Strain identifier

BacDive ID: 106

Type strain: Yes

Species: Acidimicrobium ferrooxidans

Strain Designation: ICP

Strain history: NBRC 103882 <-- DSM 10331 <-- P. R. Norris strain ICP.

NCBI tax ID(s): 525909 (strain), 53635 (species)

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General

@ref: 3908

BacDive-ID: 106

DSM-Number: 10331

keywords: genome sequence, 16S sequence, Bacteria, autotroph, thermophilic, Gram-positive, motile, rod-shaped

description: Acidimicrobium ferrooxidans ICP is an autotroph, thermophilic, Gram-positive bacterium that was isolated from hot spring run-off.

NCBI tax id

NCBI tax idMatching level
53635species
525909strain

strain history

@refhistory
3908<- P. R. Norris; ICP <- P. R. Norris {1993}
67770NBRC 103882 <-- DSM 10331 <-- P. R. Norris strain ICP.

doi: 10.13145/bacdive106.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Acidimicrobiia
  • order: Acidimicrobiales
  • family: Acidimicrobiaceae
  • genus: Acidimicrobium
  • species: Acidimicrobium ferrooxidans
  • full scientific name: Acidimicrobium ferrooxidans Clark and Norris 1996

@ref: 3908

domain: Bacteria

phylum: Actinobacteria

class: Acidimicrobiia

order: Acidimicrobiales

family: Acidimicrobiaceae

genus: Acidimicrobium

species: Acidimicrobium ferrooxidans

full scientific name: Acidimicrobium ferrooxidans Clark and Norris 1996 emend. Nouioui et al. 2018

strain designation: ICP

type strain: yes

Morphology

cell morphology

  • @ref: 22968
  • gram stain: positive
  • cell length: 1.0-1.5 µm
  • cell width: 0.35-0.4 µm
  • cell shape: rod-shaped
  • motility: yes

multimedia

  • @ref: 66793
  • multimedia content: EM_DSM_10331_1.jpg
  • caption: electron microscopic image
  • intellectual property rights: © HZI/Manfred Rohde

Culture and growth conditions

culture medium

  • @ref: 3908
  • name: ACIDIMICROBIUM MEDIUM (DSMZ Medium 709)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/709
  • composition: Name: ACIDIMICROBIUM MEDIUM (DSMZ Medium 709) Composition: MgSO4 x 7 H2O 0.5 g/l (NH4)2SO4 0.4 g/l Yeast extract 0.25 g/l K2HPO4 0.2 g/l KCl 0.1 g/l FeSO4 x 7 H2O 0.01 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
3908positivegrowth45thermophilic
22968positiveoptimum45.0-50.0thermophilic
67770positivegrowth45thermophilic

culture pH

  • @ref: 22968
  • ability: positive
  • type: optimum
  • pH: 2.0
  • PH range: acidophile

Physiology and metabolism

nutrition type

@reftype
22968autotroph
22968heterotroph

spore formation

@refspore formationconfidence
69481no100
69480no99.994

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
3908hot spring run-offIcelandISLEurope
22968warm,acidic,iron-,sulphur-or mineral-sulphide-rich environments
67770Icelandic geothermal site

isolation source categories

Cat1Cat2Cat3
#Condition#Thermophilic (>45°C)
#Environmental#Aquatic#Thermal spring
#Condition#Acidic
#Condition#Sulfuric

Safety information

risk assessment

  • @ref: 3908
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Acidimicrobium ferrooxidans DSM 10331 16S ribosomal RNA gene, partial sequence
  • accession: U75647
  • length: 1465
  • database: ena
  • NCBI tax ID: 525909

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidimicrobium ferrooxidans DSM 10331GCA_000023265completencbi525909
66792Acidimicrobium ferrooxidans DSM 10331525909.11completepatric525909
66792Acidimicrobium ferrooxidans ICP, DSM 10331644736322completeimg525909
66792Acidimicrobium ferrooxidans DSM 10331 MH-08apr19-249GCA_945862375contigncbi525909
66792Acidimicrobium ferrooxidans DSM 10331 MsH-30jul19-148GCA_945865395contigncbi525909
66792Acidimicrobium ferrooxidans DSM 10331 MiH-22jul19-254GCA_945866315contigncbi525909
66792Acidimicrobium ferrooxidans DSM 10331 MiE-14oct19-144GCA_945882605contigncbi525909
66792Acidimicrobium ferrooxidans DSM 10331 MH-21oct19-73GCA_945887445contigncbi525909
66792Acidimicrobium ferrooxidans DSM 10331 MoE-23oct19-202GCA_945897875contigncbi525909
66792Acidimicrobium ferrooxidans DSM 10331 MsH-30apr19-324GCA_945900735contigncbi525909
66792Acidimicrobium ferrooxidans DSM 10331 strain MsH-30jul19-148525909.41wgspatric525909
66792Acidimicrobium ferrooxidans DSM 10331 strain MsH-30apr19-324525909.39wgspatric525909
66792Acidimicrobium ferrooxidans DSM 10331 strain MoE-23oct19-202525909.38wgspatric525909
66792Acidimicrobium ferrooxidans DSM 10331 strain MiH-22jul19-254525909.42wgspatric525909
66792Acidimicrobium ferrooxidans DSM 10331 strain MiE-14oct19-144525909.36wgspatric525909
66792Acidimicrobium ferrooxidans DSM 10331 strain MH-21oct19-73525909.37wgspatric525909
66792Acidimicrobium ferrooxidans DSM 10331 strain MH-08apr19-249525909.40wgspatric525909

GC content

@refGC-contentmethod
390867.3
2296867-68.5
6777068.29genome sequence analysis
6777067.3thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes77.461yes
flagellatedno95.431no
gram-positiveyes52.719no
anaerobicno94.578no
aerobicyes87.683no
halophileno94.733no
spore-formingno94.267no
thermophileyes84.774no
glucose-utilyes85.731no
glucose-fermentno77.305no

External links

@ref: 3908

culture collection no.: DSM 10331, NBRC 103882, JCM 15462

straininfo link

  • @ref: 69789
  • straininfo: 48814

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19329622Iamia majanohamensis gen. nov., sp. nov., an actinobacterium isolated from sea cucumber Holothuria edulis, and proposal of Iamiaceae fam. nov.Kurahashi M, Fukunaga Y, Sakiyama Y, Harayama S, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.005611-02009Actinobacteria/chemistry/*classification/genetics/*isolation & purification, Animals, Bacterial Typing Techniques, Base Composition, Carbohydrates/analysis, Cell Wall/chemistry, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Holothuria/*microbiology, Japan, Molecular Sequence Data, Peptidoglycan/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vitamin K 2/analysisGenetics
Phylogeny19590147Ilumatobacter fluminis gen. nov., sp. nov., a novel actinobacterium isolated from the sediment of an estuary.Matsumoto A, Kasai H, Matsuo Y, Omura S, Shizuri Y, Takahashi YJ Gen Appl Microbiol10.2323/jgam.55.2012009Actinobacteria/*classification/*cytology/physiology, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Geologic Sediments/*microbiology, Phylogeny, Rivers/*microbiology, Sequence Homology, *Water Microbiology

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
3908Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 10331)https://www.dsmz.de/collection/catalogue/details/culture/DSM-10331
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
22968Darren A. Clark,Paul R. Norris10.1099/00221287-142-4-785Acidimicrobium ferrooxidans gen. nov., sp. nov.: mixed-culture ferrous iron oxidation with Sulfobacillus speciesIJSEM 142: 785-790 199633725781
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)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life 35: 676-683 201728604660
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
69789Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID48814.1StrainInfo: A central database for resolving microbial strain identifiers