A modular and reusable model of epithelial transport in the proximal convoluted tubule

We review a collection of published renal epithelial transport models, from which we build a consistent and reusable mathematical model able to reproduce many observations and predictions from the literature. The flexible modular model we present here can be adapted to specific configurations of epithelial transport, and in this work we focus on transport in the proximal convoluted tubule of the renal nephron. Our mathematical model of the epithelial proximal convoluted tubule describes the cellular and subcellular mechanisms of the transporters, intracellular buffering, solute fluxes, and other processes. We provide free and open access to the Python implementation to ensure our multiscale proximal tubule model is accessible; enabling the reader to explore the model through setting their own simulations, reproducibility tests, and sensitivity analyses.

The physical basis for ecohydrologic separation: the roles of soil hydraulics and climate

The degree of water mixing in the critical zone is under intense debate. Field measurements of isotope ratios indicate varying degrees of separation between pools of water that supply streams and vegetation. The exact physical mechanisms behind ecohydrologic separation are unknown, but local conditions such as soil heterogeneities likely influence the extent of mixing and separation of subsurface water pools. Using a well-established soil physics model, we simulated if isotopic separations occur within 650 distinct configurations of soil properties, climatologies, and mobile/immobile soil-water domains. Simulations demonstrated separations in isotope ratios between storage and drainage waters during periods of high precipitation, soil water content, and drainage. Separations grew with larger immobile domains and, to a lesser extent, higher mobile-immobile transfer rates. Across soil types and climates, lower saturated hydraulic conductivity and higher rainfall rates amplified isotopic differences, illustrating how mobile and immobile domains interact with local conditions to physically result in subsurface separations. These results show how different critical-zone solute fluxes can be generated by representing contrasting transport dynamics in distinct domains across a range of soils and climate conditions.

Cosmogenic nuclide and solute flux data from central Cuba emphasize the importance of both physical and chemical denudation in highly weathered landscapes

We consider measurements of both in situ produced cosmogenic nuclides and dissolved load flux to characterize the processes and pace of landscape change in central Cuba. The tropical landscape of Cuba is losing mass in multiple ways, making it difficult to quantify total denudation rates and thus to assess the impact of agricultural practices on rates of contemporary landscape change. Long-term sediment generation rates inferred from 26Al and 10Be concentrations in quartz extracted from central Cuban river sand range from 3.7–182 tons km−2 yr−1 (mean = 62, median = 57). Rock dissolution rates (24–154 tons km−2 yr−1; mean = 84, median = 78) inferred from stream solute loads exceed measured cosmogenic nuclide-derived sediment generation rates in 15 of 22 basins, indicating significant landscape-scale mass loss not reflected in the cosmogenic nuclide measurements. 26Al / 10Be ratios lower than that of surface production are consistent with the presence of a deep, mixed, regolith layer in the five basins that have the greatest disagreement between rock dissolution rates (high) and sediment generation rates inferred from cosmogenic nuclide concentrations (low). Our data show that accounting for the contribution of mineral dissolution at depth in calculations of total denudation is particularly important in the humid tropics, where dissolved load fluxes are high, and where mineral dissolution can occur many meters below the surface, beyond the penetration depth of most cosmic rays and thus the production of most cosmogenic nuclides. Relying on cosmogenic nuclide data or stream solute fluxes alone would both lead to underestimates of total landscape denudation in the central Cuba, emphasizing the importance of combining these approaches to fully capture mass loss in tropical landscapes.

Possible link between Earth’s rotation rate and oxygenation

The biotic and abiotic controls on major shifts in atmospheric oxygen and the persistence of low-oxygen periods over a majority of Earth’s history remain under debate. Explanations of Earth’s stepwise pattern of oxygenation have mostly neglected the effect of changing diel illumination dynamics linked to daylength, which has increased through geological time due to Earth’s rotational deceleration caused by tidal friction. Here we used microsensor measurements and dynamic modelling of interfacial solute fluxes in cyanobacterial mats to investigate the effect of changing daylength on Precambrian benthic ecosystems. Simulated increases in daylength across Earth’s historical range boosted the diel benthic oxygen export, even when the gross photosynthetic production remained constant. This fundamental relationship between net productivity and daylength emerges from the interaction of diffusive mass transfer and diel illumination dynamics, and is amplified by metabolic regulation and microbial behaviour. We found that the resultant daylength-driven surplus organic carbon burial could have shaped the increase in atmospheric oxygen that occurred during the Great and Neoproterozoic Oxidation Events. Our suggested mechanism, which links the coinciding increases in daylength and atmospheric oxygen via enhanced net productivity, reveals a possible contribution of planetary mechanics to the evolution of Earth’s biology and geochemistry.

A two-step strategy for delivering particles to targets hidden within microfabricated porous media

The delivery of small particles into porous environments remains highly challenging because of the low permeability to the fluids that carry these colloids. Even more challenging is that the specific location of targets in the porous environment usually is not known and cannot be determined from the outside. Here, we demonstrate a two-step strategy to deliver suspended colloids to targets that are “hidden” within closed porous media. The first step serves to automatically convert any hidden targets into soluto-inertial “beacons,” capable of sustaining long-lived solute outfluxes. The second step introduces the deliverable objects, which are designed to autonomously migrate against the solute fluxes emitted by the targets, thereby following chemical trails that lead to the target. Experimental and theoretical demonstrations of the strategy lay out the design elements required for the solute and the deliverable objects, suggesting routes to delivering colloidal objects to hidden targets in various environments and technologies.

A State-Of-The-Art Perspective on the Characterization of Subterranean Estuaries at the Regional Scale

Subterranean estuaries the, subsurface mixing zones of terrestrial groundwater and seawater, substantially influence solute fluxes to the oceans. Solutes brought by groundwater from land and solutes brought from the sea can undergo biogeochemical reactions. These are often mediated by microbes and controlled by reactions with coastal sediments, and determine the composition of fluids discharging from STEs (i.e., submarine groundwater discharge), which may have consequences showing in coastal ecosystems. While at the local scale (meters), processes have been intensively studied, the impact of subterranean estuary processes on solute fluxes to the coastal ocean remains poorly constrained at the regional scale (kilometers). In the present communication, we review the processes that occur in STEs, focusing mainly on fluid flow and biogeochemical transformations of nitrogen, phosphorus, carbon, sulfur and trace metals. We highlight the spatio-temporal dynamics and measurable manifestations of those processes. The objective of this contribution is to provide a perspective on how tracer studies, geophysical methods, remote sensing and hydrogeological modeling could exploit such manifestations to estimate the regional-scale impact of processes in STEs on solute fluxes to the coastal ocean.

The Interplay of Macrofauna Functional Groups Shapes Nitrogen Cycling in Oligotrophic Estuarine Sediments

The effects of single macrofauna species on benthic nitrogen (N) cycling has been extensively studied, whereas the effect of macrofauna communities on N-related processes remains poorly explored. In this study, we characterized benthic N-cycling in bioturbated sediments of an oligotrophic northern Baltic waters (Öre estuary). Solute fluxes and N transformations (N2 fixation, denitrification and DNRA) were measured in sediments and in macrofauna-bacteria holobionts to partition the role of three dominant macrofauna taxa (Limnecola balthica, Marenzelleria sp. and Monoporeia affinis) in shaping N-cycling, and to disentangle the contribution of different functional groups within the community. In the studied area, benthic macrofauna comprised a low diversity community with extremely high local dominance of three macrofauna taxa, which are widespread and dominant in the Baltic. The biomass of these three taxa in the benthic community explained up to 30% of variation in measured biogeochemical processes, confirming their role in ecosystem functioning. The results also show that these taxa significantly contributed to the benthic metabolism and N-cycling (direct effect) as well as reworked sediments with positive feedback to dissimilative nitrate reduction (indirect effect). Taken together, these functions promoted a re-use of nutrient at the benthic level, limiting net losses (e.g. denitrification) and effluxes to bottom water. Finally, the detection of multiple N transformations in dominating macrofauna holobionts suggested a community-associated active and versatile microbiome, which alternatively contributes to the biogeochemical processes. The present study highlights hidden and interactive effects among microbes and macrofauna, which should be considered in analysing benthic functioning.

Linking soil water and solutes fluxes to soil properties and vegetation types: insights from a case-study in the high tropical Andes of Ecuador

<p>The high tropical Andes ecosystem, known as páramo, provides important hydrological services to densely populated areas in the Andean region. In order to manage these services sustainably, it is crucial to understand the biotic and abiotic processes that control both water quality and fluxes. Recent research in the páramo highlights a knowledge gap regarding the role played by soil-vegetation interactions in controlling soil-water processes and resulting water and solute fluxes.</p><p>Here, we determine the hydrological and geochemical fluxes in four soil profiles in the páramo of the Antisana´s water conservation area in northern Ecuador. Water fluxes were measured biweekly with field fluxmeters in the hydrological year Apr/2019- Mar/2020 under two contrasting vegetation types: tussock-like grass (TU) and cushion-forming plants (CU). Soil solution was collected in parallel with wick samplers and suction caps for assessing the concentrations of dissolved cations, anions and organic carbon (DOC). In addition, soil moisture was measured continuously in the upper meter of the soil profile, i.e. first three horizons (A, 2A and 2BC), using water content reflectometers. The vertical water flux in the upper meter of each soil profile was simulated using the 1D HYDRUS model. We carried out a Sobol analysis to identify sensitive soil hydraulic parameters. We then derived water fluxes by inverse modeling, based on the measured soil moisture. We validated the calculated water fluxes using the fluxmeter data. Solute fluxes were estimated by combining the water fluxes and the soil solution compositions.</p><p>Our preliminary results suggest that water fluxes and DOC concentration vary under different vegetation types. The fluxmeter data from the 2A horizon indicates that the cumulative water flux under TU (2.8 - 5.7 l) was larger than under CU (0.8 – 1.1 l) during the dry season (Aug-Sep and Dec-Jan). However, the opposite trend was observed in the wet season for maximum water fluxes. Moreover, the DOC concentration in the uppermost horizon was higher under CU (47.3 ±2.2 mg l<sup>-1</sup>) than under TU (3.1 ±0.2 mg l<sup>-1</sup>) vegetation during the monitoring period. We associate the water and solute responses under different vegetation types to the contrasting soil hydro-physical and chemical properties (e.g., saturated hydraulic conductivity and organic carbon content) in the uppermost soil horizon. Our study illustrates the existence of a spatial association between vegetation types, water fluxes and solute concentrations in Antisana´s water conservation area. By modelling the hydrological balance of the upper meter of the soil mantle, the water and solute fluxes will be estimated for soils with different vegetation cover.</p><p> </p>

LysimeterGEO for modelling soil-vegetation-atmosphere 1D system in the Critical Zone

<p>Measuring and modelling of water and solute fluxes in the Critical Zone across soil-vegetation-atmosphere system is nowadays a very important challenge because of the complexity of both soil and plants. Considering the one-dimensional problem, we implement a virtual lysimeter model, LysimeterGEO, in which we coupled infiltration and evapotranspiration by using stress factor (Jarvis, 1976; Ball et al., 1987), with which we can compute effective evapotranspiration and remove it from Richards’ equation balance (Casulli and Zanolli, 2010).</p><p>As regards the IT implementation, LysimeterGEO is a system of components built upon the Object Modelling System v3 (OMS3). The infiltration component of the virtual lysimeter is WHETGEO 1D - Water, Heat and Transport in GEOframe (Tubini N. 2021), which solves the mass and energy balance for the one-dimensional case. The mass balance is represented by the Richards equation and the non-linear system is solved using the nested Newton algorithm (Casulli and Zanolli, 2010). Evapotranspiration flows are instead estimated using the GEOframe-Prospero model (Bottazzi M. 2020) which estimates the effective transpiration through the equilibrium temperature of the canopy as a function of the stomatal conductance. Finally, the transpiration is calculated starting from the method of Schymanski and Or (2017) and modified by including the dependence on the transpiring surface, the model of conductance of the stomata, as well as the conservation of mass. In LysimeterGEO the interaction between infiltration and evapotranspiration is made possible by BrokerGEO component (D’Amato C. 2021), which computes the water stress factor for vegetation by using Jarvis or Ball-Berry model. BrokerGEO computes the water stress factor considering the water content information by WHETGEO in each control volumes of the soil column discretization. Moreover, it computes a representative water stress factor for the whole column of soil for the evapotranspiration component. Finally, the density root distribution is considered to remove water into the soil used for evapotranspiration flows.</p><p>The modelling of water and solute fluxes across soil-vegetation-atmosphere is made possible by implementation of travel times of waters within vegetation, the growing of the roots and in general the growing of the plants. The idea of a joint infiltration-evapotranspiration model allows us to investigate also problems related to radical growth and the different effect of roots on vegetation. Furthermore, the implementation of travel times on a vegetation scale allows a careful analysis of the behaviour of the same as the soil moisture conditions vary.</p>

Predicting Solute Transport in Soil Water Flow with Estimated, Effective Material Properties

<div> <div>Soil water flow is a key hydrological process supporting several ecosystem services. The non-linear soil hydraulic material properties have a profound influence on the flow dynamics and cannot be measured directly. They can be estimated with data assimilation based on measurements of the soil hydraulic state. As soils feature a multi-scale architecture, these measurements typically cannot resolve the soil heterogeneity on the relevant spatial and estimating it becomes difficult. In a previous study, we estimated a one-dimensional effective representation of a synthetic, two-dimensional, heterogeneous domain based on a vertical measurement profile using an ensemble Kalman filter. The estimated one-dimensional model represented the dynamics of the soil water movement sufficiently well, but it remained unclear if these results can be transferred to associated physical processes.</div> <br><div>Soil water flow also transports solutes between surface and groundwater. The accurate description of solute fluxes and concentrations is crucial for predicting groundwater quality and contamination. In this study, we use the aforementioned estimated, one-dimensional representation of the domain to simulate and forecast passive solute transport within the soil water flow. We examine its predictive capabilities by comparing these results with results obtained from the two-dimensional, heterogeneous synthetic truth from which artificial measurements are extracted.</div> </div>