Strain identifier

BacDive ID: 13253

Type strain: Yes

Species: Amycolatopsis plumensis

Strain history: DSM 44776 <-- H. Amir strain SBHS Strp1 <-- D. Saintpierre-Bonaccio.

NCBI tax ID(s): 236508 (species)

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General

@ref: 12081

BacDive-ID: 13253

DSM-Number: 44776

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

description: Amycolatopsis plumensis DSM 44776 is an aerobe, mesophilic, Gram-positive bacterium that was isolated from brown hypermagnesian soil sasmple.

NCBI tax id

  • NCBI tax id: 236508
  • Matching level: species

strain history

@refhistory
12081<- H. Amir; SBHs Strp1 <- D. Saintpierre-Bonaccio
67770DSM 44776 <-- H. Amir strain SBHS Strp1 <-- D. Saintpierre-Bonaccio.

doi: 10.13145/bacdive13253.20230509.8.1

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 plumensis
  • full scientific name: Amycolatopsis plumensis Saintpierre-Bonaccio et al. 2005

@ref: 12081

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Pseudonocardiaceae

genus: Amycolatopsis

species: Amycolatopsis plumensis

full scientific name: Amycolatopsis plumensis Saintpierre-Bonaccio et al. 2005

type strain: yes

Morphology

cell morphology

  • @ref: 31468
  • gram stain: positive
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
20114Yellow orange (2000)10-14 daysISP 2
20114Yellow orange (2000)10-14 daysISP 3
20114Yellow orange (2000)10-14 daysISP 4
20114Yellow orange (2000)10-14 daysISP 5
20114Beige (1001)10-14 daysISP 6
20114Brown beige (1011)10-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
20114noISP 2
20114noISP 3
20114noISP 4
20114noISP 5
20114noISP 6
20114noISP 7

pigmentation

  • @ref: 31468
  • production: no

multimedia

  • @ref: 12081
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_44776.jpg
  • caption: Medium 65 28°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12081GYM 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
20114ISP 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
20114ISP 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:
20114ISP 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
20114ISP 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
20114ISP 6yesName: ISP 6 (5318) Composition Peptone 15.0 g/l Proteose peptose 5.0 g/l Ferric ammonium citrate 0.5 g/l Sodium glycerophosphate 1.0 g/l Sodium thiosulfate 0.08 g/l Yeast extract 1.0 g/l Agar 15.0 g/l Sterilisation: 20 minutes at 121°C pH before sterilisation: Usage: Production of melanoid pigments Organisms: All Actinomycetes
20114ISP 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
12081positivegrowth28mesophilic
20114positiveoptimum28mesophilic
31468positivegrowth20-37
31468positiveoptimum28.5mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
31468positivegrowth04-12alkaliphile
31468positiveoptimum8

Physiology and metabolism

oxygen tolerance

  • @ref: 31468
  • oxygen tolerance: aerobe

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2011417234glucose-
2011422599arabinose-
2011417992sucrose-
2011418222xylose-
2011417268myo-inositol+
2011429864mannitol-
2011428757fructose-
2011426546rhamnose-
2011416634raffinose+
2011462968cellulose+
3146822599arabinose+carbon source
3146817057cellobiose+carbon source
3146828757fructose+carbon source
3146817306maltose+carbon source
3146829864mannitol+carbon source
3146827082trehalose+carbon source
3146853426tween 80+carbon source

metabolite production

  • @ref: 31468
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31468catalase+1.11.1.6
31468gelatinase+
31468urease+3.5.1.5
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
20114++++++-++++++++++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12081brown hypermagnesian soil sasmplePlum regionNew CaledoniaNCLAustralia and Oceania
67770Brown hypermagnesian ultramafic soilNew CaledoniaFrench OverseasFRA

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_13301.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_10;96_408;97_462;98_532;99_13301&stattab=map
  • Last taxonomy: Amycolatopsis
  • 16S sequence: AY262825
  • Sequence Identity:
  • Total samples: 1230
  • soil counts: 1065
  • aquatic counts: 20
  • animal counts: 41
  • plant counts: 104

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
120811Risk group (German classification)
201141German classification

Sequence information

16S sequences

  • @ref: 31468
  • description: Amycolatopsis plumensis strain SBHS Strp1 16S ribosomal RNA gene, partial sequence
  • accession: AY262825
  • length: 1488
  • database: nuccore
  • NCBI tax ID: 236508

External links

@ref: 12081

culture collection no.: DSM 44776, CIP 108939, JCM 13852, NRRL B-24324, SBHs Strp1, NBRC 102106, NCIMB 14257

straininfo link

  • @ref: 82457
  • straininfo: 215500

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16166709Amycolatopsis plumensis sp. nov., a novel bioactive actinomycete isolated from a New-Caledonian brown hypermagnesian ultramafic soil.Saintpierre-Bonaccio D, Amir H, Pineau R, Tan GYA, Goodfellow MInt J Syst Evol Microbiol10.1099/ijs.0.63630-02005Actinomycetales/*classification/genetics/isolation & purification/*physiology, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Genotype, Magnesium, Molecular Sequence Data, New Caledonia, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil/analysis, *Soil MicrobiologyGenetics
Phylogeny25744584Amycolatopsis rhabdoformis sp. nov., an actinomycete isolated from a tropical forest soil.Souza WR, Silva RE, Goodfellow M, Busarakam K, Figueiro FS, Ferreira D, Rodrigues-Filho E, Moraes LAB, Zucchi TDInt J Syst Evol Microbiol10.1099/ijs.0.0001762015Actinomycetales/*classification/genetics/isolation & purification, Bacteria, Aerobic/genetics, Bacterial Typing Techniques, Brazil, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Forests, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, *Soil Microbiology, Vitamin K 2/analogs & derivatives/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12081Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44776)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44776
20114Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44776.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
31468Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2776828776041
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
82457Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID215500.1StrainInfo: A central database for resolving microbial strain identifiers