Accounting for soil architecture and microbial dynamics in microscale models: Current practices in soil science and the path ahead

Pot, Valérie; Portell, Xavier; Otten, Wilfred; Garnier, Patricia; Monga, Olivier; Baveye, Philippe C.

doi:10.1111/ejss.13142

Cited by 29 publications

(34 citation statements)

References 190 publications

(303 reference statements)

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“…The geometry of the pore space in many soils may be so convoluted as to preclude microorganisms, and even their exoenzymes, access to potential substrates. These insights are increasingly reflected by a new generation of mathematical models that take the microscale heterogeneity of soils explicitly into account when describing the fate of organic matter (e.g., Falconer et al, 2015;Golparvar et al, 2021;König et al, 2020;Pot et al, 2022;Vogel et al, 2015).…”

Section: Mineralization Kinetics: Patterns and Inherent Complexitymentioning

confidence: 99%

Soil carbon sequestration for climate change mitigation: Mineralization kinetics of organic inputs as an overlooked limitation

Berthelin¹,

Laba

Lemaire³

et al. 2022

European J Soil Science

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Over the last few years, the question of whether soil carbon sequestration could contribute significantly to climate change mitigation has been the object of numerous debates. All of these debates so far appear to have entirely overlooked a crucial aspect of the question. It concerns the short-term mineralization kinetics of fresh organic matter added to soils, which is occasionally alluded to in the literature, but is almost always subsumed in a broader modelling context. In the present article, we first summarise what is currently known about the kinetics of mineralization of plant residues added to soils, and about its modelling in the long run. We then argue that in the short run, this microbially-mediated process has important practical consequences that cannot be ignored. Specifically, since at least 90% of plant residues added to soils to increase their carbon content over the long term are mineralized relatively rapidly and are released as CO 2 to the atmosphere, farmers would have to apply to their fields 10 times more organic carbon annually than what they would eventually expect to sequester. Over time, because of a well-known sink saturation effect, the multiplier may even rise significantly above 10, up to a point when no net carbon sequestration takes place any longer.

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Section: Mineralization Kinetics: Patterns and Inherent Complexitymentioning

confidence: 99%

Soil carbon sequestration for climate change mitigation: Mineralization kinetics of organic inputs as an overlooked limitation

Berthelin¹,

Laba

Lemaire³

et al. 2022

European J Soil Science

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“…These include physicochemical control mechanisms limiting bioavailability, such as chemisorption onto humic substances (Mudhoo and Garg, 2011), physical stabilization in soil micro aggregates (Hochman et al, 2021), or the spatial encounter of substrates and degraders (Shi et al, 2021). Including these additional mechanisms by applying better sorption and stabilization model formulations (van Genuchten and Wagenet, 1989;Streck et al, 1995;Altfelder and Streck, 2006;Villaverde et al, 2009;Kästner et al, 2014;Yu et al, 2020) and spatially resolved modeling approaches (Babey et al, 2017;König et al, 2020;Pagel et al, 2020;Pot et al, 2021) might further improve predicting the persistence of AT and other pesticides in soil. Our study investigated to what extent mass-transfer limitations and bioenergetic constraints can explain the longterm fate of atrazine and its major metabolite hydroxyatrazine in soils.…”

Section: Pesticide Persistence In Soilmentioning

confidence: 99%

Modeling Bioavailability Limitations of Atrazine Degradation in Soils

Rodriguez

Ingalls

Meierdierks

et al. 2021

Front. Environ. Sci.

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Pesticide persistence in soils is a widespread environmental concern in agro-ecosystems. One particularly persistent pesticide is atrazine, which continues to be found in soils and groundwater in the EU despite having been banned since 2004. A range of physical and biological barriers, such as sorption and mass-transfer into bacterial cells, might limit atrazine degradation in soils. These effects have been observed in experiments and models working with simplified systems. We build on that work by developing a biogeochemical model of the degradation process. We extended existing engineered system models by including refined representations of mass-transfer processes across the cell membrane as well as thermodynamic growth constraints. We estimated model parameters by calibration with data on atrazine degradation, metabolite (hydroxyatrazine) formation, biomass, and isotope fractionation from a set of controlled retentostat/chemostat experiments. We then produced site-specific model predictions for arable topsoil and compared them with field observations of residual atrazine concentrations. We found that the model overestimated long-term atrazine biodegradation in soils, indicating that this process is likely not limited by bioavailability or energetic constraints of microbial growth. However, sorption-limited bioavailability, could explain the long-term fate and persistence of the main degradation metabolite hydroxyatrazine. Future studies should seek alternative controls that drive the observed atrazine persistence in soil. This work helps to bridge the gap between engineered and natural systems, allowing us to use laboratory setups to gain insight into real environmental systems.

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“…There are a number of excellent recent reviews on challenges in imaging and predictive modelling of rhizosphere processes (Pot et al 2021;Roose et al 2016), challenges in modelling soil processes (Vereecken et al 2016), or plant-soil modelling (Ruiz et al 2020b). The objective of this opinion paper is to present a series of modelling scenarios, which integrate detailed rhizosphere processes into a plant-scale and soil profile-scale modelling concept.…”

Section: Introductionmentioning

confidence: 99%

Linking rhizosphere processes across scales: Opinion

et al. 2022

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Purpose Simultaneously interacting rhizosphere processes determine emergent plant behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. However, these processes occur on multiple scales, challenging modelling of rhizosphere and plant behaviour. Current advances in modelling and experimental methods open the path to unravel the importance and interconnectedness of those processes across scales. Methods We present a series of case studies of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images. Results Each case study includes a model that links scales and experimental data to explain and predict spatial and temporal distribution of rhizosphere components. We exemplify the state-of-the-art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling, and functional-structural plant modelling. We show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties. Furthermore, we demonstrate ways of modelling the links between rhizodeposition and plant nutrient uptake or soil microbial activity. Conclusion Modelling allows to integrate new experimental data across different rhizosphere processes and scales and to explore more variables than is possible with experiments. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes including the dynamics of root growth is the logical next step for future research.

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Accounting for soil architecture and microbial dynamics in microscale models: Current practices in soil science and the path ahead

Abstract: Macroscopic models of soil organic matter (SOM) turnover have faced difficul-

Cited by 29 publications

References 190 publications

Soil carbon sequestration for climate change mitigation: Mineralization kinetics of organic inputs as an overlooked limitation

Soil carbon sequestration for climate change mitigation: Mineralization kinetics of organic inputs as an overlooked limitation

Modeling Bioavailability Limitations of Atrazine Degradation in Soils

Linking rhizosphere processes across scales: Opinion

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