Strain identifier
BacDive ID: 130138
Type strain:
Species: Acidithiobacillus ferridurans
Strain Designation: 11Fe
Strain history: D. B. Johnson <-- V. Bonnefoy <-- D. E. Rawlings <-- ATCC 33020 <-- H. M. Tsuchiya <-- N. Tomizuka 11Fe.
NCBI tax ID(s): 1232575 (species)
General
@ref: 21446
BacDive-ID: 130138
DSM-Number: 29468
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped
description: Acidithiobacillus ferridurans 11Fe is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from ore, uranium mine.
NCBI tax id
- NCBI tax id: 1232575
- Matching level: species
strain history
@ref | history |
---|---|
21446 | <- T. Itoh, JCM <- D. B. Johnson <- V. Bonnefoy <- D. E. Rawlings <- ATCC; ATCC 33020 |
67770 | D. B. Johnson <-- V. Bonnefoy <-- D. E. Rawlings <-- ATCC 33020 <-- H. M. Tsuchiya <-- N. Tomizuka 11Fe. |
doi: 10.13145/bacdive130138.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Acidithiobacillia
- order: Acidithiobacillales
- family: Acidithiobacillaceae
- genus: Acidithiobacillus
- species: Acidithiobacillus ferridurans
- full scientific name: Acidithiobacillus ferridurans Hedrich and Johnson 2013
@ref: 21446
domain: Bacteria
phylum: Proteobacteria
class: Acidithiobacillia
order: Acidithiobacillales
family: Acidithiobacillaceae
genus: Acidithiobacillus
species: Acidithiobacillus ferridurans
full scientific name: Acidithiobacillus ferridurans Hedrich and Johnson 2013
strain designation: 11Fe
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | confidence |
---|---|---|---|---|---|
31013 | negative | 1.5 µm | 1.5 µm | rod-shaped | |
69480 | negative | 100 |
colony morphology
- @ref: 21446
- incubation period: 3-7 days
pigmentation
- @ref: 31013
- production: yes
Culture and growth conditions
culture medium
- @ref: 21446
- name: LEPTOSPIRILLUM (HH) MEDIUM (DSMZ Medium 882)
- growth: yes
- link: https://mediadive.dsmz.de/medium/882
- composition: Name: LEPTOSPIRILLUM (HH) MEDIUM (DSMZ Medium 882) Composition: FeSO4 x 7 H2O 19.98 g/l CaCl2 x 2 H2O 0.146853 g/l (NH4)2SO4 0.131868 g/l MgCl2 x 6 H2O 0.0529471 g/l KH2PO4 0.0269731 g/l MnCl2 x 4 H2O 7.59241e-05 g/l ZnCl2 6.79321e-05 g/l CuCl2 x 2 H2O 6.69331e-05 g/l CoCl2 x 6 H2O 6.39361e-05 g/l H3BO3 3.0969e-05 g/l Na2MoO4 9.99001e-06 g/l H2SO4 Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
21446 | positive | growth | 30 | mesophilic |
31013 | positive | optimum | 29 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 31013
- ability: positive
- type: optimum
- pH: 2.1
- PH range: acidophile
Physiology and metabolism
oxygen tolerance
- @ref: 31013
- oxygen tolerance: facultative anaerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
31013 | no | |
69481 | no | 99 |
69480 | no | 99.999 |
observation
- @ref: 67770
- observation: quinones: Q-8
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
21446 | ore, uranium mine | Okayama prefecture, Ningyo-toge mine | Japan | JPN | Asia |
67770 | Ore from Ningyo-toge mine | Okayama | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Other | #Mine |
#Environmental | #Terrestrial | #Geologic |
taxonmaps
- @ref: 69479
- File name: preview.99_16623.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_163;96_544;97_628;98_885;99_16623&stattab=map
- Last taxonomy: Acidithiobacillus
- 16S sequence: FN686779
- Sequence Identity:
- Total samples: 73
- soil counts: 4
- aquatic counts: 68
- animal counts: 1
Safety information
risk assessment
- @ref: 21446
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
31013 | Acidithiobacillus ferrooxidans partial 16S rRNA gene, strain ATCC33020 | FN686779 | 1407 | nuccore | 1232575 |
21446 | Acidithiobacillus ferrooxidans 16S partial 16S rRNA gene, strain ATCC33020 | AJ278719 | 1408 | ena | 1232575 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Acidithiobacillus ferridurans JCM 18981 | GCA_003966655 | complete | ncbi | 1232575 |
66792 | Acidithiobacillus ferridurans ATCC 33020 | GCA_018854555 | contig | ncbi | 1232575 |
66792 | Acidithiobacillus ferridurans strain ATCC 33020 | 1232575.20 | wgs | patric | 1232575 |
66792 | Acidithiobacillus ferridurans strain ATCC 33020 | 1232575.4 | plasmid | patric | 1232575 |
66792 | Acidithiobacillus ferridurans strain JCM 18981 | 1232575.7 | complete | patric | 1232575 |
66792 | Acidithiobacillus ferrooxidans JCM 18981 | 2824077352 | complete | img | 920 |
GC content
@ref | GC-content | method |
---|---|---|
31013 | 58 | |
21446 | 58 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 99 | no |
motile | no | 78.147 | no |
flagellated | no | 97.987 | no |
gram-positive | no | 97.993 | yes |
anaerobic | no | 96.019 | yes |
aerobic | no | 84.491 | yes |
halophile | no | 85.646 | no |
spore-forming | no | 94.577 | no |
glucose-util | yes | 50.742 | no |
thermophile | no | 97.753 | no |
glucose-ferment | no | 86.136 | no |
External links
@ref: 21446
culture collection no.: DSM 29468, ATCC 33020, JCM 18981
straininfo link
- @ref: 88692
- straininfo: 40282
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23710060 | Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium. | Hedrich S, Johnson DB | Int J Syst Evol Microbiol | 10.1099/ijs.0.049759-0 | 2013 | Acidithiobacillus/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, Chemoautotrophic Growth, Fatty Acids/chemistry, Genes, Bacterial, Hydrogen/*metabolism, Iron/*metabolism, Molecular Sequence Data, Multilocus Sequence Typing, Nucleic Acid Hybridization, Oxidation-Reduction, Sulfur/*metabolism, Ubiquinone/chemistry | Metabolism |
Genetics | 30533903 | Complete Genome Sequence of Acidithiobacillus ferridurans JCM 18981. | Miyauchi T, Kouzuma A, Abe T, Watanabe K | Microbiol Resour Announc | 10.1128/MRA.01028-18 | 2018 |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
21446 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-29468 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29468) | |||
31013 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 27343 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
69479 | João 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
88692 | Reimer, 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 identifiers | 10.60712/SI-ID40282.1 |