Exploring Methane Emission Drivers in Wetlands: The Cases of Massaciuccoli and Porta Lakes (Northern Tuscany, Italy)

Wetlands are hotspots of CH4 emissions to the atmosphere, mainly sustained by microbial decomposition of organic matter in anoxic sediments. Several knowledge gaps exist on how environmental drivers shape CH4 emissions from these ecosystems, posing challenges in upscaling efforts to estimate global emissions from waterbodies. In this work, CH4 and CO2 diffusive fluxes, along with chemical and isotopic composition of dissolved ionic and gaseous species, were determined from two wetlands of Tuscany (Italy): (i) Porta Lake, a small wetland largely invaded by Phragmites australis reeds experiencing reed die-back syndrome, and (ii) Massaciuccoli Lake, a wide marsh area including open-water basins and channels affected by seawater intrusion and eutrophication. Both wetlands were recognized as net sources of CH4 to the atmosphere. Our data show that the magnitude of CH4 diffusive emission was controlled by CH4 production and consumption rates, being mostly governed by (i) water temperature and availability of labile carbon substrates and (ii) water column depth, wind exposure and dissolved O2 contents, respectively. This evidence suggests that the highest CH4 diffusive fluxes were sustained by reed beds, providing a large availability of organic matter supporting acetoclastic methanogenesis, with relevant implications for global carbon budget and future climate models.

Stratification in drying films: a diffusion–diffusiophoresis model

This research is motivated by the desire to control the solids distribution during the drying of a film containing particles of two different sizes. A variety of particle arrangements in dried films has been seen experimentally, including a thin layer of small particles at the top surface. However, it is not fully understood why this would occur. This work formulates and solves a colloidal hydrodynamics model for (i) diffusion alone and (ii) diffusion plus excluded volume diffusiophoresis, to determine their relative importance in affecting the particle arrangement. The methodology followed is to derive partial differential equations (PDEs) describing the motion of two components in a drying film. The diffusive fluxes are predicted by generalising the Stokes–Einstein diffusion coefficient, with the dispersion compressibility used to produce equations valid up until close packing. A further set of novel equations incorporating diffusiophoresis is derived. The diffusiophoretic mechanism investigated in this work is the small particles being excluded from a volume around the large particles. The resulting PDEs are scaled and solved numerically using a finite volume method. The model includes the chemical potentials of the particles, allowing for incorporation of any interaction term. The relative magnitudes of the fluxes of the differently sized particles are compared using scaling arguments and via numerical results. The diffusion results, without any inter-particle interactions, predict stratification of large particles to the top surface. Addition of excluded volume diffusiophoresis introduces a downwards flux on the large particles, that can result in small-on-top stratification, thus providing a potential explanation of the experimental observations.

Geochemical consequences of oxygen diffusion from the oceanic crust into overlying sediments and its significance for biogeochemical cycles based on sediments of the northeast Pacific

Exchange of dissolved substances at the sediment–water interface provides an important link between the short-term and long-term geochemical cycles in the ocean. A second, as yet poorly understood sediment–water exchange is supported by low-temperature circulation of seawater through the oceanic basement underneath the sediments. From the basement, upwards diffusing oxygen and other dissolved species modify the sediment, whereas reaction products diffuse from the sediment down into the basement where they are transported by the basement fluid and released to the ocean. Here, we investigate the impact of this “second” route with respect to transport, release and consumption of oxygen, nitrate, manganese, nickel and cobalt on the basis of sediment cores retrieved from the Clarion Clipperton Zone (CCZ) in the equatorial Pacific Ocean. We show that in this abyssal ocean region characterised by low organic carbon burial and sedimentation rates vast areas exist where the downward- and upward-directed diffusive fluxes of oxygen meet so that the sediments are oxic throughout. This is especially the case where sediments are thin or in the proximity of faults. Oxygen diffusing upward from the basaltic crust into the sediment contributes to the degradation of sedimentary organic matter. Where the sediments are entirely oxic, nitrate produced in the upper sediment by nitrification is lost both by upward diffusion into the bottom water and by downward diffusion into the fluids circulating within the basement. Where the oxygen profiles do not meet, they are separated by a suboxic sediment interval characterised by Mn2+ in the porewater. Where porewater Mn2+ in the suboxic zones remains low, nitrate consumption is low and the sediment continues to deliver nitrate to the ocean bottom waters and basement fluid. We observe that at elevated porewater manganese concentrations, nitrate consumption exceeds production and nitrate diffuses from the basement fluid into the sediment. Within the suboxic zone, not only manganese but also cobalt and nickel are released into the porewater by reduction of Mn oxides, diffusing towards the oxic–suboxic fronts above and below where they precipitate, effectively removing these metals from the suboxic zone and concentrating them at the two oxic–suboxic redox boundaries. We show that not only do diffusive fluxes in the top part of deep-sea sediments modify the geochemical composition over time but also diffusive fluxes of dissolved constituents from the basement into the bottom layers of the sediment. Hence, the palaeoceanographic interpretation of sedimentary layers should carefully consider such deep secondary modifications in order to prevent the misinterpretation of primary signatures.

A thermalized electrokinetics model including stochastic reactions suitable for multiscale simulations of reaction-advection-diffusion systems

We introduce a scheme to simulate the spatial and temporal evolution of the densities of charged species, taking into account diffusion, thermal fluctuations, coupling to a carrier fluid, and chemical reactions. To this end, the diffusive fluxes in the electrokinetic model by Capuani et al. [1] are supplemented with thermal fluctuations. Chemical reactions are included via an additional source term in the mass balance equation. The diffusion-reaction model is then coupled to a solver for fluctuating hydrodynamics based on the lattice Boltzmann method. We describe our implementations, one based on the automatic code generation tools using pystencils and lbmpy, and another one contained as in the molecular dynamics package ESPResSo which allows the coupling of particles to the density fields. We validate our implementations by demonstrating that the expected influence of density fluctuations on the reaction rate for chemical reactions of order > 1 is reproduced. Our novel algorithm will be applicable to coarse-grained catalysis problems as well as to many other multi-scale problems that require the coupling of explicit-particle simulations with flow fields, diffusion, and reaction problems in arbitrary geometries.

A Novel Measurement-Based Model for Calculating Diffusive Fluxes Across Substrate-Water Interfaces of Marine Aggregates, Sediments and Biofilms

Our understanding of the small-scale processes that drive global biogeochemical cycles and the Earth’s climate is dependent on accurate estimations of interfacial diffusive fluxes to and from biologically-active substrates in aquatic environments. In this study, we present a novel model approach for accurate calculations of diffusive fluxes of dissolved gases, nutrients, and solutes from concentration profiles measured across the substrate-water interfaces using microsensors. The model offers a robust computational scheme for automatized determination of the interface position and enables precise calculations of the interfacial diffusive fluxes simultaneously. In contrast to other methods, the new approach is not restricted to any particular substrate geometry, does not require a priori determination of the interface position for the flux calculation, and, thus, reduces the uncertainties in calculated fluxes arising from partly subjective identification of the interface position. In addition, it is robust when applied to measured profiles containing scattered data points and insensitive to reasonable decreases of the spatial resolution of the data points. The latter feature allows for significantly reducing measurement time which is a crucial factor for in situ experiments.

Effective Source Term Discretizations for Higher Accuracy Finite Volume Discretization of Parabolic Equations

A finite volume method is applied to develop space-time discretizations for parabolic equations based on an equation error method.A space-time expansion of the local equation error based on flux integral formulation of the equation is first designed using a desiredframework of neighboring quadrature points for the solution and local source terms. The quadrature weights are then determined through aminimization process for the error which constitutes all local compact fluxes about each centroid within the computational domain.In utilizing a local source term distribution to account for diffusive fluxes, the right minimizing quadrature weights and collocationpoints including subgrid points for the source terms may be determined and optimized for higher accuracies as well as robust higher-ordercomputational convergence. The resulting local residuals form a more complete description of the truncation errors which are then utilizedto assess the computational performances of the resulting schemes. The effectiveness of the discretization method is demonstrated by theresults and analysis of the schemes.

Geochemical consequences of oxygen diffusion from the oceanic crust into overlying sediments and its significance for biogeochemical cycles based on sediments of the NE Pacific

Exchange of dissolved substances at the sediment–water interface provides an important link between the short–term and long–term geochemical cycles in the ocean. A second, as yet poorly understood sediment–water exchange is supported by low–temperature circulation of seawater through the oceanic basement underneath the sediments. From the basement, upwards diffusing oxygen and other dissolved species modify the sediment whereas reaction products diffuse from the sediment down into the basement, where they are transported by the basement fluid and released to the ocean. Here, we investigate the impact of this “second” route with respect to transport, release and consumption of oxygen, nitrate, manganese, nickel, and cobalt on the basis of sediment cores retrieved from the Clarion Clipperton Zone (CCZ) in the equatorial Pacific Ocean. We show that in this abyssal ocean region characterised by low organic–carbon burial and sedimentation rates vast areas exist where the downward and upward directed diffusive fluxes of oxygen meet so that the sediments are oxic throughout. This is especially the case where sediments are thin or in the proximity of faults. Oxygen diffusing upward from the basaltic crust into the sediment contributes to the degradation of sedimentary organic matter. Where the oxygen profiles do not meet, they are separated by a suboxic sediment interval characterised by Mn2+ in the pore–water. Where the sediments are entirely oxic, nitrate produced in the upper sediment by nitrification is lost both by upward diffusion into the bottom water and by downward diffusion into the fluids circulating within the basement. Where pore–water manganese in the suboxic zones remains low, nitrate consumption is low and the sediment continues to deliver nitrate to the ocean bottom waters and basement fluid. We observe that at elevated pore–water manganese concentrations, nitrate consumption exceeds production and the basement becomes a nitrate source. Within the suboxic zone, not only manganese but also cobalt and nickel are released into the pore–water by reduction of oxides, diffuse towards the oxic/suboxic fronts above and below where they precipitate, effectively removing these metals from the suboxic zone and concentrating them at the oxic/suboxic redox boundaries. We show that not only diffusive fluxes in the top part of deep–sea sediments modify the geochemical composition over time, but also diffusive fluxes of dissolved constituents from the basement into the bottom layers of the sediment. Hence, paleoceanographic interpretation of sedimentary layers should carefully consider such deep secondary modifications in order to prevent misinterpretation as primary signatures.

A diffusiophoretic mechanism for ATP-driven transport without motor proteins

The healthy growth and maintenance of a biological system depends on the precise spatial organization of molecules within the cell through the dissipation of energy. Reaction–diffusion mechanisms can facilitate this organization, as can directional cargo transport orchestrated by motor proteins, by relying on specific protein interactions. However, transport of material through the cell can also be achieved by active processes based on non-specific, purely physical mechanisms, a phenomenon that remains poorly explored. Here, using a combined experimental and theoretical approach, we discover and describe a hidden function of the Escherichia coli MinDE protein system: in addition to forming dynamic patterns, this system accomplishes the directional active transport of functionally unrelated cargo on membranes. Remarkably, this mechanism enables the sorting of diffusive objects according to their effective size, as evidenced using modular DNA origami–streptavidin nanostructures. We show that the diffusive fluxes of MinDE and non-specific cargo couple via density-dependent friction. This non-specific process constitutes a diffusiophoretic mechanism, as yet unknown in a cell biology setting. This nonlinear coupling between diffusive fluxes could represent a generic physical mechanism for establishing intracellular organization.

Non-equilibrium thermodynamics model for calculating diffusion fluxes under phase transformations in alloy steels

The phase transformations in alloyed iron-carbon alloys is largely related to diffusion of components, foremost to the carbon. For the analysis of diffusive processes in alloy steels, it is possible to use the mathematical methods of non-equilibrium thermodynamics. The equation for the diffusive fluxes of the system contains unknown in general case of coefficients activity of elements and vacancies, and their derivatives for to the concentrations, that extraordinarily makes it difficult being of values of cross coefficients. In the article a non-equilibrium thermodynamics methodology of calculation of diffusive fluxes at presence of two phases in alloy steels is described. It allows one to calculate both direct- and cross coefficients in the Onsager equations. Formulas for calculation of thermodynamics forces in the alloy steel – for iron, alloying element of substitution – chrome, of element of introduction – carbon and vacancies, are presented. Common expressions are suggested for calculation of cross-factors, motive forces and fluxes in the Onsager’s equations for a multicomponent thermodynamic system. The example of using the developed model to find changes in concentrations and diffusion fluxes over time is given. For the model system used, it was established that at the stage of predominant diffusion of carbon in the alloy steel, cementite inclusions with a size of about 18 nm are formed rather quickly (within ~ 200 s). The technique developed in the article allows one to perform diffusion kinetics calculations in multicomponent thermodynamic systems, which are also iron-carbon alloys and to control the size of the phases formed, for example, of carbide nanoparticles.