Strain identifier

BacDive ID: 130138

Type strain: Yes

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)

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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

@refhistory
21446<- T. Itoh, JCM <- D. B. Johnson <- V. Bonnefoy <- D. E. Rawlings <- ATCC; ATCC 33020
67770D. 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

@refgram staincell lengthcell widthcell shapeconfidence
31013negative1.5 µm1.5 µmrod-shaped
69480negative100

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

@refgrowthtypetemperaturerange
21446positivegrowth30mesophilic
31013positiveoptimum29mesophilic
67770positivegrowth30mesophilic

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

@refspore formationconfidence
31013no
69481no99
69480no99.999

observation

  • @ref: 67770
  • observation: quinones: Q-8

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
21446ore, uranium mineOkayama prefecture, Ningyo-toge mineJapanJPNAsia
67770Ore from Ningyo-toge mineOkayamaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
31013Acidithiobacillus ferrooxidans partial 16S rRNA gene, strain ATCC33020FN6867791407nuccore1232575
21446Acidithiobacillus ferrooxidans 16S partial 16S rRNA gene, strain ATCC33020AJ2787191408ena1232575

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidithiobacillus ferridurans JCM 18981GCA_003966655completencbi1232575
66792Acidithiobacillus ferridurans ATCC 33020GCA_018854555contigncbi1232575
66792Acidithiobacillus ferridurans strain ATCC 330201232575.20wgspatric1232575
66792Acidithiobacillus ferridurans strain ATCC 330201232575.4plasmidpatric1232575
66792Acidithiobacillus ferridurans strain JCM 189811232575.7completepatric1232575
66792Acidithiobacillus ferrooxidans JCM 189812824077352completeimg920

GC content

@refGC-contentmethod
3101358
2144658thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno78.147no
flagellatedno97.987no
gram-positiveno97.993yes
anaerobicno96.019yes
aerobicno84.491yes
halophileno85.646no
spore-formingno94.577no
glucose-utilyes50.742no
thermophileno97.753no
glucose-fermentno86.136no

External links

@ref: 21446

culture collection no.: DSM 29468, ATCC 33020, JCM 18981

straininfo link

  • @ref: 88692
  • straininfo: 40282

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23710060Acidithiobacillus ferridurans sp. nov., an acidophilic iron-, sulfur- and hydrogen-metabolizing chemolithotrophic gammaproteobacterium.Hedrich S, Johnson DBInt J Syst Evol Microbiol10.1099/ijs.0.049759-02013Acidithiobacillus/*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/chemistryMetabolism
Genetics30533903Complete Genome Sequence of Acidithiobacillus ferridurans JCM 18981.Miyauchi T, Kouzuma A, Abe T, Watanabe KMicrobiol Resour Announc10.1128/MRA.01028-182018

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
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
21446Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29468Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29468)
31013Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172734328776041
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
88692Reimer, 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-ID40282.1