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 Ascontaminated soils. Our study underlines the usefulness of the aoxB gene as a functional marker of aerobic As(III) oxidizers.Arsenic (As) exists mainly in two toxic soluble forms, arsenite, As(III), and arsenate, As(V), with the latter tending to associate with some oxyhydroxides and clay minerals. The bacterial oxidation of As(III) can thus contribute to a natural attenuation of As contamination by decreasing As bioavailability. These properties have recently been used to develop a bioprocess for removing As from a mining effluent by using the activity of As-metabolizing bacteria indigenous to the contaminated site (4). The feasibility of such a process depends on a good knowledge of the ability of the indigenous microflora to oxidize As(III) and requires reliable methods for detecting, identifying, and monitoring As(III) oxidizers in the environment.More than 50 phylogenetically diverse As(III)-oxidizing strains distributed among 25 genera have been isolated from various environments so far. Bacterial aerobic As(III) oxidation is performed by a dedicated enzyme, the As(III) oxidase (1,36,40), which belongs to the dimethyl sulfoxide (DMSO) reductase of the molybdenum family (9). In Alcaligenes faecalis, it is an ␣ 1 ␤ 1 heterodimer comprising a large subunit incorporating a molybdenum center and a [3Fe-4S] cluster and a small subunit incorporating a Rieske-type [2Fe-2S] cluster (9). Genes encoding these subunits are cotranscribed as an operon and have been successively characterized in Herminiimonas arsenicoxydans (26), Rhizobium sp. strain , and Agrobacterium tumefaciens (21). They have also been found in the genome of Chloroflexus aurantiacus, on a plasmid in Thermus thermophilus, in two aerobic thermophilic As(III) oxidizers, and in the genome of strains for which the ability to oxidize As(III) has not been experimentally proven (27).Due to the polyphyly of As(III)-oxidizing bacteria, the aoxB gene encoding the catalytic subunit of the enzyme seems to be a valuable molecular marker for investigating its ecology and the potential of As(III) oxidation in the environment. To this end, a recent study described primers targeting the first quarter of the aoxB gene to detect its presence and expression in the environment and suggested that the gene is widely distributed among the Bacteria and also is widespread in soil-water systems containing As (16).In our present study, we designed...

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.

International audienceTo reduce the environmental footprint of human activities, the quality of environmental media such as water, soil and the atmosphere should be first assessed. Microorganisms are well suited for a such assessment because they respond fast to environmental changes, they have a huge taxonomic and genetic diversity, and they are actively involved in biogeochemical cycles. Here, we review microbiological methods that provide sensitive and robust indicators for environmental diagnosis. Methods include genomics, transcriptomics, proteomics and metabolomics to study the abundance, diversity, activity and functional potentials of indigenous microbial communities in various environmental matrices such as water, soil, air and waste. We describe the advancement, technical limits and sensitivity of each method. Examples of method application to farming, industrial and urban impact are presented. We rank the most advanced indicators according to their level of operability in the different environmental matrices based on a technology readiness level scale

A novel bacterium, strain b6(T) (T=type strain), was isolated from a disused mine site by growth using arsenite [As(III)] as energy source in a simple mineral medium. Cells of strain b6(T) were rod-shaped, Gram-negative, non-sporulating and motile. Optimum growth occurred at temperatures between 20 and 30 degrees C, and at pH between 4.0 and 7.5. Strain b6(T) grew chemoautotrophically on As(III), sulphur and thiosulphate, and also heterotrophically on yeast extract and a variety of defined organic compounds. Several other Thiomonas strains, including the type species Thiomonas (Tm.) intermedia, were able to oxidize As(III), though only strain b6(T) and strain NO115 could grow using As(III) as sole energy source in the absence of any organic compound. The G+C content of the DNA of strain b6(T) was 65.1 mol %. Comparative small subunit (SSU) ribosomal RNA (rRNA) analysis indicated that strain b6(T) belongs to the genus Thiomonas in the beta-subdivision of the Proteobacteria. It was closely related to an unnamed Thiomonas strain (NO115) isolated from a Norwegian mining site, though sequence identities between strain b6(T) and characterized Thiomonas species were less than 95%. DNA-DNA hybridization between strain b6(T) and the type species of the genus Tm. intermedia showed less than 50% homology. On the basis of phylogenetic and phenotypic characteristics, strain b6(T) (DSM 16361(T), LMG 22795(T)) is proposed as the type strain of the new species Thiomonas arsenivorans, sp. nov.

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