Strain identifier

BacDive ID: 17634

Type strain: Yes

Species: Actinospica acidiphila

Strain Designation: GE134766

Strain history: NBRC 102107 <-- NRRL B-24431 <-- L. Cavaletti GE134766.

NCBI tax ID(s): 304899 (species)

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General

@ref: 12199

BacDive-ID: 17634

DSM-Number: 44926

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

description: Actinospica acidiphila GE134766 is an aerobe, spore-forming, mesophilic bacterium that was isolated from forest soil.

NCBI tax id

  • NCBI tax id: 304899
  • Matching level: species

strain history

@refhistory
12199<- L. Cavaletti; GE134766
67770NBRC 102107 <-- NRRL B-24431 <-- L. Cavaletti GE134766.

doi: 10.13145/bacdive17634.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Catenulisporales
  • family: Actinospicaceae
  • genus: Actinospica
  • species: Actinospica acidiphila
  • full scientific name: Actinospica acidiphila Cavaletti et al. 2006

@ref: 12199

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Actinospicaceae

genus: Actinospica

species: Actinospica acidiphila

full scientific name: Actinospica acidiphila Cavaletti et al. 2006

strain designation: GE134766

type strain: yes

Morphology

cell morphology

  • @ref: 31589
  • gram stain: positive
  • cell length: 0.6-0.8 µm
  • cell width: 0.5 µm
  • cell shape: rod-shaped
  • motility: no

colony morphology

@refcolony colorincubation periodmedium used
19889Beige10-14 daysISP 2
19889Beige10-14 daysISP 3
1988910-14 daysISP 4
1988910-14 daysISP 5
1988910-14 daysISP 6
1988910-14 daysISP 7

multicellular morphology

@refforms multicellular complexmedium name
19889noISP 2
19889noISP 3
19889noISP 4
19889noISP 5
19889noISP 6
19889noISP 7

pigmentation

  • @ref: 31589
  • production: yes

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_44926_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44926_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44926_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44926_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_44926_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12199ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84)yeshttps://mediadive.dsmz.de/medium/84Name: ROLLED OATS MINERAL MEDIUM (DSMZ Medium 84) Composition: Agar 20.0 g/l Rolled oats 20.0 g/l ZnSO4 x 7 H2O 0.001 g/l MnCl2 x 4 H2O 0.001 g/l FeSO4 x 7 H2O 0.001 g/l Distilled water
12199ISP2 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
19889ISP 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
19889ISP 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:
19889ISP 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
19889ISP 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
19889ISP 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
19889ISP 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
12199positivegrowth28mesophilic
31589positivegrowth17-33
31589positiveoptimum28mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepH
31589positivegrowth4.2-6
31589positiveoptimum5

Physiology and metabolism

oxygen tolerance

  • @ref: 31589
  • oxygen tolerance: aerobe

spore formation

  • @ref: 31589
  • spore formation: yes

halophily

@refsaltgrowthtested relationconcentration
31589NaClpositivegrowth0-1 %
31589NaClpositiveoptimum0-1 %

observation

@refobservation
31589aggregates in chains
67770quinones: MK-9(H4), MK-9(H6), MK-9(H8)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3158922599arabinose+carbon source
3158918222xylose+carbon source

metabolite production

  • @ref: 31589
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31589catalase+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
19889++++++---+++++++++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12199forest soilLombardia, GerenzanoItalyITAEurope
67770Soil in a wooded areaGerenzanoItalyITAEurope

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Forest
#Environmental#Terrestrial#Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_50127.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_15873;96_110;97_117;98_36040;99_50127&stattab=map
  • Last taxonomy: Actinospica
  • 16S sequence: AJ865861
  • Sequence Identity:
  • Total samples: 1636
  • soil counts: 1356
  • aquatic counts: 70
  • animal counts: 76
  • plant counts: 134

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
121991Risk group (German classification)
198891Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12199
  • description: Actinospica acidiphila partial 16S rRNA gene, type strain GE134766T
  • accession: AJ865861
  • length: 1446
  • database: ena
  • NCBI tax ID: 304899

Genome sequences

  • @ref: 67770
  • description: Actinospica acidiphila NRRL B-24431
  • accession: GCA_000717315
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 304899

GC content

@refGC-contentmethod
1219969.2
6777069.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.363no
flagellatedno97.681no
gram-positiveyes91.023no
anaerobicno99.305yes
halophileno89.193no
spore-formingyes95.948yes
thermophileno98.181yes
glucose-utilyes89.07no
aerobicyes94.922yes
glucose-fermentno87.943no

External links

@ref: 12199

culture collection no.: DSM 44926, NRRL B-24431, JCM 14896, BCRC 16838, NBRC 102107

straininfo link

  • @ref: 86626
  • straininfo: 295938

literature

  • topic: Phylogeny
  • Pubmed-ID: 16902002
  • title: Actinospica robiniae gen. nov., sp. nov. and Actinospica acidiphila sp. nov.: proposal for Actinospicaceae fam. nov. and Catenulisporinae subord. nov. in the order Actinomycetales.
  • authors: Cavaletti L, Monciardini P, Schumann P, Rohde M, Bamonte R, Busti E, Sosio M, Donadio S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63859-0
  • year: 2006
  • mesh: Actinomycetales/chemistry/*classification/genetics/ultrastructure, Amino Acids, Diamino/analysis, Base Composition, Cyanoacrylates/analysis, DNA, Bacterial/chemistry, Fatty Acids/analysis, Microscopy, Electron, Scanning, Molecular Sequence Data, Monosaccharides/analysis, Peptidoglycan/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Soil Microbiology, Species Specificity, Trees, Vitamin K 2/analysis
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
12199Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 44926)https://www.dsmz.de/collection/catalogue/details/culture/DSM-44926
19889Wink, J.http://www.dsmz.de/microorganisms/wink_pdf/DSM44926.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
31589Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2787828776041
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
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
86626Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID295938.1StrainInfo: A central database for resolving microbial strain identifiers