Strain identifier

BacDive ID: 132249

Type strain: Yes

Species: Acidipila rosea

Strain Designation: AP8

Strain history: <- KCTC; KCTC 23427

NCBI tax ID(s): 768535 (species)

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General

@ref: 24038

BacDive-ID: 132249

DSM-Number: 103428

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Acidipila rosea AP8 is a mesophilic, Gram-negative bacterium that was isolated from acid mine drainage.

NCBI tax id

  • NCBI tax id: 768535
  • Matching level: species

strain history

  • @ref: 24038
  • history: <- KCTC; KCTC 23427

doi: 10.13145/bacdive132249.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/acidobacteriota
  • domain: Bacteria
  • phylum: Acidobacteriota
  • class: Terriglobia
  • order: Terriglobales
  • family: Acidobacteriaceae
  • genus: Acidipila
  • species: Acidipila rosea
  • full scientific name: Acidipila rosea Okamura et al. 2015

@ref: 24038

domain: Bacteria

phylum: Acidobacteria

class: Acidobacteriia

order: Acidobacteriales

family: Acidobacteriaceae

genus: Acidipila

species: Acidipila rosea

full scientific name: Acidipila rosea Okamura et al. 2015

strain designation: AP8

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.968

Culture and growth conditions

culture medium

  • @ref: 24038
  • name: SSE/HD1:10 (DSMZ Medium 1426)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1426
  • composition: Name: SSE/HD 1:10 MEDIUM (DSMZ Medium 1426) Composition: MES 1.95 g/l Peptone 0.5 g/l CaSO4 x 2 H2O 0.4303 g/l MgSO4 x 7 H2O 0.3695 g/l Yeast extract 0.25 g/l Na NO3 0.212 g/l CaCl2 x 2 H2O 0.1469 g/l Ca(NO3)2 x 4 H2O 0.118 g/l MgCl2 x 6 H2O 0.1018 g/l Glucose 0.1 g/l (NH4)2SO4 0.09915 g/l NH4Cl 0.05345 g/l K2SO4 0.0435 g/l FeSO4 x 7 H2O 0.00555 g/l KH2PO4 0.00340213 g/l HCl 0.0025 g/l FeCl2 x 4 H2O 0.0015 g/l CoCl2 x 6 H2O 0.00019 g/l MnCl2 x 4 H2O 0.0001 g/l ZnCl2 7e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l Pyridoxine hydrochloride 1e-05 g/l H3BO3 6e-06 g/l Lipoic acid 5e-06 g/l D-Calcium pantothenate 5e-06 g/l Nicotinic acid 5e-06 g/l Riboflavin 5e-06 g/l Thiamine-HCl x 2 H2O 5e-06 g/l p-Aminobenzoic acid 5e-06 g/l Folic acid 2e-06 g/l Biotin 2e-06 g/l CuCl2 x 2 H2O 2e-06 g/l Vitamin B12 1e-07 g/l Distilled water

culture temp

  • @ref: 24038
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.995

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase-1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
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
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

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
24038-+++/-+/-+++/-+-+++++-++-+

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
24038-----+-+-------------

Isolation, sampling and environmental information

isolation

  • @ref: 24038
  • sample type: acid mine drainage
  • geographic location: Matsuo mine, Iwate Prefecture
  • country: Japan
  • origin.country: JPN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Aquatic
#Condition#Acidic

Safety information

risk assessment

  • @ref: 24038
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24038
  • description: Acidopila rosea gene for 16S rRNA, partial sequence
  • accession: AB561884
  • length: 1461
  • database: ena
  • NCBI tax ID: 768535

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidipila rosea DSM 103428GCA_004339725scaffoldncbi768535
66792Acidipila rosea strain DSM 103428768535.4wgspatric768535
66792Acidipila rosea DSM 1034282757320406draftimg768535

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno57.316no
flagellatedno90.972no
gram-positiveno97.813no
anaerobicno98.713no
aerobicyes86.169no
halophileno92.286no
spore-formingno92.85no
thermophileno87.451yes
glucose-utilyes57.708yes
glucose-fermentno91.844yes

External links

@ref: 24038

culture collection no.: DSM 103428, KCTC 23427, NBRC 107607

straininfo link

  • @ref: 90599
  • straininfo: 397443

literature

  • topic: Phylogeny
  • Pubmed-ID: 21255071
  • title: Acidipila rosea gen. nov., sp. nov., an acidophilic chemoorganotrophic bacterium belonging to the phylum Acidobacteria.
  • authors: Okamura K, Kawai A, Yamada T, Hiraishi A
  • journal: FEMS Microbiol Lett
  • DOI: 10.1111/j.1574-6968.2011.02224.x
  • year: 2011
  • mesh: Base Composition/genetics, Gram-Negative Bacteria/*classification/genetics/*metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Vitamin K 2/metabolism
  • topic2: Metabolism

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
24038Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103428Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103428)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90599Reimer, 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 identifiers10.60712/SI-ID397443.1