Strain identifier
BacDive ID: 125
Type strain:
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)
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 id | Matching level |
---|---|
637390 | strain |
930 | species |
strain history
@ref | history |
---|---|
5601 | <- ATCC <- NCIMB <- K. R. Butlin, Chemical Research Laboratory, Department of Scientific and Industrial Research, Teddington, Middlesex, UK; 3/TA {1930} |
67770 | Y. Katayama THI142 <-- IAM 12134. |
123524 | CIP <- 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
@ref synonym 20215 Acidithiobacillus concretivorus 20215 Thiobacillus concretivorus 20215 Thiobacillus 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
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 91.423 | ||
69480 | 99.998 | negative | ||
123524 | yes | negative | rod-shaped |
colony morphology
- @ref: 5601
- incubation period: 3-7 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5601 | ACIDITHIOBACILLUS THIOOXIDANS MEDIUM (DSMZ Medium 71) | yes | https://mediadive.dsmz.de/medium/71 | Name: 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 |
35699 | MEDIUM 124 - for Thiobacillus | yes | Distilled 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 | |
123524 | CIP Medium 124 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=124 | |
123524 | CIP Medium 249 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=249 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5601 | positive | growth | 25 | mesophilic |
35699 | positive | growth | 25 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.998 |
observation
- @ref: 67770
- observation: quinones: Q-8
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
123524 | 4853 | esculin | - | hydrolysis |
123524 | 17632 | nitrate | - | reduction |
123524 | 16301 | nitrite | - | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | - | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | - | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | - | 3.1.3.1 |
123524 | oxidase | - | |
123524 | beta-galactosidase | - | 3.2.1.23 |
123524 | alcohol dehydrogenase | - | 1.1.1.1 |
123524 | gelatinase | - | |
123524 | catalase | - | 1.11.1.6 |
123524 | lysine decarboxylase | - | 4.1.1.18 |
123524 | ornithine decarboxylase | - | 4.1.1.17 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
123524 | - | - | + | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent |
---|---|---|---|---|
5601 | Kimmeridge clay | United Kingdom | GBR | Europe |
67770 | Kimmeridge clay | United Kingdom | GBR | Europe |
123524 | Kimmeridge 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
@ref | biosafety level | biosafety level comment |
---|---|---|
5601 | 1 | Risk group (German classification) |
123524 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Acidithiobacillus thiooxidans gene, 16S-23S rDNA region, strain: JCM 3867 | AB189141 | 456 | ena | 930 |
20218 | Acidithiobacillus 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 sequence | AF512812 | 514 | ena | 637390 |
20218 | Acidithiobacillus thiooxidans 16S rRNA gene, strain ATCC 19377 | AJ459803 | 1434 | ena | 637390 |
20218 | Acidithiobacillus thiooxidans strain ATCC 19377 16S ribosomal RNA gene, partial sequence | AY552087 | 1485 | ena | 637390 |
20218 | Acidithiobacillus thiooxidans strain ATCC 19377 16S ribosomal RNA gene, partial sequence; 16S-23S ribosomal RNA intergenic spacer, complete sequence; and 23S ribosomal RNA gene, partial sequence | EF059790 | 632 | ena | 637390 |
20218 | Thiobacillus thiooxidans 16S rRNA sequence | M79397 | 355 | ena | 930 |
20218 | Thiobacillus thiooxidans 16S rRNA sequence | M79398 | 406 | ena | 930 |
5601 | Acidithiobacillus thiooxidans 16S rRNA gene, type strain ATCC19377 | Y11596 | 1472 | ena | 930 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Acidithiobacillus thiooxidans ATCC 19377 | GCA_009662475 | complete | ncbi | 637390 |
66792 | Acidithiobacillus thiooxidans ATCC 19377 | 637390.18 | wgs | patric | 637390 |
66792 | Acidithiobacillus thiooxidans ATCC 19377 | 637390.5 | wgs | patric | 637390 |
66792 | Acidithiobacillus thiooxidans ATCC 19377 | 637390.19 | complete | patric | 637390 |
66792 | Acidithiobacillus thiooxidans ATCC 19377 | 2510461056 | draft | img | 637390 |
67770 | Acidithiobacillus thiooxidans ATCC 19377 | GCA_000227215 | contig | ncbi | 637390 |
67770 | Acidithiobacillus thiooxidans ATCC 19377 | GCA_006718285 | scaffold | ncbi | 637390 |
GC content
@ref | GC-content | method |
---|---|---|
5601 | 52.1 | |
67770 | 52 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 87.215 | no |
flagellated | no | 84.409 | no |
gram-positive | no | 98.262 | no |
anaerobic | no | 96.347 | no |
aerobic | no | 72.497 | no |
halophile | no | 84.593 | no |
spore-forming | no | 93.843 | no |
glucose-util | yes | 66.925 | no |
thermophile | no | 91.83 | yes |
glucose-ferment | no | 82.628 | no |
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
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 11054160 | Physiology and taxonomy of thiobacillus strain TJ330, which oxidizes carbon disulphide (CS2). | Hartikainen T, Ruuskanen J, Raty K, Von Wright A, Martikainen PJ | J Appl Microbiol | 10.1046/j.1365-2672.2000.01150.x | 2000 | Carbon Disulfide/*metabolism, Culture Media, DNA, Bacterial/analysis, Hydrogen-Ion Concentration, Oxidation-Reduction, Temperature, Thiobacillus/classification/genetics/growth & development/*physiology | Cultivation |
Phylogeny | 15313256 | Differentiation 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 LM | Res Microbiol | 10.1016/j.resmic.2004.03.009 | 2004 | Bacterial 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 Acid | Transcriptome |
Enzymology | 15676194 | Detection of Acidithiobacillus ferrooxidans in acid mine drainage environments using fluorescent in situ hybridization (FISH). | Mahmoud KK, Leduc LG, Ferroni GD | J Microbiol Methods | 10.1016/j.mimet.2004.10.022 | 2005 | Acidithiobacillus/genetics/*isolation & purification, DNA, Bacterial/genetics, Image Processing, Computer-Assisted, In Situ Hybridization, Fluorescence/*methods, *Industrial Waste, Microscopy, Fluorescence, *Mining, *Water Pollutants, Chemical | Phylogeny |
Genetics | 22123759 | Draft 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 DS | J Bacteriol | 10.1128/JB.06281-11 | 2011 | Acidithiobacillus/genetics/metabolism, Acidithiobacillus thiooxidans/*genetics/metabolism, Acids/*metabolism, Base Sequence, *Evolution, Molecular, *Genome, Bacterial, Mining, Molecular Sequence Data, Sulfur/metabolism | Metabolism |
Enzymology | 24797809 | A 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 J | Environ Microbiol | 10.1111/1462-2920.12494 | 2014 | Acidithiobacillus thiooxidans/drug effects/enzymology/*genetics, Copper/*toxicity, *Gene Knockout Techniques, Molecular Sequence Data, Monophenol Monooxygenase/metabolism, Mutation, Oxidoreductases/*genetics, beta-Galactosidase/genetics | Genetics |
Genetics | 25148779 | A 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 A | Res Microbiol | 10.1016/j.resmic.2014.08.004 | 2014 | Acidithiobacillus 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 Acid | Biotechnology |
Metabolism | 32231653 | New 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 LA | Front Microbiol | 10.3389/fmicb.2020.00411 | 2020 | ||
33472156 | Bioaugmentation 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 L | J Hazard Mater | 10.1016/j.jhazmat.2020.124988 | 2021 | |||
34745076 | Sticky 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 JC | Front Microbiol | 10.3389/fmicb.2021.767639 | 2021 | |||
Metabolism | 35962820 | Organic 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 J | Extremophiles | 10.1007/s00792-022-01274-z | 2022 | *Ectothiorhodospiraceae/metabolism, Oxidation-Reduction, Sulfur/metabolism |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5601 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 14887) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-14887 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
35699 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16523 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68382 | Automatically annotated from API zym | |||||
69479 | João 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 | |||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
69808 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID45621.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
123524 | Curators of the CIP | Collection of Institut Pasteur (CIP 104597) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104597 |