Modelling Biogeochemical Cycles Across Scales: From Whole-Lake Phosphorus Dynamics to Microbial Reaction Systems

Lakes are ecologically, economically, and culturally significant resources that are, at the same time, very fragile and sensitive to human disturbances. During the last decades, intensified urbanization and discharge of nutrients lead to the increase of lake eutrophication in many regions of the world. Moreover, biogeochemical cycles within the lakes are changing due to climate warming, which increases water temperature and affects physical and hydrological lake regimes. In this thesis, I investigate a vast scope of the natural and anthropogenic processes affecting the biogeochemical cycles in lakes at different scales. In particular, I examine the cascading effect of the climate, regional weather, human interventions, and microbial control on phosphorus dynamics in lakes. In Chapter 2, I demonstrate that on the lake scale, phosphorus cycle is driven by internal loading and iron recycling, while it is vulnerable to the reduction of ice cover. To achieve that, I expand the existing MyLake model by incorporating a sediment diagenesis module. Moreover, I develop the continuous reaction network that couples biogeochemical reactions taking place both in water column and sediment. In the modeling scenarios, I assess the importance of the sediment processes and the effects of the climatic and anthro- pogenic drivers on water quality in Lake Vansjø, Norway. I also highlight the importance of phosphorus accumulation within the lake that controls timing and magnitude of bio- geochemical lake responses to external forcing. This includes projected changes in the air temperature, absence of ice cover, and potential management practices. In Chapter 3, I contribute to the long-standing understanding that on the scales of microbial systems, the respiration reactions exert substantial control on biogeochemi- cal cycles by regulating the availability of the electron donors and acceptors, secondary minerals, adsorption sites, and alkalinity. Moreover, I develop a new conceptual model to simulate the preferential catabolic reaction pathways based on power produced in reactions. In contrast to common kinetic rate expressions, I demonstrate that new ther- modynamically based formulations can be applied to describe the microbial respiration of arbitrary large reaction networks. New approach substantially improves the robustness, transferability, and allows the generalization of the model-derived parameters. In Chapter 4, I show that on the regional scale, weather defines hydrodynamic flush rates and water circulation patterns, which, in turn, control the phosphorus transport in Lake Erie, Canada. Specifically, precipitation controls the release of phosphorus from the watershed in the spring, while wind governs the water circulation and transport of the phosphorus released from sediment in the central basin during summer. I also illustrate that climate and weather in the upper Laurentian Great Lakes regulate changes in the water level of Lake Erie. Overall, this thesis improves the fundamental understanding of the phosphorus cycle in lakes, which is being controlled by numerous biogeochemical and physical processes at various scales. In particular, I show that the climate has a cascading effect on the phosphorus cycle in lakes. First, climate controls regional precipitation, wind, and air temperature, which in turn control phosphorus supply from the watershed and basin- wide phosphorus transport. Second, being vulnerable to climate warming, the duration of ice cover impacts the phosphorus cycle through changes in light attenuation, water temperature, mixing regimes, and water column ventilation. Lastly, local environmental perturbations (e.g., pH, temperature, or redox state) define thermodynamic properties of the sediment, which control microbial metabolism and, therefore, the internal phosphorus loading. Finally, this thesis provides new open-source tools for reactive transport simula- tions in lakes as well as in saturated media. In addition to the coupled lake-sediment model developed in Chapter 3, I develop a computer program PorousMediaLab, which performs biogeochemical simulations in water-saturated media and described In Chapter 5. PorousMediaLab is the core component of the numerical investigations presented in the thesis. For example, PorousMediaLab is applied in Chapter 2 to design and test the initial reaction network, calculate fluxes at the sediment-water interface, and estimate re- action timescales. In Chapter 3, PorousMediaLab is used to simulate the reaction rates of batch and one-dimensional sediment column using a novel approach based on the thermo- dynamic switch function. In Chapter 4, PorousMediaLab is used to build a mass balance model and to improve the current understanding of the inter-basin exchange. Both tools are open-source, and they are available online

Coupling Water Column and Sediment Biogeochemical Dynamics: Modeling Internal Phosphorus Loading, Climate Change Responses, and Mitigation Measures in Lake Vansjø, Norway

We expanded the existing one‐dimensional MyLake model by incorporating a vertically resolved sediment diagenesis module and developing a reaction network that seamlessly couples the water column and sediment biogeochemistry. The application of the MyLake‐Sediment model to boreal Lake Vansjø illustrates the model's ability to reproduce daily water quality variables and predict sediment‐water column exchange fluxes over a long historical period. In prognostic scenarios, we assessed the importance of sediment processes and the effects of various climatic and anthropogenic drivers on the lake's biogeochemistry and phytoplankton dynamics. First, MyLake‐Sediment was used to simulate the potential impacts of increasing air temperature on algal growth and water quality. Second, the key role of ice cover in controlling water column mixing and biogeochemical cycles was analyzed in a series of scenarios that included a fully ice‐free end‐member. Third, in another end‐member scenario P loading from the watershed to the lake was abruptly halted. The model results suggest that remobilization of legacy P stored in the bottom sediments could sustain the lake's primary productivity on a time scale of several centuries. Finally, while the majority of management practices to reduce excessive algal growth in lakes focus on reducing external P loads, other efforts rely on the addition of reactive materials that sequester P in the sediment. Therefore, we investigated the effectiveness of ferric iron additions in decreasing the dissolved phosphate efflux from the sediment and, consequently, limit phytoplankton growth in Lake Vansjø.publishedVersio

Speciation dynamics of oxyanion contaminants (As, Sb, Cr) in argillaceous suspensions during oxic-anoxic cycles

The final publication is available at Elsevier via http://dx.doi.org/10.1016/j.apgeochem.2017.12.012 © 2018. This manuscript version is made available under the CC-BY 4.0 license https://creativecommons.org/licenses/by/4.0/Argillaceous geological formations are considered promising repositories for waste containing inorganic contaminants. However, the sequestration capacity of an argillaceous natural barrier may change as a result of dynamic environmental conditions, in particular changes in redox state. Here, we imposed redox cycles to argillaceous suspensions amended with a mixture of the inorganic contaminants As(V), Sb(V), Cr(VI), by alternating 7-day cycles of sparging with either oxic or anoxic gas mixtures. During the redox cycles, we assessed the relative importance of different contaminant sequestration mechanisms under sterile and non-sterile conditions. The non-sterile experiments were carried out 1) with the argillaceous material as is, that is, containing the native microbial population, 2) with the addition of ethanol as a source of labile organic carbon, and 3) with the addition of both ethanol and a soil microbial inoculum. In order to capture the observed solid-solution partitioning trends, a series of mixed thermodynamic-kinetic models representing the dynamic conditions in the experiments were developed using PHREEQC. Parameter values for processes such as adsorption, which occurred in all experiments, were kept constant across all the simulations. Additional formulations were introduced as needed to account for the microbial detoxification and respiration of the contaminants in the increasing complexity experiments. Abiotic adsorption of As and abiotic reductive precipitation of Cr dominated sequestration of these two contaminants under all experimental conditions, whereas the presence of microorganisms was essential to decrease the aqueous Sb concentration. Once reduced, As(III), Sb(III), and Cr(III) were not re-oxidized upon exposure to dissolved O2 in any of the experiments. Neither the mineralogy nor the native microbiota catalysed contaminant oxidation processes. Thus, kinetically, the reduction of As(V), Sb(V), and Cr(VI) was irreversible over the experimental duration (49 days). The capacity of the argillaceous matrix to reduce and sequester the aqueous contaminants, without subsequent remobilization to the aqueous phase during the oxic periods, supports the use of argillaceous barriers for geologic waste storage.Andra (French National Radioactive Waste Management Agency)Geochemistry group at ISTerre, a part of Labex OSUG@2020 (ANR 10 LABX 56)Canada Excellence Research Chair progra

biogeochemistry/PorousMediaLab: Released version of PorousMediaLab

PorousMediaLa

Strategy of Organization and Safety of Road Traffic in the Russian Federation in the Conditions of Modern Urbanization

Abstract Directions of the modern approach to the organization and safety of traffic in the conditions of the emerging tendency to creation of agglomerations in the Russian Federation are defined. The complex of innovative concepts in the country related to the effective development of these agglomerations is considered. The functions of the Center providing the unifying beginning of the concepts under consideration are defined

Lysine Dendrigraft Nanocontainers. Influence of Topology on Their Size and Internal Structure

Poly-l-ysine dendrigrafts are promising systems for biomedical applications due to their biodegradability, biocompatibility, and similarity to dendrimers. There are many papers about the use of dendrigrafts as nanocontainers for drug delivery. At the same time, the number of studies about their physical properties is limited, and computer simulations of dendrigrafts are almost absent. This paper presents the results of a systematic molecular dynamics simulation study of third-generation lysine dendrigrafts with different topologies. The size and internal structures of the dendrigrafts were calculated. We discovered that the size of dendrigrafts of the same molecular weight depends on their topology. The shape of all studied dendrigrafts is close to spherical. Density profile of dendrigrafts depends on their topology

Coupling Water Column and Sediment Biogeochemical Dynamics: Modeling Internal Phosphorus Loading, Climate Change Responses, and Mitigation Measures in Lake Vansjø, Norway

We expanded the existing one‐dimensional MyLake model by incorporating a vertically resolved sediment diagenesis module and developing a reaction network that seamlessly couples the water column and sediment biogeochemistry. The application of the MyLake‐Sediment model to boreal Lake Vansjø illustrates the model's ability to reproduce daily water quality variables and predict sediment‐water column exchange fluxes over a long historical period. In prognostic scenarios, we assessed the importance of sediment processes and the effects of various climatic and anthropogenic drivers on the lake's biogeochemistry and phytoplankton dynamics. First, MyLake‐Sediment was used to simulate the potential impacts of increasing air temperature on algal growth and water quality. Second, the key role of ice cover in controlling water column mixing and biogeochemical cycles was analyzed in a series of scenarios that included a fully ice‐free end‐member. Third, in another end‐member scenario P loading from the watershed to the lake was abruptly halted. The model results suggest that remobilization of legacy P stored in the bottom sediments could sustain the lake's primary productivity on a time scale of several centuries. Finally, while the majority of management practices to reduce excessive algal growth in lakes focus on reducing external P loads, other efforts rely on the addition of reactive materials that sequester P in the sediment. Therefore, we investigated the effectiveness of ferric iron additions in decreasing the dissolved phosphate efflux from the sediment and, consequently, limit phytoplankton growth in Lake Vansjø

Comparison of Structure and Local Dynamics of Two Peptide Dendrimers with the Same Backbone but with Different Side Groups in Their Spacers

In this paper, we perform computer simulation of two lysine-based dendrimers with Lys-2Lys and Lys-2Gly repeating units. These dendrimers were recently studied experimentally by NMR (Sci. Reports, 2018, 8, 8916) and tested as carriers for gene delivery (Bioorg. Chem., 2020, 95, 103504). Simulation was performed by molecular dynamics method in a wide range of temperatures. We have shown that the Lys-2Lys dendrimer has a larger size but smaller fluctuations as well as lower internal density in comparison with the Lys-2Gly dendrimer. The Lys-2Lys dendrimer has larger charge but counterions form more ion pairs with its NH 3 + groups and reduce the bare charge and zeta potential of the first dendrimer more strongly. It was demonstrated that these differences between dendrimers are due to the lower flexibility and the larger charge (+2) of each 2Lys spacers in comparison with 2Gly ones. The terminal CH2 groups in both dendrimers move faster than the inner CH2 groups. The calculated temperature dependencies of the spin-lattice relaxation times of these groups for both dendrimers are in a good agreement with the experimental results obtained by NMR