Strain identifier

BacDive ID: 6145

Type strain: Yes

Species: Thiobacillus thioparus

Strain history: CIP <- 2013, DSMZ <- NCIB <- KR Butlin <- RL Starkey

NCBI tax ID(s): 1123393 (strain), 931 (species)

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General

@ref: 243

BacDive-ID: 6145

DSM-Number: 505

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative

description: Thiobacillus thioparus DSM 505 is a Gram-negative bacterium that was isolated from agricultural soil.

NCBI tax id

NCBI tax idMatching level
931species
1123393strain

strain history

@refhistory
243<- NCIB; NCIB 8370 <- K. R. Butlin <- R. L. Starkey {1934}
67770Y. Katayama THI111 <-- ATCC 8158 <-- R. L. Starkey.
123527CIP <- 2013, DSMZ <- NCIB <- KR Butlin <- RL Starkey

doi: 10.13145/bacdive6145.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Nitrosomonadales
  • family: Thiobacillaceae
  • genus: Thiobacillus
  • species: Thiobacillus thioparus
  • full scientific name: Thiobacillus thioparus Beijerinck 1904 (Approved Lists 1980)

@ref: 243

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Hydrogenophilales

family: Thiobacillaceae

genus: Thiobacillus

species: Thiobacillus thioparus

full scientific name: Thiobacillus thioparus Beijerinck 1904

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
123527negativerod-shapedyes
69480negative98

colony morphology

  • @ref: 243
  • incubation period: 2-3 days

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_505_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_505_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_505_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_505_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_505_5.jpgelectron microscopic image© HZI/Manfred Rohde

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
243THIOBACILLUS MEDIUM (DSMZ Medium 36)yeshttps://mediadive.dsmz.de/medium/36Name: THIOBACILLUS MEDIUM (DSMZ Medium 36) Composition: Agar 12.0 g/l (optional) Na2S2O3 x 5 H2O 10.0 g/l K2HPO4 4.0 g/l KH2PO4 4.0 g/l CaCl2 0.1 g/l MgSO4 x 7 H2O 0.1 g/l (NH4)2SO4 0.1 g/l FeCl3 x 6 H2O 0.02 g/l MnSO4 x H2O 0.02 g/l Distilled water
123527CIP Medium 249yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=249
123527CIP Medium 124yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=124

culture temp

@refgrowthtypetemperature
243positivegrowth26
67770positivegrowth30
123527positivegrowth15-37

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no90.821
69481no100

compound production

  • @ref: 243
  • compound: glutamate synthase

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
1235274853esculin-hydrolysis
12352717632nitrate+reduction
12352716301nitrite-reduction

metabolite production

  • @ref: 123527
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

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
123527oxidase+
123527beta-galactosidase+/-3.2.1.23
123527alcohol dehydrogenase-1.1.1.1
123527gelatinase-
123527catalase-1.11.1.6
123527lysine decarboxylase-4.1.1.18
123527ornithine decarboxylase-4.1.1.17
123527urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
123527--++-------+--------

Isolation, sampling and environmental information

isolation

  • @ref: 243
  • sample type: agricultural soil
  • geographic location: Rutgers University, New Jersey
  • country: USA
  • origin.country: USA
  • continent: North America

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Engineered#Agriculture

taxonmaps

  • @ref: 69479
  • File name: preview.99_4650.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_421;96_1931;97_2322;98_2865;99_4650&stattab=map
  • Last taxonomy: Thiobacillus thioparus
  • 16S sequence: HM173629
  • Sequence Identity:
  • Total samples: 62
  • soil counts: 14
  • aquatic counts: 45
  • animal counts: 1
  • plant counts: 2

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
2431Risk group (German classification)
1235271Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Thiobacillus thioparus culture-collection DSM:505 16S ribosomal RNA gene, partial sequenceGU9676791382nuccore931
20218Thiobacillus thioparus strain ATCC 8158 16S ribosomal RNA gene, partial sequenceM794261237nuccore931
243Thiobacillus thioparus strain Starkey 16S ribosomal RNA (rrs) gene, partial sequenceHM1736291403nuccore931
124043Thiobacillus thioparus strain NCIMB 8370 16S ribosomal RNA (rrs) gene, partial sequence.HM1736301403nuccore931
124043Thiobacillus thioparus strain THI 111 16S ribosomal RNA gene, partial sequence.HM5352261460nuccore931

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thiobacillus thioparus DSM 5051123393.3wgspatric1123393
66792Thiobacillus thioparus DSM 5052515154076draftimg1123393
67770Thiobacillus thioparus DSM 505GCA_000373385scaffoldncbi1123393

GC content

@refGC-contentmethod
24363.0
6777062thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69481spore-formingspore-formingAbility to form endo- or exosporesno100no
69480gram-positivegram-positivePositive reaction to Gram-stainingno98no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no71.781no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.821no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no53.542no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno95.16yes
69480flagellatedmotile2+Ability to perform flagellated movementyes82.936no

External links

@ref: 243

culture collection no.: DSM 505, ATCC 8158, CIP 104484, NCIMB 8370, JCM 3859, BCRC 11089, IAM 12101, IAM 12113, NBRC 103402

straininfo link

  • @ref: 75632
  • straininfo: 34928

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21858648Phylogenetic assessment of culture collection strains of Thiobacillus thioparus, and definitive 16S rRNA gene sequences for T. thioparus, T. denitrificans, and Halothiobacillus neapolitanus.Boden R, Cleland D, Green PN, Katayama Y, Uchino Y, Murrell JC, Kelly DPArch Microbiol10.1007/s00203-011-0747-02011Genes, rRNA, Halothiobacillus/*classification/genetics, Molecular Sequence Data, *Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/*genetics, Sequence Analysis, RNA, Thiobacillus/*classification/geneticsGenetics
Metabolism27542742Response of cbb gene transcription levels of four typical sulfur-oxidizing bacteria to the CO2 concentration and its effect on their carbon fixation efficiency during sulfur oxidation.Wang YN, Wang L, Tsang YF, Fu X, Hu J, Li H, Le YEnzyme Microb Technol10.1016/j.enzmictec.2016.06.0152016Alphaproteobacteria/genetics/metabolism, Bacteria/*genetics/*metabolism, Bacterial Proteins/genetics/metabolism, Betaproteobacteria/genetics/metabolism, Carbon Cycle/genetics, Carbon Dioxide/metabolism, Genes, Bacterial, Halothiobacillus/genetics/metabolism, Oxidation-Reduction, Ribulose-Bisphosphate Carboxylase/genetics/metabolism, Sulfur/*metabolism, Thiobacillus/genetics/metabolism, Transcription, Genetic
28127420Permanent draft genome of Thiobacillus thioparus DSM 505(T), an obligately chemolithoautotrophic member of the Betaproteobacteria.Hutt LP, Huntemann M, Clum A, Pillay M, Palaniappan K, Varghese N, Mikhailova N, Stamatis D, Reddy T, Daum C, Shapiro N, Ivanova N, Kyrpides N, Woyke T, Boden RStand Genomic Sci10.1186/s40793-017-0229-32017
Phylogeny28581923Reclassification of Thiobacillus aquaesulis (Wood & Kelly, 1995) as Annwoodia aquaesulis gen. nov., comb. nov., transfer of Thiobacillus (Beijerinck, 1904) from the Hydrogenophilales to the Nitrosomonadales, proposal of Hydrogenophilalia class. nov. within the 'Proteobacteria', and four new families within the orders Nitrosomonadales and Rhodocyclales.Boden R, Hutt LP, Rae AWInt J Syst Evol Microbiol10.1099/ijsem.0.0019272017Bacterial Typing Techniques, Betaproteobacteria/*classification, DNA, Bacterial/genetics, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Thiobacillus/*classificationTranscriptome
Cultivation29306128Inhibitory effect of self-generated extracellular dissolved organic carbon on carbon dioxide fixation in sulfur-oxidizing bacteria during a chemoautotrophic cultivation process and its elimination.Wang YN, Tsang YF, Wang L, Fu X, Hu J, Li H, Le YBioresour Technol10.1016/j.biortech.2017.12.0892017Bacteria, Bioreactors, *Carbon, Carbon Cycle, *Carbon Dioxide, Sulfur
Metabolism29965370[Effect of Thiosulfate on the Carbon Fixation Capability of Thiobacillus thioparus and Its Mechanism].Li H, Wang L, Wang YNHuan Jing Ke Xue10.13227/j.hjkx.2016100432017Carbon/*chemistry, *Carbon Cycle, Ribulose-Bisphosphate Carboxylase/genetics, Thiobacillus/*metabolism, Thiosulfates/*chemistry
Cultivation32579519Key internal factors leading to the variability in CO2 fixation efficiency of different sulfur-oxidizing bacteria during autotrophic cultivation.Wang YN, Kai Y, Wang L, Tsang YF, Fu X, Hu J, Xie YJ Environ Manage10.1016/j.jenvman.2020.1109572020Alphaproteobacteria, Bacteria, Burkholderiales, *Carbon Dioxide, Oxidation-Reduction, *Sulfur

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
243Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 505)https://www.dsmz.de/collection/catalogue/details/culture/DSM-505
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
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
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
75632Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID34928.1StrainInfo: A central database for resolving microbial strain identifiers
123527Curators of the CIPCollection of Institut Pasteur (CIP 104484)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104484
124043Dr. Isabel Schober, Dr. Julia KoblitzData extracted from sequence databases, automatically matched based on designation and taxonomy