François Lafolie

Root clumping may affect the root water potential and the resistance to soil-root water transport

We have appraised for clumped root systems the widely-accepted view that the resistance to water flux from soil to roots (‘soil resistance’) is low under most field conditions, so that root water potential would closely follow the mean soil water potential. Three root spatial arrangements were studied, simulating either the regular pattern generally assumed in models, or two degrees of root clumping frequently observed in the field. We used a numerical 2-dimensional model of water transfer which assumes a control of evapotranspiration by root signalling. Calculations were carried out at two evaporative demands and for two contrasting soil hydraulic properties. The rate of soil depletion, the timing of the reduction in evapotranspiration and the difference between root water potential and mean soil water potential were all affected by the root spatial arrangement, with a greater effect at high evaporative demand and low soil hydraulic conductivity. Almost all the soil water reserve was available to plants without reduction in evapotranspiration in the regular case, while only a part of it was available in clumped cases. In the regular case, calculated ‘soil resistances’ were similar to those calculated using Newmans (1969) method. Conversely they were higher by up to two orders of magnitude in clumped root spatial arrangements. These results place doubt on the generality of the view that ‘soil resistance’ is low under common field conditions. They are consistent with the results of field experiments, especially with recent data dealing with root-to-shoot communication.

Modelling competition for water in intercrops : Theory and comparison with field experiments

A knowledge of plant interactions above and below ground with respect to water is essential to understand the performance of intercrop systems. In this study, a physically based framework is proposed to analyse the competition for soil water in the case of intercropped plants. A radiative transfer model, associated with a transpiration-partitioning model based on a modified form of the Penman-Monteith equation, was used to estimate the evaporative demand of maize (Zea mays L.) and sorghum ( Sorghum vulgare R.) intercrops. In order to model soil–root water transport, the root water potential of each species was calculated so as to minimise the difference between the evaporative demand and the amount of water taken up by each species. A characterisation of the micrometeorological conditions (net radiation, photosynthetically active radiation, air temperature and humidity, rain), plant water relations (leaf area index, leaf water potential, stomatal conductance, sap flow measurements), as well as the two-component root systems and water balance (soil–root impacts, soil evaporation) was carried out during a 7-day experiment with densities of about 4.2 plant m-2 for both maize and sorghum. Comparison of the measured and calculated transpiration values shows that the slopes of the measured versus predicted regression lines for hourly transpiration were 0.823 and 0.778 for maize and sorghum, respectively. Overall trends in the variation of volumetric water content profiles are also reasonably well described. This model could be useful for analysing competition where several root systems are present under various environmental conditions.

Emigration of the plant pathogen Pseudomonas syringae from leaf litter contributes to its population dynamics in alpine snowpack

The recently discovered ubiquity of the plant pathogen Pseudomonas syringae in headwaters and alpine ecosystems worldwide elicits new questions about the ecology of this bacterium and subsequent consequences for disease epidemiology. Because of the major contribution of snow to river run-off during crop growth, we evaluated the population dynamics of P.syringae in snowpack and the underlying leaf litter during two years in the Southern French Alps. High population densities of P.syringae were found on alpine grasses, and leaf litter was identified as the main source of populations of P.syringae in snowpack, contributing more than the populations arriving with the snowfall. The insulating properties of snow foster survival of P.syringae throughout the winter in the 10 cm layer of snow closest to the soil. Litter and snowpack harboured populations of P.syringae that were very diverse in terms of phenotypes and genotypes. Neither substrate nor sampling site had a marked effect on the structure of P.syringae populations, and snow and litter had genotypes in common with other non-agricultural habitats and with crops. These results contribute to the mounting evidence that a highly diverse P.syringae metapopulation is disseminated throughout drainage basins between cultivated and non-cultivated zones.

Modeling soil-root water transport with non-uniform water supply and heterogeneous root distribution

A 2D physically based framework is proposed to analyze the effect of a non-uniform water supply at the soil surface generated by rainfall interception and stemflow on soil-root water transport in the case of heterogeneous distribution of the roots in the soil profile. To model soil-root water transport, the root water potential of two plants placed in two adjacent rows was simulated so as to minimize the difference between the evaporative demand and the amount of water taken up by each plant. A characterization of the throughfall to incident rainfall, soil hydrodynamic properties, soil-root contacts, and maize evapotranspiration, was carried out during a 10-day experiment with a leaf area index of about 4 to 5 m2 m−2. Mean rainfall interception percentages were in the [47.4%–52.6%] range at half the distance between two adjacent rows, whereas an interception percentage higher than 80% was found near the stems along the rows. As a result, the mean estimated stemflow was 1 L per plant per 16.4 mm water supply above the canopy. Good agreement was found between the measured and predicted transpiration values. As the soil started to moisten, the predicted root water potential rapidly increased, in line with the predicted number of active roots that rapidly decreased. Effects due to stemflow during infiltration disappeared progressively when drying was in progress. The proposed approach could be useful for analyzing soil-root water transport and possible pollution when solutes move with water under various realistic conditions where non-uniform water supply is involved.

Modeling soil-root water transport and competition for single and mixed crops

A knowledge of above and below ground plant interactions for water is essential to understand the performance of intercropped systems. In this work, root water potential dynamics and water uptake partitioning were compared between single crops and intercrops, using a simulation model. Four root maps having 498, 364, 431 and 431 soil-root contacts were used. In the first and second cases, single crops with ‘deep’ and ‘surface’ roots were considered, whereas in the third and fourth cases, roots of two mixed crops were simultaneously considered with different row spacing (40 cm and 60 cm). Two soils corresponding to a clay and a silty clay loam were used in the calculations. A total maximum evapotranspiration of 6 mm d-1 for both single or mixed crops was considered, for the mixed crops however, two transpiration distributions between the crops were analyzed (3:3 mm d-1, or 4:2 mm d-1 for each crop, respectively). The model was based on a previous theoretical framework applied to single or intercropped plants having spatially distributed roots in a two-dimensional domain. Although water stress occurred more rapidly in the loam than in the clay, due to the rapid decrease of the soil water reserve in the loam, the role of the root arrangement appeared to be crucial for water availability. Interactions between the distribution of transpiration among mixed crops and the architecture of the root systems which were in competition led to water movements from zones with one plant to another, or vice versa, which corresponded to specific competition or facilitation effects. Decreasing the distances between roots may increase competition for water, although it may determine greater water potential gradients in the soil that increase lateral or vertical water fluxes in the soil profile. The effects of the root competition on water uptake were quite complicated, depending on both environmental conditions, soil hydrodynamic properties, and time scales. Although some biological adaptive mechanisms were disregarded in the analysis, the physically 2-D based model may be considered as a tool to study the exploitation of environmental heterogeneity at microsite scales.

Potential for fluorescence spectroscopy to assess the quality of soil water-extracted organic matter

Fluorescence spectroscopy has potential for characterizing the water soluble fraction of soil organic matter. However, some questions remain unanswered: (i) can this technique be applied to a complex and evolving mixture of compounds and (ii) can the quality parameter obtained from fluorescence analysis be linked to climatic parameters and soil microbial activity. To answer these questions, a set of 98 soil water extracts, from a study of a 2.50-m-thick soil section in the vadose zone during a 7-month experiment was analyzed. Water-extracted organic matter (WEOM) content and the potential aerobic respiratory activity were measured in the laboratory, whereas environmental factors (rainfall, soil temperature) were monitored on site. The humification index (HIX) was also calculated for the 98 samples. Results showed a significant positive correlation (R2 = 0.87, P < 0.001) between the fluorescence signal and the WEOM content. A higher proportion of low molecular weight and size compounds was observed in the deepest layers than in the surface soils. The decrease in aerobic respiratory activity (from 0.9 to 0.4 μgO2 g−1dw h−1) and in HIX (from 3.7 to 2.1) from the surface to the 1.5-m depth suggest that the small fluorescent compounds were more recalcitrant to biodegradation in the deep vadose zone. Heavy rainfall events (60 mm) resulted in a sharp decrease of HIX values (from 2.6 to 1.3) at the 1.5-m depth, probably the result of leaching of small compounds, whereas the WEOM content was stable (2 mg C L−1). Fluorescence spectroscopy was demonstrated to be useful for analyzing the fate of agricultural organic residues in soils.

Soil water flow is a source of the plant pathogen Pseudomonas syringae in subalpine headwaters

The airborne plant pathogenic bacterium Pseudomonas syringae is ubiquitous in headwaters, snowpack and precipitation where its populations are genetically and phenotypically diverse. Here, we assessed its population dynamics during snowmelt in headwaters of the French Alps. We revealed a continuous and significant transport of P.syringae by these waters in which the population density is correlated with water chemistry. Via in situ observations and laboratory experiments, we validated that P.syringae is effectively transported with the snow melt and rain water infiltrating through the soil of subalpine grasslands, leading to the same range of concentrations as measured in headwaters (10(2) -10(5) CFU l(-1) ). A population structure analysis confirmed the relatedness between populations in percolated water and those above the ground (i.e. rain, leaf litter and snowpack). However, the transport study in porous media suggested that water percolation could have different efficiencies for different strains of P.syringae. Finally, leaching of soil cores incubated for up to 4 months at 8°C showed that indigenous populations of P.syringae were able to survive in subalpine soil under cold temperature. This study brings to light the underestimated role of hydrological processes involved in the long distance dissemination of P.syringae.

A coordinated set of ecosystem research platforms open to international research in ecotoxicology, AnaEE-France

The infrastructure for Analysis and Experimentation on Ecosystems (AnaEE-France) is an integrated network of the major French experimental, analytical, and modeling platforms dedicated to the biological study of continental ecosystems (aquatic and terrestrial). This infrastructure aims at understanding and predicting ecosystem dynamics under global change. AnaEE-France comprises complementary nodes offering access to the best experimental facilities and associated biological resources and data: Ecotrons, seminatural experimental platforms to manipulate terrestrial and aquatic ecosystems, in natura sites equipped for large-scale and long-term experiments. AnaEE-France also provides shared instruments and analytical platforms dedicated to environmental (micro) biology. Finally, AnaEE-France provides users with data bases and modeling tools designed to represent ecosystem dynamics and to go further in coupling ecological, agronomical, and evolutionary approaches. In particular, AnaEE-France offers adequate services to tackle the new challenges of research in ecotoxicology, positioning its various types of platforms in an ecologically advanced ecotoxicology approach. AnaEE-France is a leading international infrastructure, and it is pioneering the construction of AnaEE (Europe) infrastructure in the field of ecosystem research. AnaEE-France infrastructure is already open to the international community of scientists in the field of continental ecotoxicology.

Combined time-lapse magnetic resonance imaging and modeling to investigate colloid deposition and transport in porous media

Colloidal particles can act as vectors of adsorbed pollutants in the subsurface, or be themselves pollutants. They can reach the aquifer and impair groundwater quality. The mechanisms of colloid transport and deposition are often studied in columns filled with saturated porous media. Time-lapse profiles of colloid concentration inside the columns have occasionally been derived from magnetic resonance imaging (MRI) data recorded in transport experiments. These profiles are valuable, in addition to particle breakthrough curves (BTCs), for testing and improving colloid transport models. We show that concentrations could not be simply computed from MRI data when both deposited and suspended colloids contributed to the signal. We propose a generic method whereby these data can still be used to quantitatively appraise colloid transport models. It uses the modeled suspended and deposited particle concentrations to compute modeled MRI data that are compared to the experimental data. We tested this method by performing transport experiments with sorbing colloids in sand, and assessed for the first time the capacity of the model calibrated from BTCs to reproduce the MRI data. Interestingly, the dispersion coefficient and deposition rate calibrated from the BTC were respectively overestimated and underestimated compared with those calibrated from the MRI data, suggesting that these quantities, when determined from BTCs, need to be interpreted with care. In a broader perspective, we consider that combining MRI and modeling offers great potential for the quantitative analysis of complex MRI data recorded during transport experiments in complex environmentally relevant porous media, and can help improve our understanding of the fate of colloids and solutes, first in these media, and later in soils.

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.