Microbial Alkalinity Production and Silicate Alteration in Methane Charged Marine Sediments: Implications for Porewater Chemistry and Diagenetic Carbonate Formation

A numerical reaction-transport model was developed to simulate the effects of microbial activity and mineral reactions on the composition of porewater in a 230-m-thick Pleistocene interval drilled in the Peru-Chile Trench (Ocean Drilling Program, Site 1230). This site has porewater profiles similar to those along many continental margins, where intense methanogenesis occurs and alkalinity surpasses 100 mmol/L. Simulations show that microbial sulphate reduction, anaerobic oxidation of methane, and ammonium release from organic matter degradation only account for parts of total alkalinity, and excess CO2 produced during methanogenesis leads to acidification of porewater. Additional alkalinity is produced by slow alteration of primary aluminosilicate minerals to kaolinite and SiO2. Overall, alkalinity production in the methanogenic zone is sufficient to prevent dissolution of carbonate minerals; indeed, it contributes to the formation of cemented carbonate layers at a supersaturation front near the sulphate-methane transition zone. Within the methanogenic zone, carbonate formation is largely inhibited by cation diffusion but occurs rapidly if cations are transported into the zone via fluid conduits, such as faults. The simulation presented here provides fundamental insight into the diagenetic effects of the deep biosphere and may also be applicable for the long-term prediction of the stability and safety of deep CO2 storage reservoirs.

Modern perspectives on near-equilibrium analysis of Turing systems

In the nearly seven decades since the publication of Alan Turing’s work on morphogenesis, enormous progress has been made in understanding both the mathematical and biological aspects of his proposed reaction–diffusion theory. Some of these developments were nascent in Turing’s paper, and others have been due to new insights from modern mathematical techniques, advances in numerical simulations and extensive biological experiments. Despite such progress, there are still important gaps between theory and experiment, with many examples of biological patterning where the underlying mechanisms are still unclear. Here, we review modern developments in the mathematical theory pioneered by Turing, showing how his approach has been generalized to a range of settings beyond the classical two-species reaction–diffusion framework, including evolving and complex manifolds, systems heterogeneous in space and time, and more general reaction-transport equations. While substantial progress has been made in understanding these more complicated models, there are many remaining challenges that we highlight throughout. We focus on the mathematical theory, and in particular linear stability analysis of ‘trivial’ base states. We emphasize important open questions in developing this theory further, and discuss obstacles in using these techniques to understand biological reality. This article is part of the theme issue ‘Recent progress and open frontiers in Turing’s theory of morphogenesis’.

Application of CO2-water-rock reaction transport simulation in NPs-CO2 flooding and storage

As a hot issue in geological engineering, CO2 flooding and sequestration still face many challenges. Injection of nanoparticles into CO2 can improve the injectability and effective reserves of CO2. However, the migration law of the mixed fluid of CO2 and nanoparticles (NPs-CO2) in the reservoir under the condition of chemical reaction is still unclear. Based on chemical reaction kinetics, a mass transfer model of NPs-CO2 nanofluid in reservoir is established by combining the micro-pore structure change of porous media under CO2-water-rock reactions condition and the migration law of NPs-CO2 fluid. The geochemical reaction process between CO2 and reservoir and the influence of heterogeneity caused by rock microstructure on the miscibility and migration of NPs-CO2 brine fluid are simulated. The results show that the CO2-water-rock reaction increases the heterogeneity of reservoir, and the porosity and permeability are rising as a whole; the increase of reservoir heterogeneity caused by chemical reaction can makes the migration of NPs-CO2 selective. The local accumulation of NPs-CO2 in the unconnected pores will weaken the original oil displacement efficiency to some extent; in the process of CO2 sequestration, the density difference between NPs-CO2 and formation water can not only promote the miscibility of NPs-CO2-brine fluid, but also inhibit the acid fluid under buoyancy. The upward diffusion is moved to the cover layer to prevent the chemical reaction of the rocks in the cap layer, so as ensuring the permanent storage of greenhouse gases.

Phosphorus recycling and retention in Lake of the Woods: Reactive-transport diagenetic modeling across spatial and temporal Scales

<p>The dynamics of sediment phosphorus (P) remobilization and recycling in many polymictic systems due to distinct external and internal loading conditions are poorly understood. Here we used a multifaceted approach of quantifying sediment P binding forms and corresponding metal contents in sediment cores down to 30 cm from 8 different locations at Lake of Woods (LOW) in different seasons. We also measured pH, redox potential and dissolved oxygen uptake across the sediment-water interface and the concentration of nutrient and metals in pore water at different depths. Additionally, we applied a reaction-transport diagenetic model to construct the spatial and temporal trend of internal P loading in response to environmental variations. The summer diffusive fluxes of P ranged between 3 and 83 µmol m<sup>-2</sup> d<sup>-1 </sup>whereas the winter fluxes were lower ranged from 0.1 to 0.35 µmol m<sup>-2</sup> d<sup>-1</sup>. P recycling efficiency were 13% to 77%. P bound to redox sensitive iron (Fe)-P binding forms in sediments were the major source of P release in all stations, while P immobilization is controlled by redox-insensitive calcium (Ca)-P phases. The modeling results supported the notion that P release was mostly driven by the diagenetic recycling of redox sensitive and organic bound P.</p>

Impact of Thiomargarita on the rates of N, S and P turnover in mudbelt sediments from the Benguela Upwelling System: a model study

<p>The availability of major nutrients, nitrogen (N) and phosphorus (P), largely controls primary productivity in eastern boundary upwelling systems. The oxygen minimum zone (OMZ) on the Namibian shelf is characterized by high productivity and extraordinarily high particulate organic carbon (POC) contents (up to 19 % dry weight) in the surface sediments. The anaerobic degradation of POC by bacterial sulfate reduction leads to the production of hydrogen sulfide (H<sub>2</sub>S) that supports extensive communities of large sulfur bacteria <em>Thiomargarita namibiensis</em> in surface shelf sediments. These bacteria oxidize sulfide by reducing nitrate (NO<sub>3</sub><sup>-</sup>) to either ammonium (NH<sub>4</sub><sup>+</sup>) or dinitrogen (N<sub>2</sub>). <em>Thiomargarita</em> also affect phosphorus cycling by intracellular incorporation of polyphosphates and extracellular formation of hydroxyapatites. In order to understand and quantify the complexity of the coupled benthic cycles of C, N, P, S, Fe in the Benguela Upwelling System, a reaction-transport model (RTM) was used to simulate sediment biogeochemical data collected from the RV Meteor cruise (M157, August 4th-September 16th 2019) off Namibia. This allowed deeper insights into the role of sulfur-oxidizing bacteria on P and N fluxes across the sediment surface. Results are presented that point toward potentially strong feedbacks by <em>Thiomargarita</em> on primary production in response to ongoing global warming and ocean deoxygenation.</p>

Multi-spike solutions of a hybrid reaction–transport model

Simulations of classical pattern-forming reaction–diffusion systems indicate that they often operate in the strongly nonlinear regime, with the final steady state consisting of a spatially repeating pattern of localized spikes. In activator–inhibitor systems such as the two-component Gierer–Meinhardt (GM) model, one can consider the singular limit D a ≪ D h , where D a and D h are the diffusivities of the activator and inhibitor, respectively. Asymptotic analysis can then be used to analyse the existence and linear stability of multi-spike solutions. In this paper, we analyse multi-spike solutions in a hybrid reaction–transport model, consisting of a slowly diffusing activator and an actively transported inhibitor that switches at a rate α between right-moving and left-moving velocity states. Such a model was recently introduced to account for the formation and homeostatic regulation of synaptic puncta during larval development in Caenorhabditis elegans . We exploit the fact that the hybrid model can be mapped onto the classical GM model in the fast switching limit α → ∞, which establishes the existence of multi-spike solutions. Linearization about the multi-spike solution yields a non-local eigenvalue problem that is used to investigate stability of the multi-spike solution by combining analytical results for α → ∞ with a graphical construction for finite α .

Thermochemical Aerobic Oxidation Catalysis in Water Proceeds via Coupled Electrochemical Half-Reactions

Heterogeneous aqueous-phase aerobic oxidations are an important emerging class of catalytic transformations, particularly for upgrading next generation bio-derived substrates. The mechanism of these reactions and the precise role of O2 in particular remains unclear. Herein, we test the hypothesis that thermochemical aerobic oxidation proceeds via two coupled electrochemical half-reactions for oxygen reduction and substrate oxidation. We collect electrochemical and thermochemical data on common noble metal catalysts under identical reaction/transport environments, and find that the electrochemical polarization curves of the O2 reduction and the substrate oxidation half-reaction closely predict the mixed potential of the catalyst measured in operando during thermochemical catalysis across 13 diverse variables spanning reaction conditions, catalyst composition, reactant identity, and pH. Additionally, we find that driving the oxidation half-reaction reaction electrochemically in the absence of O2 at the mixed potential leads to very similar rates and selectivities as for the thermochemical reaction in all cases examined. These findings strongly indicate that the role of O2 in thermochemical aerobic oxidation is solely as an electron scavenger that provides an incipient electrochemical driving force for substrate oxidation. These studies provide a quantitative and predictive link between thermochemical and electrochemical catalysis, thereby enabling the rational design of new thermochemical liquid-phase aerobic oxidation schemes by applying the principles of electrochemistry.

Thermochemical Aerobic Oxidation Catalysis in Water Proceeds via Coupled Electrochemical Half-Reactions

<div> <p><b>Heterogeneous aqueous-phase aerobic oxidations are an important emerging class of catalytic transformations, particularly for upgrading next generation bio-derived substrates. The mechanism of these reactions and the precise role of O₂ in particular remains unclear. Herein, we test the hypothesis that thermochemical aerobic oxidation proceeds via two coupled electrochemical half-reactions for oxygen reduction and substrate oxidation. We collect</b><b> electrochemical and thermochemical data on common noble metal catalysts under identical reaction/transport environments, and find that the electrochemical polarization curves of the O₂ reduction and the substrate oxidation half-reaction closely predict the mixed potential of the catalyst measured <i>in operando</i> during thermochemical catalysis across 13 diverse variables spanning </b><b>reaction conditions, catalyst composition, reactant identity, and pH</b><b>. Additionally, we find that driving the oxidation half-reaction reaction electrochemically in the absence of O₂ at the mixed potential leads to very similar rates and selectivities as for the thermochemical reaction in all cases examined. These findings strongly indicate that the role of O₂ in thermochemical aerobic oxidation is solely as an electron scavenger that provides an incipient electrochemical driving force for substrate oxidation. These studies provide a </b><b>quantitative and predictive link between thermochemical and electrochemical catalysis, thereby enabling the rational design of new thermochemical liquid-phase aerobic oxidation schemes by applying the principles of electrochemistry.</b></p> </div> <br>