Browsing by Author "Garnier, Patricia"

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    Accounting for soil architecture and microbial dynamics in microscale models: current practices in soil science and the path ahead
    (Wiley, 2021-07-04) Pot, Valérie; Portell, Xavier; Otten, Wilfred; Garnier, Patricia; Monga, Olivier; Baveye, Philippe C.
    Macroscopic models of soil organic matter (SOM) turnover have faced difficulties in reproducing SOM dynamics or in predicting the spatial distribution of carbon stocks. These models are based on a largely inadequate linear response of soil microorganisms to bulk concentrations of nutrients and it is clear that a new approach to SOM modelling is required. Introducing explicit microbial activity and organic matter (OM) reactivity in macroscopic models represents a challenge because of the fine spatial scales at which the processes occur. To get a better grasp on interactions that take place at the microscale, a new generation of SOM models have been developed at the spatial scale of the soil microenvironments where microorganisms evolve. These models are well adapted to challenge traditional hypotheses about the influence of soil architecture on soil microbial activity. Soil architecture provides the stage for a dynamic spatial accessibility of resources to microbes and the emergence of interactions between the actors in SOM decomposition. In this context, we review microscale models of microbial activity that have been designed for soils and soil analogues. To understand how these models account for spatial accessibility, we look in detail at how soil microenvironments are described in the different approaches and how microbial colonies are spatialized in these microenvironments. We present the advantages and disadvantages of the developed strategies and we discuss their limits.
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    Data underpinning "Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: Insights from computer simulations"
    (Cranfield University, 2018-07-30 11:12) Portell-Canal, Xavier; Pot, Valérie; Garnier, Patricia; Otten, Wilfred; Baveye, Philippe
    Figures and data used in the paper "Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: Insights from computer simulations". See readme.txt file in the compressed files (.7z) for a description of the files included in the folder.
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    Emergent properties of microbial activity in heterogeneous soil microenvironments: different research approaches are slowly converging, yet major challenges remain
    (Frontiers Media, 2018-08-27) Baveye, Philippe C.; Otten, Wilfred; Kravchenko, Alexandra; Balseiro-Romero, María; Beckers, Éléonore; Chalhoub, Maha; Darnault, Christophe; Eickhorst, Thilo; Garnier, Patricia; Hapca, Simona; Kiranyaz, Serkan; Monga, Olivier; Mueller, Carsten W.; Nunan, Naoise; Pot, Valérie; Schlüter, Steffen; Schmidt, Hannes; Vogel, Hans-Jörg
    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.
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    Lessons from a landmark 1991 article on soil structure: distinct precedence of non-destructive assessment and benefits of fresh perspectives in soil research
    (CSIRO Publishing, 2022-01-19) Baveye, Philippe C.; Balseiro-Romero, María; Bottinelli, Nicolas; Briones, María; Capowiez, Yvan; Garnier, Patricia; Kravchenko, Alexandra; Otten, Wilfred; Pot, Valérie; Schlüter, Steffen; Vogel, Hans-Jörg
    In 1991, at the launch of a national symposium devoted to soil structure, the Australian Society of Soil Science invited Professor John Letey to deliver a keynote address, which was later published in the society’s journal. In his lecture, he shared the outcome of his reflexion about what the assessment of soil structure should amount to, in order to produce useful insight into the functioning of soils. His viewpoint was that the focus should be put on the openings present in the structure, rather than on the chunks of material resulting from its mechanical dismantlement. In the present article, we provide some historical background for Letey’s analysis, and try to explain why it took a number of years for the paradigm shift that he advocated to begin to occur. Over the last decade, his perspective that soil structure needs to be characterised via non-destructive methods appears to have gained significant momentum, which is likely to increase further in the near future, as we take advantage of recent technological advances. Other valuable lessons that one can derive from Letey’s pioneering article relate to the extreme value for everyone, even neophytes, to constantly ask questions about where research on given topics is heading, what its goals are, and whether the methods that are used at a certain time are optimal.
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    Microscale heterogeneity of the spatial distribution of organic matter can promote bacterial biodiversity in soils: Insights from computer simulations
    (Frontiers Media, 2018-07-27) Portell, Xavier; Pot, Valérie; Garnier, Patricia; Otten, Wilfred; Baveye, Philippe C.
    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.
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    Pore-scale monitoring of the effect of microarchitecture on fungal growth in a two-dimensional soil-like micromodel
    (Frontiers Media, 2018-07-03) Soufan, Raghad; Delaunay, Yolaine; Vieublé Gonod, Laure; Shor, Leslie M.; Garnier, Patricia; Otten, Wilfred; Baveye, Philippe C.
    In spite of the very significant role that fungi are called to play in agricultural production and climate change over the next two decades, very little is known at this point about the parameters that control the spread of fungal hyphae in the pore space of soils. Monitoring of this process in 3 dimensions is not technically feasible at the moment. The use of transparent micromodels simulating the internal geometry of real soils affords an opportunity to approach the problem in 2 dimensions, provided it is confirmed that fungi would actually want to propagate in such artificial systems. In this context, the key objectives of the research described in this article are to ascertain, first, that the fungus Rhizoctonia solani can indeed grow in a micromodel of a sandy loam soil, and, second, to identify and analyze in detail the pattern by which it spreads in the tortuous pores of the micromodel. Experimental observations show that hyphae penetrate easily inside the micromodel, where they bend frequently to adapt to the confinement to which they are subjected, and branch at irregular intervals, unlike in current computer models of the growth of hyphae, which tend to describe them as series of straight tubular segments. A portion of the time, hyphae in the micromodels also exhibit thigmotropism, i.e., tend to follow solid surfaces closely. Sub-apical branching, which in unconfined situations seems to be controlled by the fungus, appears to be closely connected with the bending of the hyphae, resulting from their interactions with surfaces. These different observations not only indicate different directions to follow to modify current mesoscopic models of fungal growth, so they can apply to soils, but they also suggest a wealth of further experiments using the same set-up, involving for example competing fungal hyphae, or the coexistence of fungi and bacteria in the same pore space.
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    Scenario modelling of carbon mineralization in 3D soil architecture at the microscale: toward an accessibility coefficient of organic matter for bacteria
    (Wiley, 2021-07-07) Mbé, Bruno; Monga, Olivier; Pot, Valérie; Otten, Wilfred; Hecht, Frédéric; Raynaud, Xavier; Nunan, Naoise; Chenu, Claire; Baveye, Philippe C.; Garnier, Patricia
    The microscale physical characteristics of microbial habitats considerably affect the decomposition of organic matter in soils. One of the challenges is to identify microheterogeneities in soil that can explain the extent of carbon mineralization. The aim of this study was therefore to identify descriptors of μm-scale soil heterogeneity that can explain CO2 fluxes obtained at the mm scale. A suite of methods and models that visualize soil heterogeneity at scales relevant to microorganisms has been developed over the last decade. Among the existing 3D models that simulate microbial activity in soils, Mosaic is able to simulate, within a short computation time, the microbial degradation of organic matter at the microhabitat scale in soil using real 3D images of soil porosity. Our approach was to generate scenarios of carbon mineralization for various microscale environmental conditions and determine how the descriptors of soil structure could explain CO2 evolution. First, we verified that the simulated diffusion of solutes in the soil samples obtained with Mosaic were the same as those obtained using the same parameter set from a robust 3D model based on a lattice Boltzmann approach. Then, we ran scenarios considering different soil pore architectures, water saturations and microorganism and organic matter placements. We found that the CO2 emissions simulated for the different scenarios could be explained by the distance between microorganisms and organic matter, the diffusion of the substrate and the concentration of the available substrate. For some of the scenarios, we proposed a descriptor of accessibility based on the geodesic distance between microorganisms and organic matter weighted by the amount of organic matter. This microscale descriptor is correlated to the simulated CO2 flux with a correlation coefficient of 0.69.
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    Soil aggregates as biogeochemical reactors: Not a way forward in the research on soil‐atmosphere exchange of greenhouse gases
    (Wiley, 2019-04-08) Kravchenko, Alexandra; Otten, Wilfred; Garnier, Patricia; Pot, Valérie; Baveye, Philippe C.
    Over the last two decades, the fact that soils are significant sources of greenhouse gases (GHG), e.g., carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and water vapor, has received considerable attention from the scientific community. Many laboratory and field experiments have been carried out to investigate the release of GHG by soils, and a wide range of computer modeling approaches have been explored to encapsulate what is known about the process, as well as to improve its prediction at various spatial and temporal scales.
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    Understanding the joint impacts of soil architecture and microbial dynamics on soil functions: insights derived from microscale models
    (Wiley, 2022-06-23) Pot, Valérie; Portell, Xavier; Otten, Wilfred; Garnier, Patricia; Monga, Olivier; Baveye, Philippe C.
    Over the last decades, a new generation of microscale models has been developed to simulate soil microbial activity. An earlier article (Pot et al., 2021) presented a detailed review of the description of soil architecture and microbial dynamics in these models. In the present article, we summarise the main results obtained by these models according to six model outputs: growth and spatial organisation of microbial colonies, soil hydraulic conductivity, coexistence and trophic interactions of microorganisms, temporal dynamics of the amount of solid and dissolved organic matter in soil and, microbial production of CO2. For each of these outputs, we draw particular attention to the respective roles of soil architecture and microbial dynamics, and we report how microscale models allow for disentangling and quantifying them. We finally discuss limitations and future directions of microscale models in combination with the on-going development of high-performance imaging tools revealing the spatial heterogeneity of the actors of soil microbial activity.