Strain identifier
BacDive ID: 126
Type strain: 
Species: Acidithiobacillus caldus
Strain Designation: KU
Strain history: <- K. B. Hallberg; KU
NCBI tax ID(s): 637389 (strain), 33059 (species)
version 9.1 (current version)
General
@ref: 3313
BacDive-ID: 126
DSM-Number: 8584
keywords: genome sequence, 16S sequence, Bacteria, Gram-negative
description: Acidithiobacillus caldus KU is a Gram-negative bacterium that was isolated from coal spoil enrichment culture K of P. Norris, Univ. of Warwick.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 33059 | species |
| 637389 | strain |
strain history
- @ref: 3313
- history: <- K. B. Hallberg; KU
doi: 10.13145/bacdive126.20240916.9.1
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 caldus
- full scientific name: Acidithiobacillus caldus (Hallberg and Lindström 1995) Kelly and Wood 2000
synonyms
@ref synonym 20215 Fervidacidithiobacillus caldus 20215 Thiobacillus caldus
@ref: 3313
domain: Bacteria
phylum: Proteobacteria
class: Acidithiobacillia
order: Acidithiobacillales
family: Acidithiobacillaceae
genus: Acidithiobacillus
species: Acidithiobacillus caldus
full scientific name: Acidithiobacillus caldus (Hallberg and Lindström 1995) Kelly and Wood 2000
strain designation: KU
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 97.97
colony morphology
- @ref: 3313
- incubation period: 2-3 days
Culture and growth conditions
culture medium
- @ref: 3313
- name: ACIDITHIOBACILLUS CALDUS MEDIUM (DSMZ Medium 150a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/150a
- composition: Name: ACIDITHIOBACILLUS CALDUS MEDIUM (DSMZ Medium 150a) Composition: Sulfur 4.9505 g/l (NH4)2SO4 2.9703 g/l K2HPO4 x 3 H2O 0.49505 g/l MgSO4 x 7 H2O 0.49505 g/l KCl 0.0990099 g/l Ca(NO3)2 x 4 H2O 0.019802 g/l FeCl3 x 6 H2O 0.0108911 g/l MnSO4 x H2O 0.0019802 g/l H3BO3 0.0019802 g/l ZnSO4 x 7 H2O 0.000891089 g/l Na2MoO4 x 2 H2O 0.000792079 g/l CoCl2 x 6 H2O 0.000594059 g/l CuSO4 x 5 H2O 0.00049505 g/l Distilled water
culture temp
- @ref: 3313
- growth: positive
- type: growth
- temperature: 45
Physiology and metabolism
spore formation
- @ref: 69481
- spore formation: no
- confidence: 100
Isolation, sampling and environmental information
isolation
- @ref: 3313
- sample type: coal spoil enrichment culture K of P. Norris, Univ. of Warwick
- geographic location: Kingsbury
- country: United Kingdom
- origin.country: GBR
- continent: Europe
isolation source categories
- Cat1: #Engineered
- Cat2: #Laboratory
- Cat3: #Lab enrichment
taxonmaps
- @ref: 69479
- File name: preview.99_1394.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_163;96_805;97_939;98_1102;99_1394&stattab=map
- Last taxonomy: Acidithiobacillus caldus subclade
- 16S sequence: Z29975
- Sequence Identity:
- Total samples: 1453
- soil counts: 217
- aquatic counts: 855
- animal counts: 359
- plant counts: 22
Safety information
risk assessment
- @ref: 3313
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 20218 | Acidithiobacillus caldus strain DSM8584 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 | AF512808 | 438 | nuccore | 637389 |
| 3313 | T.caldus (DSM 8584) gene for 16S ribosomal RNA | Z29975 | 1460 | nuccore | 637389 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Acidithiobacillus caldus ATCC 51756 | GCA_000175575 | contig | ncbi | 637389 |
| 66792 | Acidithiobacillus caldus KU | GCA_018853545 | contig | ncbi | 33059 |
| 66792 | Acidithiobacillus caldus ATCC 51756 DSM 8584 | GCA_018853615 | contig | ncbi | 637389 |
| 66792 | Acidithiobacillus caldus ATCC 51756 | 637389.19 | plasmid | patric | 637389 |
| 66792 | Acidithiobacillus caldus ATCC 51756 | 637389.17 | plasmid | patric | 637389 |
| 66792 | Acidithiobacillus caldus ATCC 51756 | 637389.3 | wgs | patric | 637389 |
| 66792 | Acidithiobacillus caldus ATCC 51756 | 637389.18 | plasmid | patric | 637389 |
| 66792 | Acidithiobacillus caldus ATCC 51756 strain DSM 8584 | 637389.29 | wgs | patric | 637389 |
| 66792 | Acidithiobacillus caldus ATCC 51756 | 2811995294 | complete | img | 637389 |
GC content
- @ref: 3313
- GC-content: 63.9
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
| @ref | trait | model | description | prediction | confidence | training_data |
|---|---|---|---|---|---|---|
| 69481 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 100 | no |
| 69480 | gram-positive | gram-positive | Positive reaction to Gram-staining | no | 97.97 | no |
| 69480 | anaerobic | anaerobic | Ability to grow under anoxygenic conditions (including facultative anaerobes) | no | 82.514 | no |
| 69480 | aerobic | aerobic | Ability to grow under oxygenic conditions (including facultative aerobes) | yes | 55.682 | no |
| 69480 | spore-forming | spore-forming | Ability to form endo- or exospores | no | 89.217 | no |
| 69480 | thermophilic | thermophile | Ability to grow at temperatures above or equal to 45°C | no | 92.532 | no |
| 69480 | flagellated | motile2+ | Ability to perform flagellated movement | yes | 52.47 | no |
External links
@ref: 3313
culture collection no.: DSM 8584, ATCC 51756
straininfo link
- @ref: 69809
- straininfo: 43164
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 7533596 | Characterization of Thiobacillus caldus sp. nov., a moderately thermophilic acidophile. | Hallberg KB, Lindstrom EB | Microbiology (Reading) | 10.1099/13500872-140-12-3451 | 1994 | Base Composition, DNA, Bacterial/genetics, Hydrogen-Ion Concentration, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sulfur/metabolism, Temperature, Thiobacillus/*classification/genetics/metabolism | Genetics |
| Genetics | 19617360 | Draft genome sequence of the extremely acidophilic bacterium Acidithiobacillus caldus ATCC 51756 reveals metabolic versatility in the genus Acidithiobacillus. | Valdes J, Quatrini R, Hallberg K, Dopson M, Valenzuela PD, Holmes DS | J Bacteriol | 10.1128/JB.00843-09 | 2009 | Acidithiobacillus/genetics/*metabolism, *Bacterial Proteins/genetics/metabolism, Computational Biology, Genes, Bacterial, *Genome, Bacterial, Genomic Library, Molecular Sequence Data, *Sequence Analysis, DNA | Metabolism |
| Phylogeny | 20580751 | Isolation and characterization of Acidithiobacillus caldus from a sulfur-oxidizing bacterial biosensor and its role in detection of toxic chemicals. | Hassan SH, Van Ginkel SW, Kim SM, Yoon SH, Joo JH, Shin BS, Jeon BH, Bae W, Oh SE | J Microbiol Methods | 10.1016/j.mimet.2010.05.008 | 2010 | Acidithiobacillus/classification/*isolation & purification/*metabolism, Bacteria, Biosensing Techniques/*methods, *Biotransformation, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Electric Conductivity, Hydrogen-Ion Concentration, Metals, Heavy/*analysis, Oxidation-Reduction, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sulfur/*metabolism, Water Pollutants, Chemical/*analysis, Water Pollution, Chemical | Metabolism |
| Genetics | 23087115 | Complete genome sequence of temperate bacteriophage AcaML1 from the extreme acidophile Acidithiobacillus caldus ATCC 51756. | Tapia P, Flores FM, Covarrubias PC, Acuna LG, Holmes DS, Quatrini R | J Virol | 10.1128/JVI.02261-12 | 2012 | Acidithiobacillus/*virology, Bacteriophages/*genetics, Computational Biology/methods, DNA, Viral, Databases, Genetic, Genes, Viral, Genetic Techniques, *Genome, Viral, Models, Genetic, Molecular Sequence Data, Multigene Family, Sequence Analysis, DNA | Transcriptome |
| Metabolism | 24250794 | Architecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus. | Acuna LG, Cardenas JP, Covarrubias PC, Haristoy JJ, Flores R, Nunez H, Riadi G, Shmaryahu A, Valdes J, Dopson M, Rawlings DE, Banfield JF, Holmes DS, Quatrini R | PLoS One | 10.1371/journal.pone.0078237 | 2013 | Acidithiobacillus/*genetics/metabolism, Bacterial Proteins/genetics, Computational Biology, Conjugation, Genetic, DNA Transposable Elements/*genetics, *Genome, Bacterial, Plasmids/genetics, Sulfur/*metabolism | Genetics |
| Metabolism | 25689133 | Diguanylate cyclase null mutant reveals that C-Di-GMP pathway regulates the motility and adherence of the extremophile bacterium Acidithiobacillus caldus. | Castro M, Deane SM, Ruiz L, Rawlings DE, Guiliani N | PLoS One | 10.1371/journal.pone.0116399 | 2015 | Acidithiobacillus/*physiology, *Bacterial Adhesion, Bacterial Proteins/chemistry/genetics/metabolism, Cyclic GMP/*analogs & derivatives/metabolism, Escherichia coli Proteins/chemistry/*genetics/metabolism, Genetic Complementation Test, *Metabolic Networks and Pathways, *Mutation, Phosphorus-Oxygen Lyases/chemistry/*genetics/metabolism, Protein Interaction Domains and Motifs, Signal Transduction | |
| Metabolism | 30138723 | Occurrence, integrity and functionality of AcaML1-like viruses infecting extreme acidophiles of the Acidithiobacillus species complex. | Covarrubias PC, Moya-Beltran A, Atavales J, Moya-Flores F, Tapia PS, Acuna LG, Spinelli S, Quatrini R | Res Microbiol | 10.1016/j.resmic.2018.07.005 | 2018 | Acidithiobacillus/genetics/metabolism/*virology, Bacterial Proteins/genetics/metabolism, Bacteriophages/genetics/isolation & purification/*physiology, Proviruses/genetics/isolation & purification/*physiology, Viral Proteins/genetics/metabolism, Virus Integration | Enzymology |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 3313 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 8584) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-8584 | |||
| 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 | |
| 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) | |||
| 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 | |||
| 69809 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID43164.1 | StrainInfo: A central database for resolving microbial strain identifiers |