Strain identifier

BacDive ID: 108

Type strain: Yes

Species: Ferrimicrobium acidiphilum

Strain Designation: T23

Strain history: <- D. B. Johnson, School Biol. Sci., Bangor Univ., United Kingdom; T23 <- D. B. Johnson {1991}

NCBI tax ID(s): 1121877 (strain), 121039 (species)

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General

@ref: 8120

BacDive-ID: 108

DSM-Number: 19497

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

description: Ferrimicrobium acidiphilum T23 is a mesophilic, Gram-negative, motile bacterium that was isolated from pyrite enrichment cultures inoculated with mine water .

NCBI tax id

NCBI tax idMatching level
121039species
1121877strain

strain history

  • @ref: 8120
  • history: <- D. B. Johnson, School Biol. Sci., Bangor Univ., United Kingdom; T23 <- D. B. Johnson {1991}

doi: 10.13145/bacdive108.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Acidimicrobiia
  • order: Acidimicrobiales
  • family: Acidimicrobiaceae
  • genus: Ferrimicrobium
  • species: Ferrimicrobium acidiphilum
  • full scientific name: Ferrimicrobium acidiphilum Johnson et al. 2009

  • synonyms

    • @ref: 20215
    • synonym: Ferromicrobium acidophilus

@ref: 8120

domain: Bacteria

phylum: Actinobacteria

class: Acidimicrobiia

order: Acidimicrobiales

family: Acidimicrobiaceae

genus: Ferrimicrobium

species: Ferrimicrobium acidiphilum

full scientific name: Ferrimicrobium acidiphilum Johnson et al. 2009

strain designation: T23

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
22969negative1.0-3.0 µm0.5 µmrod-shapedyes
69480negative99.534

colony morphology

  • @ref: 22969
  • colony size: 1.0-3.0 mm
  • medium used: Feo solid medium

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8120FERROUS SULFATE/YEAST EXTRACT MEDIUM (DSMZ Medium 1190)yeshttps://mediadive.dsmz.de/medium/1190Name: FERROUS SULFATE/YEAST EXTRACT MEDIUM (DSMZ Medium 1190) Composition: FeSO4 x 7 H2O 5.56 g/l MgSO4 x 7 H2O 0.5 g/l (NH4)2SO4 0.45 g/l Yeast extract 0.2 g/l Na2SO4 x 10 H2O 0.15 g/l KH2PO4 0.05 g/l KCl 0.05 g/l Ca(NO3)2 x 4 H2O 0.014 g/l Distilled water
22969Feo solid mediumyes

culture temp

@refgrowthtypetemperaturerange
8120positivegrowth32mesophilic
22969nogrowth>37.0
22969positiveoptimum35.0

culture pH

@refabilitytypepHPH range
22969positiveoptimum2.0acidophile
22969positiveminimum1.4

Physiology and metabolism

spore formation

@refspore formationconfidence
22969no
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2296933403elemental sulfur-oxidation
2296917754glycerol+carbon source
2296917754glycerol+electron donor
2296917754glycerol+energy source
2296916947citrate+growth
2296929987glutamate+growth
2296917754glycerol+growth
22969yeast extract+growth
2296918248iron+oxidation
2296986471pyrite+oxidation

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentenrichment cultureenrichment culture compositionenrichment culture temperature
8120pyrite enrichment cultures inoculated with mine water (pH 2.0 - 3.0)
8120mine waterNorth Wales, abandoned Cae Coch sulfur mineUnited KingdomGBREurope
22969sulfur minesolid mediaferrous iron,ferrous iron,tryptone soya broth,potassium tetrathionate30.0

isolation source categories

Cat1Cat2Cat3
#Engineered#Laboratory#Lab enrichment
#Environmental#Aquatic
#Condition#Acidic
#Engineered#Other#Mine
#Condition#Sulfuric

taxonmaps

  • @ref: 69479
  • File name: preview.99_6387.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_568;96_3028;97_3721;98_4719;99_6387&stattab=map
  • Last taxonomy: Ferrimicrobium acidiphilum subclade
  • 16S sequence: AF251436
  • Sequence Identity:
  • Total samples: 2086
  • soil counts: 565
  • aquatic counts: 948
  • animal counts: 527
  • plant counts: 46

Safety information

risk assessment

  • @ref: 8120
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 8120
  • description: Ferrimicrobium acidiphilum strain T23 16S ribosomal RNA gene, partial sequence
  • accession: AF251436
  • length: 1466
  • database: ena
  • NCBI tax ID: 121039

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Ferrimicrobium acidiphilum DSM 19497GCA_000745905scaffoldncbi1121877
66792Ferrimicrobium acidiphilum DSM 19497 T23GCA_000949255contigncbi1121877
66792Ferrimicrobium acidiphilum DSM 194971121877.3wgspatric1121877
66792Ferrimicrobium acidiphilum DSM 19497 strain T231121877.6wgspatric1121877
66792Ferrimicrobium acidiphilum DSM 194972571042004draftimg1121877
66792Ferrimicrobium acidiphilum DSM 194972585428130draftimg1121877

GC content

@refGC-contentmethod
812054.9±0.3thermal denaturation, midpoint method (Tm)
2296954.6-55.2thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno79no
motileyes76.838yes
flagellatedno94.029no
gram-positiveyes52.416yes
anaerobicno96.064no
aerobicyes87.791no
halophileno94.97no
spore-formingno92.429yes
thermophileno52.868yes
glucose-utilyes84.768no
glucose-fermentno80.348no

External links

@ref: 8120

culture collection no.: DSM 19497, ATCC BAA 1647, DSM 11138

straininfo link

@refstraininfo
69790405480
69791412342

literature

  • topic: Phylogeny
  • Pubmed-ID: 19406797
  • title: Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteria.
  • authors: Johnson DB, Bacelar-Nicolau P, Okibe N, Thomas A, Hallberg KB
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65409-0
  • year: 2009
  • mesh: Actinobacteria/*classification/genetics/isolation & purification/physiology, Bacterial Typing Techniques, Culture Media, DNA, Bacterial/analysis, Fresh Water/microbiology, *Heterotrophic Processes, Hot Springs/microbiology, Hydrogen-Ion Concentration, Iron/*metabolism, Mining, Molecular Sequence Data, Oxidation-Reduction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Species Specificity, Sulfur, Wales, Wyoming
  • topic2: Cultivation

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
8120Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19497)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19497
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
22969D. Barrie Johnson,Paula Bacelar-Nicolau,Naoko Okibe,Angharad Thomas,Kevin B. Hallberg10.1099/ijs.0.65409-0Ferrimicrobium acidiphilum gen. nov., sp. nov. and Ferrithrix thermotolerans gen. nov., sp. nov.: heterotrophic, iron-oxidizing, extremely acidophilic actinobacteriaIJSEM 59: 1082-1089 200919406797
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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)
69790Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID405480.1StrainInfo: A central database for resolving microbial strain identifiers
69791Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID412342.1StrainInfo: A central database for resolving microbial strain identifiers