Diffusion of strongly sorbed solutes in soil: a dual-porosity model allowing for slow access to sorption sites and time-dependent sorption reactions

We use homogenization techniques to derive a dual (or double) porosity model of solute diffusion and reaction in soil, allowing for slow access to sorption sites within micro-aggregates and time-dependent sorption reactions. We give a means for determining the conditions in which micro-scale concentration gradients affect macro-scale gradients and fluxes. We present equations for a unit volume of soil represented as a series of uniformly-spaced, porous spherical particles, containing and surrounded by solution through which solutes diffuse. The methods we use can, in principle, be applied to more complex geometries. We compare the model's predictions with those of the equivalent single porosity model for commonly used boundary conditions. We show that failure to allow for slow access to reaction sites can lead to seriously erroneous results. Slow access has the effect of decreasing the sorption of solute into soil from a source or desorption from soil to a sink. As a result of slow access, the diffusion coefficients of strongly-sorbed solutes measured at the macro-scale will be time-dependent and will depend on the method of measurement. We also show that slow access is more often likely to limit macro-scale diffusion than rates of slow chemical reactions per se . In principle, the unimportance of slow reactions except at periods longer than several weeks of diffusion simplifies modelling because, if slow access is correctly allowed for, sorption can be described with equilibrium relations with an understanding of speciation and rapid sorption-desorption reactions.     

The effect of non-instantaneous exchange on the self-diffusion of phosphate in soil

The kinetics of isotopic exchange of phosphate in a soil were studied using three techniques: (a) in shaken suspension, (b) in a system where solution circulated through a thin disc of soil, and (c) in moist soil from which solution was extracted by centrifugation with a dense immiscible liquid.
The exchange kinetics of isotope diffusing in moist soil were inferred from the concentration profile of the isotope after diffusion periods of 10-60 days. The proportion of the exchange that is effectively instantaneous in this diffusion system was much lower than in systems in which isotope is uniformly applied to the soil.
It is postulated that the difference arises because exchange of diffusing isotope is limited by access to exchange sites and not, during the period considered, by slow exchange at the solid-liquid interface.     

Three approaches to the simulation of the self-diffusion and non-instantaneous isotopic exchange of phosphate in soil

Three models of the self-diffusion of phosphate in moist soil are presented, and their predictions compared to experimental data. The latter appeared to show that isotopic exchange was limited by access to exchange sites. The apparent rate of access was first described by a series of first-order reactions, then as the diffusion of isotope into, and within, uniformly distributed, porous spherical aggregates, where the majority of exchange sites were situated, and finally as an Nth order ( N 1) reversible reaction. All models were solved using Crank-Nicolson finite difference methods.
The first two gave similar predictions; they were not capable of giving an adequate fit to experimental results. The third, although purely an empirical model, not based on a possible mechanism, was able to simulate data well.
The mechanistic implications of each model, and of its relative success in simulating phosphate diffusion are discussed.     

SWORM: an agent-based model to simulate the effect of earthworms on soil structure

Soil structure can be defined as the spatial organization of solid mineral and organic particles, and pore space. It is of great importance for soil functioning as it drives ecosystem functions (carbon sequestration, emission of greenhouse gases, nutrient cycling, primary productivity, etc.). Soil structure results from biotic and abiotic factors. Among biotic factors, numerous studies have shown the importance of organic matter, microorganisms, roots and invertebrates. Earthworms are known to play a key role in soil structure formation and maintenance through a continuous production of biogenic structures (casts and burrows). As far as we know, no models describe or quantify the effect of soil invertebrates on soil aggregation and porosity. It is a challenge to describe the physical soil environment for purposes of modelling because a soil is a multi‐scale heterogeneous, three‐dimensional and dynamic environment. An approach based on fractal theory (often used in soil sciences) was chosen to model such a real complex environment; it was integrated into a multi‐agent system (MAS), which allows us to simulate agents (e.g. earthworms) situated in a virtual world (e.g. soil). It is a bottom‐up approach that allows us to describe a system at a micro level (e.g. earthworms and their local soil environment) in order to observe, during simulations, macroscopic changes (e.g. soil structure evolution, organic matter dynamics, and microbial functions). In this paper we describe the SWORM (for ‘Simulated Worms’) model and the simulator, and present the results of the simulation applied to a case study. The effect of compacting and decompacting earthworm species on the structure of humid savanna soil at Lamto in Côte d’Ivoire has been widely studied. Quantitative and graphical outputs (e.g. thin sections of the virtual soil) indicate that the simulator was able to reproduce the effects of both compacting and decompacting species. Different ways to improve the model are discussed.     

Uptake of cations by annual ryegrass as related to cations adsorbed onto root exchange sites

Abstract

Previously published results on exchange capacities for Ca²⁺, Mg²⁺, Mn²⁺, and K⁺ in the Donnan free space of roots of two ryegrass cultivars (Lolium multiflorum Lam. cv. Marshall and Wilo) grown at two Al levels in the nutrient solution (0 and 74 μM) were correlated with the average net uptakes of the same cations. For Al‐treated plants regressed separately, significant correlations r=0.906 and r=0.963 were found for Mn²⁺ and Ca²⁺/Mg²⁺, respectively. No significant correlations were observed for these cations in control plants. In contrast, when data of control and Al‐treated plants were combined, significant linear correlations r=0.805, r=0.924, and r=0.968 were found for Ca²⁺, K⁺, and K⁺/(Ca²⁺+Mg²⁺)^1/2, respectively. The influence of cations adsorbed onto the root exchange sites and the effect of Al on the cation uptake processes were discussed.     

黑土有机碳变化的DNDC模拟预测

为探讨黑土有机碳的长期变化规律及DNDC模型在土壤有机碳预测方面的适用性,本文利用吉林省公主岭地区黑土不同施肥措施下的长期定位试验数据,选取不施肥(CK)、单施化肥(NPK)、配施有机肥(NPKM)和增施有机肥(M2+NPK)4个处理进行土壤有机碳分析,并将数据用作DNDC模型验证。验证结果表明:各处理DNDC验证中RMSE值均小于10%(分别为5.09%、6.11%、9.38%、8.36%),说明模拟值与观测值一致性良好,模型可用于该地区土壤有机碳模拟。选取了化肥施用、有机肥施用、秸秆还田比率、温度及降水5个因子进行模型的敏感性分析,结果表明:有机肥的施用对土壤有机碳含量的影响最显著,且这种影响具有持久性。最后模拟了4种施肥情境下未来(至2100年)的土壤有机碳变化情况。结果表明:对照不施肥处理(CK)土壤有机碳含量略有下降,至2100年土壤有机碳含量为11.55 g·kg-1,较试验前土壤初始有机碳(13.2 g·kg-1)下降约12.5%。单施化肥处理(NPK)土壤有机碳含量较为稳定,并未出现土壤有机碳含量下降。配施有机肥(NPKM)和增施有机肥(M2+NPK)处理土壤有机碳含量增加明显,至2100年土壤有机碳含量为24.4 g·kg-1和27.6 g·kg-1,分别较初始有机碳含量上升84.8%和109.1%。     

Application of a two-dimensional model to simulate flow and transport in a macroporous agricultural soil with tile drains

It is essential that important field processes are taken into account to model water flow and chemical transport accurately in agricultural fields. Recent field studies indicate that transport through macropores can play a major role in the export of solutes and particulates from drained agricultural land into surface water. Non‐ideal drain behaviour may further modify the flow and transport. We extended an existing two‐dimensional flow and transport model for variably saturated soils (SWMS_2D) by adding a macropore domain and an additional Hooghoudt drain boundary condition. The Hooghoudt boundary condition accounts for an entrance head needed to initiate flow into the drains. This paper presents the application of the new model (M‐2D) to an agricultural field in Switzerland. To understand interactions between macropore flow and drains better we simulated water flow and bromide transport for four different field scenarios. We considered both collector drains only with an ideal drain boundary condition (with and without macropores) and collectors and laterals with a Hooghoudt boundary condition (also with and without macropores). For each scenario, inverse modelling was used to identify model parameters using 150 days of data on observed cumulative discharge, water table depth, and tracer concentration. The models were subsequently tested against a 390‐day validation data set. We found that the two additional components (macropore flow, drain entrance head) of the M‐2D model were essential to describe adequately the flow regime and the tracer transport data in the field.     

The self-diffusion of sodium in soil: factors affecting the surface mobility

A study is presented of the self-diffusion of sodium in a sub-soil. Impedance factors (f_s)associated with the surface phase have been derived, representing the mobility of sorbed sodium ions relative to mobility in an ideal solution. Effects of drying, of cationic com-position and of enrichment with either native clay fraction or ‘pure’ clay minerals were investigated. The liquid phase impedance factor (f_L) without added clay was 0.29: clay enrichment affected soil structure and hence f_L. Values of f_s were in the range 0.19–0.05, and were about one-third of f_L. The value off, decreased as clay content increased, being halved when 50% native clay or 10% clay mineral was added. In a sodium saturated soil f_s was 0.06, less than half that in a calcium saturated soil.     

Using the ecosys mathematical model to simulate temporal variability of nitrous oxide emissions from a fertilized agricultural soil

Large temporal variability of N₂O emissions complicates calculation of emission factors (EFs) needed for N₂O inventories. To contribute towards improving these inventories, a process-based, 3-dimensional mathematical model, ecosys, was used to model N₂O emissions from a canola crop. The objective of this study was to test the hypothesis in ecosys that large temporal variability of N₂O is due to transition among alternative reduction reactions in nitrification/denitrification caused by small changes in soil water-filled pore space (WFPS) following a threshold response, which controls diffusivity (D_g) and solubility of O₂. We simulated emissions at field scale, using a 20 × 20 matrix of 36 m × 36 m grid cells rendered in ArcGIS from a digital elevation model of the fertilized agricultural field. Modelled results were compared to measured N₂O fluxes using the flux-gradient technique from a micrometeorological tower equipped with a tunable diode laser, to assess temporal N₂O variability. Grid cell simulations were performed using original, earlier and later planting and fertilizer dates, to show the influence of changing precipitation and temperature on EFs. Fertilizer application (112 kg N ha^?1), precipitation and temperature were the main factors responsible for N₂O emissions. Ecosys represented the temporal variation of N₂O emissions measured at the tower by modelling significant emissions at WFPS > 60% which reduced the oxygen diffusivity, causing a rising need for alternative electron acceptors, thus greater N₂O production via nitrification/denitrification. Small changes in WFPS above a threshold value caused comparatively large changes in N₂O flux not directly predictable from soil temperature and WFPS. In ecosys, little N₂O production occurred at WFPS < 60% because the oxygen diffusivity was large enough to meet microbial demand. Coefficients of diurnal temporal variation in N₂O fluxes were high, ranging from 25–51% (modelled) and 24–63% (measured), during emission periods (0–0.8 mg N₂O–N m² h^?1). This variation was shown to rise strongly with temperature during nitrification of N fertilizer so that EFs were affected by timing of fertilizer application. EFs almost quadrupled when fertilizer applications were delayed (average: 1.67% (fertilizer-induced emissions), causing nitrification to occur in warmer soils (18 °C), compared to earlier applications (average: 0.45%) when nitrification occurred in cooler soils (12 °C). Large temporal variation caused biases in seasonal emissions if calculated from infrequent (daily and weekly) measurements. These results show the importance of the use of models that include climate impact on N₂O, with appropriate time-steps that capture its temporal variation.     

Comparison of soil nitrate extracted by potassium chloride and adsorbed on an anion exchange membrane in situ

Abstract

The 2M potassium chloride (KCl) extraction method used to measure soil nitrate (NO₃ ^‐‐N) concentrations in soils may introduce some artifacts caused by soil sampling, processing, and handling. Furthermore, this method provides soil NO₃ ^‐‐N concentrations for soil sampled at a particular time, whereas the dynamics of this anion in situ need to be better understood. In order to develop a reliable in situ method as an alternative, an anion exchange membrane (AEM) was tested for its ability to adsorb NO₃ ^‐‐N from a soil cropped to corn (Zea mays L.) and amended with manure or inorganic nitrogen (N). In a field study, we compared the amount of NO₃ ^‐‐N adsorbed on an AEM and extracted with the 2M KCl method. The AEM was calibrated in the laboratory and placed at 15‐cm soil depth for 2‐wk periods during the corn growing season. Nitrate adsorption on the AEM and KCl‐extractable NO₃ ^‐‐N were larger in the inorganic N treatment than in the manure or the control treatments throughout the growing season. The NO₃ ^‐‐N concentrations measured by the AEM method were correlated with NO₃ ^‐‐N extracted with 2M KCl (r² = 0.78***), suggesting that the AEM method could be used to measure NO₃ ^‐‐N concentrations in agricultural soils.     

The chemistry of aluminium in strongly acidified sandy soil in Poland

Organically-bound Al in acidic, base-poor sandy soils seems to be a major contributor to dissolved Al. This hypothesis has been tested under field conditions at two intensely acidified sites. The research was conducted at the agricultural trial fields at Lyczyn, Poland, which have been fertilized continuously for 30 yr with 130 kg ha^?1 a^?1 N (as NH₄NO₃ or urea). The effect of depletion of Al on its solubility was also studied. Field data confirmed that mobilized Al originates largely in the organically bound fraction of soil Al. Depletion of this fraction resulted in a considerable decrease in the mobility of Al such that, at pH = 3.0 and reaction times of a few weeks, small amounts of Al were mobilized. Apparently, the rate at which Al is dissolved from structural silicates, which are abundant in the soil investigated, is small. This suggests that at sites in Poland most exposed to acid deposition, where the rates of soil acidification and depletion of organically-bound Al are greatest, both the concentration of Al and the soil solution pH are expected to decline with time.     

Bacterial and fungal growth in soil heated at different temperatures to simulate a range of fire intensities

The intensity of a fire is an important factor determining the recovery of soil microorganisms after a forest fire, since it can alter the quality and quantity of carbon sources. Recovery of the microbial community was studied in a Mediterranean pine forest soil subjected to different temperatures to simulate the short-term effects of fire intensity on bacterial and fungal growth, estimated using leucine incorporation for bacteria and acetate incorporation into ergosterol for fungi. Soil samples were heated for 15 min at 50, 80, 120, 200, 300, 400 and 500 °C. After inoculation with fresh soil, and adding water to achieve 60% WHC, the soils were incubated at 20 °C for 21 days. Bacterial growth was initially inhibited in the samples heated above 50 °C (totally inhibited ≥ 200 °C), but recovered within days to levels much higher than the control, except for the samples heated at 500 °C, where growth remained low throughout the incubation period due to the destruction of most of the organic matter. After the first week of incubation, the bacterial response decreased to values close to, but still above, that of the control. Samples heated at 200 °C showed the highest cumulative bacterial growth. Fungal growth was initially lower than in the control in all the heated samples (totally inhibited ≥ 200 °C). Fungal growth recovered slowly during incubation in soils heated at ≤ 300 °C, but the cumulative growth in heated soils did not exceed that in the control. No fungal growth was observed in samples heated at the two highest temperatures. Soil respiration was initially totally inhibited in soil heated at ≥ 200 °C, but recovered rapidly in all soils; the highest respiration being observed already 1 day after inoculation. This is the first time both fungal and bacterial growth has been directly estimated in heated soils. High soil pH favouring bacteria can explain these results, but the differences in fungal and bacterial responses suggest a competitive interaction between these groups.     

SUNFLO, a model to simulate genotype-specific performance of the sunflower crop in contrasting environments

Yield improvement certainly depends on breeding new genotypes, but also on identifying the best genotype for a given location and crop management system. Hence we need to quickly evaluate the performance of each new variety in different cropping systems and environmental conditions.Our objective was to develop a model (SUNFLO) which can help to improve genotypic assessment in the sunflower crop. The present work aimed at identifying, quantifying and modelling the phenotypic variability of crop performance in response to the main abiotic stresses occurring in the field (light, temperature, water, nitrogen) but also in the expression of genotypic variability.We therefore include just enough genetic information to enable the model to be used with new genotypes. Each genotype was thus defined by chosen phenotypic traits which were transcribed into a set of 12 genotype-specific parameters.The model's performance was evaluated in both specific field experiments and generic multi-environment trials (MET). The first evaluation assessed model robustness: no variables had a large prediction error, indicating that the final output error results more from poor prediction for all variables than from error compensation. An ANOVA on the simulated MET dataset showed that although the model simulates less variability than in reality (60%), there was genotype-environment interaction and the ranking of the ANOVA factors was identical in both observed and simulated networks. The model's accuracy was sufficient to discriminate between genotypes from different breeding periods, but was similar to the difference in performance between actual genotypes (∼0.2 t ha⁻¹).To improve the understanding of crop physiology and crop-environment interactions, this kind of model shows weaknesses, especially when dealing with environmental stress integration or biomass allocation. On the other hand, SUNFLO seems sufficiently robust to estimate the influence on yield of breeding traits or to explore new management practices.     

应用CropSyst模型模拟东北黑土区春小麦生长

Available water and fertilizer have been the main limiting factors for yields of spring wheat, which occupies a large area of the black soil zone in northeast China; thus, the need to set up appropriate models for scenario analysis of cropping system models has been increasing. The capability of CropSyst, a cropping system simulation model, to simulate spring wheat growth of a widely grown spring cultivar, ‘Longmai 19＇, in the black soil zone in northeast China under different water and nitrogen regimes was evaluated. Field data collected from a rotation experiment of three growing seasons （1992- 1994） were used to calibrate and validate the model. The model was run for 3 years by providing initial conditions at the beginning of the rotation without reinitializing the model in later years in the rotation sequence. Crop input parameters were set based on measured data or taken from CropSyst manual. A few cultivar-specific parameters were adjusted within a reasonable range of fluctuation. The results demonstrated the robustness of CropSyst for simulating evapotranspiration, aboveground biomass, and grain yield of ＇Longmai 19＇ spring wheat with the root mean square errors being 7%, 13% and 13% of the observed means for evapotranspiration （ET）, grain yield and aboveground biomass, respectively. Although CropSyst was able to simulate spring production reasonably well, further evaluation and improvement of the model with a more detailed field database was desirable for agricultural systems in northeast China.     

曲线数值法(SCS模型)在北京温榆河流域降雨-径流关系中的应用研究

为研究北京城市化进程中降雨-径流关系变化,在温榆河流域应用SCS模型,对该流域部分实测次降雨-径流过程及不同频率年降雨-径流进行模拟,得出SCS模型在温榆河流域预测径流是可行的,无论哪种前期土壤湿润条件,不同频率降雨的年径流量随着时间的推移有增大的趋势,相同前期土壤湿润情况下年径流量绝对增量顺序为,丰水年＞平水年＞枯水年,而相对增量是枯水年＞平水年＞丰水年.相同前期土壤湿润程度及相同频率降雨条件下,城市化水平越高,径流量越大.     

阴离子对应用于红壤中的微生物量的镉毒害的影响

A laboratory incubation experiment was conducted to elucidat the effects of associated anions on toxicity of cadmium applied to microbial biomass in the red soil. Cadmium was applied at six different levels,i.e.,O(background),5,15,30,60 and 100μg g^-1 soil in the form of either cadmium acetate or cadmium chloride. Application of cadmium as cadmium acetate markedly reduced the soil microbial biomass carbon compared to cadmium applied as cadmium chlorde at all the tested levels.Similarly,organic carbon to biomass carbon ration in the soil was markedly increased by increasing the level of the cadmium in the soil as cadmium acetate,while the change wa much smaller in the case of cadmium chloride at the same cadmium levels.The results suggested that due consideration should be given to the source of cadmium while deciding the cadmium levles in experiments.     

Antibiotic-resistant mutants identified from nodules of uninoculated soybeans grown in a strongly acidic soil

Two hypotheses that antibiotic-resistant nodule isolates from uninoculated soybeans grown in a strongly acidic soil were naturally occurring rhizobia which had acquired resistance to spectinomycin and streptomycin or were contaminants from adjacent, inoculated treatments, were tested in laboratory experiments. Soybean nodule isolates (166) as well as 48 cowpea and 89 Rhizobium japonicum strains were used in tests of resistance to six concentrations (0–500 μg ml^?1) of kanamycin, spectinomycin and streptomycin, tolerance of stresses of pH 4.6, with or without 50 μm Al, and serological cross-reactivity.More strains from the strongly acidic soil were resistant to the antibiotics than from slightly acidic soils, but resistance to antibiotics did not necessarily entail resistance to pH 4.6 or to 50 μm Al. Twenty-three nodule isolates which were resistant to spectinomycin or streptomycin cross-reacted with antisera of the inoculum strains, indicating that they were contaminants. None of 59 antibiotic-sensitive nodule isolates from uninoculated plants and none of 31 from inoculated plants cross-reacted with the antisera. All 53 antibiotic-resistant isolates from nodules of plants in inoculated plots cross-reacted with test antisera, indicating stability of the antibiotic markers.Cowpea rhizobia were generally more resistant to the antibiotics and more tolerant of pH 4.6 and 50 μm Al than were R. japonicum. Among strains of R. japonicum, slow growers were more resistant to antibiotics than moderately fast growers.