Structure, Function, and Evolution of the Thiomonas spp. Genome

Bacteria of the Thiomonas genus are ubiquitous in extreme environments, such as arsenic-rich acid mine drainage (AMD). The genome of one of these strains, Thiomonas sp. 3As, was sequenced, annotated, and examined, revealing specific adaptations allowing this bacterium to survive and grow in its highly toxic environment. In order to explore genomic diversity as well as genetic evolution in Thiomonas spp., a comparative genomic hybridization (CGH) approach was used on eight different strains of the Thiomonas genus, including five strains of the same species. Our results suggest that the Thiomonas genome has evolved through the gain or loss of genomic islands and that this evolution is influenced by the specific environmental conditions in which the strains live

Diversity of bacterial arsenic oxido-reduction mechanisms : from cultivable strains to communities

Les bactéries sont retrouvés dans des milieux très variés allant des plus communs aux plus extrêmes, comme les sites miniers arséniés de Carnoulès, de Salsigne ou de Sainte-Marie-aux-Mines. De nombreuses bactéries sont impliquées dans le cycle bio-géochimique de l'arsenic et jouent un rôle crucial dans sa biodisponibilité. Certaines possèdent l'arsénite-oxydase (Aox) qui catalyse l'oxydation de l'AsIII en AsV, constituant la première étape de détoxication. L'objectif de ce travail est d'étudier la diversité des mécanismes d'oxydo-réduction de l'arsenic chez les bactéries. Mon travail s'est focalisé sur l'analyse de la diversité des gènes aox observée chez des isolats en condition de laboratoire et au sein de communautés complexes en conditions in situ. Ces travaux ont conduit à la caractérisation de trois souches : Pseudomonas S11, Leptothrix S1.1 et Thiomonas 3As. Une analyse génétique a complété l'analyse physiologique de Thiomonas. Ces études ont de plus conduit à la mise en évidence d'arsénite-oxydases particulières dont l'activité est exprimée de manière constitutive ou présentant une activité enzymatique élevée. Puis l'analyse des séquences AoxB issues de diverses bactéries cultivables et de communautés bactériennes a permis la mise en évidence d'une variabilité de séquences AoxB et nous a conduit à proposer le gène aoxB comme marqueur moléculaire des bactéries arsénite-oxydantes aérobies. Enfin l'analyse des gènes aox par une étude de génomique environnementale sur la communauté bactérienne du site de Carnoulès, a permis de mieux appréhender les interactions trophiques entre les souches et de mettre en évidence le rôle pivot de Thiomonas sp. dans cet environnement.Microorganisms are found in several environments from the friendliest to the most extreme such as arsenical environment as frnch mining sites of Carnoules, Salsigne or Sainte-Marie-aux-Mines. Some of them are involved in arsenic biochemical cycle and play a crucial role in its mobilization/immobilization and thus in its biodisponibility. These bacteria contain arsenite oxidase (coded by aox genes) catalyzing the oxidation of As III in As V. This oxidation constitutes the first arsenical environment detoxification stage. The aim of this work is the study of the diversity of bacterial arsenic oxido-reduction mechanisms. This study focuses on the diversity of aoxB genes from isolated strains or complex communities. Physiological characterizations of three strains have been first realized on Pseudomonas S11, Leptothrix S1.1 and Thiomonas 3As. A genetic approach supplements the physiological data of Thiomonas 3As. Particular arsenite oxidases demonstrating a high or a constitutive arsenite oxidase activity have been highlighted. In a second time AoxB sequences analyses from cultivable bacteria or bacterial communities have underlined a sequence variability and allowed to consider aoxB gene as molecular marker for aerobic arsenite oxidizing strains. Lastly an environmental genomic approach on bacterial community from Carnoulès mining site allowed to decipher the bacterial trophic interactions and the key role of the arsenite oxidizing strain Thiomonas sp. in this study site

Diversity of bacterial arsenic oxido-reduction mechanisms : from cultivable strains to communities

Les bactéries sont retrouvés dans des milieux très variés allant des plus communs aux plus extrêmes, comme les sites miniers arséniés de Carnoulès, de Salsigne ou de Sainte-Marie-aux-Mines. De nombreuses bactéries sont impliquées dans le cycle bio-géochimMicroorganisms are found in several environments from the friendliest to the most extreme such as arsenical environment as frnch mining sites of Carnoules, Salsigne or Sainte-Marie-aux-Mines. Some of them are involved in arsenic biochemical cycle and pla

Diversity Surveys and Evolutionary Relationships of aoxB Genes in Aerobic Arsenite-Oxidizing Bacteria▿ †

A new primer set was designed to specifically amplify ca. 1,100 bp of aoxB genes encoding the As(III) oxidase catalytic subunit from taxonomically diverse aerobic As(III)-oxidizing bacteria. Comparative analysis of AoxB protein sequences showed variable conservation levels and highlighted the conservation of essential amino acids and structural motifs. AoxB phylogeny of pure strains showed well-discriminated taxonomic groups and was similar to 16S rRNA phylogeny. Alphaproteobacteria-, Betaproteobacteria-, and Gammaproteobacteria-related sequences were retrieved from environmental surveys, demonstrating their prevalence in mesophilic As-contaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers

Taxonomic and functional prokaryote diversity in mildly arsenic-contaminated sediments

International audienceArsenic-resistant prokaryote diversity is far from being exhaustively explored. In this study, the arsenic-adapted prokaryotic community present in a moderately arsenic-contaminated site near Sainte-Marie-aux-Mines (France) was characterized, using metaproteomic and 16S rRNA-encoding gene amplification. High prokaryotic diversity was observed, with a majority of Proteobacteria, Acidobacteria and Bacter-oidetes, and a large archaeal community comprising Euryarchaeaota and Thaumarchaeota. Metaproteomic analysis revealed that Proteobacteria, Planctomycetes and Cyanobacteria are among the active bacteria in this ecosystem. Taken together, these results highlight the unsuspected high diversity of the arsenic-adapted prokaryotic community, with some phyla never having been described in highly arsenic-exposed sites

Unsuspected Diversity of Arsenite-Oxidizing Bacteria as Revealed by Widespread Distribution of the aoxB Gene in Prokaryotes ▿ †

In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity of aoxB genes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterial aoxB genes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading of aoxB in prokaryotic communities