Carbon efflux from soils is the largest terrestrial carbon source to the atmosphere, yet it remains one of the most uncertain fluxes in the Earth’s carbon budget. A dominant component of this flux is heterotrophic respiration, influenced by several environmental factors, most notably soil temperature and moisture. We developed a mechanistic model from micro to global scale to explore how changes in soil water content and temperature affect soil heterotrophic respiration. Simulations, laboratory measurements, and field observations validate the new approach. Estimates from the model show that heterotrophic respiration has been increasing since the 1980s at a rate of about 1.7% per decade globally. Using future projections of surface temperature and soil moisture, the model predicts a global increase of about 40% in heterotrophic respiration by the end of the century under the worst-case emission scenario, which is driven principally by the reduction of soil moisture rather than temperature increase.

How to cite: Nissan, A., Alcolombri, U., Peleg, N., Galili, N., Jimenez-Martinez, J., Molnar, P., and Holzner, M.: Global warming accelerates soil heterotrophic respiration, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-4948, https://doi.org/10.5194/egusphere-egu23-4948, 2023.

Laboratory quantification and computer modeling of soil organic carbon (SOC) and radiocarbon (¹⁴C) rarely align well. Diverse lab methods exist to separate SOC into “fractions” with operationally defined boundaries which include physical, chemical, and biological thresholds. Compartmental soil models, on the other hand, use homogeneous “pools” to group SOC by its rate of decay. However, the stochastic nature of organic matter decomposition makes it virtually impossible to isolate model pools through fractionation or to model fractions as pools. Radiocarbon is a powerful metric that integrates C fluxes in and out of a system, but fraction and pool ¹⁴C valuesrepresent an average which may be composed of widely different C ages. In order to advance and constrain our understanding of SOC dynamics, we need to go beyond mean ¹⁴C values of operationally defined pools and instead use radiocarbon distributions. Thermal (oxidative) fractionation of SOC produces continuous C data as a function of temperature (20˚C to 900˚C), and discrete ¹⁴C measurements by collecting evolved gas. By fitting splines to ¹⁴C data and weighing by C release over temperature, a continuous mass-weighted distribution of ¹⁴C can be estimated. Recent modeling advances can similarly estimate system ¹⁴C distributions, and models may thus be constrained for the first time by continuous lab data. This convergence is a first step beyond pools and fractions that may significantly increase constraining power. We will present lab and mathematical methods, limitations, and outlooks for advancing soil SOC modeling.

How to cite: Stoner, S., Trumbore, S., Schrumpf, M., Doetterl, S., and Sierra, C.: Beyond fractions and pools: Radiocarbon distributions as a constraint for soil organic carbon models, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-16144, https://doi.org/10.5194/egusphere-egu23-16144, 2023.

The increasing demand for biomass for food, animal feed, fiber and bioenergy requires optimization of soil productivity, while, at the same time, protecting other soil functions such as nutrient cycling and buffering, carbon storage, habitat for biological activity, and water filter and storage. Therefore, one of the main challenges for sustainable agriculture is to produce high yields while maintaining all the other soil functions. Mechanistic simulation models are an essential tool for predicting soil functions as well as the complex interactions between these functions.

Here, we present our process-based systemic soil model BODIUM which integrates biological, physical and chemical processes to predict the effect of management activities on soil functions at the field scale. We first present simulations of a long-term field experiment to validate our model along the different soil functions. Then we apply different management scenarios to show the potential of our model for explorative scenario simulations, including tillage, different organic fertilizer treatments, and cover crops.

Finally, we discuss ongoing model developments to further extend BODIUM such as bioturbation, phosphorous dynamics, and fungal-bacterial interactions.

How to cite: Weller, U., König, S., Lang, B., Betancur-Corredor, B., Reitz, T., Wiesmeier, M., Wollschläger, U., and Vogel, H.-J.: BODIUM - a systemic approach to model the dynamics of soil functions: validation and scenario simulations, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-5287, https://doi.org/10.5194/egusphere-egu23-5287, 2023.

The rhizosphere, or the soil directly influenced by plant roots, is a complex and dynamic environment shaped by both plant and soil processes. Plant processes include root growth, rhizodeposition, root water and nutrient uptake or signalling; soil processes include water flow, reactive transport, organic matter decomposition or soil microbe and fauna-related processes. In this contribution, we focus on the soil-related aspects of modelling the interactions within the rhizosphere and how these interactions lead to the emergence of specific properties. Factors such as radial transport, root growth, and diurnal variation all play a role in the formation of patterns within the rhizosphere. However, modelling these processes is challenging due to their interconnected nature and the fact that they occur on multiple temporal and spatial scales. Recent research by Vetterlein et al. (2020) and Schnepf et al. (2022) have addressed these challenges and advances in our understanding of modelling the rhizosphere. For example can the effect of root elongation rate on the radial extension of the rhizosphere be quantified by means of the rhizosphere Péclet number, a dimensionless number that compares the importance of diffusive transport relative to root elongation rate. New findings of Kuppe et al. (2022), who have organized rhizosphere models within a collective framework that allows for the incorporation of microorganisms and their activity and motility, and Deckmyn et al. (2020), who combined soil carbon and food web ecosystem models, will further enhance a mechanistic description of the rhizosphere

Deckmyn G, Flores O, Mayer M, Domene X, Schnepf A, Kuka K, Van Looy K, Rasse DP, Briones MJI, Barot S, Berg M, Vanguelova E, Ostonen I, Vereecken H, Suz LM, Frey B, Frossard A, Tiunov A, Frouz J, Grebenc T, Öpik M, Javaux M, Uvarov A, Vinduskova O, Henning Krogh P, Franklin O, Jiménez J, Curiel Yuste J. 2020. KEYLINK: towards a more integrative soil representation for inclusion in ecosystem scale models. I. review and model concept. PeerJ 8:e9750 DOI 10.7717/peerj.9750

Kuppe CW, Schnepf A, von Lieres E, Watt M, Postma JA (2022) Rhizosphere models: their concepts and application to plant-soil ecosystems. Plant Soil 474, 17–55. doi: 10.1007/s11104-021-05201-7

Schnepf A, Carminati A, Ahmed MA, Ani M, Benard P, Bentz J, Bonkowski M, Knott M, Diehl D, Duddek P, Kröner E, Javaux M, Landl M, Lehndorff E, Lippold E, Lieu A, Mueller CW, Oburger E, Otten W, Portell X, Phalempin M, Prechtel A, Schulz R, Vanderborght J, Vetterlein D (2022) Linking rhizosphere processes across scales: Opinion. Plant and Soil 478: 5-42. doi: 10.1007/s11104-022-05306-7.

Vetterlein D, Carminati A, Kögel-Knabner I, Bienert GP, Smalla K, Oburger E, Schnepf A, Banitz T, Tarkka MT, Schlüter S (2020) Rhizosphere Spatiotemporal Organization–A Key to Rhizosphere Functions. Frontiers in Agronomy 2. doi: 10.3389/fagro.2020.00008.

How to cite: Schnepf, A.: Mechanistic modelling of the rhizosphere across scales, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-9473, https://doi.org/10.5194/egusphere-egu23-9473, 2023.

We present a mechanistic, spatially and temporally explicit microscale model to investigate the interactions between a growing root, its exudates and the soil structure. Our model allows us to simultaneously simulate and study the dynamic rearrangement of soil particles, the input and turnover of organic matter, the root growth and decay, as well as the deposition, redistribution and decomposition of mucilage into the rhizosphere. The interactions between these components are realized within a cellular automaton framework. Mechanistic rules lead to the formation and break-up of soil structures. The most stable configuration is determined by the amount and attractivity of surface contacts between the particles. Alteration of surface types due to addition and decomposition of organic matter and the root growth induced movements of particles result in varying aggregation dynamics over time and space.

We illustrate the capability of our model by simulating the growth and shrinkage period of a fine root in a two-dimensional, horizontal cross section through the soil. We evaluate various scenarios to identify the impact of the root and further influencing factors that shape soil aggregation in the rhizosphere. More precisely, we address how the soil structure formation is influenced by soil texture and the amount of mucilage. We quantify the variations in local porosity due to the change in available pore space as influenced by the root growth. We further identify attractive properties of the soil surface induced by root exudation as key factors for the creation of stable soil structures.

How to cite: Rötzer, M., Prechtel, A., and Ray, N.: Pore scale modeling of the influence of roots on soil aggregation in the rhizosphere, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-13567, https://doi.org/10.5194/egusphere-egu23-13567, 2023.

Root hairs, tubular protrusions of epidermal root cells, are considered a key rhizosphere feature: by substantially increasing the contact area between roots and soil, they enhance the ability of plants to capture soil resources. Hence, they are considered a breeding target for improving drought tolerance and yield stability of crops. While their pivotal role in the uptake of immobile nutrients such as phosphorus is well accepted, their effect on root water uptake remains controversial as it varies across plant species. 
By means of image-based modelling, our objective was to identify environmental conditions (e.g. soil water content) and hair traits (e.g. root hair length and density) that determine the effectiveness of root hairs in root water uptake. Furthermore, we investigated the effect of drought stress-induced root hair shrinkage on root water uptake.

We scanned root compartments of 8 days old maize seedlings (Zea Mays L.) grown in a loamy soil using synchrotron radiation X-ray CT. Based on the collected image-data, we implemented a 3D root water uptake model. By solving Richards equation numerically, we computed the propagation of water potential gradients across the root-soil continuum which allowed to quantify root water uptake. The high spatial resolution of the acquired images enabled us to explicitly take rhizosphere features, such as root hairs and root-soil matrix contact into account. We determined the key parameters governing the effectiveness of root hairs in water uptake by comparing a set of six maize root compartments before and after digitally removing their hairs. The quantification of root hair turgor-loss in response to progressive soil drying allowed us to implement hair shrinkage within our model.

We found that the effect of root hairs in root water uptake is governed by 1) the root hair induced increase in root soil contact and 2) root hair length. Furthermore, our results suggest that root hairs potentially facilitate root water uptake under dry soil conditions (< -0.1MPa). However, in the dry range, root hair shrinkage severely reduces the effect of hairs. Depending on their turgor-loss curve, root hairs may still provide a positive effect on root water uptake in a narrow range of soil matric potential. 

In summary, the effect of root hairs on root water uptake depends on soil water content, root-soil contact, root hair length and the turgor-loss point of hairs.

How to cite: Duddek, P., Ahmed, M. A., Javaux, M., Vanderborght, J., Lovric, G., King, A., and Carminati, A.: The role of root hairs in root water uptake - Insights from an image-based 3D model, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-13626, https://doi.org/10.5194/egusphere-egu23-13626, 2023.

The establishment of microbes in the rhizosphere requires a complex sequence of mobility, proliferation, and attachment/detachment from the root as well as soil surfaces. Most research has focused on proliferation and biofilm formation while the mobility and attachment of microbes in soil has remained mysterious and hidden. We combined novel microscopy technologies and mathematical models to capture and characterise the dynamic movement of bacteria through soil during the early stages of root colonisation. The study revealed how bacteria behave as a flock to exploit the pore space and move towards plant roots where they collectively interact with the root tip before forming biofilms on more mature root zones. Results in this study add significantly to our understanding of the biophysical mechanisms enabling microbial colonisation dynamics in soil.

References

Liu Y., Patko D, Engelhardt I.C, George T.S., Stanley-Wall N.P., Ladmiral V., Ameduri B., Daniell T.J., Holden N., MacDonald M.P., Dupuy L.X. (2021). Whole plant-environment microscopy reveals how Bacillus subtilis utilises the soil pore space to colonise plant roots. 118 (48) e2109176118

Engelhardt I. C., Patko D., Liu Y., Mimault M., de las Heras Martinez G., George T. S., MacDonald M., Ptashnyk M., Sukhodub T., Stanley-Wall N. R., Holden N., Daniell T. J. & Dupuy  L. X. The ISME Journal volume 16, pages2337–2347 (2022)

How to cite: Dupuy, L., Engelhardt, I., Mimault, M., Liu, Y., Patko, D., Ptashnyk, M., and MacDonald, M.: Mechanisms of migration of bacteria the pore space, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-7639, https://doi.org/10.5194/egusphere-egu23-7639, 2023.

Microbes play a key role in the degradation of organic matter across all ecosystems. A significant fraction of the organic matter pool available to microorganisms consists of structural polysaccharides, e.g. biopolymers such as cellulose, or chitin, that cannot be directly taken up and have to be broken down outside the cell. For that mean microbes have to produce a variety of extracellular enzymes catalyzing different steps of polymer degradation. Within any substrate-specific enzyme group, e.g. hydrolases that act on a certain polysaccharide such as chitin, we highlight two enzyme types with different kinetic strategies: exo-enzymes that cleave the ends of polysaccharide chains, thereby releasing mono- or dimers, and endo-enzymes that act on all intermittent bonds, thereby generating oligosaccharides of various sizes. Since depolymerization works as a bottleneck for nutrient acquisition and is a multi-step process, the trade-offs of investing in the production of one or the other enzyme type have highly non-trivial consequences for microorganisms. Despite its relevance, the depolymerization dynamics is incorporated in oversimplified manner into microbial growth models, where the general assumption is that all enzymes have exo-like kinetics. In this work we bridge this gap, by theoretically analyzing the consequences of production of different ratios of these enzymes on microbial growth. Our objective was to estimate the possible trade-offs faced by microorganisms growing on biopolymers and compare them to known strategies found in soil bacteria.

To investigate how the interplay of enzyme production strategies within a microbial population affect organic matter degradation, we incorporate polymer degradation by means of population balance equations into an individual-based spatially-explicit microscale microbial community model. This approach allows us to track the spatial distribution of biopolymer molecules of different sizes in space and time, as well as the microbes feeding on them. Our results show that microorganisms are limited not only by the amount of carbon in the system, but also by its form (biopolymer chain size). First we have analysed specialists, producing one or the other enzyme type. We found that the producers of exo-enzymes are well adapted to nutrient rich conditions or when carbon is trapped into small oligomers. We therefore suggest to consider them as copiotrophs. Endo-enzyme producers on the contrary can be considered as oligotrophs, as we found them to thrive in poor nutrient conditions with few long chain molecules. However, endo-producers were completely unable to start growing when too many long chains of nutrients are present. Moreover they are much more susceptible to exploitation as they loose larger parts of their intermediate products to diffusion. For generalists, i.e. microorganisms producing both enzymes, our results show that there is an optimum fraction of endo and exo-enzymes that boosts substrate degradation of long biopolymers and such tuned enzyme production speeds-up microbial growth. Overall, our analysis shows that there are incentive to regulate enzyme production towards this optimum ratio in mixed consortia of cooperating exo and endo-producers.

How to cite: Guseva, K., Mohrlok, M., Alteio, L., and Kaiser, C.: Theoretical model uncovering trade-offs faced by bacteria in the decomposition of large oligosaccharides, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-9524, https://doi.org/10.5194/egusphere-egu23-9524, 2023.

Soils contain the largest terrestrial reservoir of organic carbon, and dynamics in soil organic carbon turnover will drive carbon-climate feedbacks over the coming century. To date, most SOC dynamics have been simulated with pool-based models, which assume homogeneous physical properties in soil. However, there is increasing evidence which suggests that soil carbon turnover is not just determined by carbon inputs, but by restrictions on microbial access to organic matter in a spatially heterogeneous soil environment. Pore geometry is a critical factor in affecting the accessibility of organic matter for microorganisms, but this accessibility has not been explicitly considered in models. Therefore, we have a challenge to mechanistically predict how environmental change will impact on the balance between soil stored in soil and in the atmosphere.

We will exemplify the impact of pore-connectivity on organic matter turn-over by modelling fungal mediated processes in soil. The fungal model includes important fungal processes such as growth, death and spread, secretion of enzymes to degrade soil organic matter, and translocation of dissolved organic matter through its hyphal structure. For such a complex system the question of what constitutes a connected habitat and how this affects soil processes may not be as easy to address and needs to consider more than the pore connectivity often highlighted. For example, for these fungal mediated processes, habitat connectivity may be determined by various characteristics, namely: (i) the total volume of the connected pore space; (ii) the connected air-filled pore volume, through which fungal spread predominantly occurs and gasses diffuse, (iii) the connected water phase volume, through which dissolved C diffuses, (iv) the distribution of particulate organic matter that fuels fungal growth, and (v) biological traits such as those enabling translocation through for example fungal hyphal networks. We demonstrate how various aspects of habitat connectivity differentially impact on two contrasting fungal species, representing e.g. R and K strategists. The results suggest that: i) connectivity of the water phase is critical as it regulates diffusion of dissolved organic matter; this is even so for fungi that preferentially spread through air-filled pores, and ii) whether fungi behave as R or K strategists is not just determined by fungal traits but to a large extend depends on the physical environment. Consequently, selective pressures can be exerted by physical conditions. It was however not possible to identify a key physical driver as the dynamics were mostly determined by interactions between the various types of connectivity. These different pathways tend to compensate each other, enhancing stability of the function. We argue that the fact that multiple connected pathways underpin a soil function leads to resilience of soils to perturbations and underpins soil health. 

How to cite: Otten, W., Portell-Canal, X., and Falconer, R.: The role connectivity in soil for stability of soil organic matter degradation: a biophysical model, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-13245, https://doi.org/10.5194/egusphere-egu23-13245, 2023.

We present a spatially and temporally explicit mechanistic model for soil aggregation at the microscale. This consists of a cellular automaton model for the dynamic rearrangement of solid building units whose size and shape are derived from dynamic image analysis of wet-sieved, water stable aggregates. This model is combined with a particulate organic matter (POM) turnover model or a model for a growing fine root which exudes and distributes mucilage into the soil. Along this line the mutually interacting soil and POM dynamics and the intertwined processes at the root-soil interface are captured and evaluated simultaneously at the biologically relevant scale. Our comprehensive modeling toolbox allows us to conduct various simulation scenarios and to discriminate and evaluate the underlying processes and different drivers such as texture. We quantify our results by evaluating the stability of the created structures or the dynamical change in local porosity around a growing root. Finally, the insights gained at the microscale are used to parametrize a CO2 transport model at the profile scale. Thereby, the microbially mediated CO2 source is taken into account as well as the driver soil texture, and changing ambient environmental conditions such as water saturation, oxygen concentration and POM content.

How to cite: Ray, N., Prechtel, A., Rötzer, M., and Zech, S.: Cellular automaton based modeling of dynamic soil structures and their functions across scales, EGU General Assembly 2023, Vienna, Austria, 23–28 Apr 2023, EGU23-13407, https://doi.org/10.5194/egusphere-egu23-13407, 2023.