Strain identifier

BacDive ID: 125

Type strain: Yes

Species: Acidithiobacillus thiooxidans

Strain Designation: 3/TA

Strain history: CIP <- 1995, NCIMB <- K.R. Butlin: strain 3/TA

NCBI tax ID(s): 637390 (strain), 930 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 5601

BacDive-ID: 125

DSM-Number: 14887

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, motile

description: Acidithiobacillus thiooxidans 3/TA is a mesophilic, motile bacterium that was isolated from Kimmeridge clay.

NCBI tax id

NCBI tax idMatching level
637390strain
930species

strain history

@refhistory
5601<- ATCC <- NCIMB <- K. R. Butlin, Chemical Research Laboratory, Department of Scientific and Industrial Research, Teddington, Middlesex, UK; 3/TA {1930}
67770Y. Katayama THI142 <-- IAM 12134.
123524CIP <- 1995, NCIMB <- K.R. Butlin: strain 3/TA

doi: 10.13145/bacdive125.20230509.8.1

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 thiooxidans
  • full scientific name: Acidithiobacillus thiooxidans (Waksman and Joffe 1922) Kelly and Wood 2000
  • synonyms

    @refsynonym
    20215Acidithiobacillus concretivorus
    20215Thiobacillus concretivorus
    20215Thiobacillus thiooxidans

@ref: 5601

domain: Bacteria

phylum: Proteobacteria

class: Acidithiobacillia

order: Acidithiobacillales

family: Acidithiobacillaceae

genus: Acidithiobacillus

species: Acidithiobacillus thiooxidans

full scientific name: Acidithiobacillus thiooxidans (Waksman and Joffe 1922) Kelly and Wood 2000

strain designation: 3/TA

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes91.423
6948099.998negative
123524yesnegativerod-shaped

colony morphology

  • @ref: 5601
  • incubation period: 3-7 days

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5601ACIDITHIOBACILLUS THIOOXIDANS MEDIUM (DSMZ Medium 71)yeshttps://mediadive.dsmz.de/medium/71Name: ACIDITHIOBACILLUS THIOOXIDANS MEDIUM (DSMZ Medium 71) Composition: Na2S2O3 x 5 H2O 5.0 g/l (NH4)2SO4 3.0 g/l KH2PO4 3.0 g/l MgSO4 x 7 H2O 0.5 g/l CaCl2 x 2 H2O 0.25 g/l Distilled water
35699MEDIUM 124 - for ThiobacillusyesDistilled water make up to (1000.000 ml);ManganeseII chloride tetrahydrate(2.000 mg);Magnesium sulphate heptahydrate (0.100 g);Calcium chloride dihydrate (0.100 g);Agar (12.000 g);Ammonium sulphate (0.100 g);Potassium di-hydrogen phosphate (4.000 g);Sodiu
123524CIP Medium 124yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=124
123524CIP Medium 249yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=249

culture temp

@refgrowthtypetemperaturerange
5601positivegrowth25mesophilic
35699positivegrowth25mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1235244853esculin-hydrolysis
12352417632nitrate-reduction
12352416301nitrite-reduction

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase-3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)-
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
123524oxidase-
123524beta-galactosidase-3.2.1.23
123524alcohol dehydrogenase-1.1.1.1
123524gelatinase-
123524catalase-1.11.1.6
123524lysine decarboxylase-4.1.1.18
123524ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123524--+-------++--------

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
5601Kimmeridge clayUnited KingdomGBREurope
67770Kimmeridge clayUnited KingdomGBREurope
123524Kimmeridge clay

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Geologic

taxonmaps

  • @ref: 69479
  • File name: preview.99_922.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_163;96_544;97_628;98_726;99_922&stattab=map
  • Last taxonomy: Acidithiobacillus
  • 16S sequence: Y11596
  • Sequence Identity:
  • Total samples: 1758
  • soil counts: 228
  • aquatic counts: 1330
  • animal counts: 187
  • plant counts: 13

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
56011Risk group (German classification)
1235241Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Acidithiobacillus thiooxidans gene, 16S-23S rDNA region, strain: JCM 3867AB189141456ena930
20218Acidithiobacillus thiooxidans strain ATCC 19377 16S ribosomal RNA gene, partial sequence; intergenic spacer, tRNA-Ile (trnI) and tRNA-Ala (trnA) genes, complete sequence; and 23S ribosomal RNA gene, partial sequenceAF512812514ena637390
20218Acidithiobacillus thiooxidans 16S rRNA gene, strain ATCC 19377AJ4598031434ena637390
20218Acidithiobacillus thiooxidans strain ATCC 19377 16S ribosomal RNA gene, partial sequenceAY5520871485ena637390
20218Acidithiobacillus thiooxidans strain ATCC 19377 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequenceEF059790632ena637390
20218Thiobacillus thiooxidans 16S rRNA sequenceM79397355ena930
20218Thiobacillus thiooxidans 16S rRNA sequenceM79398406ena930
5601Acidithiobacillus thiooxidans 16S rRNA gene, type strain ATCC19377Y115961472ena930

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Acidithiobacillus thiooxidans ATCC 19377GCA_009662475completencbi637390
66792Acidithiobacillus thiooxidans ATCC 19377637390.18wgspatric637390
66792Acidithiobacillus thiooxidans ATCC 19377637390.5wgspatric637390
66792Acidithiobacillus thiooxidans ATCC 19377637390.19completepatric637390
66792Acidithiobacillus thiooxidans ATCC 193772510461056draftimg637390
67770Acidithiobacillus thiooxidans ATCC 19377GCA_000227215contigncbi637390
67770Acidithiobacillus thiooxidans ATCC 19377GCA_006718285scaffoldncbi637390

GC content

@refGC-contentmethod
560152.1
6777052thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes87.215no
flagellatedno84.409no
gram-positiveno98.262no
anaerobicno96.347no
aerobicno72.497no
halophileno84.593no
spore-formingno93.843no
glucose-utilyes66.925no
thermophileno91.83yes
glucose-fermentno82.628no

External links

@ref: 5601

culture collection no.: DSM 14887, ATCC 19377, JCM 3867, NCIMB 8343, CIP 104597, IAM 12134

straininfo link

  • @ref: 69808
  • straininfo: 45621

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11054160Physiology and taxonomy of thiobacillus strain TJ330, which oxidizes carbon disulphide (CS2).Hartikainen T, Ruuskanen J, Raty K, Von Wright A, Martikainen PJJ Appl Microbiol10.1046/j.1365-2672.2000.01150.x2000Carbon Disulfide/*metabolism, Culture Media, DNA, Bacterial/analysis, Hydrogen-Ion Concentration, Oxidation-Reduction, Temperature, Thiobacillus/classification/genetics/growth & development/*physiologyCultivation
Phylogeny15313256Differentiation of Acidithiobacillus ferrooxidans and A. thiooxidans strains based on 16S-23S rDNA spacer polymorphism analysis.Bergamo RF, Novo MT, Verissimo RV, Paulino LC, Stoppe NC, Sato MI, Manfio GP, Prado PI, Garcia O Jr, Ottoboni LMRes Microbiol10.1016/j.resmic.2004.03.0092004Bacterial Typing Techniques, DNA, Ribosomal/*analysis/genetics, DNA, Ribosomal Spacer/*analysis/genetics, Gammaproteobacteria/*classification/genetics/isolation & purification, Phylogeny, Polymerase Chain Reaction, Polymorphism, Restriction Fragment Length, RNA, Ribosomal, 23S/genetics, *Ribotyping, Sequence Analysis, DNA, Sequence Homology, Nucleic AcidTranscriptome
Enzymology15676194Detection of Acidithiobacillus ferrooxidans in acid mine drainage environments using fluorescent in situ hybridization (FISH).Mahmoud KK, Leduc LG, Ferroni GDJ Microbiol Methods10.1016/j.mimet.2004.10.0222005Acidithiobacillus/genetics/*isolation & purification, DNA, Bacterial/genetics, Image Processing, Computer-Assisted, In Situ Hybridization, Fluorescence/*methods, *Industrial Waste, Microscopy, Fluorescence, *Mining, *Water Pollutants, ChemicalPhylogeny
Genetics22123759Draft genome sequence of the extremely acidophilic biomining bacterium Acidithiobacillus thiooxidans ATCC 19377 provides insights into the evolution of the Acidithiobacillus genus.Valdes J, Ossandon F, Quatrini R, Dopson M, Holmes DSJ Bacteriol10.1128/JB.06281-112011Acidithiobacillus/genetics/metabolism, Acidithiobacillus thiooxidans/*genetics/metabolism, Acids/*metabolism, Base Sequence, *Evolution, Molecular, *Genome, Bacterial, Mining, Molecular Sequence Data, Sulfur/metabolismMetabolism
Enzymology24797809A versatile and efficient markerless gene disruption system for Acidithiobacillus thiooxidans: application for characterizing a copper tolerance related multicopper oxidase gene.Wen Q, Liu X, Wang H, Lin JEnviron Microbiol10.1111/1462-2920.124942014Acidithiobacillus thiooxidans/drug effects/enzymology/*genetics, Copper/*toxicity, *Gene Knockout Techniques, Molecular Sequence Data, Monophenol Monooxygenase/metabolism, Mutation, Oxidoreductases/*genetics, beta-Galactosidase/geneticsGenetics
Genetics25148779A new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment.Travisany D, Cortes MP, Latorre M, Di Genova A, Budinich M, Bobadilla-Fazzini RA, Parada P, Gonzalez M, Maass ARes Microbiol10.1016/j.resmic.2014.08.0042014Acidithiobacillus thiooxidans/*genetics/isolation & purification/physiology, Adaptation, Biological, DNA, Bacterial/*chemistry/*genetics, Drug Tolerance, Environmental Microbiology, Genes, Bacterial, *Genome, Bacterial, Industrial Microbiology, Interspersed Repetitive Sequences, Metabolic Networks and Pathways, Metals/toxicity, Molecular Sequence Data, *Sequence Analysis, DNA, Sequence Homology, Nucleic AcidBiotechnology
Metabolism32231653New Insights Into Acidithiobacillus thiooxidans Sulfur Metabolism Through Coupled Gene Expression, Solution Chemistry, Microscopy, and Spectroscopy Analyses.Camacho D, Frazao R, Fouillen A, Nanci A, Lang BF, Apte SC, Baron C, Warren LAFront Microbiol10.3389/fmicb.2020.004112020
33472156Bioaugmentation with Acidithiobacillus species accelerates mineral weathering and formation of secondary mineral cements for hardpan development in sulfidic Pb-Zn tailings.Liu Y, Wu S, Southam G, Chan TS, Lu YR, Paterson DJ, Huang LJ Hazard Mater10.1016/j.jhazmat.2020.1249882021
34745076Sticky Bacteria: Understanding the Behavior of a D-Galactose Adapted Consortium of Acidophilic Chemolithotroph Bacteria and Their Attachment on a Concentrate of Polymetallic Mineral.Aguirre P, Saavedra A, Moncayo E, Hedrich S, Guerrero K, Gentina JCFront Microbiol10.3389/fmicb.2021.7676392021
Metabolism35962820Organic layer characteristics and microbial utilization of the biosulfur globules produced by haloalkaliphilic Thioalkalivibrio versutus D301 during biological desulfurization.Liu Z, Yang M, Mu T, Liu J, Chen L, Miao D, Xing JExtremophiles10.1007/s00792-022-01274-z2022*Ectothiorhodospiraceae/metabolism, Oxidation-Reduction, Sulfur/metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
5601Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14887)https://www.dsmz.de/collection/catalogue/details/culture/DSM-14887
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
35699Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16523
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/
68382Automatically annotated from API zym
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)
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
69808Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID45621.1StrainInfo: A central database for resolving microbial strain identifiers
123524Curators of the CIPCollection of Institut Pasteur (CIP 104597)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104597