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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General

@ref: 6239

BacDive-ID: 67

DSM-Number: 16009

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

description: Acidisphaera rubrifaciens HS-AP3 is an aerobe, mesophilic, Gram-negative bacterium 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

@refhistory
6239<- JCM/RIKEN <- A. Hiraishi, Dept. Ecological Engineering, Toyohashi Univ. Technol., Japan; HS-AP3
67770A. Hiraishi HS-AP3.

doi: 10.13145/bacdive67.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • 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

Morphology

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

pigmentation

@refproductionname
23249yesSpirilloxanthin
23249yescarotenoids
23249yesBacteriochlorophyll a

Culture and growth conditions

culture medium

  • @ref: 6239
  • name: GNYS MEDIUM (DSMZ Medium 1119)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1119
  • 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

@refgrowthtypetemperaturerange
6239positivegrowth30mesophilic
23249positivegrowth20-40
23249positiveoptimum30-35mesophilic
67770positivegrowth30mesophilic

culture pH

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

Physiology and metabolism

oxygen tolerance

  • @ref: 23249
  • oxygen tolerance: aerobe

observation

  • @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
23249casein-hydrolysis
2324928017starch-hydrolysis
2324953426tween 80-hydrolysis
2324917632nitrate-reduction
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

@refChebi-IDmetaboliteproduction
6777030033bacteriochlorophyll ayes
6777023044carotenoidyes

Isolation, sampling and environmental information

isolation

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

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Aquatic#Surface water
#Environmental#Aquatic#Thermal spring
#Condition#Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3138.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_29;96_1637;97_1959;98_2409;99_3138&stattab=map
  • Last taxonomy: Acidisphaera rubrifaciens subclade
  • 16S sequence: D86512
  • Sequence Identity:
  • Total samples: 4564
  • soil counts: 3255
  • aquatic counts: 658
  • animal counts: 249
  • plant counts: 402

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-AP31231350.12wgspatric1231350
67770Acidisphaera rubrifaciens HS-AP3GCA_000964365scaffoldncbi1231350

GC content

@refGC-contentmethod
2324969.1-69.8high performance liquid chromatography (HPLC)
6777069.3high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes65.345yes
gram-positiveno97.93yes
anaerobicno95.859yes
aerobicyes90.572yes
halophileno89.403no
spore-formingno92.827no
thermophileno95.514no
glucose-utilyes74.066no
flagellatedno92.372yes
glucose-fermentno94.061no

External links

@ref: 6239

culture collection no.: DSM 16009, JCM 10600

straininfo link

  • @ref: 69751
  • straininfo: 100464

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10939661Acidisphaera rubrifaciens gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from acidic environments.Hiraishi A, Matsuzawa Y, Kanbe T, Wakao NInt J Syst Evol Microbiol10.1099/00207713-50-4-15392000Acids, Aerobiosis, Alphaproteobacteria/*classification/cytology/physiology, Bacteriochlorophylls/*metabolism, Base Composition, Culture Media, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fresh Water/microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/analysis, Species Specificity, *Water Microbiology, Zinc SulfateCultivation
Phylogeny19282632Rhodovastum atsumiense gen. nov., sp. nov., a phototrophic alphaproteobacterium isolated from paddy soil.Okamura K, Hisada T, Kanbe T, Hiraishi AJ Gen Appl Microbiol10.2323/jgam.55.432009Acetobacteraceae/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Bacteriochlorophyll A/metabolism, Base Composition, DNA, Bacterial/analysis/genetics, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, *Geologic Sediments, Japan, Molecular Sequence Data, *Phototrophic Processes, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity, Xanthophylls/metabolismMetabolism
Phylogeny31355740Acidibrevibacterium fodinaquatile gen. nov., sp. nov., isolated from acidic mine drainage.Muhadesi JB, Huang Y, Wang BJ, Jiang CY, Liu SJInt J Syst Evol Microbiol10.1099/ijsem.0.0036182019Acetobacteraceae/*classification/isolation & purification, Acids, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6239Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16009)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16009
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
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
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
69751Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100464.1StrainInfo: A central database for resolving microbial strain identifiers