New developments in early diagenetic modeling: pH distributions, calcite dissolution and compaction

The goal of this thesis is to advance the modeling of physical, chemical, and biological transformations that define the early diagenetic processes in sediments. Early diagenetic models encompass the mathematical formulation and numerical solution of complex biogeochemical reaction systems, and thus contribute to and profit from the advances made in the broader field of reaction transport models (RTMs). In chapter 2, the available information on individual biogeochemical reactions common to many natural systems (e.g. redox reactions, mineral dissolution/precipitation processes, and acid/base equilibria) is systematically compiled based on the concept of a Knowledge Base (KB), in order to facilitate the assemblage of RTMs. The KB is interfaced with one-dimensional transport descriptions relevant to many compartments of the Earth system (rivers, estuaries, groundwater or sediments) to yield a unified simulation environment. The flexibility of this modeling framework is illustrated in two applications dealing with biogeochemical processes in sediments and groundwater environments. A new approach is proposed in chapter 3 that yields the reaction-specific proton production and consumption rates, since the quantitative interpretation of pH distribution is a diagnostic indicator of biogeochemical processes. This method also provides a means to interpret the saturation state of pore waters with respect to mineral phases. Here, the chemical species participating in equilibrium reactions appear explicitly in the kinetic reaction stoichiometries and are treated as unknowns. The model is applied by simulating continental shelf sediments. Simulations are also used to determine the response of pH to variations in calcite dissolution kinetics and irrigation intensity. The developed RTM is used to interpret pore water oxygen and pH microprofiles in deep-sea sediments. Two pools of degradable organic matter (OM) are necessary and sufficient to reproduce the oxygen profiles. In contrast, the successful simulation of pH profiles is limited, due to the larger number of processes that affect the proton balance. As OM is unstable in early diagenetic environments, fitting the O2 distribution yields estimates of its deposition flux, while it is not possible to constrain the deposition flux of CaCO3 from the pH data, since the pore waters reach equilibrium with respect to calcite. Thus, the depth-integrated calcite dissolution rate is obtained from the best-fit pH profiles. The nonlinear calcite dissolution rate laws yield the best agreement between modeled and measured pH profiles. The last chapter presents a model of physical and chemical compaction for the interpretation of porosity profiles based on the conservation of mass and momentum. It is used to separate the effects of mechanical compaction from mineral dissolution or precipitation reactions. The hydraulic conductivity and elastic response of a set of deep-sea sediments are estimated through an inverse modeling approach. Preliminary results indicate an inverse relationship between the elastic response coefficient and the lithogenic content of the sediment. This highlights the possibility of linking the sediment compaction behavior to its composition. The simulation results indicate a slightly improved porosity fit to available data with the nonlinear calcite dissolution rate laws, and suggest that treating porosity as an unknown enhances the current early diagenetic modeling efforts

Quantitative interpretation of pH distributions in aquatic sediments: A reaction-transport modeling approach

Despite its status of master variable, there have been relatively few attempts to quantitatively predict the distributions of pH in biogeochemical reactive transport systems. Here, we propose a theoretical approach for calculating the vertical pore water profiles of pH and the rates of proton production and consumption in aquatic sediments. In this approach, the stoichiometric coefficients of species that participate in acid-base equilibrium reactions are treated as unknown variables in the biogeochemical reaction network. The mixed kinetic-equilibrium reaction system results in a set of coupled differential and algebraic equations and is solved using a new numerical solver. The diagnostic capabilities of the model are illustrated for depositional conditions representative of those encountered on the continental shelf. The early diagenetic reaction network includes the major microbial degradation pathways of organic matter and associated secondary redox reactions, mineral precipitation and dissolution processes, and homogeneous acid-base reactions. The resulting pH profile in this baseline simulation exhibits a sharp decrease below the sediment-water interface, followed by an increase with depth and again a decrease. The features of the pH profile are explained in terms of the production and consumption of protons by the various biogeochemical processes. Secondary oxygenation reactions are the principal proton producers within the oxic zone, while reduction of iron and manganese oxyhydroxides are primarily responsible for the reversal in the pH gradient in the suboxic zone. Proton production in the zone of sulfate reduction outweighs alkalinity production, maintaining the undersaturation of the pore waters with respect to calcite. Integrated over the entire depth of early diagenesis, dissolution of CaCO3 is the main sink for protons. Variations in the reaction rate order and rate constant for CaCO3 dissolution do not fundamentally alter the shape of the pH profile. An entirely different shape is obtained, however, when the pore waters are assumed to remain in thermodynamic equilibrium with calcite at all depths. Pore water (bio)irrigation decreases the amplitude of pH changes in the sediment and may modify the shape of the pH profile

Reactive transport modeling as a technique for understanding coupled biogeochemical processes in surface and subsurface environments

info:eu-repo/semantics/publishe

Quantitative interpretation of pH distributions in aquatic sediments: a reaction transport modeling approach

info:eu-repo/semantics/publishe

Organic matter mineralization in sediment of a coastal freshwater lake and response to salinization

Solid phase and pore water chemical data collected in a sediment of the Haringvliet Lake are interpreted using a multi-component reactive transport model. This freshwater lake, which was formed as the result of a river impoundment along the southwestern coast of the Netherlands, is currently targeted for restoration of estuarine conditions. The model is used to assess the present-day biogeochemical dynamics in the sediment, and to forecast possible changes in organic carbon mineralization pathways and associated redox reactions upon salinization of the bottom waters. Model results indicate that oxic degradation (55%), denitrification (21%), and sulfate reduction (17%) are currently the main organic carbon degradation pathways in the upper 30 cm of sediment. Unlike in many other freshwater sediments, methanogenesis is a relatively minor carbon mineralization pathway (5%), because of significant supply of soluble electron acceptors from the well-mixed bottom waters. Although ascorbate-reducible Fe(III) mineral phases are present throughout the upper 30 cm of sediment, the contribution of dissimilatory iron reduction to overall sediment metabolism is negligible. Sensitivity analyses show that bioirrigation and bioturbation are important processes controlling the distribution of organic carbon degradation over the different pathways. Model simulations indicate that sulfate reduction would rapidly suppress methanogenesis upon seawater intrusion in the Haringvliet, and could lead to significant changes in the sediment’s solid-state iron speciation. The changes in Fe speciation would take place on time-scales of 20–100 years

Agrobacterium tumefaciens-mediated introduction of polygalacturonase inhibiting protein 2 gene (pvpgip2) from Phaseolus vulgaris into sugar beet (Beta vulgaris L.)

Sugar beet (Beta vulgaris L.) is an important industrial crop, the yield of which is strongly affected by numerous diseases caused by fungal pathogens. To the aim of developing transgenic plants resistant to fungi, two transgenic diploid sugar beet genotypes expressing the gene encoding the polygalacturonase inhibiting protein 2 of Phaseolus vulgaris (PvPGIP2) were generated by Agrobacterium tumefaciens-mediated transformation. PGIPs are plant cell wall leucine-rich repeat (LRR) proteins that bind to and inhibit fungal polygalacturonase (PG), thus slowing down the plant cell wall degradation and limiting fungal colonization of the plant tissues. Leaf blade explants carrying the bases of regenerated shoots, a highly regenerative tissue, were used for transformation. PCR screening using specific primers showed the presence of the transgene in more than 40% of the regenerated kanamycin-resistant plants. A transformation rate of 4.4-4.2% (depending on the genotype) was achieved as revealed by agarose diffusion assay of the PvPGIP2 activity in the crude protein extracts of shoot tissues. The intact integration of the transgene cassette into the genome was confirmed by Southern blot analysis. The inhibitory activity against Fusarium phyllophilum polygalacturonase (FpPG) was found at various levels in several transgenic plants. No alterations of growth and development of the transgenic plants were observed

Methane transport during a controlled release in the vadose zone

Shallow, small-rate releases of ethanol-blended fuels from underground storage tanks (USTs) may be quite common and result in subsurface CH4 generation. However, vadose zone transport of CH4 generated from these fuel releases is poorly understood, despite the potential to promote vapor intrusion or create explosion hazards. In this study, we simulated shallow CH4 generation with a controlled subsurface CH4 release from July 2014 to February 2015 to characterize subsurface CH4 migration and surface emissions and to determine environmental controls on CH4 fate and transport. July 2014 through November 2014 was an extended period of drought followed by precipitation during December 2014. Throughout the experiment, under varied CH4 injection rates, CH4 formed a radially symmetrical plume around the injection point. Surface efflux during the drought period of the experiment was relatively high and stable, with approximately 10 to 11 and 34 to 52% of injected CH4 reaching the ground surface during the low-and high-rate injections, respectively. Following the period of precipitation and increased soil moisture, efflux dropped and stabilized at approximately 1% of injected CH4, even as soil moisture began to decrease again. Tracer and inhibitor experiments and estimates of soil diffusivity suggest that microbial CH4 oxidation was responsible for the observed drop in efflux. The decrease in efflux only after soil moisture increased suggests a strong environmental control over the transport and oxidation of vadose zone CH4