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UMR ECOSYS - Ecologie fonctionnelle et écotoxicologie des agroécosystèmes

RL3. Studying soil organic matter dynamics, C storage and its controlling factors at different spatial organization levels

Managing soil organic matter is a key issue for a sustainable agriculture as well as for adapting to climate change and mitigating climate change. Despite dedicated research efforts, the processes leading to soil organic matter biodegradation or stabilization and storage are still insufficiently understood for a robust prediction of SOM stocks and associated properties as affected by management and climate change. Recent research resulted in a change of paradigm in the vision of soil organic matter dynamics, this being more controlled in the long-term by SOM interactions with the environment (physical and chemical conditions, interactions with soils mineral constituents, accessibility to microbial decomposers) than by its intrinsic chemical recalcitrance.

In this context and given our previous achievements, our aims for the last 5 years were to:

A - Understand the processes of soil organic matter stabilization and destabilization, and assess their relative importance at different time scales;

B - Understand and predict microbial transformations of carbon in the complex and structured environment of soils at the scale of the microbial habitat, as affected by climate change, focusing on water availability and developing for this innovative modeling approaches;

C - Evaluate the effect of agricultural soil management on soil carbon stocks and organic matter quality.

The research developed at ECOSYS is largely based on the use of long-term experiments (LTE), which are prime research infrastructures in soil science and biogeochemistry (e. g. Chabbi and Loescher, 2017). The LTEs are either managed by ECOSYS (QualiAgro organic wastes, Les Closeaux C3-C4 chronosequence, “42 parcelles” and “36 parcelles” long term bare fallows – see Appendix 2), or through collaborations (Lusignan SOERE-ACBB, INRA Lusignan grassland management, La Cage and SIC alternative cropping systems, INRA Agronomie, Restinclières Agroforestry, INRA System). On these, SOC and SON stocks are measured, a range of chemical and physical fractionation methods are applied as well as biological characterizations (e.g. microbial biomass, PLFAs, SOC and SON mineralization). Soil organic carbon dynamics is deciphered using 13C natural abundance. The research unit also has strong expertise regarding incubation microcosms experiments in which soil structure and the placement of organic substrates and microorganisms may be manipulated. Modeling with compartment models is used to predict stocks and fluxes as well as to test hypotheses and a new generation of models has been developed at the soil microscale.

The expertise of the soil team allows for its implication into national research networks (CarboSMS, Resmo), and national expert assessments (INRA expert assessment on GHG mitigation in agriculture, ongoing INRA expert assessment on SOC storage). The recognition of carbon storage in soils as an additional and potentially important mitigation option at the COP21 has fostered international initiatives and networking in which the team is involved (4p1000 initiative, Global Research Alliance, FAO GSOC) and has raised the demand for political and management decision making support.

A-  The different processes that explain soil organic matter persistence are at play in all soils, but their relative importance depends on the pedoclimatic context and soil management (Stockman et al., 2013; Dignac et al., 2017) and is not yet fully evaluated.

During the last 5 years, we:

  • Quantified the effect of agricultural management and of the pedoclimatic context on the dynamics of SOM molecular fractions (e.g. Armas Herrera et al., 2016)
  • Quantified the effect of grassland management on the physical protection of soil organic matter (Panettieri et al., 2017)
  • Investigated the importance of clay mineralogy in the stabilization of soil organic matter by organo-mineral associations (e.g. Barré et al., 2015). Using powerful visualization methods, we showed that a diversity of organic compounds interacted with metal oxides (nanoSIMS, STXM, e.g. Lutfalla, PhD 2015).

Biochars are organic amendments to soils gaining considerable interest in the scientific community. During the last 5 years, we contributed to demonstrate their diversity in terms of decomposability and effect on the SOM via priming (e.g. Paestch et al., 2017).

Isolating SOM compartments with contrasted residence times is an ever-challenging issue in soil science. We proposed to use long term bare fallows, i.e. field experiments kept free of vegetation, in which with time soils become gradually depleted in labile organic matter as it decomposes and relatively enriched in persistent soil organic matter. During the last 5 years, thanks to the European network of Long Term Bare Fallows we have developed, we showed that:

  • The mineralization of stable SOC is more sensitive to temperature than that of labile SOC, answering to an active international debate (Lefevre et al., 2014, R. Lefevre, PhD 2015);
  • Pyrogenic C decomposes in the long term;
  • Physical protection contributed to about a quarter of SOC persistence over 80 years (Paradelo et al., 2016);
  • Priming effect does not seem to be quantitatively important in the long term (50 y) (Cardinael et al., 2015);
  • Stable SOC has a low energy content, which may be attributed to a combination of reduced content of energetic C–H bonds or stronger interactions between OM and the mineral matrix, explaining partly its persistence in soils (Barré et al., 2016). The use of these Long-term Bare Fallow showed that thermal methods and in particular Rock Eval pyrolysis are very promising method to evaluate the biological stability of soil organic carbon (Cecillon et al., 2018).

B-  The insufficiently accurate prediction of SOM stocks and fluxes with current compartment models is now ascribed largely to ignoring the high level of heterogeneity at the particle and pore scale caused by soil structure, which leads to a spatial disconnection between soil carbon, energy sources, and the organisms that are involved in carbon transformations. Our team has invested in the study of the microbial transformations of organic matter at the microscale in soils since a decade now, with an original combination of experimental and modeling studies. In the last 5 years, this topic was developed in the framework of two ANR projects, MEPSOM and Soilµ3D that we coordinated.

We have improved our description of the importance of accessibility in the mineralization of organic substrates (Pinheiro et al. 2015), have shown that the heterogeneity of habitats at the pore scale affected more the mineralisation of labile organic substrates than microbial diversity (e.g. Juarez et al., 2013). Water availability is indeed a strong driver of microbial decomposition of organic matter in the soil structure (Moyano al., 2013).

We developed a series of breakthrough models for describing the mineralisation of organic substrates in the soil structure, that are based on an explicit description of the heterogeneity of soil pore system, water and air distribution and bacteria or fungi and organic matter distribution in the soil structure. These models are based on lattice-Boltzmann formalisms (e.g. Vogel et al., 2015; see Highlight 6) or on a representation of soil pore system with geometrical primitives (e.g. Monga et al. 2014). The spatial distribution of solids and voids is obtained from X-ray computed micro tomography µCT images, although the resolution of these techniques needs improvement when dealing with microbial processes in soils (Baveye et al., 2017). We invested in describing the three-dimensional distribution of water and air in soil pores, using two-relaxation-times lattice-Boltzmann modeling, with the aid of synchrotron X-ray computed tomography studies (e.g. Pot et al., 2015). The spatial distribution of organic matter is ascribed a priori or could be located as well using µCT. For this, we have developed an innovative method for localizing organic matter in µCT tomography (Peth et al., 2014). The spatial distribution of microorganisms is implemented either at random or based on literature reports. We have been able so far to model the mineralisation of simple organic compounds (Monga et al., 2014; Vogel et al., 2015; 2018) and the spread of fungal hyphae in soils.

C-  Our research aims also at evaluating the effects of agricultural soil management on soil carbon stocks and organic matter quality, which is needed to identify mitigation options in agriculture (Chabbi et al., 2017; Chenu et al., 2018).

The recycling of OWPs is one of these managements and has been specifically presented in the research line 1. In the last 5 years:

We showed that, regarding grassland management, ley-arable rotations improved GHG emissions and carbon balance compared to continuous arable systems, and also affected the phosphorus cycle (Crème et al., 2016). The introduction of alfalfa in the leys had however little effect on SOC stocks and SOM biochemical composition. We found that the model DaylyDayCent could successfully describe GHG fluxes in these systems (Senapati et al., 2016).

Thanks to long term experiments, we provided the first estimates of additional SOC storage rates for two alternative cropping systems in France: conservation agriculture (i.e. no tillage with a permanent cover crop, Autret et al., 2016,), and alley cropping agroforestry (Cardinael et al., 2015, 2017). Combining measurements of SOC stocks, C inputs to soil and modeling we found that in these different cropping systems, the additional SOC storage could be explained entirely by increased organic inputs to soil (Autret et al., 2016; Cardinael et al., 2018), raising questions about the effects of no tillage on SOC mineralization rates.