Strain identifier
BacDive ID: 67
Type strain: 
Species: Acidisphaera rubrifaciens
Strain Designation: HS-AP3
Strain history: A. Hiraishi HS-AP3.
NCBI tax ID(s): 50715 (species)
version 6 (current version)
General
@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
LPSN
- @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
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
| @ref | production | name |
|---|---|---|
| 23249 | yes | Spirilloxanthin |
| 23249 | yes | carotenoids |
| 23249 | yes | Bacteriochlorophyll a |
Culture and growth conditions
culture medium
- @ref: 6239
- name: GNYS MEDIUM (DSMZ Medium 1119)
- growth: yes
- link: https://bacmedia.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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 6239 | positive | growth | 30 | mesophilic |
| 23249 | positive | growth | 20-40 | |
| 23249 | positive | optimum | 30-35 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
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
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 23249 | 30089 | acetate | - | carbon source |
| 23249 | 16150 | benzoate | - | carbon source |
| 23249 | 28885 | butanol | - | carbon source |
| 23249 | 17968 | butyrate | - | carbon source |
| 23249 | casamino acids | - | carbon source | |
| 23249 | 16947 | citrate | - | carbon source |
| 23249 | 16236 | ethanol | - | carbon source |
| 23249 | 15740 | formate | - | carbon source |
| 23249 | 28757 | fructose | - | carbon source |
| 23249 | 17268 | myo-inositol | - | carbon source |
| 23249 | 30849 | L-arabinose | - | carbon source |
| 23249 | 17716 | lactose | - | carbon source |
| 23249 | 37684 | mannose | - | carbon source |
| 23249 | 17790 | methanol | - | carbon source |
| 23249 | peptone | - | carbon source | |
| 23249 | 28831 | propanol | - | carbon source |
| 23249 | 17272 | propionate | - | carbon source |
| 23249 | 17992 | sucrose | - | carbon source |
| 23249 | casein | - | hydrolysis | |
| 23249 | 28017 | starch | - | hydrolysis |
| 23249 | 53426 | tween 80 | - | hydrolysis |
| 23249 | 17632 | nitrate | - | reduction |
| 23249 | 65327 | D-xylose | + | carbon source |
| 23249 | 29806 | fumarate | + | carbon source |
| 23249 | 28260 | galactose | + | carbon source |
| 23249 | 24265 | gluconate | + | carbon source |
| 23249 | 17234 | glucose | + | carbon source |
| 23249 | 17754 | glycerol | + | carbon source |
| 23249 | 24996 | lactate | + | carbon source |
| 23249 | 25115 | malate | + | carbon source |
| 23249 | 29864 | mannitol | + | carbon source |
| 23249 | 15361 | pyruvate | + | carbon source |
| 23249 | 30911 | sorbitol | + | carbon source |
| 23249 | 30031 | succinate | + | carbon source |
| 23249 | yeast extract | + | carbon source |
metabolite production
| @ref | Chebi-ID | metabolite | production |
|---|---|---|---|
| 67770 | 30033 | bacteriochlorophyll a | yes |
| 67770 | 23044 | carotenoid | yes |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 6239 | surface water and sediment from an acidic hot spring | Kanagawa Prefecture, Hakone | Japan | JPN | Asia |
| 67770 | Hot spring water | Hakone, Kanagawa Pref. | Japan | JPN | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Aquatic | #Surface water |
| #Environmental | #Aquatic | #Thermal spring |
| #Condition | #Acidic |
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
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Acidisphaera rubrifaciens HS-AP3 HS-AP3 | GCA_000964365 | scaffold | ncbi | 1231350 |
| 66792 | Acidisphaera rubrifaciens HS-AP3 | 1231350.12 | wgs | patric | 1231350 |
| 67770 | Acidisphaera rubrifaciens HS-AP3, whole genome shotgun sequencing project | BANB00000000 | ncbi | 1231350 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 23249 | 69.1-69.8 | high performance liquid chromatography (HPLC) |
| 67770 | 69.3 | high performance liquid chromatography (HPLC) |
External links
@ref: 6239
culture collection no.: DSM 16009, JCM 10600
straininfo link
| @ref | passport |
|---|---|
| 20218 | http://www.straininfo.net/strains/692079 |
| 20218 | http://www.straininfo.net/strains/301705 |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 6239 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16009) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16009 | |||
| 20215 | D.Gleim, M.Kracht, N.Weiss et. al. | http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date.html | Prokaryotic 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 23249 | A Hiraishi, Y Matsuzawa, T Kanbe, N Wakao | 10.1099/00207713-50-4-1539 | Acidisphaera rubrifaciens gen. nov., sp. nov., an aerobic bacteriochlorophyll-containing bacterium isolated from acidic environments. | IJSEM 50: 1539-1546 2000 | 10939661 | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ |