Role of microbial processes in arsenic cycling

Arsenic (As) is a toxic metalloid of geogenic origins that can lead to groundwater contamination and serious health consequences. South and Southeast Asia, the most populated regions of the world, are particularly affected as the access to water treatment facilities is limited and many people, mainly in rural areas still rely on shallow groundwater wells. Various mechanisms of As release to the groundwater have been suggested to date. Yet, the most commonly accepted one is that As is released from aquifer sediments during microbially-mediated reductive dissolution of As-bearing Fe(III) (oxyhydr)oxide minerals. This process, however, requires the presence of bioavailable carbon (C) that Fe(III)-reducing microorganisms need as energy, electron and carbon sources for their activity. Most laboratory studies, however, used simple fatty acids or sugars, often at high and not environmentally relevant concentrations, instead of naturally-occurring organic matter (OM). Therefore, in this work extracted in-situ OM was characterized (FTIR, NMR, EEM and Pyrolysis GC/MS), and used in 100-day microcosm experiments to determine Fe(III) mineral reduction, As mobilization and the microbial community composition compared to easily bioavailable fatty acids. Furthermore, this work explored the potential of single C compound such as methane (CH4) as the electron donor and driver of reductive dissolution of Fe- and As-bearing sediments. This work for the first time demonstrated that CH4, widely abundant in many As contaminated aquifers across South and Southeast Asia, can be efficiently used by methanotrophic archaea such as Candidatus Methanoperedens to reduce Fe(III) and consequently mobilize As to groundwater. Finally, this PhD thesis revealed main microbial processes occurring in As contaminated aquifer in Vietnam. Some of these process such as SO42- reduction, Fe(III) reduction, Fe2+ oxidation or methanotrophy can directly affect the fate of As in groundwater. Other processes that were found dominant in situ such as methanogenesis and fermentation indirectly favor As mobilization by providing wide range of electron donors. Overall this PhD thesis broadened our understanding of As biogeochemical cycling and filled some knowledge gaps about microbial contribution to this cycle

Microbial transformation of biogenic and abiogenic Fe minerals followed by in-situ incubations in an As-contaminated vs. non-contaminated aquifer

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Carbon and methane cycling in arsenic-contaminated aquifers

Geogenic arsenic (As) contamination of groundwater is a health threat to millions of people worldwide, particularly in alluvial regions of South and Southeast Asia. Mitigation measures are often hindered by high heterogeneities in As concentrations, the cause(s) of which are elusive. Here we used a comprehensive suite of stable isotope analyses and hydrogeochemical parameters to shed light on the mechanisms in a typical high-As Holocene aquifer near Hanoi where groundwater is advected to a low-As Pleistocene aquifer. Carbon isotope signatures (δ$^{13}$C-CH$_{4}$, δ$^{13}$C-DOC, δ$^{13}$C-DIC) provided evidence that fermentation, methanogenesis and methanotrophy are actively contributing to the As heterogeneity. Methanogenesis occurred concurrently where As levels are high (>200 µg/L) and DOC-enriched aquitard pore water infiltrates into the aquifer. Along the flowpath to the Holocene/Pleistocene aquifer transition, methane oxidation causes a strong shift in δ$^{13}$C-CH$_{4}$ from -87‰ to +47‰, indicating high reactivity. These findings demonstrate a previously overlooked role of methane cycling and DOC infiltration in high-As aquifers

Spatial and temporal evolution of groundwater arsenic contamination in the Red River delta, Vietnam: Interplay of mobilisation and retardation processes

Geogenic arsenic (As) contamination of groundwater poses a major threat to global health, particularly in Asia. To mitigate this exposure, groundwater is increasingly extracted from low-As Pleistocene aquifers. This, however, disturbs groundwater flow and potentially draws high-As groundwater into low-As aquifers. Here we report a detailed characterisation of the Van Phuc aquifer in the Red River Delta region, Vietnam, where high-As groundwater from a Holocene aquifer is being drawn into a low-As Pleistocene aquifer. This study includes data from eight years (2010–2017) of groundwater observations to develop an understanding of the spatial and temporal evolution of the redox status and groundwater hydrochemistry. Arsenic concentrations were highly variable (0.5–510 μg/L) over spatial scales of <200 m. Five hydro(geo)chemical zones (indicated as A to E) were identified in the aquifer, each associated with specific As mobilisation and retardation processes. At the riverbank (zone A), As is mobilised from freshly deposited sediments where Fe(III)-reducing conditions occur. Arsenic is then transported across the Holocene aquifer (zone B), where the vertical intrusion of evaporative water, likely enriched in dissolved organic matter, promotes methanogenic conditions and further release of As (zone C). In the redox transition zone at the boundary of the two aquifers (zone D), groundwater arsenic concentrations decrease by sorption and incorporations onto Fe(II) carbonates and Fe(II)/Fe(III) (oxyhydr)oxides under reducing conditions. The sorption/incorporation of As onto Fe(III) minerals at the redox transition and in the Mn(IV)-reducing Pleistocene aquifer (zone E) has consistently kept As concentrations below 10 μg/L for the studied period of 2010–2017, and the location of the redox transition zone does not appear to have propagated significantly. Yet, the largest temporal hydrochemical changes were found in the Pleistocene aquifer caused by groundwater advection from the Holocene aquifer. This is critical and calls for detailed investigations

Biochar as a potential inoculant carrier for plant-beneficial bacteria

In recent years, biochar has gained importance as a way to deal with global climate change, by sequestering C into soil, also as a soil amendment and bioremediation tool. Many studies have demonstrated the positive influence of biochar on soil quality and subsequently, plant growth, although the results are not consistent and climate seems to be the main reason for this inconsistency. Biochar, with its highly porous structure, is believed to provide a suitable habitat for many microorganisms by protecting them from predation and desiccation; additionally it might also provide reduced carbon as an energy source and mineral nutrients. However, not much attention has been focused on biochar and microbial interactions. In this study, we propose the use of biochar as an inoculant carrier for plant-beneficial bacteria. Presently the most commonly used carrier for bacterial inoculants is peat moss. However, peat is a natural and non-renewable resource; its overuse is of great environmental concern. Moreover, rapidly decreasing reserves of peat have led to price increases, which ultimately limit its use. A good bacterial carrier must possess a number of key features. It should be unlimited, locally available and inexpensive; furthermore, it should have good water holding capacity and aeration properties and furthermore, it should sustain growth and survival of bacteria over time. Additionally, the right inoculant carrier should be non-toxic, environmentally friendly, and easily produced, sterilized and handled in the field. Finally, it should easily release bacteria into the soil, be simply converted to powder, mixable, packageable and adhere to the seed. I hypothesised that biochar can fulfill the conditions of a suitable carrier; its chemical and physical properties can create appropriate conditions for bacteria habitat and provide some nutrients that sustain survival and growth of bacteria over time. Moreover, it was expected that biochar can be successfully used as seed-coating material. Therefore the objectives of this research were to: 1) determine whether biochar can serve as a carrier for beneficial bacteria, 2) identify biochar(s) which sustains bacteria viability at the highest population density, 3) create a seed-coating system which could potentially be used in agriculture, 4) evaluate the effect of biochar inoculant and seed-coating on plant growth. Two bacteria, P- solubilizing Pseudomonas libanensis and N2-fixing Bradyrhizobium japonicum, were selected as model bacteria. P. libanensis biochar inoculant and seed-coating were tested on corn plants, while B. japonicum was tested on soybean. The results of the storage time experiment demonstrated that not every biochar can be a suitable carrier; however, two out of the four were able to sustain B. japonicum survival for as long as 8 months at a population density high enough to secure efficient soybean nodulation. Moreover, I demonstrated that biochar is a suitable material for seed-coating. The storage time experiment showed that biochar seed-coating can support the survival of P.libanensis and B. japonicum for up to four months at a relatively high population density; however, the abundance of the population strongly depends on storage temperature. I also demonstrated that the main reason behind a quick decline in the bacteria population is related to the pH of the carrier. Finally, a germination assay and greenhouse experiment were carried out to evaluate biochar inoculant and seed-coating effect on plant growth. This research clearly demonstrated that biochar can be a suitable bacterial carrier and can successfully replace commercially used peat moss. Biochar rhizobial inoculant can significantly improve soybean growth and reduce N fertilizer demand. Finally, biochar seed-coating might be considered an efficient end easy way to provide beneficial bacteria to the crop.Dans les dernières années, le biocharbon a gagné en importance, autant pour régler les changements climatiques, que comme amendement pour le sol et outil de bioremédiation. De études ont démontré l’influence positive du biocharbon sur la qualité du sol et des plantes qui y poussent. Par contre, les résultats de ces études manquent de cohérence, le climat semblant en être la cause principale. Il y a lieu de croire que la structure hautement poreuse du biocharbon pourrait offrir un habitat convenable aux microorganismes, en les protégeant de la prédation et de la dessiccation. De plus, le biocharbon pourrait offrir une source énergétique et des éléments minéraux sous forme de carbone. Jusqu’à maintenant, l’attention des chercheurs n’était toutefois pas rivée sur l’interaction entre le biocharbon et les microbes. Dans cette étude, nous proposons l’utilisation du biocharbon comme vecteur d’inoculation pour les bactéries. En ce moment, le vecteur le plus utilisé est la tourbe-mousse. Par contre, la tourbe est une ressource non renouvelable, dont l’usage excessif est problématique pour l’environnement. Qui plus est, la baisse des réserves de tourbe a provoqué une hausse des prix qui limite son usage. Un bon vecteur doit posséder certaines caractéristiques pour accomplir sa fonction : être illimité, disponible localement et peu coûteux; avoir une bonne capacité de rétention d’eau et des propriétés d’aération; et, surtout, soutenir la croissance et la survie des bactéries pour une certaine période de temps. Il doit aussi être non toxique, respectueux de l’environnement, facile à produire et manipulé dans les champs. Finalement, il doit facilement libérer les bactéries dans le sol, se convertir aisément en poudre, se mélanger, s’emballer et coller à la graine. Nous avons formulé l’hypothèse que le biocharbon remplit ces conditions. De plus, nous nous attendions à ce que le biocharbon soit utilisé avec succès comme matériel de pelliculage des semences. Les objectifs de cette recherche étaient donc de : 1) déterminer si le biocharbon peut servir de vecteur pour des bactéries bénéfiques; 2) choisir le biocharbon qui soutient la viabilité bactérienne à la densité de population la plus élevée; 3) créer un système de pelliculage des semences utilisable en agriculture; et 4) évaluer l’effet de l’inoculant de biocharbon et du pelliculage des semences sur la croissance des plantes. Deux bactéries, la Pseudomonas libanensis qui solubilise le phosphore et la Bradyrhizobium japonicum qui fixe l’azote atmosphérique, ont été choisies comme bactéries modèles. L’inoculant et le pelliculage des semences développés à partir du biocharbon P. libanensis ont été testés sur du maïs et ceux développés à partir de B. japonicum sur du soja. Les résultats de l’expérience de temps de conservation démontrent que deux vecteurs sur quatre ont permis la survie de la bactérie B. japonicum, pour huit mois, à une densité de population assez élevée pour assurer la nodulation efficace du soja. De plus, nous avons démontré que le biocharbon est un matériel adéquat au pelliculage des semences. Notre expérience de temps de conservation a démontré que le pelliculage de semences au biocharbon peut soutenir la survie des bactéries P.libanensis et B. japonicum, pour quatre mois, à une densité de population relativement élevée, bien que cette densité dépende fortement de la température de conservation. Nous avons aussi démontré que la raison principale du déclin rapide de la population de bactéries est liée au pH du vecteur. Finalement, des expériences de germination et en serre ont été menées pour évaluer les effets de l’inoculant et du pelliculage des semences développé à partir du biocharbon sur les plantes. Cette recherche a clairement démontré que le biocharbon peut être un porteur bactérien adéquat et peut remplacer la tourbe-mousse commerciale. L’inoculant rhizobien de biocharbon peut grandement améliorer la croissance du soja et réduire la demande en engrais d’azote