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PhD student (M/F) - Characterisation of the biophysical interactions that regulate microbial activity in soils

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Français - Anglais

Date Limite Candidature : samedi 9 juillet 2022

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General information

Reference : UMR7619-DAMJOU-002
Workplace : PARIS 05
Date of publication : Saturday, June 18, 2022
Scientific Responsible name : Damien Jougnot
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2022
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly

Description of the thesis topic

This PhD project will combine elements of enzymology, soil microbiology and hydrogeophysics in order to better understand how interactions between soil microbial communities and their physical environment affects their activity.

Agricultural soils are at the heart of many of societies needs. They are expected to produce food for a growing population whilst contributing to global change mitigation. However, there is significant concern over the release by agriculture fields to the atmosphere of significant amounts of greenhouse gases, suggesting a changes in agricultural practices may be beneficial. However, in order to assess the usefulness of measures taken more refined models of carbon dynamics than those that are available at present are required. The available models have been developed to date are generally plot scale models and do not describe microbial decomposition of soil organic matter adequately. Recent research on soil carbon dynamics suggests that the persistence of organic carbon (OC) in soil is more an ecosystem property (interactions between organic carbon and the mineral phase of soil, physical separation between decomposer and OC…) than an intrinsic property of the OC molecules (Schmidt et al., 2011). Therefore investigations of interactions between microbial decomposers and their environment are likely important to fully comprehend soil C dynamics.
The mineralisation of OC is frequently linear as a function of the square root of time, suggesting that the process may be diffusion limited (Nunan, 2017). In this scenario, the environmental properties that affect the diffusion pathways towards microbial decomposers are likely to have a profound influence on OC mineralisation. These diffusion pathways vary as a function of the connectivity and the tortuosity of the water phase in the soil pore network. The volume of water that is connected to decomposers could therefore be viewed as the “active volume” of the soil within which certain molecules can freely diffuse.

Scientific objectives
The objectives of the PhD are to experimentally test the hypothesis that OC decomposition is limited by diffusion and to characterise the properties of the water phase that influence diffusion (distribution and connectivity of the water phase in the soil pore network) using hydrogeophysical approaches (measurement of electrical tortuosity and connectivity).

Specific questions
1. diffusion constraints on decomposition
The rate limiting step in the decomposition of soil OC is catalysed by extracellular enzymes (mostly of microbial origin - Schimel & Weintraub, 2003). These enzymes are generally adsorbed to surfaces and their kinetics are significantly different from enzymes that are in free solution, who have Michaelis-Menten type kinetics. In biotechnology, where enzymes are immobilised on surfaces in order to slow denaturing rates (Chaplin & Bucke, 1990), studies have shown that the activity of immobilised enzymes was modulated by ratio of the maximum catalytic rate over the substrate diffusion rate, called the Damköhler number (Chaplin & Bucke, 1990). the specific kinetic characteristics of Michaelis-Menten and diffusion limited enzyme activities should allow the determination of the role of diffusion in regulating the mineralisation of soil OC.

2. Characterisation of the water phase.
The effective diffusion rate in the aqueous phase depends upon the tortuosity and connectivity of the aqueous phase within the soil pore network (Revil & Jougnot, 2008). In porous media, these parameters depend upon the interaction between the water content and the architecture of the pore network (Jougnot et al., 2018). Furthermore, it has been shown that the distribution of the aqueous phase depends not only on the organisation of the pore network but also on the structure of the pores and on saturation dynamics (Maineult et al., 2018). This means that the connectivity of the pore network and the connectivity of the aqueous phase within the pore network are not necessarily linked in unsaturated conditions and that descriptors of the pore network, as obtained by X-ray tomography, are not particularly pertinent.
Electrical resistivity is a non-intrusive and integrative geophysical method that can be used as a proxy for determining the moisture content of porous media as well as the connectivity and tortuosity of the aqueous phase in the pores (Jougnot et al., 2018). The use of appropriate petrophysical models allows the estimation of diffusion coefficients of different ionic species from such electrical measurements (Revil & Jougnot, 2008; Jougnot et al., 2009). The electrical resistivity of porous media is a property that should be considered as a tensor, especially in partially saturated media which can display significant anisotropy (Jougnot et al., 2018). The use of several measurements of electrical resistivity with different configurations makes it possible to account for both anisotropy and for temporal changes, and therefore for changes in the connectivity of the aqueous phase (Maineult et al., 2018; Jougnot et al., 2019).

There will be two experimental work packages in this PhD program: (1) investigation of diffusion constraints on microbial decomposition of organic carbon and (2) characterisation of the connectivity of the aqueous phase. Both experimental work packages will use a range of soils (10-15 soils with different textures and organic C contents) in order to ensure that the results are generalisable.
1. diffusion constraints on decomposition. Subsoil microbial communities, and therefore decomposition sites, are more spatially dispersed than in surface soils (Nunan et al., 2002). This means that the distances among decomposition sites are, on average, greater and the diffusion pathways of substrates longer. We will test the hypothesis that diffusional constraints on OC decomposition are greater in subsoil samples than in surface samples. This will be achieved by adding different concentrations of 13C labelled (stable C isotope) to undisturbed soil cores taken from surface soil and subsoil and measuring the mineralisation of the added labelled substrate.
2. Characterisation of the aqueous phase. Much progress has been made recently in the use of geophysical measurements, through the use of petrophysics approaches in hydrogeophysics, particularly that of electrical resistivity, which has been been used as a proxy for transport properties in partially saturated porous media such as the tortuosity of the aqueous phase (e.g., Clennel, 1997). We will use this rapid (~1s) and easily implemented method to link the distribution and anisotropy of electrical resistivity in order to quantify and monitor changes in diffusion pathways as a function of water potential. In addition to these measurements, a series of more routine measurements will also be made (porosity, texture, x-ray tomography).

Chaplin, M.F., Bucke, C. (1990) Enzyme technology. Cambridge University Press, R-U.
Clennell, B. (1997). Tortuosity: A guide through the maze. Geological Society, London, Special Publications, 122(1), 299–344.
Davidson, E.A., Janssens, I.A. (2006) Temperature sensitivity of soil carbon decomposition and feedbacks to climate change. Nature 440, 165–173.
Guérin, R. (2005) Borehole and surface-based hydrogeophysics. Hydrogeology Journal, 13(1), 251-254.
Jougnot, D., Revil, A., Leroy, P. (2009) Diffusion of ionic tracers in the Callovo-Oxfordian clay-rock using the Donnan equilibrium model and the formation factor. Geochimica et Cosmochimica Acta, 73(10), 2712-2726.
Jougnot D., Jimenez-Martinez, J., Legendre, R., Le Borgne, T., Meheust, Y., Linde, N. (2018) Impact of small-scale saline tracer heterogeneity on electrical resistivity monitoring in fully and partially saturate d porous me dia: Insights from geoelectrical milli-fluidic experiments. Advances in Water Resources 113, 295–309.
Jougnot D., A. Mendieta, P. Leroy, A. Maineult (2019) Exploring the effect of the pore size distribution on the streaming potential generation in saturated porous media, insight from pore network simulations, Journal of Geophysical Research - Solid Earth, 124(6), 5315-5335, doi:10.1029/2018JB017240.
Juarez, S., Nunan, N., Duday, A.-C., Pouteau, V., Schmidt, S., Hapca, S., Falconer, R., Otten, W., Chenu, C. (2013) Effects of different soil structures on the decomposition of native and added organic carbon. European Journal of Soil Biology 58, 81–90.
Maineult, A., Jougnot, D., Revil, A. (2018) Variations of petrophysical properties and spectral induced polarization in response to drainage and imbibition: a study on a correlated random tube network. Geophysical Journal International 212(2), 1398–1411.
Nunan, N. (2017) The microbial habitat in soil: Scale, heterogeneity and functional consequences. Journal of Plant Nutrition & Soil Science 180, 425–429.
Nunan, N., Wu, K., Young, I.M., Crawford, J.W., Ritz, K. (2002) In situ spatial patterns of soil bacterial populations, mapped at multiple scales, in an arable soil. Microbial Ecology 44, 296–305.
Raynaud, X, Nunan, N. (2014) Spatial Ecology of Bacteria at the Microscale in Soil. PLoS ONE 9, e87217.
Revil, A., Jougnot, D. (2008). Diffusion of ions in unsaturated porous materials. Journal of Colloid and Interface Science, 319(1), 226-235.
Ruamps, L.S., Nunan, N., Chenu, C. (2011) Microbial biogeography at the soil pore scale. Soil Biology and Biochemistry 43, 280–286.
Ruamps, L.S., Nunan, N., Pouteau, V., Leloup, J., Raynaud, X., Roy, V., Chenu, C. (2013) Regulation of soil organic C mineralisation at the pore scale. FEMS Microbiology Ecology 86, 26–35.
Schmidt et al., 2011 Persistence of soil organic matter as an ecosystem property. Nature 478, 49–56.
Schimel, J.P., Weintraub, M.N. (2003) The implications of exoenzyme activity on microbial carbon and nitrogen limitation in soil: a theoretical model. Soil Biology & Biochemistry 35, 549–563.

Work Context

The experimental work will be carried out in the laboratories of two mixed research units (UMR), Metis and IEES Paris, both of which are located on the Pierre and Marie Campus of Sorbonne University. The two supervisors (D. Jougnot and N. Nunan) already have all the equipment necessary for the successful completion of the project. The thesis is part of the BIOMASS (BIOgeophysical characterization of Microbial Activity in SoilS) project, which is funded by the MITI 80|PRIME initiative of the CNRS. The thesis will also interact with the TERRA FORMA EQUIPEX project, which started in 2022 and one work package of which is lead by D. Jougnot.

Constraints and risks

Not applicable

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