Strain identifier

BacDive ID: 17953

Type strain: Yes

Species: Thiomonas arsenitoxydans

Strain Designation: 3As

Strain history: CIP <- 2009, V. Bonnefoy, CNRS IMM, Marseille, France: strain 3As

NCBI tax ID(s): 426114 (species)

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General

@ref: 16472

BacDive-ID: 17953

DSM-Number: 22701

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

description: Thiomonas arsenitoxydans 3As is an obligate aerobe, mesophilic, motile bacterium that was isolated from acid mine drainage.

NCBI tax id

  • NCBI tax id: 426114
  • Matching level: species

strain history

@refhistory
336752009, V. Bonnefoy, CNRS IMM, Marseille, France: strain 3As
16472<- V. Bonnefoy, CNRS, Marseille; 3As <- K. Duquesne {2001}
116506CIP <- 2009, V. Bonnefoy, CNRS IMM, Marseille, France: strain 3As

doi: 10.13145/bacdive17953.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Thiomonas
  • species: Thiomonas arsenitoxydans
  • full scientific name: Thiomonas arsenitoxydans Slyemi et al. 2011

@ref: 16472

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Thiomonas

species: Thiomonas arsenitoxydans

full scientific name: Thiomonas arsenitoxydans Slyemi et al. 2011

strain designation: 3As

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes90.191
69480100negative
116506yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
16472THIOMONAS MEDIUM (DSMZ Medium 35a)yeshttps://mediadive.dsmz.de/medium/35aName: THIOMONAS MEDIUM (DSMZ Medium 35a; with strain-specific modifications) Composition: Agar 19.4175 g/l (optional) Na2S2O3 x 5 H2O 4.85437 g/l KH2PO4 2.91262 g/l Yeast extract 0.5 g/l CaCl2 x 2 H2O 0.135922 g/l MgCl2 x 6 H2O 0.0970874 g/l NH4Cl 0.0970873 g/l Distilled water
33675MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
116506CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
16472positivegrowth30mesophilic
33675positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 116506
  • oxygen tolerance: obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
11650617632nitrate-reduction
11650616301nitrite-reduction

metabolite production

  • @ref: 116506
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
116506oxidase+
116506catalase+1.11.1.6
116506urease+3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase-
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
116506-+++-+--+-++--------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
16472acid mine drainageGard, CarnoulèsFranceFRAEurope
116506Environment, Arsenite-containing acid mine drainage watersCarnoulèsFranceFRAEurope2001

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Aquatic
#Condition#Acidic

taxonmaps

  • @ref: 69479
  • File name: preview.99_3097.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_1616;97_1933;98_2377;99_3097&stattab=map
  • Last taxonomy: Thiomonas
  • 16S sequence: AM492684
  • Sequence Identity:
  • Total samples: 3123
  • soil counts: 388
  • aquatic counts: 2269
  • animal counts: 312
  • plant counts: 154

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
164721Risk group (German classification)
1165061Risk group (French classification)

Sequence information

16S sequences

  • @ref: 16472
  • description: Thiomonas arsenitoxydans partial 16S rRNA gene, type strain 3AsT
  • accession: AM492684
  • length: 1442
  • database: ena
  • NCBI tax ID: 426114

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thiomonas arsenitoxydans 3AsGCA_000253115chromosomencbi426114
66792Thiomonas arsenitoxydans 3As651053077completeimg426114

GC content

  • @ref: 16472
  • GC-content: 64.2

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 16472

culture collection no.: DSM 22701, CIP 110005

straininfo link

  • @ref: 86940
  • straininfo: 377780

literature

  • topic: Phylogeny
  • Pubmed-ID: 21409355
  • title: Characteristics of a phylogenetically ambiguous, arsenic-oxidizing Thiomonas sp., Thiomonas arsenitoxydans strain 3As(T) sp. nov.
  • authors: Slyemi D, Moinier D, Brochier-Armanet C, Bonnefoy V, Johnson DB
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-011-0684-y
  • year: 2011
  • mesh: Arsenic/*metabolism, Betaproteobacteria/*classification/genetics/growth & development/*metabolism, Chemoautotrophic Growth, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Multilocus Sequence Typing, Phylogeny, RNA, Ribosomal, 16S/genetics, Sulfur/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitle
16472Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22701)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22701
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
33675Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7815
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)
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
86940Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID377780.1StrainInfo: A central database for resolving microbial strain identifiers
116506Curators of the CIPCollection of Institut Pasteur (CIP 110005)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110005