Strain identifier

BacDive ID: 4303

Type strain: Yes

Species: Acidiferrobacter thiooxydans

Strain Designation: m-1

Strain history: D. B. Johnson <-- DSM 2392 <-- A. P. Harrison, Jr. strain m-1 <-- B. Jarvis.

NCBI tax ID(s): 163359 (species)

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General

@ref: 1071

BacDive-ID: 4303

DSM-Number: 2392

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Acidiferrobacter thiooxydans m-1 is a mesophilic, Gram-negative bacterium that was isolated from coal strip mine refuse.

NCBI tax id

  • NCBI tax id: 163359
  • Matching level: species

strain history

@refhistory
1071<- Harrison, A. P., Jr, Univ. Missouri, USA; m-1 <- B. Jarvis
67770D. B. Johnson <-- DSM 2392 <-- A. P. Harrison, Jr. strain m-1 <-- B. Jarvis.

doi: 10.13145/bacdive4303.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Acidiferrobacterales
  • family: Acidiferrobacteraceae
  • genus: Acidiferrobacter
  • species: Acidiferrobacter thiooxydans
  • full scientific name: Acidiferrobacter thiooxydans Hallberg et al. 2011

@ref: 1071

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Chromatiales

family: Acidiferrobacteraceae

genus: Acidiferrobacter

species: Acidiferrobacter thiooxydans

full scientific name: Acidiferrobacter thiooxydans Hallberg et al. 2011

strain designation: m-1

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.999

colony morphology

  • @ref: 1071
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

  • @ref: 1071
  • name: ACIDIFERROBACTER (MS) MEDIUM (DSMZ Medium 670)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/670
  • composition: Name: ACIDIFERROBACTER (MS) MEDIUM (DSMZ Medium 670) Composition: FeSO4 x 7 H2O 20.0 g/l (NH4)2SO4 2.0 g/l MgSO4 x 7 H2O 0.25 g/l K2HPO4 0.1 g/l KCl 0.1 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
1071positivegrowth30mesophilic
67770positivegrowth37mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
1071coal strip mine refuseMississipi, Calloway countyUSAUSANorth America
67770Forty-year-old coal refuse, Bevier coal seamCalloway county, MOUSAUSANorth America

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Engineered#Waste#Solid waste
#Environmental#Terrestrial#Geologic

Safety information

risk assessment

  • @ref: 1071
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Acidiferrobacter thiooxydans partial 16S rRNA gene, type strain DSM 2392TAJ4598001329ena163359
20218Thiobacillus ferrooxidans (DSM 2392) 16S rRNA sequenceM79416736ena920
20218Thiobacillus ferrooxidans (DSM 2392) 16S rRNA sequenceM79417354ena920
1071Acidiferrobacter thiooxydans strain m-1 16S ribosomal RNA gene, partial sequenceAF3873011475ena163359

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidiferrobacter thiooxydans strain m-1163359.15wgspatric163359
67770Acidiferrobacter thiooxydans m-1GCA_003333315contigncbi163359

GC content

@refGC-contentmethod
107163.1±0.4
107165.0
6777063.1thermal denaturation, midpoint method (Tm)
6777065thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno70.416no
gram-positiveno97.838no
anaerobicno93.269no
aerobicno90.28no
halophileno90.656no
spore-formingno92.6no
glucose-utilyes53.194no
flagellatedno94.01no
thermophileno93.314yes
glucose-fermentno84.449no

External links

@ref: 1071

culture collection no.: DSM 2392, JCM 17358

straininfo link

  • @ref: 73795
  • straininfo: 47609

literature

  • topic: Phylogeny
  • Pubmed-ID: 21311931
  • title: Acidiferrobacter thiooxydans, gen. nov. sp. nov.; an acidophilic, thermo-tolerant, facultatively anaerobic iron- and sulfur-oxidizer of the family Ectothiorhodospiraceae.
  • authors: Hallberg KB, Hedrich S, Johnson DB
  • journal: Extremophiles
  • DOI: 10.1007/s00792-011-0359-2
  • year: 2011
  • mesh: Carbon/chemistry, Culture Media/chemistry, Ectothiorhodospiraceae/*enzymology/*genetics, Hydrogen-Ion Concentration, Iron/*chemistry, Metals/chemistry, Nitrogen/chemistry, Nitrogen Fixation, Osmosis, Phylogeny, Seawater, Species Specificity, Sulfur/*chemistry, Temperature
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
1071Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 2392)https://www.dsmz.de/collection/catalogue/details/culture/DSM-2392
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
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
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
73795Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID47609.1StrainInfo: A central database for resolving microbial strain identifiers