Soil aggregates as biogeochemical reactors: Not a way forward in the research on soil-atmosphere exchange of greenhouse gases.

The goal of this comment is to show that the "aggregate reactor" framework recently proposed in an article published in this journal is severely limited by two kinds of indeterminacy. The first is related to the size of aggregates, which is not defined precisely. The second issue is with the impossibility to replicate boundary conditions that are identical to what chunks of soils would have experienced in their natural state. We suggest that the study of GHG release in undisturbed soil samples is a better way to proceed forward.

Predicting the Stability of Organic Matter Originating from Different Waste Treatment Procedures.

Recycling organic wastes into farmland faces a double challenge: increasing the carbon storage of soil while mitigating CO2 emission from soil. Predicting the stability of organic matter (OM) in wastes and treatment products can be helpful in dealing with this contradiction. This work proposed a modeling approach integrating an OM characterization protocol into partial least squares (PLS) regression. A total of 31 organic wastes, and their products issued from anaerobic digestion, composting, and digestion-composting treatment were characterized using sequential extraction and three-dimension (3D) fluorescence spectroscopy. The apportionment of carbon in different fractions and fluorescence spectra revealed that the OM became less accessible and biodegradable after treatments, especially the composting. This was proven by the decrease in CO2 emission from soil incubation. The PLS model successfully predicted the stability of solid digestate, compost, and compost of solid digestate in the soil by using only the characterized variables of non-treated wastes. The results suggested that it would be possible to predict the stability of OM from organic wastes after different treatment procedures. It is helpful to choose the most suitable and economic treatment procedure to stabilize labile organic carbon in wastes and hence minimize CO2 emission after the application of treatment products to the soil.

Changes in soil carbon mineralization related to earthworm activity depend on the time since inoculation and their density in soil.

Earthworms play a key role in soil carbon mineralization, but their effect is highly uncertain and suspected to vary as a function of several factors, particularly the earthworm density and time from earthworm inoculation. We conducted a meta-analysis considering these factors based on 42 experiments comparing carbon mineralization in the absence and presence of earthworms at different times. The results reveal an average carbon mineralization increase of 24% (sd 41%) in the presence of earthworms with an initial median earthworm density of 1.95 mg/g soil DM (Dry Mass) (sd 48%). We show that carbon mineralization due to earthworms was related to their density and time from inoculation. From a simple regression model using these two variables, the estimated impact of earthworms on carbon mineralization was 20% increase from 0 to 60 days and 14% decrease at day 350 for a density of worms commonly found in soils (0.5 mg/g soil DM). Finally, we proposed a simple equation that could be used in organic matter decomposition models that do not take macrofauna into account.

Fate of 14C-acetyl sulfamethoxazole during the activated sludge process.

Compared to antibiotic parent molecule, human metabolites are generally more polar and sometimes not less toxic in wastewater. However, most researches focus on the fate of parent molecule. Therefore, behaviors of human metabolites are little known. Moreover, though much has been done on the fate of antibiotics during activated sludge process, there are still some limitations and gaps. In the present study, [Ring-14C] acetyl sulfamethoxazole (14C-Ac-SMX) was used to investigate the fate of human metabolite of SMX during activated sludge process at environmentally relevant concentration. At the end of 216 h, 3.1% of the spiked activity in the initial aqueous phase was mineralized, 50% was adsorbed onto the solid phase, and 36.5% still remained in the aqueous phase, indicating that adsorption, not biodegradation, was the main dissipation pathway. In the existence of microbial activities, accumulation into the solid phase was much higher, which was less bioavailable by chemical sequential extraction. The multimedia kinetic model simultaneously depicted the fate of Ac-SMX in the gas, aqueous, and solid phases, and demonstrated that microbially accelerated accumulation onto the solid phase was attributed to lower desorption rate from the solid phase to the aqueous phase, where adsorption rate was not the key factor. Therefore, Ac-SMX cannot be efficiently mineralized and remain in the aqueous or the solid phases. The accumulation in the solid phase is less bioavailable and is hard to be desorbed in the existence of microbial activities, and should not be easily degraded, and may lead to the development of antibiotic-resistant bacteria and genes after discharge into the environment.

Environmental availability of sulfamethoxazole and its acetylated metabolite added to soils via sludge compost or bovine manure.

The fate of antibiotics and their metabolites in soils after application of organic waste depends on their environmental availability, which depends on the quality and biodegradability of the added exogenous organic matter (EOM). This study aimed at better understanding the fate of sulfamethoxazole (SMX) and N-acetyl-sulfamethoxazole (AcSMX) metabolite added to soils via sludge compost or cow manure application, during a 28-day incubation. Experimental results obtained for mineralized, extractable, and non-extractable fractions as well as EOM mineralization were used to couple SMX and AcSMX dynamics to the EOM evolution using the COP-Soil model. According to various mechanisms of extraction, CaCl2, EDTA and cyclodextrin solutions extracted contrasted available fractions (31-96% on day 0), resulting in different sets of parameter values in the model. CaCl2 extraction was the best method to assess the sulfonamide availability, leading to low relative root mean squared errors and best simulations of SMX and AcSMX dynamics. The decrease of SMX and AcSMX availability over time went with the formation of non-extractable residues, mostly of physicochemical origin. Using the COP-Soil model, the co-metabolism was assumed to be responsible for the formation of biogenic non-extractable residues and the low mineralization of SMX and AcSMX.

Mulch of plant residues at the soil surface impact the leaching and persistence of pesticides: A modelling study from soil columns.

Crop residues left on the soil surface as mulch greatly influence the fate of pesticides in conservation agricultural practices because most of the applied pesticide is intercepted by mulch before passing to the soil. Modelling of pesticide losses from wash-off and leaching will greatly improve our understanding of the environmental consequences of pesticides in these systems. The PASTIS model, which simulates water transfer, mulch decomposition, and pesticide dynamics, was adapted in this new version to model the interactions between pesticides and mulch in order to simulate the impact of mulch on pesticide dynamic. Parameters of mulch dynamics and pesticide degradation and retention processes were estimated using independent incubation experiments. The PASTIS model was tested with experimental laboratory data that were obtained from two pesticides (Glyphosate and s-metolachlor) applied to soil columns where mulch composed of maize and dolichos was placed at the soil surface impacted by two rain intensities (a high and infrequent intensity and a light and frequent intensity). Simulations indicated good agreement between simulated and experimental values. After 1 day, 45-46% of the pesticides leached from the mulch and 54-55% remained in the mulch for both pesticides and both rain intensities. During the experiment, pesticide wash-off was greater for the high and infrequent rain (56-57%) compare to light and frequent rain (39-45%) for both pesticides. A smaller amount of S-metolachlor washed off with the light and frequent rain intensity (39%) than glyphosate (45%) because of its lower desorption rate from mulch residues. Glyphosate was more degraded (37-45%) than s-metolachlor (17-37%), which agrees with preliminary incubation experiments that were used for parameter estimation. A sensitivity analysis indicated that the saturation index of mulch at which pesticides started their diffusion in the rainwater and the time of the first rainfall were the two parameters that influenced the most output variables of our model. This study suggests that the PASTIS model developed for pesticide dissipation in mulch is a useful tool to evaluate the potential risk of pesticide leaching to the groundwater in conservation agriculture systems.

Modelling the fate of PAH added with composts in amended soil according to the origin of the exogenous organic matter.

A new model that was able to simulate the behaviours of polycyclic aromatic hydrocarbons (PAH) during composting and after the addition of the composts to agricultural soil is presented here. This model associates modules that describe the physical, biological and biochemical processes involved in PAH dynamics in soils, along with a module describing the compost degradation resulting in PAH release. The model was calibrated from laboratory incubations using three 14C-PAHs, phenanthrene, fluoranthene and benzo(a)pyrene, and three different composts consisting of two mature and one non-mature composts. First, the labelled PAHs were added to the compost over 28days, and spiked composts were then added to the soil over 55days. The model calculates the proportion of biogenic and physically bound residues in the non-extractable compartment of PAHs at the end of the compost incubation to feed the initial conditions of the model for soil amended with composts. For most of the treatments, a single parameter set enabled to simulate the observed dynamics of PAHs adequately for all the amended soil treatments using a Bayesian approach. However, for fluoranthene, different parameters that were able to simulate the growth of a specific microbial biomass had to be considered for mature compost. Processes that occurred before the compost application to the soil strongly influenced the fate of PAHs in the soil. Our results showed that the PAH dissipation during compost incubation was higher in mature composts because of the higher specific microbial activity, while the PAH dissipation in amended soil was higher in the non-mature compost because of the higher availability of PAHs and the higher co-metabolic microbial activity.

In situ long-term modeling of phenanthrene dynamics in an aged contaminated soil using the VSOIL platform.

Management and remediation actions of polycyclic aromatic hydrocarbons (PAH) contaminated sites require an accurate knowledge of the dynamics of these chemicals in situ under real conditions. Here we developed, under the Virtual Soil Platform, a global model for PAH that describes the principal physical and biological processes controlling the dynamics of PAH in soil under real climatic conditions. The model was applied first to simulate the observed dynamics of phenanthrene in situ field experimental plots of industrial contaminated soil. In a second step, different long-term scenarios of climate change or bioavailability increase were applied. Our results show that the model can adequately predict the fate of phenanthrene and can contribute to clarify some of unexplored aspects regarding the behavior of phenanthrene in soil like its degradation mechanism and stabilization. Tested prospective scenarios showed that bioavailability increase (through the addition of solvent or surfactants) resulted in significant increase in substrate transfer rate, hence reducing remediation time. Regarding climate change effect, the model indicated that phenanthrene concentration decreased by 54% during 40years with a natural attenuation and both scenarios chosen for climatic boundaries provided very similar results.

Microscale Heterogeneity of the Spatial Distribution of Organic Matter Can Promote Bacterial Biodiversity in Soils: Insights From Computer Simulations.

There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic matter, in addition to the spatial connectivity of the soil moisture, might account for the observed microbial biodiversity in soils. A multi-species, individual-based, pore-scale model is developed and parameterized with data from 3 Arthrobacter sp. strains, known to be, respectively, competitive, versatile, and poorly competitive. In the simulations, bacteria of each strain are distributed in a 3D computed tomography (CT) image of a real soil and three water saturation levels (100, 50, and 25%) and spatial heterogeneity levels (high, intermediate, and low) in the distribution of the soil organic matter are considered. High and intermediate heterogeneity levels assume, respectively, an amount of particulate organic matter (POM) distributed in a single (high heterogeneity) or in four (intermediate heterogeneity) randomly placed fragments. POM is hydrolyzed at a constant rate following a first-order kinetic, and continuously delivers dissolved organic carbon (DOC) into the liquid phase, where it is then taken up by bacteria. The low heterogeneity level assumes that the food source is available from the start as DOC. Unlike the relative abundances of the 3 strains, the total bacterial biomass and respiration are similar under the high and intermediate resource heterogeneity schemes. The key result of the simulations is that spatial heterogeneity in the distribution of organic matter influences the maintenance of bacterial biodiversity. The least competing strain, which does not reach noticeable growth for the low and intermediate spatial heterogeneities of resource distribution, can grow appreciably and even become more abundant than the other strains in the absence of direct competition, if the placement of the resource is favorable. For geodesic distances exceeding 5 mm, microbial colonies cannot grow. These conclusions are conditioned by assumptions made in the model, yet they suggest that microscale factors need to be considered to better understand the root causes of the high biodiversity of soils.

Impact of sludge treatments on the extractability and fate of acetyl sulfamethoxazole residues in amended soils.

Sludge recycled in agriculture may bring antibiotics into cropped soils. The nature, total amount, and availability of the antibiotics in soil partly depend on the sludge treatments. Our paper compares the fate of N-acetyl sulfamethoxazole (AC-SMX) residues between soils incubated with the same sludge but submitted to different processes before being added in soil. The fate of 14C-AC-SMX residues was studied in mixtures of soil and sludges at different treatment levels: 1) activated and 2) centrifuged sludges, both enriched with 14C-AC-SMX, and 3) limed and 4) heat-dried sludges obtained by treating the previously contaminated centrifuged sludge. The evolution of the extractability of 14C residues (CaCl2, methanol) and their mineralization were followed during 119 days. More than 80% of the initial 14C-activity was no longer extractable after 14 days, except in soil with limed sludge. Liming and drying the centrifuged sludge decreased the mineralized 14C fraction from 5.7-6.4% to 1.2-1.8% and consequently, the corresponding soils contained more 14C residues after 119 days. Although 14C residues were more CaCl2-extractable in soil with limed sludge, they seemed to be poorly bioavailable for biodegradation. For all solid sludges, the mineralization rate of 14C-AC-SMX residues was strongly correlated to that of sludge organic carbon, with a coefficient three times lower for the limed and dried sludges than for the centrifuged sludge after 14 days.

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain.

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

Impact of liming and drying municipal sewage sludge on the amount and availability of (14)C-acetyl sulfamethoxazole and (14)C-acetaminophen residues.

Acetyl Sulfamethoxazole (AC-SMX) and acetaminophen (ACM) can be found in municipal sewage sludge, and their content and availability may be influenced by sludge treatments, such as drying and liming. A sludge similarly centrifuged with/without a flocculant was spiked with (14)C-labelled AC-SMX or ACM. Then, it was either limed (20% CaO) or/and dried under different laboratory conditions (1 week at ambient temperature; and 48 h at 40 or 80 °C). The total amount and distribution of the (14)C-compounds among several chemical fractions, based on the sludge floc definition, were assessed at the end of the treatments. All the (14)C-activity brought initially was recovered in the limed and/or dried sludges for AC-SMX but only between 44.4 and 84.9% for ACM, with the highest rate obtained for the limed sludge. Drying at 80 °C or liming increased the percentage of the sludge total organic carbon recovered in the extracts containing soluble extracellular polymeric substances (S-EPS) and the percentage of the total (14)C-activity extracted simultaneously. The non-extractable residues represented only 3.9-11.6% of the total (14)C-activity measured in the treated sludges for AC-SMX and 16.9-21.8% for ACM. The presence of AC-SMX and ACM residues in the treated sludges, after liming and drying under different conditions, was shown using some (14)C-labelled molecules. At this time scale and according to the extraction method selected, most of the (14)C-residues remained soluble and easily extractable for both compounds. This result implies that certain precautions should be taken when storing sludges before being spread on the field. Sludge piles, particularly the limed sludge, should be protected from rain to limit the production of lixiviates, which may contain residues of AC-SMX and ACM.

Using a Bayesian approach to improve and calibrate a dynamic model of polycyclic aromatic hydrocarbons degradation in an industrial contaminated soil.

A novel kinetics model that describes the dynamics of polycyclic aromatic hydrocarbons (PAHs) in contaminated soils is presented. The model includes two typical biodegradation pathways: the co-metabolic pathway using pseudo first order kinetics and the specific biodegradation pathway modeled using Monod kinetics. The sorption of PAHs to the solid soil occurs through bi-phasic fist order kinetics, and two types of non-extractible bounded residues are considered: the biogenic and the physically sequestrated into soil matrix. The PAH model was developed in Matlab, parameterized and tested successfully on batch experimental data using a Bayesian approach (DREAM). Preliminary results led to significant model simplifications. They also highlighted that the specific biodegradation pathway was the most efficient at explaining experimental data, as would be expected for an old industrial contaminated soil. Global analysis of sensitivity showed that the amount of PAHs ultimately degraded was mostly governed by physicochemical interactions rather than by biological activity.

Effect of rainfall regimes and mulch decomposition on the dissipation and leaching of S-metolachlor and glyphosate: a soil column experiment.

BACKGROUND: Interception by plant residues is a major process affecting pesticide persistence and leaching in conservation agriculture. Dissipation and leaching of S-metolachlor and glyphosate was studied in repacked soil columns covered with a mulch of maize and lablab residues. The columns were submitted to two contrasting simulated rainfall regimes: one with light but frequent rain (LF) and one with less frequent but more intense rain (HI). In both treatments, columns received the same amount of rainwater by the end of the experiment. RESULTS: Decomposing crop residues on the soil surface retained more than 50% of the applied amount of pesticide. S-metolachlor dissipation in mulch residues was faster under the LF rainfall regime. This was attributed to more humid surface conditions, under which mulch decomposition was also faster. The formation of metabolites of both molecules was higher under the LF rainfall regime. However, leaching of S-metolachlor and its metabolites to deeper soil layers was greater under the HI rainfall regime, whereas they accumulated in the surface layer under the LF rainfall regime. Glyphosate remained in the surface soil layer because of its strong adsorption capacity, whereas aminomethylphosphonic acid leached down in small amounts without any difference between the two rainfall regimes. CONCLUSION: The impact of mulch residues on herbicide dissipation was strongly dependent on molecule type and rainfall regime. © 2014 Society of Chemical Industry.

Modeling the release of organic contaminants during compost decomposition in soil.

Composts, incorporated in soils as amendments, may release organic contaminants during their decomposition. COP-Soil is presented here as a new model to simulate the interaction between organic contaminants and compost, using one module for organic matter and one for organic pollutants, with these modules being linked by several assumptions. Published results of laboratory soil incubations using labeled carbon pollutants from compost were used to test the model for one polycyclic aromatic hydrocarbon (PAH), two surfactants and one herbicide. Several simulation scenarios were tested using (i) the organic pollutant module either alone or coupled to the organic matter module, (ii) various methods to estimate the adsorption coefficients (Kd) of contaminants on organic matter and (iii) different degrading biomasses. The simulations were improved if the organic pollutant module was coupled with the organic matter module. Multiple linear regression model for Kd as a function of organic matter quality yielded the most accurate simulation results. The inclusion of specific biomass in the model made it possible to successfully predict the PAH mineralization.

Preferential transport of Cryptosporidium parvum oocysts in variably saturated subsurface environments.

When oocysts of the protozoan Cryptosporidium parvum contaminate drinking water supplies, they can cause outbreaks of Cryptosporidiosis, a common waterborne disease. Of the different pathways by which oocysts can wind up in drinking water, one has received little attention to date; that is, because soils are often considered to be perfect filters, the transport of oocysts through the subsoil to groundwater is generally ignored. To evaluate the significance of this pathway, a series of laboratory experiments investigated subsurface transport of oocysts. Experiment 1 was carried out in a vertical 18-cm-long column filled either with glass beads or silica sand, under conditions known to foster fingered flow. Experiment 2 involved undisturbed, macroporous soil columns subjected to macropore flow. Experiment 3 aimed to study the lateral flow on an undisturbed soil block. The columns and soil samples were subjected to artificial rainfall and were allowed to reach steady state. At that point, feces of contaminated calves were applied at the surface along with a known amount of potassium chloride to serve as a tracer, and rainfall was continued at the same rate. The breakthrough of oocysts and chloride, monitored in the effluent, demonstrate the importance of preferential flow on the transport of oocysts. Compared with chloride, peak oocyst concentrations were not appreciably delayed and, in some cases, occurred even before the chloride peak. Recovery rates for oocysts were low, ranging from 0.1 to 10.4% of the oocysts originally applied on the columns. However, the numbers of oocysts present in the effluents were still orders of magnitude higher than 10 oocysts, the infectious dose considered by the U.S. Food and Drug Administration, Center for Food Safety and Applied Nutrition, to be sufficient to cause Cryptosporidiosis in healthy adults. These results suggest that the transport of oocysts in the subsurface via preferential flow may create a significant risk of groundwater contamination in some situations.

Adsorption and desorption behavior of selected pesticides as influenced by decomposition of maize mulch.

Assessing pesticide fate in conservation agricultural systems requires a detailed understanding of their interaction with decomposing surface crop residues (mulch). Adsorption and desorption behavior of glyphosate, s-metolachlor and epoxiconazole was investigated on maize mulch residues decomposed under laboratory and field conditions. Our conceptual approach included characterization of chemical composition and hydrophobicity of mulch residues in order to generate parameters to predict sorption behavior. Adsorption of s-metolachlor and epoxiconazole greatly increased with mulch decomposition, whereas glyphosate adsorption was less affected but its desorption was increased. Mulch characteristics including aromaticity, hydrophobicity and polarity indices were strongly correlated to Koc of the non-ionic pesticides. A predictive model based on compositional data (CoDa) analysis revealed that the sorption capacity of decomposing mulch can be predicted from descriptors such as aromatic and alkyl C corresponding respectively to lignin and NDF biochemical fractions. The decomposition degree of mulch residues should be taken into account while predicting the fate of pesticides.

Remediation of polycyclic aromatic hydrocarbon (PAH) contaminated soil through composting with fresh organic wastes.

INTRODUCTION: Composting may enhance bioremediation of PAH-contaminated soils by providing organic substrates that stimulate the growth of potential microbial degraders. However, the influence of added organic matter (OM) together with the microbial activities on the dissipation of PAHs has not yet been fully assessed. MATERIALS AND METHODS: An in-vessel composting-bioremediation experiment of a contaminated soil amended with fresh wastes was carried out. Four different experimental conditions were tested in triplicate during 60 days using laboratory-scale reactors: treatment S (100% soil), W (100% wastes), SW (soil/waste mixture), and SWB (soil/waste mixture with inoculation of degrading microorganisms). RESULTS AND DISCUSSION: A dry mass loss of 35 ± 5% was observed in treatments with organic wastes during composting in all the treatments except treatment S. The dissipation of the 16 USEPA-listed PAHs was largely enhanced from no significant change to 50.5 ± 14.8% (for SW)/63.7 ± 10.0% (for SWB). More obvious dissipation was observed when fresh wastes were added at the beginning of composting to the contaminated soil, without significant difference between the inoculated and non-inoculated treatments. Phospholipid fatty acid (PLFA) profiling showed that fungi and G-bacteria dominated at the beginning of experiment and were probably involved in PAH dissipation. Subsequently, greater relative abundances of G + bacteria were observed as PAH dissipation slowed down. CONCLUSIONS: The results suggest that improving the composting process with optimal organic compositions may be a feasible remediation strategy in PAH-contaminated soils through stimulation of active microbial populations.