Browsing by Author "Portell, Xavier"

Now showing 1 - 8 of 8
  • Thumbnail Image
    ItemOpen Access
    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.
  • Thumbnail Image
    ItemOpen Access
    Bypass and hyperbole in soil science: a perspective from the next generation of soil scientists
    (Wiley, 2020-11-23) Portell, Xavier; Sauzet, Ophélie; Balseiro-Romero, María; Benard, Pascal; Cardinael, Rémi; Couradeau, Estelle; Danra, Dieudonné D.; Evans, Daniel L.; Fry, Ellen L.; Hammer, Edith C.; Mamba, Danielle; Merino‐Martín, Luis; Mueller, Carsten W.; Paradelo, Marcos; Rees, Frédéric; Rossi, Lorenzo M. W.; Schmidt, Hannes; Schnee, Laura S.; Védère, Charlotte; Vidal, Alix
  • Thumbnail Image
    ItemOpen Access
    Digital image analysis of yeast single calls growing in two different oxygen concentrations to analyze the population growth and to assist individual-based modeling
    (Frontiers Media, 2018-01-04) Ginovart, Marta; Carbó, Rosa; Blanco, Mónica; Portell, Xavier
    Nowadays control of the growth of Saccharomyces to obtain biomass or cellular wall components is crucial for specific industrial applications. The general aim of this contribution is to deal with experimental data obtained from yeast cells and from yeast cultures to attempt the integration of the two levels of information, individual and population, to progress in the control of yeast biotechnological processes by means of the overall analysis of this set of experimental data, and to assist in the improvement of an individual-based model, namely, INDISIM-Saccha. Populations of S. cerevisiae growing in liquid batch culture, in aerobic and microaerophilic conditions, were studied. A set of digital images was taken during the population growth, and a protocol for the treatment and analyses of the images obtained was established. The piecewise linear model of Buchanan was adjusted to the temporal evolutions of the yeast populations to determine the kinetic parameters and changes of growth phases. In parallel, for all the yeast cells analyzed, values of direct morphological parameters, such as area, perimeter, major diameter, minor diameter, and derived ones, such as circularity and elongation, were obtained. Graphical and numerical methods from descriptive statistics were applied to these data to characterize the growth phases and the budding state of the yeast cells in both experimental conditions, and inferential statistical methods were used to compare the diverse groups of data achieved. Oxidative metabolism of yeast in a medium with oxygen available and low initial sugar concentration can be taken into account in order to obtain a greater number of cells or larger cells. Morphological parameters were analyzed statistically to identify which were the most useful for the discrimination of the different states, according to budding and/or growth phase, in aerobic and microaerophilic conditions. The use of the experimental data for subsequent modeling work was then discussed and compared to simulation results generated with INDISIM-Saccha, which allowed us to advance in the development of this yeast model, and illustrated the utility of data at different levels of observation and the needs and logic behind the development of a microbial individual-based model.
  • Thumbnail Image
    ItemOpen Access
    Linking rhizosphere processes across scales: opinion
    (Springer, 2022-01-31) Schnepf, A.; Carminati, A.; Ahmed, M. A.; Ani, M.; Benard, P.; Bentz, J.; Bonkowski, M.; Knott, M.; Diehl, D.; Duddek, P.; Kröner, E.; Javaux, M.; Landl, M.; Lehndorf, E.; Lippold, E.; Lieu, A.; Mueller, C. W.; Oburger, E.; Otten, Wilfred; Portell, Xavier; Phalempin, M.; Prechtel, A.; Schulz, R.; Vanderborght, J.; Vetterlein, D.
    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.
  • Thumbnail Image
    ItemOpen Access
    A microfluidics and agent-based modeling framework for investigating spatial organization in bacterial colonies: The case of Pseudomonas Aeruginosa amd H1-type VI secretion interactions
    (Frontiers Media, 2018-02-06) Wilmoth, Jared L.; Doak, Peter W.; Timm, Andrea; Halsted, Michelle; Anderson, John D.; Ginovart, Marta; Prats, Clara; Portell, Xavier; Retterer, Scott T.; Fuentes-Cabrera, Miguel
    The factors leading to changes in the organization of microbial assemblages at fine spatial scales are not well characterized or understood. However, they are expected to guide the succession of community development and function toward specific outcomes that could impact human health and the environment. In this study, we put forward a combined experimental and agent-based modeling framework and use it to interpret unique spatial organization patterns of H1-Type VI secretion system (T6SS) mutants of P. aeruginosa under spatial confinement. We find that key parameters, such as T6SS-mediated cell contact and lysis, spatial localization, relative species abundance, cell density and local concentrations of growth substrates and metabolites are influenced by spatial confinement. The model, written in the accessible programming language NetLogo, can be adapted to a variety of biological systems of interest and used to simulate experiments across a broad parameter space. It was implemented and run in a high-throughput mode by deploying it across multiple CPUs, with each simulation representing an individual well within a high-throughput microwell array experimental platform. The microfluidics and agent-based modeling framework we present in this paper provides an effective means by which to connect experimental studies in microbiology to model development. The work demonstrates progress in coupling experimental results to simulation while also highlighting potential sources of discrepancies between real-world experiments and idealized models.
  • Thumbnail Image
    ItemOpen Access
    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.
  • Thumbnail Image
    ItemOpen Access
    Three-dimensional study of F. graminearum colonisation of stored wheat: post-harvest growth patterns, dry matter losses and mycotoxin contamination
    (MDPI, 2020-08-01) Portell, Xavier; Verheecke-Vaessen, Carol; Torrelles-Ràfales, Rosa; Medina, Angel; Otten, Wilfred; Magan, Naresh; García-Cela, Esther
    Fusarium causes significant post-harvest quality losses and mycotoxin contamination in stored wheat but the colonisation dynamics of the grain and how this may be affected by the initial inoculum position in the grain mass is poorly understood. This study examined the 3D growth kinetics and mycotoxin production (deoxynivalenol and zearalenone) by F. graminearum during hyphal colonisation from different initial inoculum positions in wheat microcosms (top-centre, bottom-centre, and bottom-side) maintained at two water activities (aw; 0.95 and 0.97). Clear jars were used to visually follow the colonisation dynamics. Fungal respiration and associated dry matter loss (DML) and ergosterol were also quantified. Colonisation dynamics was shown to be affected by the inoculation position. At the end of the colonisation process, fungal respiration and DML were driven by the inoculation position, and the latter also by the prevailing aw. Fungal biomass (ergosterol) was mainly affected by the aw. The initial inoculum position did not affect the relative mycotoxin production. There was a positive correlation between respiration and ergosterol, and between mycotoxin production and colonisation indicators. We suggest that spatially explicit predictive models can be used to better understand the colonisation patterns and mycotoxin contamination of stored cereal commodities and to aid more effective post-harvest management.
  • Thumbnail Image
    ItemOpen Access
    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.