10.13145/bacdive13273.20230509.8.1

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 samaneae
  • full scientific name: Amycolatopsis samaneae Duangmal et al. 2011

@ref: 17974

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis samaneae

full scientific name: Amycolatopsis samaneae Duangmal et al. 2011

type strain: yes

Morphology

cell morphology

  • @ref: 29853
  • gram stain: positive
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
21390Maize yellow (1006)10-14 daysISP 2
21390Sand yellow (1002)10-14 daysISP 3
21390Traffic yellow (1023)10-14 daysISP 4
21390Traffic yellow (1023)10-14 daysISP 5
21390Sun yellow (1037)10-14 daysISP 7
21390Ochre yellow (1024)10-14 daysSuter with tyrosine
21390Golden yellow (1004)10-14 daysSuter without tyrosine

multicellular morphology

@refforms multicellular complexcomplex namecomplex colormedium name
21390yesAerial MyceliumOyster white (1013)ISP 2
21390yesAerial MyceliumCream (9001)ISP 3
21390yesAerial MyceliumCream (9001)ISP 4
21390yesAerial MyceliumLight ivory (1015)ISP 5
21390yesAerial MyceliumGrey white (9002)ISP 7
21390yesAerial MyceliumOyster white (1013)Suter with tyrosine
21390yesAerial MyceliumGolden yellow (1004)Suter without tyrosine

pigmentation

  • @ref: 29853
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
17974GPHF-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
21390ISP 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
21390ISP 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:
21390ISP 4yesName: ISP 4; DSM 547 Solution I: Difco soluble starch, 10.0 g. Make a paste of the starch with a small amount of cold distilled water and bring to a volume of 500 ml. Solution II: CaCO3 2.0 g K2HPO4 (anhydrous) 1.0 g MgSO4 x 7 H2O 1.0 g NaCl 1.0 g (NH4)2SO4 2.0 g Distilled water 500.0 ml Trace salt solution (see below) 1.0 ml The pH should be between 7.0 and 7.4. Do not adjust if it is within this range. Mix solutions I and II together. Add 20.0 g agar. Liquify agar by steaming at 100°C for 10 to 20 min. Trace element solution: FeSO4 x 7 H2O 0.1 g MnCl2 x 4 H2O 0.1 g ZnSO4 x 7 H2O 0.1 g Distilled water 100.0 ml
21390ISP 5yesName: ISP 5 (5323) Composition L-Asparagine 1.0 g/l Glycerol 10.0 g/l K2HPO4 1.0 g/l Salt solution (see preparation) 1.0 ml/l Agar 20.0 g/l Preparation: Salt solution 1.0 g FeSO4 x 7 H2O 1.0 g MnCl2 x 4 H2O 1.0 g ZNSO4 x 7 H2O in 100 ml water Sterilisation: 20 minutes at 121°C pH before sterilisation: 7.2 Usage: Maintenance and taxonomy Organisms: All Actinomycetes
21390ISP 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
21390Suter with tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes
21390Suter without tyrosineyesName: Synthetically suter medium (5337) with and without tyrosine - see Kutzner,H.J., R. M. Kroppensted and F. Korn-Wendisch. (1986) Composition: Glycerol 15.0 g/l Tyrosine 1.0 (optional, see preparation comment) L-arginine 5.0 g/l L-glutamic acid 5.0 g/l L-methionine 0.3 g/l L-isoleucine 0.3 g/l K2HPO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l Agar 20.0 g/l Trace element solution (5341) 1.0 ml Composition of Trace element solution (5341): CuSO4 x 5 H2O 10.0 g/l CaCl2 x 2 H2O 10.0 g/l FeSO4 x 7 H2O 10.0 g/l ZnSO4 x 7 H2O 10.0 g/l MnSO4 x 7 H2O 40.0 g/l Preparation: Control medium is prepared without tyrosine Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigment Organisms: All Actinomycetes

culture temp

@refgrowthtypetemperaturerange
17974positivegrowth28mesophilic
29853positivegrowth16-40
29853positiveoptimum29.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
29853positivegrowth05-11alkaliphile
29853positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 29853
  • oxygen tolerance: aerobe

spore formation

  • @ref: 29853
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
21390NaClpositivemaximum5 %
29853NaClpositivegrowth0-10 %
29853NaClpositiveoptimum5 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2139017234glucose+
2139022599arabinose-
2139017992sucrose-
2139018222xylose-
2139017268myo-inositol+
2139037684mannose+
2139028757fructose+
2139026546rhamnose-
2139016634raffinose-
2139062968cellulose-
298534853esculin+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

enzymes

@refvalueactivityec
29853acid phosphatase+3.1.3.2
29853alkaline phosphatase+3.1.3.1
29853catalase+1.11.1.6
29853urease+3.5.1.5
68379gelatinase+
68379urease+3.5.1.5
68379N-acetyl-beta-glucosaminidase+3.2.1.52
68379beta-galactosidase-3.2.1.23
68379beta-glucuronidase-3.2.1.31
68379alkaline phosphatase+3.1.3.1
68379pyrrolidonyl arylamidase+3.4.19.3
68382alkaline phosphatase+3.1.3.1
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
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
68382beta-glucosidase+3.2.1.21
68382N-acetyl-beta-glucosaminidase+3.2.1.52
68382alpha-fucosidase-3.2.1.51

API coryne

@refNITPYZPYRAPALbeta GURbeta GALalpha GLUbeta NAGESCUREGELGLURIBXYLMANMALLACSACGLYGControl
21390-+++--++-++--------
17974--++---++++---------

API zym

@refAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- FucosidaseControl
21390+++-+++/--+++---+++--
17974++/---+++/--+++---+/-+++--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinenthost species
17974roots of Samanea samanBangkok, Kasetsart UniversityThailandTHAAsia
67770Roots of Samanea saman (Jacq.) Merr. from Kasetsart Univ.BangkokThailandTHAAsiaSamanea saman

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Tree
#Host Body-Site#Plant#Root (Rhizome)

Safety information

risk assessment

  • @ref: 17974
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17974
  • description: Amycolatopsis samaneae strain RM287 16S ribosomal RNA gene, partial sequence
  • accession: GQ381310
  • length: 1417
  • database: ena
  • NCBI tax ID: 664691

GC content

@refGC-contentmethod
1797471.7
6777071.7high performance liquid chromatography (HPLC)

External links

@ref: 17974

culture collection no.: DSM 45649, BCC 35842, NBRC 106095, TISTR 1919, RM 287, JCM 17934

straininfo link

  • @ref: 82477
  • straininfo: 403813

literature

  • topic: Phylogeny
  • Pubmed-ID: 20511469
  • title: Amycolatopsis samaneae sp. nov., isolated from roots of Samanea saman (Jacq.) Merr.
  • authors: Duangmal K, Mingma R, Pathom-Aree W, Thamchaipenet A, Inahashi Y, Matsumoto A, Takahashi Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.022699-0
  • year: 2010
  • mesh: Actinomycetales/chemistry/*classification/genetics/*isolation & purification, Arabinose/analysis, Base Composition, Cell Wall/chemistry, Cluster Analysis, Cytoplasm/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fabaceae/*microbiology, Fatty Acids/analysis, Galactose/analysis, Molecular Sequence Data, Phylogeny, Plant Roots/microbiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thailand, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17974Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45649)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45649
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
21390Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM45649.pdfCompendium of Actinobacteria. HZI-Helmholtz-Centre for Infection Research, Braunschweig
29853Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2622728776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68379Automatically annotated from API Coryne
68382Automatically annotated from API zym
82477Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID403813.1StrainInfo: A central database for resolving microbial strain identifiers