Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta- and proteo-genomics

Abstract

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.

In situ proteo-metabolomics reveals metabolite secretion by the acid mine drainage bio-indicator, Euglena mutabilis

“…and Ca. F. communificans according to our previous analysis are represented in green and in brown, respectively (Bertin et al, 2011). observed in AMDs (Olaveson and Nalewajko, 2000), which suggests that this protist is able to cope with most of these environmental stresses. Indeed, our proteo-metabolomic approach highlighted the expression of multiple defense mechanisms expressed in situ.…”

“…These analyses were performed at the sampling site called COWG, located 30 m downstream from the spring, where E. mutabilis forms abundant green mats and where the bacterial community has been recently characterized (Bertin et al, 2011). The physico-chemistry of the running water covering the sediments revealed a low pH (3.1), a high dissolved oxygen content at the sediment/water interface (5.72 mg l À1 ) and a high concentration of sulfate (3409 ( ± 341) mg l À1 ).…”

“…Bacteria related to Acidithiobacillus ferrooxidans and Thiomonas spp. have been shown to oxidize Fe(II) and As(III), respectively, leading to co-precipitation of less bio-available As-Fe complexes Duquesne et al, 2003;Bertin et al, 2011). Besides these two bacteria, the Carnoulès AMD prokaryotic community has also been shown to be dominated by five other bacteria, of which two are related to a novel phylum (Bertin et al, 2011).…”

“…have been shown to oxidize Fe(II) and As(III), respectively, leading to co-precipitation of less bio-available As-Fe complexes Duquesne et al, 2003;Bertin et al, 2011). Besides these two bacteria, the Carnoulès AMD prokaryotic community has also been shown to be dominated by five other bacteria, of which two are related to a novel phylum (Bertin et al, 2011). Interestingly, several of these dominant bacteria, including those having a role in bio-attenuation processes, express in situ biological functions involved in metabolite transport and recycling (Bertin et al, 2011).…”

“…Besides these two bacteria, the Carnoulès AMD prokaryotic community has also been shown to be dominated by five other bacteria, of which two are related to a novel phylum (Bertin et al, 2011). Interestingly, several of these dominant bacteria, including those having a role in bio-attenuation processes, express in situ biological functions involved in metabolite transport and recycling (Bertin et al, 2011). Such an observation suggests that the organic matter present at the study site may be crucial for the activities of the prokaryotic community as a whole.…”