RESUMO
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.
Assuntos
Betaproteobacteria/genética , Evolução Molecular , Genoma Bacteriano/genética , Adaptação Fisiológica/genética , Arsênio/metabolismo , Carbono/metabolismo , Hibridização Genômica Comparativa , Metabolismo Energético/genética , Meio Ambiente , Transferência Genética Horizontal/genética , Genes Bacterianos/genética , Genes Duplicados/genética , Variação Genética , Ilhas Genômicas/genética , Redes e Vias Metabólicas/genética , Plasmídeos/genética , Prófagos/genéticaRESUMO
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.
Assuntos
Archaea/enzimologia , Archaea/metabolismo , Arsenitos/metabolismo , Bactérias/enzimologia , Bactérias/metabolismo , Microbiologia Ambiental , Oxirredutases/genética , Archaea/genética , Archaea/isolamento & purificação , Bactérias/genética , Bactérias/isolamento & purificação , Análise por Conglomerados , DNA Arqueal/química , DNA Arqueal/genética , DNA Bacteriano/química , DNA Bacteriano/genética , França , Dados de Sequência Molecular , Oxirredução , Filogenia , Análise de Sequência de DNA , Homologia de SequênciaRESUMO
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.
Assuntos
Arsenitos/metabolismo , Bactérias/enzimologia , Bactérias/genética , Oxirredutases/genética , Sequência de Aminoácidos , Sequência de Bases , Biodiversidade , Crescimento Quimioautotrófico , Sequência Conservada , Primers do DNA , DNA Bacteriano/isolamento & purificação , Genes Bacterianos , Marcadores Genéticos , Variação Genética , Dados de Sequência Molecular , Oxirredução , Filogenia , Reação em Cadeia da Polimerase , Proteobactérias/enzimologia , Proteobactérias/genética , RNA Ribossômico 16S/isolamento & purificação , Análise de Sequência de DNA , Análise de Sequência de Proteína , Microbiologia do Solo , Poluentes do Solo/metabolismoRESUMO
Pseudomonas xanthomarina S11 is an arsenite-oxidizing bacterium isolated from an arsenic-contaminated former gold mine in Salsigne, France. This bacterium showed high resistance to arsenite and was able to oxidize arsenite to arsenate at concentrations up to 42.72 mM As[III]. The genome of this strain was sequenced and revealed the presence of three ars clusters. One of them is located on a plasmid and is organized as an "arsenic island" harbouring an aio operon and genes involved in phosphorous metabolism, in addition to the ars genes. Neither the aioXRS genes nor a specific sigma-54-dependent promoter located upstream of aioBA genes, both involved in regulation of arsenite oxidase expression in other arsenite-oxidizing bacteria, could be identified in the genome. This observation is in accordance with the fact that no difference was observed in expression of arsenite oxidase in P. xanthomarina S11, whether or not the strain was grown in the presence of As[III].
Assuntos
Arsênio/metabolismo , Proteínas de Bactérias/genética , Oxirredutases/genética , Oxirredutases/metabolismo , Pseudomonas/genética , Arseniatos/metabolismo , Arsênio/farmacologia , ATPases Transportadoras de Arsenito/genética , ATPases Transportadoras de Arsenito/metabolismo , Arsenitos/metabolismo , Arsenitos/farmacologia , Proteínas de Bactérias/metabolismo , Sequência de Bases , DNA Bacteriano , Farmacorresistência Bacteriana , França , Regulação Bacteriana da Expressão Gênica , Mineração , Óperon , Oxirredução , Filogenia , Plasmídeos , Pseudomonas/enzimologia , Pseudomonas/crescimento & desenvolvimento , Pseudomonas/isolamento & purificaçãoRESUMO
Arsenic-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 Bacteroidetes, 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.
Assuntos
Archaea/genética , Arsênio/metabolismo , Bactérias/genética , Sedimentos Geológicos/microbiologia , Consórcios Microbianos/fisiologia , Proteômica , Rios/microbiologia , Adaptação Fisiológica , Archaea/classificação , Archaea/isolamento & purificação , Archaea/metabolismo , Bactérias/classificação , Bactérias/isolamento & purificação , Bactérias/metabolismo , Biodiversidade , DNA Arqueal/análise , DNA Arqueal/genética , DNA Bacteriano/análise , DNA Bacteriano/genética , Ecossistema , Poluentes Ambientais/metabolismo , França , Transferência Genética Horizontal , Filogenia , Reação em Cadeia da Polimerase , RNA Ribossômico 16S/análise , RNA Ribossômico 16S/genéticaRESUMO
By their metabolic activities, microorganisms have a crucial role in the biogeochemical cycles of elements. The complete understanding of these processes requires, however, the deciphering of both the structure and the function, including synecologic interactions, of microbial communities. Using a metagenomic approach, we demonstrated here that an acid mine drainage highly contaminated with arsenic is dominated by seven bacterial strains whose genomes were reconstructed. Five of them represent yet uncultivated bacteria and include two strains belonging to a novel bacterial phylum present in some similar ecosystems, and which was named 'Candidatus Fodinabacter communificans.' Metaproteomic data unravelled several microbial capabilities expressed in situ, such as iron, sulfur and arsenic oxidation that are key mechanisms in biomineralization, or organic nutrient, amino acid and vitamin metabolism involved in synthrophic associations. A statistical analysis of genomic and proteomic data and reverse transcriptase-PCR experiments allowed us to build an integrated model of the metabolic interactions that may be of prime importance in the natural attenuation of such anthropized ecosystems.