Dynamics of Bacterial Communities Mediating the Treatment of an As-Rich Acid Mine Drainage in a Field Pilot

Passive treatment based on iron biological oxidation is a promising strategy for Arsenic (As)-rich acid mine drainage (AMD) remediation. In the present study, we characterized by 16S rRNA metabarcoding the bacterial diversity in a field-pilot bioreactor treating extremely As-rich AMD in situ, over a 6 months monitoring period. Inside the bioreactor, the bacterial communities responsible for iron and arsenic removal formed a biofilm (“biogenic precipitate”) whose composition varied in time and space. These communities evolved from a structure at first similar to the one of the feed water used as an inoculum to a structure quite similar to the natural biofilm developing in situ in the AMD. Over the monitoring period, iron-oxidizing bacteria always largely dominated the biogenic precipitate, with distinct populations (Gallionella, Ferrovum, Leptospirillum, Acidithiobacillus, Ferritrophicum), whose relative proportions extensively varied among time and space. A spatial structuring was observed inside the trays (arranged in series) composing the bioreactor. This spatial dynamic could be linked to the variation of the physico-chemistry of the AMD water between the raw water entering and the treated water exiting the pilot. According to redundancy analysis (RDA), the following parameters exerted a control on the bacterial communities potentially involved in the water treatment process: dissolved oxygen, temperature, pH, dissolved sulfates, arsenic and Fe(II) concentrations and redox potential. Appreciable arsenite oxidation occurring in the bioreactor could be linked to the stable presence of two distinct monophylogenetic groups of Thiomonas related bacteria. The ubiquity and the physiological diversity of the bacteria identified, as well as the presence of bacteria of biotechnological relevance, suggested that this treatment system could be applied to the treatment of other AMD

Acteurs et mécanismes des bio-transformations de l’arsenic, de l’antimoine et du thallium pour la mise en place d’éco-technologies appliquées à la gestion d’anciens sites miniers

Sulfide wastes from the extraction of metal ores generate acidic mine drainage (AMD), containing toxic elements such as arsenic (As), antimony (Sb) and thallium (Tl). Remediation processes using microbial communities have been developed to remove these pollutants from AMD, but the biological processes involved in these treatments still need to be controlled to ensure their effectiveness. The scientific obstacles, which are the subject of the thesis, lie in (1) a lack of knowledge on direct and indirect microbial transformations of Sb and Tl, and (2) for As, a weak understanding of relationships that exist between dynamics of microbial communities, their functional potential, water physico-chemistry and efficiency of treatments applied to AMD. A multidisciplinary approach, mainly based on microbial ecology and physico-chemistry tools, allowed to characterize the diversity of microbial communities capable of directly or indirectly transforming As and Sb at increasing experimental scales: batch reactor, laboratory continuously fed systems, and pilot on site. A microbial consortium able of tolerating up to 100 mM of antimonite and oxidizing it under acidic conditions (pH <4), equivalent to those of AMD, was obtained in a batch system in the laboratory from contaminated soil at Sb. A laboratory column bioreactor, fed continuously with a real AMD and inoculated with a bacterial sulfate-reducing consortium enriched from this AMD, allowed the elimination of almost all the As, Sb and Tl present in the water. Finally, the dynamics of the bacterial communities was described under real conditions in an aerobic pilot for the treatment of an AMD rich in As and installed on site. These communities were dominated by Fe-oxidizing bacteria, and their spatial and temporal structure modifications appeared to be associated to variations of water physico-chemistry (dissolved oxygen, temperature, pH, redox potential, sulfate, arsenic and iron(II) concentrations). The knowledge acquired during this thesis may serve as a basis for the design of passive and inexpensive eco-technologies applicable to the management and remediation of former mining sites.Les déchets sulfurés issus de l’extraction des minerais métalliques génèrent des drainages miniers acides (DMA), contenant des éléments toxiques tels que l’arsenic (As), l’antimoine (Sb) et le thallium (Tl). Des procédés de remédiation utilisant des communautés microbiennes ont été développés afin d’éliminer ces polluants des DMA, mais les processus biologiques en jeu dans ces traitements doivent encore être maîtrisés pour garantir leur efficacité. Les verrous scientifiques, objets de la thèse, résident dans (1) la méconnaissance des transformations microbiennes, directe et indirectes, de Sb et Tl, et, (2) pour l’As, la faible compréhension des relations qui existent entre la dynamique des communautés microbiennes, leur potentiel fonctionnel, la physico-chimie des eaux et l’efficacité des traitements appliqués aux DMA. Une approche pluridisciplinaire, principalement basée sur des outils d’écologie microbienne et de physico-chimie, a permis de caractériser la diversité des communautés microbiennes capables de transformer directement ou indirectement As et Sb, à différentes échelles expérimentales : réacteur batch, dispositif à flux continu de laboratoire et pilote de terrain. Un consortium microbien capable de tolérer jusqu’à 100 mM d’antimonite et de l’oxyder en conditions acides (pH < 4), équivalentes à celles des DMA, a été obtenu à partir d’un sol contaminé au Sb. Un bioréacteur colonne de laboratoire, alimenté en continu avec un DMA réel et inoculé avec un consortium bactérien sulfato-réducteur issu de ce DMA, a permis l’élimination de la quasi-totalité de l’As, du Sb et du Tl présents dans l’eau. Enfin, la dynamique des communautés bactériennes au sein d’un dispositif aérobie de traitement d’un DMA riche en As installé sur site a été décrite. Ces communautés sont dominées par des bactéries Fe-oxydantes, et les modifications spatiales et temporelles de leur structure apparaissent associées aux variations de la physico-chimie de l’eau (concentration en oxygène dissous, température, pH, potentiel rédox, concentrations en sulfate, arsenic et fer(II)). Les connaissances acquises au cours de cette thèse pourront servir de base à la conception d’éco-technologies passives et peu coûteuses applicables à la gestion et la remédiation d’anciens sites miniers

Actors and mechanisms of microbial transformation of arsenic, antimony and thallium, towards a strategy of eco-technology applied to the management of mining sites

Les déchets sulfurés issus de l’extraction des minerais métalliques génèrent des drainages miniers acides (DMA), contenant des éléments toxiques tels que l’arsenic (As), l’antimoine (Sb) et le thallium (Tl). Des procédés de remédiation utilisant des communautés microbiennes ont été développés afin d’éliminer ces polluants des DMA, mais les processus biologiques en jeu dans ces traitements doivent encore être maîtrisés pour garantir leur efficacité. Les verrous scientifiques, objets de la thèse, résident dans (1) la méconnaissance des transformations microbiennes, directe et indirectes, de Sb et Tl, et, (2) pour l’As, la faible compréhension des relations qui existent entre la dynamique des communautés microbiennes, leur potentiel fonctionnel, la physico-chimie des eaux et l’efficacité des traitements appliqués aux DMA. Une approche pluridisciplinaire, principalement basée sur des outils d’écologie microbienne et de physico-chimie, a permis de caractériser la diversité des communautés microbiennes capables de transformer directement ou indirectement As et Sb, à différentes échelles expérimentales : réacteur batch, dispositif à flux continu de laboratoire et pilote de terrain. Un consortium microbien capable de tolérer jusqu’à 100 mM d’antimonite et de l’oxyder en conditions acides (pH < 4), équivalentes à celles des DMA, a été obtenu à partir d’un sol contaminé au Sb. Un bioréacteur colonne de laboratoire, alimenté en continu avec un DMA réel et inoculé avec un consortium bactérien sulfato-réducteur issu de ce DMA, a permis l’élimination de la quasi-totalité de l’As, du Sb et du Tl présents dans l’eau. Enfin, la dynamique des communautés bactériennes au sein d’un dispositif aérobie de traitement d’un DMA riche en As installé sur site a été décrite. Ces communautés sont dominées par des bactéries Fe-oxydantes, et les modifications spatiales et temporelles de leur structure apparaissent associées aux variations de la physico-chimie de l’eau (concentration en oxygène dissous, température, pH, potentiel rédox, concentrations en sulfate, arsenic et fer(II)). Les connaissances acquises au cours de cette thèse pourront servir de base à la conception d’éco-technologies passives et peu coûteuses applicables à la gestion et la remédiation d’anciens sites miniers.Sulfide wastes from the extraction of metal ores generate acidic mine drainage (AMD), containing toxic elements such as arsenic (As), antimony (Sb) and thallium (Tl). Remediation processes using microbial communities have been developed to remove these pollutants from AMD, but the biological processes involved in these treatments still need to be controlled to ensure their effectiveness. The scientific obstacles, which are the subject of the thesis, lie in (1) a lack of knowledge on direct and indirect microbial transformations of Sb and Tl, and (2) for As, a weak understanding of relationships that exist between dynamics of microbial communities, their functional potential, water physico-chemistry and efficiency of treatments applied to AMD. A multidisciplinary approach, mainly based on microbial ecology and physico-chemistry tools, allowed to characterize the diversity of microbial communities capable of directly or indirectly transforming As and Sb at increasing experimental scales: batch reactor, laboratory continuously fed systems, and pilot on site. A microbial consortium able of tolerating up to 100 mM of antimonite and oxidizing it under acidic conditions (pH <4), equivalent to those of AMD, was obtained in a batch system in the laboratory from contaminated soil at Sb. A laboratory column bioreactor, fed continuously with a real AMD and inoculated with a bacterial sulfate-reducing consortium enriched from this AMD, allowed the elimination of almost all the As, Sb and Tl present in the water. Finally, the dynamics of the bacterial communities was described under real conditions in an aerobic pilot for the treatment of an AMD rich in As and installed on site. These communities were dominated by Fe-oxidizing bacteria, and their spatial and temporal structure modifications appeared to be associated to variations of water physico-chemistry (dissolved oxygen, temperature, pH, redox potential, sulfate, arsenic and iron(II) concentrations). The knowledge acquired during this thesis may serve as a basis for the design of passive and inexpensive eco-technologies applicable to the management and remediation of former mining sites

Microbial transformations of arsenic : from metabolism to bioremediation

International audienc

Dynamics of bacterial communities in a field-scale pilot treating As-rich acid mine drainage

International audienceArsenic rich AMDs (Acid Mine Drainages) represent a major source of pollution foraquatic ecosystems. Microbially driven iron (Fe) and arsenic (As) oxidation and precipitation represent a promising strategy to treat this pollution. A better understanding of thebiogeochemical mechanisms involved is required prior any further exploitation of this microbial potential. A field-scale pilot was implemented at the Carnoul`es mine (France) for thetreatment of AMD. It is an ergonomic and passive aerobic system: five treatment units of1.5 m2 are combined vertically in series and fed with the AMD water by gravitation flow.Biogenic precipitates (corresponding to Fe- and As-rich biofilms) covered the bottom of theunits. Inlet water and biogenic precipitates were collected over a 7 months period. Wedetermined the bacterial community structure in the precipitates by fingerprint (ARISA),metabarcoding (16S rRNA gene) and qPCR targeting arsenite oxidase gene aioA. Chemicaland mineralogical analyses were conducted on the precipitates and on the feed water. Thebacterial communities in the precipitates developed from the indigenous communities of theAMD used to feed the pilot. Our results showed an evolution of these communities overtime associated with an increase of the potential genetic for As oxidation. The proportionof As(V) in the precipitates and arsenic removal efficiency fluctuated, with maximum levelsof 99% and 97 % respectively. This work provided information about microbial dynamicsand pollution removal efficiency in a treatment pilot under field conditions. It will serve forfuture design of a bioremediation system to treat As-rich AMD

Bio-precipitation of arsenic and antimony in a sulfate-reducing bioreactor treating real acid mine drainage water

Arsenic (As) and antimony (Sb) from mining sites can seep into aquatic ecosystems by acid mine drainage (AMD). Here, the possibility of concomitantly removing As and Sb from acidic waters by precipitation of sulfides induced by sulfate-reducing bacteria (SRB) was investigated in a fixed-bed column bioreactor. The real AMD water used to feed the bioreactor contained nearly 1 mM As, while the Sb concentrations were increased (0.008 ± 0.006 to 1.01 ± 0.07 mM) to obtain an Sb/As molar ratio = 1. Results showed that the addition of Sb did not affect the efficiency of As bio-precipitation. Sb was removed efficiently (up to 97.9% removal) between the inlet and outlet of the bioreactor, together with As (up to 99.3% removal) in all conditions. Sb was generally removed as it entered the bioreactor. Appreciable sulfate reduction occurred in the bioreactor, which could have been linked to the stable presence of a major SRB operational taxonomic unit affiliated with the Desulfosporosinus genus. The bacterial community included polymer degraders, fermenters, and acetate degraders. Results suggested that sulfate reduction could be a suitable bioremediation process for the simultaneous removal of Sb and As from AMD

Bio-precipitation of arsenic and antimony from acid mine water in a sulfate-reducing bioreactor

International audienc

Role of micro-organisms in the leaching of critical metals from tungsten mine wastes: from the microscale to the field scale

International audienceThe availability of primary resources will continue to be a growing need to satisfy the increasing global demand for raw materials, with the consequence of the production of waste products from exploration and mining activities. An innovative approach is to consider tailings/wastes from mining in a circular economy concept, as secondary raw materials. The REVIVING project has been developed in this context, with coupled fundamental and applied approaches, with the objective of obtaining optimized experimental models for efficient recycling of critical metals from mining wastes, based on the manipulation of the indigenous tailing’s microbiome.We tested different leaching processes of metals of interest (Cu, Mn, Mg, Zn, W and Mo) from the mining waste of Panasqueira (Portugal). A first series of batch experiments was carried out with four bacteria isolated from this waste at increasing cell concentrations (107, 108 and 109 cells/ml) and under variable physiological conditions (live, dead, with nutrients...). Another batch reactor is also currently applied to evaluate the acidophilic leaching process via ferrooxidizing and sulfo-oxidizing micro-organisms enriched from the Panasqueira mine waste. Results from column reactors showed a limitation of the mobility of bacterial cells in the reactor due to the very small waste grain size leading to a strong filtration of the cells. The optimization of the cell transfer process is underway with a system dynamics approach in columns with different filling materials (waste, residues...) and experimental conditions (flow, saturation, geochemistry, microbiology...).The continuous monitoring of physico-chemical parameters (pH, O2, salinity and concentrations of metals and major ions...) and biological parameters (cell density by cytometry, qPCR and diversity by DNA-metabarcoding) will allow the identification of the dominant processes for a better understanding of the bioleaching phenomenon and therefore to design an efficient system for recycling metals from mining waste on a large scale

Role of micro-organisms in the leaching of critical metals from tungsten mine wastes: from the microscale to the field scale

International audienceThe availability of primary resources will continue to be a growing need to satisfy the increasing global demand for raw materials, with the consequence of the production of waste products from exploration and mining activities. An innovative approach is to consider tailings/wastes from mining in a circular economy concept, as secondary raw materials. The REVIVING project has been developed in this context, with coupled fundamental and applied approaches, with the objective of obtaining optimized experimental models for efficient recycling of critical metals from mining wastes, based on the manipulation of the indigenous tailing’s microbiome.We tested different leaching processes of metals of interest (Cu, Mn, Mg, Zn, W and Mo) from the mining waste of Panasqueira (Portugal). A first series of batch experiments was carried out with four bacteria isolated from this waste at increasing cell concentrations (107, 108 and 109 cells/ml) and under variable physiological conditions (live, dead, with nutrients...). Another batch reactor is also currently applied to evaluate the acidophilic leaching process via ferrooxidizing and sulfo-oxidizing micro-organisms enriched from the Panasqueira mine waste. Results from column reactors showed a limitation of the mobility of bacterial cells in the reactor due to the very small waste grain size leading to a strong filtration of the cells. The optimization of the cell transfer process is underway with a system dynamics approach in columns with different filling materials (waste, residues...) and experimental conditions (flow, saturation, geochemistry, microbiology...).The continuous monitoring of physico-chemical parameters (pH, O2, salinity and concentrations of metals and major ions...) and biological parameters (cell density by cytometry, qPCR and diversity by DNA-metabarcoding) will allow the identification of the dominant processes for a better understanding of the bioleaching phenomenon and therefore to design an efficient system for recycling metals from mining waste on a large scale

Fractionnement des isotopes stables de l’antimoine par un consortium microbien issu d’un sédiment contaminé

International audienc