Strain identifier

BacDive ID: 67

Type strain: Yes

Species: Acidisphaera rubrifaciens

Strain Designation: HS-AP3

Strain history: A. Hiraishi HS-AP3.

NCBI tax ID(s): 50715 (species)

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@ref: 6239

BacDive-ID: 67

DSM-Number: 16009

keywords: colony-forming, coccus-shaped, mesophilic, Gram-negative, aerobe, Bacteria, 16S sequence, genome sequence

description: Acidisphaera rubrifaciens HS-AP3 is an aerobe, mesophilic, Gram-negative Proteobacterium that forms circular colonies and was isolated from surface water and sediment from an acidic hot spring.

NCBI tax id

  • NCBI tax id: 50715
  • Matching level: species

strain history

doi: 10.13145/bacdive67.20211221.6

Name and taxonomic classification


  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/proteobacteria
  • domain: Bacteria
  • phylum: Proteobacteria
  • class: Alphaproteobacteria
  • order: Rhodospirillales
  • family: Acetobacteraceae
  • genus: Acidisphaera
  • species: Acidisphaera rubrifaciens
  • full scientific name: Acidisphaera rubrifaciens Hiraishi et al. 2000

@ref: 6239

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Acetobacteraceae

genus: Acidisphaera

species: Acidisphaera rubrifaciens

full scientific name: Acidisphaera rubrifaciens Hiraishi et al. 2000

strain designation: HS-AP3

type strain: yes


cell morphology

  • @ref: 23249
  • gram stain: negative
  • cell length: 0.8-1.2 µm
  • cell width: 0.7-1.0 µm
  • cell shape: coccus-shaped
  • motility: no

colony morphology

  • @ref: 23249
  • colony size: 2 mm
  • colony color: salmon pink to red
  • colony shape: circular
  • incubation period: 7 days
  • medium used: GNYS


23249yesBacteriochlorophyll a

Culture and growth conditions

culture medium

  • @ref: 6239
  • name: GNYS MEDIUM (DSMZ Medium 1119)
  • growth: yes
  • link:
  • composition: Name: GNYS MEDIUM (DSMZ Medium 1119) Composition: Agar 18.0 g/l Sodium gluconate 3.0 g/l Yeast extract 1.0 g/l (NH4)2SO4 1.0 g/l KH2PO4 1.0 g/l MgCl2 x 6 H2O 0.2 g/l NaCl 0.2 g/l CaCl2 x 2 H2O 0.05 g/l Na2-EDTA 0.0052 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 H3BO3 6.2e-05 g/l Na2MoO4 x 2 H2O 3.6e-05 g/l NiCl2 x 6 H2O 2.4e-05 g/l CuCl2 x 2 H2O 1.7e-05 g/l Distilled water

culture temp


culture pH

  • @ref: 23249
  • ability: positive
  • type: optimum
  • pH: 4.5-5.0

Physiology and metabolism

oxygen tolerance

  • @ref: 23249
  • oxygen tolerance: aerobe


  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2324930089acetate-carbon source
2324916150benzoate-carbon source
2324928885butanol-carbon source
2324917968butyrate-carbon source
23249casamino acids-carbon source
2324916947citrate-carbon source
2324916236ethanol-carbon source
2324915740formate-carbon source
2324928757fructose-carbon source
2324917268myo-inositol-carbon source
2324930849L-arabinose-carbon source
2324917716lactose-carbon source
2324937684mannose-carbon source
2324917790methanol-carbon source
23249peptone-carbon source
2324928831propanol-carbon source
2324917272propionate-carbon source
2324917992sucrose-carbon source
2324953426tween 80-hydrolysis
2324965327D-xylose+carbon source
2324929806fumarate+carbon source
2324928260galactose+carbon source
2324924265gluconate+carbon source
2324917234glucose+carbon source
2324917754glycerol+carbon source
2324924996lactate+carbon source
2324925115malate+carbon source
2324929864mannitol+carbon source
2324915361pyruvate+carbon source
2324930911sorbitol+carbon source
2324930031succinate+carbon source
23249yeast extract+carbon source

metabolite production

6777030033bacteriochlorophyll ayes

Isolation, sampling and environmental information


@refsample typegeographic locationcountryorigin.countrycontinent
6239surface water and sediment from an acidic hot springKanagawa Prefecture, HakoneJapanJPNAsia
67770Hot spring waterHakone, Kanagawa Pref.JapanJPNAsia

isolation source categories

#Environmental#Aquatic#Surface water
#Environmental#Aquatic#Thermal spring

Safety information

risk assessment

  • @ref: 6239
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6239
  • description: Acidisphaera rubrifaciens rrn gene for 16S rRNA
  • accession: D86512
  • length: 1451
  • database: ena
  • NCBI tax ID: 50715

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidisphaera rubrifaciens HS-AP3 HS-AP3GCA_000964365scaffoldncbi1231350
66792Acidisphaera rubrifaciens HS-AP31231350.12wgspatric1231350
67770Acidisphaera rubrifaciens HS-AP3, whole genome shotgun sequencing projectBANB00000000ncbi1231350

GC content

2324969.1-69.8high performance liquid chromatography (HPLC)
6777069.3high performance liquid chromatography (HPLC)

External links

@ref: 6239

culture collection no.: DSM 16009, JCM 10600

straininfo link



6239Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16009)
20215D.Gleim, M.Kracht, N.Weiss et. al. Nomenclature Up-to-date - compilation of all names of Bacteria and Archaea, validly published according to the Bacteriological Code since 1. Jan. 1980, and validly published nomenclatural changes since
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
23249A Hiraishi, Y Matsuzawa, T Kanbe, N Wakao10.1099/00207713-50-4-1539Acidisphaera rubrifaciens gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from acidic environments.IJSEM 50: 1539-1546 200010939661
67770Curators of the JCM