Evaluation of Silicate Minerals for pH Control During Bioremediation: Application to Chlorinated Solvents

Accurate control of groundwater pH is of critical importance for in situ biological treatment of chlorinated solvents. This study evaluated a novel approach for buffering subsurface pH that relies on the use of silicate minerals as a long-term source of alkalinity. A screening methodology based on thermodynamic considerations and numerical simulations was developed to rank silicate minerals according to their buffering efficiency. A geochemical model including the main microbial processes driving groundwater acidification and silicate mineral dissolution was developed. Kinetic and thermodynamic data for silicate minerals dissolution were compiled. Results indicated that eight minerals (nepheline, fayalite, glaucophane, lizardite, grossular, almandine, cordierite, and andradite) could potentially be used as buffering agents for the case considered. A sensitivity analysis was conducted to identify the dominant model parameters and processes. This showed that accurate characterization of mineral kinetic rate constants and solubility are crucial for reliable prediction of the acid-neutralizing capacity. In addition, the model can be used as a design tool to estimate the amount of mineral (total mass and specific surface area) required in field application

Using Silicate Mineral Particles for pH Control during in situ Bioremediation of Chlorinated Ethene Source Zones

Soil and groundwater pollution by chlorinated solvents such as tricholorethene (TCE) and tetrachloroethene (PCE) is a frequent problem in the industrialized world. Chlorinated solvents, characterized by a low solubility and a density greater than water, form dense non-aqueous phase liquids (DNAPLs) when released in the subsurface. DNAPLs accumulate along low permeability layers and slowly dissolve in groundwater acting as a long-term source of contamination that can last for decades. Remediation of chlorinated solvent DNAPLs is recognized as one of the most challenging problems in the field of environmental remediation. In situ bioremediation (ISB) is a promising and cost-effective technology for their removal that relies on the activity of specialized microorganisms able to transform chlorinated compounds to ethene (a non-toxic product) via a stepwise anaerobic process called organohalide respiration (OHR). ISB has been applied successfully for the treatment of dissolved phase plumes since the early 1980’s. However, its application for source zones, where contaminants are present as DNAPLs, is relatively recent and has only been developed in the last decade. One of the major issues limiting source zone ISB is the acidification of the groundwater due to the transformation of chlorinated compounds by organohalide-respiring bacteria (OHRB) and the production of organic acids by fermentative microbial populations. OHRB are inactivated when the pH is below 5-6 and therefore pH buffer amendments are required when the soil buffering capacity is insufficient. In field applications, the most common method used for pH adjustment is the injection of soluble buffers such as sodium bicarbonate. However, this method requires frequent injections and constant monitoring as alkalinity is rapidly consumed. Therefore, there is a need to develop more efficient and long-lasting buffering strategies. The objective of this thesis was to develop a novel method for long-term control of groundwater pH that relies on the use of ground silicate minerals. Silicate minerals may act as a long-term source of alkalinity release as i) they dissolve slowly compared to carbonates and ii) their dissolution rate and solubility is pH-dependent and increase with acidic pH. In addition, they are easily available at an affordable cost as a raw material or as a by-product of industrial processes. Silicate minerals are the most common rock forming mineral and constitute a very diverse group with highly variable dissolution rates, solubilities and compositions. Only a restricted numbers of these minerals present appropriate characteristics to act as buffering agents. A screening methodology, based on numerical simulations, thermodynamic and kinetic considerations, was developed to select potential candidates for pH control. A geochemical model including the main microbial processes driving groundwater acidification and silicate mineral dissolution was developed as well. This model provides a useful design tool to estimate the mineral requirement in the perspective of field applications. The results of numerical simulations showed that a dozen silicate minerals have the potential to act as buffering agents. Abiotic batch experiments were conducted with five silicate minerals (nepheline, fay alite, forsterite, diopside and andradite) to validate and improve the geochemical model. Abiotic experiments confirmed the buffering potential of these minerals and revealed the importance of secondary precipitation, a process not included in the original formulation of the model. Precipitation of secondary phases can decrease the reactivity of silicates, reduce the aquifer porosity and precipitate nutrients. Therefore, prediction of secondary precipitations was included in the model in order to predict this type of reaction. The influence of silicate mineral dissolution on OHRB and fermentative bacteria was investigated in batch cultures. As expected, the five silicate minerals (except nepheline) were able to maintain the pH in the tolerance range for the three microbial consortia tested. However, transformation of cA-DCE to ethene was completely inhibited in most of the experiments in the presence of minerals. These results showed that compatibility of silicate minerals with the bacterial community involved in in situ bioremediation has to be carefully evaluated prior to their use for pH control at a specific site. Subsequently, the long-term buffering potential of the most promising buffering agents (diopside, fayalite, forsterite) was tested in continuous-flow column studies simulating chloroethene source zone conditions for six and a half month and a half. In contrast to batch experiments, transformation of cis-DCE to ethene was not inhibited by mineral dissolution in continuous flow systems. Olivine minerals (such as fayalite and forsterite) appeared as suitable pH buffering agents. They successfully maintained the pH in the neutral range (7.5 for forsterite and 6.5 for fayalite) and sustained the activity of OHRB bacteria. In contrast, the buffering potential of diopside rapidly decreased due to the formation of a less-reactive cation-depleted leached layer at the mineral surface. This thesis demonstrated the potential of silicate minerals to act as a long-term source of alkalinity release for groundwater pH control. A global strategy for the selection of appropriate buffering agents based on site characteristics was developed. This methodology was applied to the particular case of chlorinated solvent ISB but can be extended to any groundwater remediation technology requiring close to neutral pH conditions

Reference-free detection of isolated SNPs

International audienceDetecting Single Nucleotide Polymorphisms (SNPs) between genomes is becoming a routine task with Next Generation Sequencing. Generally, SNP detection methods use a reference genome. As non-model organisms are increasingly investigated, the need for reference-free methods has been amplified. Most of the existing reference-free methods have fundamental limitations: they can only call SNPs between exactly two datasets, and/or they require a prohibitive amount of computational resources. The method we propose, DISCOSNP, detects both heterozygous and homozygous isolated SNPs from any number of read datasets, without a reference genome, and with very low memory and time footprints (billions of reads can be analyzed with a standard desktop computer). To facilitate downstream genotyping analyses, DISCOSNP ranks predictions and outputs quality and coverage per allele. Compared to finding isolated SNPs using a state-of-the-art assembly and mapping approach, DISCOSNP requires significantly less computational resources, shows similar precision/recall values, and highly ranked predictions are less likely to be false positives. An experimental validation was conducted on an arthropod species (the tick Ixodes ricinus) on which de novo sequencing was performed. Among the predicted SNPs that were tested, 96% were successfully genotyped and truly exhibited polymorphism

Evaluation of silicate minerals for pH control during bioremediation: Application to chlorinated solvents

Accurate control of groundwater pH is of critical importance for in situ biological treatment of chlorinated solvents. This study evaluated a novel approach for buffering subsurface pH that relies on the use of silicate minerals as a long-term source of alkalinity. A screening methodology based on thermodynamic considerations and numerical simulations was developed to rank silicate minerals according to their buffering efficiency. A geochemical model including the main microbial processes driving groundwater acidification and silicate mineral dissolution was developed. Kinetic and thermodynamic data for silicate minerals dissolution were compiled. Results indicated that eight minerals (nepheline, fayalite, glaucophane, lizardite, grossular, almandine, cordierite, and andradite) could potentially be used as buffering agents for the case considered. A sensitivity analysis was conducted to identify the dominant model parameters and processes. This showed that accurate characterization of mineral kinetic rate constants and solubility are crucial for reliable prediction of the acid-neutralizing capacity. In addition, the model can be used as a design tool to estimate the amount of mineral (totalmass and specific surface area) required in field application

Modelling migration and dissolution of mineral particles in saturated porous media

Understanding and predicting the fate in soils and other porous media of solid mineral particles with grain diameters in the micrometer range is important in a number of environmental and civil engineering applications, including subsurface hydrology, wastewater treatment and oil/gas production. In this context, deep-bed filtration theory is commonly applied to model particle detachment and deposition. Most existing models however neglect some processes that can modify groundwater flow patterns, particle concentration and attachment/detachment coefficients. The aim of this work was to develop a mechanistic model to study the transport and mobilization/immobilization of mineral particles in saturated porous media. The model accounts for particle advection and dispersion, deep-bed filtration, porosity and hydraulic conductivity changes associated with deposition and mobilization, and for particle dissolution. In addition, the deep-bed filtration coefficients vary with the characteristics and composition of the pore-solution, ionic strength and pH in particular. The groundwater flow and reactive transport simulator PHAST was used to implement the model. Measurements from a variety of deep-bed filtration and mineral dissolution experiments were used to calibrate and validate the model. A satisfactory comparison was found in most situations. A sensitivity analysis was subsequently performed to identify the conditions in which some of the processes (such as hydraulic conductivity changes and particle dissolution) can be neglected and therefore less sophisticated numerical tools can be used

Buffering soil-water acidity in chlorinated solvent bioremediation schemes

Chlorinated solvents form a significant part of groundwater contamination worldwide. They are difficult to remove via physical means, and anaerobic source-zone remediation based on provision of fermentable e-donor is an attractive clean-up dechlorination option. However, organic acids and HCl lower the groundwater pH and thereby stall the microbial consortia responsible for the biodegradation process. Often, the soil’s natural buffering capacity will be exceeded, in which case a strategy of adding buffer to the groundwater is a priori beneficial to maintain dechlorination. Geochemical modelling was used to investigate the feasibility of adding naturally occurring buffering minerals to the groundwater for pH control. The simulations revealed that anorthite has the potential to be used as a sustainable pH buffering mineral.ECOLLB

Effect of heterogeneity on enhanced reductive dechlorination: Analysis of remediation efficiency and groundwater acidification

Enhanced reductive dehalogenation is an attractive in situ treatment technology for chlorinated contaminants. The process includes two acid-forming microbial reactions: fermentation of an organic substrate resulting in short-chain fatty acids, and dehalogenation resulting in hydrochloric acid. The accumulation of acids and the resulting drop of groundwater pH are controlled by the mass and distribution of chlorinated solvents in the source zone, type of electron donor, alternative terminal electron acceptors available and presence of soil mineral phases able to buffer the pH (such as carbonates). Groundwater acidification may reduce or halt microbial activity, and thus dehalogenation, significantly increasing the time and costs required to remediate the aquifer. In previous work a detailed geochemical and groundwater flow simulator able to model the fermentation-dechlorination reactions and associated pH change was developed. The model accounts for the main processes influencing microbial activity and groundwater pH, including the groundwater composition, the electron donor used and soil mineral phase interactions. In this study, the model was applied to investigate how spatial variability occurring at the field scale affects dechlorination rates, groundwater pH and ultimately the remediation efficiency. Numerical simulations were conducted to examine the influence of heterogeneous hydraulic conductivity on the distribution of the injected, fermentable substrate and on the accumulation/dilution of the acidic products of reductive dehalogenation. The influence of the geometry of the DNAPL source zone was studied, as well as the spatial distribution of soil minerals. The results of this study showed that the heterogeneous distribution of the soil properties have a potentially large effect on the remediation efficiency. For examples, zones of high hydraulic conductivity can prevent the accumulation of acids and alleviate the problem of groundwater acidification. The conclusions drawn and insights gained from this modeling study will be useful to design improved in-situ enhanced dehalogenation remediation schemes

Traction Forces of Endothelial Cells under Slow Shear Flow

Endothelial cells are constantly exposed to fluid shear stresses that regulate vascular morphogenesis, homeostasis, and disease. The mechanical responses of endothelial cells to relatively high shear flow such as that characteristic of arterial circulation has been extensively studied. Much less is known about the responses of endothelial cells to slow shear flow such as that characteristic of venous circulation, early angiogenesis, atherosclerosis, intracranial aneurysm, or interstitial flow. Here we used a novel, to our knowledge, microfluidic technique to measure traction forces exerted by confluent vascular endothelial cell monolayers under slow shear flow. We found that cells respond to flow with rapid and pronounced increases in traction forces and cell-cell stresses. These responses are reversible in time and do not involve reorientation of the cell body. Traction maps reveal that local cell responses to slow shear flow are highly heterogeneous in magnitude and sign. Our findings unveil a low-flow regime in which endothelial cell mechanics is acutely responsive to shear stress

Oral Narrative Skills in French Adults Who Are Functionally Illiterate: Linguistic Features and Discourse Organization

International audiencePurposeTo investigate the nature and extent of oral language difficulties encountered by adults who are functionally illiterate.MethodFifty-two men and women identified as functionally illiterate, together with a group of control individuals of comparable age, sex, and socioprofessional background, produced a narrative intended for an absent recipient based on a sequence of pictures featuring a cast of 3 protagonists. All narratives were transcribed in their entirety and coded in terms of linguistic features and discourse organization.ResultsAs a group, the participants who were illiterate had great difficulty handling morphosyntactic rules, referential cohension, and the narrative schema. Furthermore, a qualitative analysis highlighted considerable interindividual variability in narrative styles, reflecting different types of difficulties.ConclusionsIndividuals who have not succeeded in learning to read also have impaired oral language abilities. This may affect different aspects of communication skills to a greater or lesser extent. These results have implications for teaching written language to adult learners