Archives of Microbiology

, 193:439 | Cite as

Characteristics of a phylogenetically ambiguous, arsenic-oxidizing Thiomonas sp., Thiomonas arsenitoxydans strain 3AsT sp. nov

  • Djamila Slyemi
  • Danielle Moinier
  • Céline Brochier-Armanet
  • Violaine Bonnefoy
  • D. Barrie Johnson
Original Paper


A moderately acidophilic, facultative chemoautotrophic, As(III)-oxidizing Thiomonas sp. (strain 3AsT) was previously shown, on the basis of comparative 16S rRNA gene sequences, to be closely related to both Tm. perometabolis DSM 18570T and Tm. intermedia DSM 18155T. While it had shared many physiological traits with Tm. intermedia T, a mean DNA–DNA hybridization value (DDHV) of 47.2% confirmed that strain 3AsT was not a strain of Tm. intermedia, though the situation with regard to Tm. perometabolis (DDHV previously determined as 72%) was more ambiguous. A comparative physiological and chemotaxonomic study of strain 3AsT and Tm. perometabolis T was therefore carried out, together with multilocus sequence analysis (MLSA) of all three bacteria. Differences in fatty acid profiles and utilization of organic substrates supported the view that strain 3AsT and Tm. perometabolis are distinct species, while MLSA showed a closer relationship between strain 3AsT and Tm. intermedia T than between strain 3AsT and Tm. perometabolis T. These apparent contradictory conclusions were explained by differences in genome of these three bacteria, which are known to be highly flexible in Thiomonas spp. A novel species designation Thiomonas arsenitoxydans is proposed for strain 3AsT (DSM 22701T, CIP 110005T), which is nominated as the type strain of this species.


Thiomonas Thiomonas arsenitoxydans Arsenic DNA–DNA hybridization Multilocus sequence analysis 



We warmly acknowledge K. Duquesne (IMM, LCB, Marseille, France), J. Ratouchniak (IMM, LCB, Marseille, France) and A. Yarzábal (Universidad de Los Andes, Merida, Venezuela) for initiating this work. The authors are grateful to B. Ollivier (IRD, Microbiologie et Biotechnologie des environnements chauds, Marseille) and P. Bauda (Université Paul Verlaine, Metz) for their advices and for helpful discussions. We wish to thank J. Euzéby for his expert advice on bacterial nomenclature. We also thank M. Bauzan (Fermentation plant unit, IMM, Marseille, France) for growing the bacteria in bioreactor, S. Verbarg (DSMZ, Braunschweig, Germany) for fatty acid analysis. Part of this work was financed by the EU framework 6 project “BioMine” (N° NM2.ct, 2005.500329). This work was partly performed in the frame of the Groupement de Recherche “Métabolisme de l’Arsenic chez les Procaryotes: de la résistance à la détoxication” (GDR2009-CNRS). DS was supported by a grant from the French Ministry of Education and Research. C.B.-A. is supported by an Action Thématique et Incitative sur Programme (ATIP) of the French Centre National de la Recherche Scientifique (CNRS). DBJ is grateful to the Royal Society (UK) for the provision of an Industrial Fellowship.

Supplementary material

203_2011_684_MOESM1_ESM.doc (310 kb)
Supplementary material 1 (DOC 310 kb)


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  2. Amouric A, Brochier-Armanet C, Johnson DB, Bonnefoy V, Hallberg KB (2011) Phylogenetic and genetic variation among Fe(II)-oxidizing acidithiobacilli supports the view that these comprise multiple species with different ferrous iron oxidation pathways. Microbiology 157:111–122PubMedCrossRefGoogle Scholar
  3. Arsene-Ploetze F, Koechler S, Marchal M, Coppee JY, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan CG, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lievremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Medigue C, Bertin PN (2010) Structure, function, and evolution of the Thiomonas spp. genome. PLoS Genet 6:e1000859Google Scholar
  4. Battaglia-Brunet F, Joulian C, Garrido F, Dictor MC, Morin D, Coupland K, Johnson DB, Hallberg KB, Baranger P (2006) Oxidation of arsenite by Thiomonas strains and characterization of Thiomonas arsenivorans sp. nov. Antonie Van Leeuwenhoek 89:1–10CrossRefGoogle Scholar
  5. Coupland K, Battaglia-Brunet F, Hallberg KB, Dictor MC, Garrido F, Johnson DB (2003) Oxidation of iron, sulfur and arsenic in mine waters and mine wastes: an important role for novel Thiomonas spp. In: Tsezos M, Remoudaki E, Hatzikioseyian A (eds) Biohydrometallurgy; a sustainable technology in evolution. National Technical University of Athens, Zografou, Greece, Athens, Greece, pp 639–646Google Scholar
  6. Duquesne K (2004) Rôle des bactéries dans la bioremédiation de l’arsenic dans les eaux acides de drainage de la mine de Carnoulès. PhD Thesis, Faculté des Sciences de Luminy, Université de la Méditerranée, Marseille, FranceGoogle Scholar
  7. Duquesne K, Lieutaud A, Ratouchniak J, Muller D, Lett MC, Bonnefoy V (2008) Arsenite oxidation by a chemoautotrophic moderately acidophilic Thiomonas sp.: from the strain isolation to the gene study. Environ Microbiol 10:228–237PubMedGoogle Scholar
  8. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91PubMedCrossRefGoogle Scholar
  9. Hallberg KB, Johnson DB (2003) Novel acidophiles isolated from moderately acidic mine drainage waters. Hydrometallurgy 71:139–148CrossRefGoogle Scholar
  10. Huber H, Stetter KO (1990) Thiobacillus cuprinus sp. nov., a novel facultatively organotrophic metal-mobilizing bacterium. Appl Environ Microbiol 56:315–322PubMedGoogle Scholar
  11. Jobb G, von Haeseler A, Strimmer K (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4:18PubMedCrossRefGoogle Scholar
  12. Johnson DB (2009) Extremophiles: acidic environments. In: Schaechter M (ed) Encyclopaedia of microbiology. Elsevier, Oxford, pp 107–126CrossRefGoogle Scholar
  13. Johnson DB, Hallberg KB (2007) Techniques for detecting and identifying acidophilic mineral-oxidizing microorganisms. In: Rawlings DE, Johnson DB (eds) Biomining. Springer, Berlin, pp 237–261CrossRefGoogle Scholar
  14. Katayama Y, Uchino Y, Wood AP, Kelly DP (2006) Confirmation of Thiomonas delicata (formerly Thiobacillus delicatus) as a distinct species of the genus Thiomonas Moreira and Amils 1997 with comments on some species currently assigned to the genus. Int J Syst Evol Microbiol 56:2553–2557PubMedCrossRefGoogle Scholar
  15. Katayama-Fujimura Y, Kuraishi H (1983) Emendation of Thiobacillus perometabolis London and Rittenberg 1967. Int J Syst. Bacteriol 33:650–651CrossRefGoogle Scholar
  16. Katayama-Fujimura Y, Enokizono Y, Kaneko T, Kuraishi H (1983) Deoxyribonucleic acid homologies among species of the genus Thiobacillus. J Gen Appl Microbiol 29:287–295CrossRefGoogle Scholar
  17. Katayama-Fujimura Y, Kawashima I, Tsuzaki N, Kuraishi H (1984) Physiological characteristics of the facultatively chemolithotrophic Thiobacillus species Thiobacillus delicatus nom. rev., emend. Thiobacillus perometabolis, and Thiobacillus intermedius. Int J Syst Bacteriol 34:139–144CrossRefGoogle Scholar
  18. Kelly DP, Uchino Y, Huber H, Amils R, Wood AP (2007) Reassessment of the phylogenetic relationships of Thiomonas cuprina. Int J Syst Evol Microbiol 57:2720–2724PubMedCrossRefGoogle Scholar
  19. Kimura S, Hallberg KB, Johnson DB (2006) Sulfidogenesis in low pH (3.8–4.2) media by a mixed population of acidophilic bacteria. Biodegradation 17:57–65CrossRefGoogle Scholar
  20. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948PubMedCrossRefGoogle Scholar
  21. Liu Z, Borne F, Ratouchniak J, Bonnefoy V (2001) Genetic transfer of IncP, IncQ and IncW plasmids to four Thiobacillus ferrooxidans strain by conjugation. Hydrometallurgy 59:339–345CrossRefGoogle Scholar
  22. London J (1963) Thiobacillus intermedius nov. sp. A novel type of facultative autotroph. Arch Mikrobiol 46:329–337CrossRefGoogle Scholar
  23. London J, Rittenberg SC (1967) Thiobacillus perometabolis nov. sp., a non-autotrophic thiobacillus. Arch Mikrobiol 59:218–225PubMedCrossRefGoogle Scholar
  24. Lovley DR, Phillips EJ (1987) Rapid assay for microbially reducible ferric iron in aquatic sediments. Appl Environ Microbiol 53:1536–1540PubMedGoogle Scholar
  25. Maiden MC (2006) Multilocus sequence typing of bacteria. Annu Rev Microbiol 60:561–588PubMedCrossRefGoogle Scholar
  26. Mizoguchi T, Sato T, Okabe T (1976) New sulfur-oxidizing bacteria capable of growing heterotrophically, Thiobacillus rubellus nov. sp. and Thiobacillus delicatus nov. sp. J Ferment Technol 54:181–191Google Scholar
  27. Moreira D, Amils R (1997) Phylogeny of Thiobacillus cuprinus and other mixotrophic thiobacilli: proposal for Thiomonas gen. nov. Int J Syst Bacteriol 47:522–528PubMedCrossRefGoogle Scholar
  28. Panda SK, Jyoti V, Bhadra B, Nayak KC, Shivaji S, Rainey FA, Das SK (2009) Thiomonas bhubaneswarensis sp. nov. an obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium. Int J Syst Evol Microbiol 59:2171–2175PubMedCrossRefGoogle Scholar
  29. Philippe H (1993) MUST, a computer package of Management Utilities for Sequences and Trees. Nucleic Acids Res 21:5264–5272PubMedCrossRefGoogle Scholar
  30. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574PubMedCrossRefGoogle Scholar
  31. Shooner F, Bousquet J, Tyagi RD (1996) Isolation, phenotypic characterization, and phylogenetic position of a novel, facultatively autotrophic, moderately thermophilic bacterium, Thiobacillus thermosulfatus sp. nov. Int J Syst Bacteriol 46:409–415PubMedCrossRefGoogle Scholar
  32. Slyemi D (2010) Caractérisation de “Thiomonas arsenitoxydans” et étude de la régulation des gènes codant pour l’arsénite oxydase. PhD Thesis, Faculté des Sciences de Luminy, Université de la Méditerranée, Marseille, FranceGoogle Scholar
  33. Vesteinsdottir H, Reynisdottir DB, Orlygsson J (2011) Thiomonas islandica sp. nov., a novel moderately thermophilic hydrogen and sulfur oxidizing betaproteobacterium isolated from an Icelandic hot spring. Int J Syst Evol Microbiol 61:132–137PubMedCrossRefGoogle Scholar
  34. Wakeman K, Auvinen H, Johnson DB (2008) Microbiological and geochemical dynamics in simulated-heap leaching of a polymetallic sulfide ore. Biotechnol Bioeng 101:739–750PubMedCrossRefGoogle Scholar
  35. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE, Stackebrandt E, Starr MP, Truper HG (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Djamila Slyemi
    • 1
  • Danielle Moinier
    • 1
  • Céline Brochier-Armanet
    • 1
  • Violaine Bonnefoy
    • 1
  • D. Barrie Johnson
    • 2
  1. 1.C.N.R.S., Institut de Microbiologie de la Méditerranée, Aix-Marseille Université, Laboratoire de Chimie BactérienneMarseilleFrance
  2. 2.School of Biological SciencesBangor UniversityBangorUK

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