Advancing microbial sciences by individual-based modelling

Remarkable technological advances have revealed ever more properties and behaviours of individual microorganisms, but the novel data generated by these techniques have not yet been fully exploited. In this Opinion article, we explain how individual-based models (IBMs) can be constructed based on the findings of such techniques and how they help to explore competitive and cooperative microbial interactions. Furthermore, we describe how IBMs have provided insights into self-organized spatial patterns from biofilms to the oceans of the world, phage-CRISPR dynamics and other emergent phenomena. Finally, we discuss how combining individual-based observations with IBMs can advance our understanding at both the individual and population levels, leading to the new approach of microbial individual-based ecology (μIBE)

Reactive transport simulations of microbial activity and biogeochemical transformations in porous environments - development and application of a pore-network model

The focus of this study was on the development and application of a model, describing the micro-scale, flexible enough to consider any arbitrary number of reactions, and able to simulate reactive transport of chemicals and microorganisms in the presence of pore-scale heterogeneities. This research aimed to unravel the relative importance of biogeochemical processes, external forces and microbial characteristics on the functioning of the porous systems as a whole, and to identify and evaluate the influence of these controlling parameters

Data for: A robust optimization technique for analysis of multi-tracer experiments

OptSFDM is a multi-tracer data assimilation program that automatically optimizes the single fissure dispersion model (suggested by Maloszewski and Zuber (1985, 1990)) using tracer experiments to estimate the hydrogeological parameters of an aquifer or a double-porosity system

Finite Element Analysis of Cahn-Hilliard equations: Mass transfer of an oil-soluble chemical for water control

Two models have been constructed and physically motivated based on the (system of) Cahn-Hilliard equation(s) and Stefan problem in order to describe the behavior of fluids in a hypothetical mixture. A finite element method is developed to solve the Cahn-Hilliard equations based on a mixed formulation where reduction of the forthorder spatial derivative is applied. The method is also extended to multiple species. Furthermore, mass conservation and energy decrease for the (system of) Cahn-Hilliard equation(s) as well as the Stefan problem are demonstrated mathematically. Then, all proved mathematical subjects have been verified by the numerical aspects for the purpose of approving the numerical results. The Cahn-Hilliard equations with a diffuse interface has been compared to a Stefan problem with a sharp interface and a reasonable agreement is obtained. To find out the advantages and disadvantages, the results and assumptions are discussed at the end for both models.Civil Engineering and GeosciencesGeoscience & EngineeringPetroleum Engineering and Geoscience

Isotope fractionation pinpoints membrane permeability as a barrier to atrazine biodegradation in gram-negative <em>Polaromonas sp. Nea-C</em>.

Biodegradation of persistent pesticides like atrazine often stalls at low concentrations in the environment. While mass transfer does not limit atrazine degradation by the Gram-positive Arthrobacter aurescens TC1 at high concentrations (&gt;1 mg/L), evidence of bioavailability limitations is emerging at trace concentrations (&lt;0.1 mg/L). To assess the bioavailability constraints on biodegradation, the roles of cell wall physiology and transporters remain imperfectly understood. Here, compound-specific isotope analysis (CSIA) demonstrates that cell wall physiology (i.e., the difference between Gram-negative and Gram-positive bacteria) imposes mass transfer limitations in atrazine biodegradation even at high concentrations. Atrazine biodegradation by Gram-negative Polaromonas sp. Nea-C caused significantly less isotope fractionation (ϵ(C) = -3.5 &permil;) than expected for hydrolysis by the enzyme TrzN (ϵ(C) = -5.0 &permil;) and observed in Gram-positive Arthrobacter aurescens TC1 (ϵ(C) = -5.4 &permil;). Isotope fractionation was recovered in cell-free extracts (ϵ(C) = -5.3 &permil;) where no cell envelope restricted pollutant uptake. When active transport was inhibited with cyanide, atrazine degradation rates remained constant demonstrating that atrazine mass transfer across the cell envelope does not depend on active transport but is a consequence of passive cell wall permeation. Taken together, our results identify the cell envelope of the Gram-negative bacterium Polaromonas sp. Nea-C as a relevant barrier for atrazine biodegradation

Data for: Simulating the chemical kinetics of CO2-methane exchange in hydrate

Comsol model for CO2-methane exchange in a pressure vesselTHIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Data for: A robust optimization technique for analysis of multi-tracer experiments

OptSFDM is a multi-tracer data assimilation program that automatically optimizes the single fissure dispersion model (suggested by Maloszewski and Zuber (1985, 1990)) using tracer experiments to estimate the hydrogeological parameters of an aquifer or a double-porosity system.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Introduction of a new platform for parameter estimation of kinetically complex environmental systems.

A modeling framework (ReKinSim - Reaction Kinetics Simulator) is introduced, within which biogeochemical reactions in environmental systems can be described and inversely fitted to experimental data. Three key features of this simulation environment are: (1) a generic mathematical tool for solving sets of unlimited, arbitrary, non-linear ordinary differential equations; (2) no limitation to the number or type of reactions or other influential dynamics (e.g., isotope fractionation or small-scale mass-transfer limitations); (3) an easy to use and flexible module for nonlinear data-fitting. It allows users to easily define any kinetic model by a set of biogeochemical reactions relevant to the experimental application and to obtain the values of the kinetic parameters by fitting of the model to data. By allowing users to include the environmentally related processes and solving them along with the chemical kinetics, ReKinSim helps the user to elucidate the extent that these processes are controlled by factors other than kinetics. The novelty of the presented program primary lays in its unique combination of flexibility, computational efficiency and user-friendliness. ReKinSim&#39;s usability is showcased by four case studies of varying complexity, and compared against a set of currently available modeling tools

How the chemotactic characteristics of bacteria can determine their population patterns

Spatial distribution of soil microorganisms is relevant for the functioning and performance of many ecosystem processes such as nutrient cycling or biodegradation of organic matters and contaminants. Beside the multitude of abiotic environmental factors controlling the distribution of microorganisms in soil systems, many microbial species exhibit chemotactic behavior by directing their movement along concentration gradients of nutrients or of chemoattractants produced by cells of their own kind. This chemotactic ability has been shown to promote the formation of complex distribution patterns even in the absence of environmental heterogeneities. Microbial population patterns in heterogeneous soil systems might be, hence, the result of the interplay between the heterogeneous environmental conditions and the microorganisms' intrinsic pattern formation capabilities.In this modeling study, we combined an individual-based modeling approach with a reactive pore-network model to investigate the formation of bacterial patterns in homogeneous and heterogeneous porous media. We investigated the influence of different bacterial chemotactic sensitivities (toward both substrate and bacteria) on bacterial distribution patterns. The emerging population patterns were classified with the support of a geostatistical approach, and the required conditions for the formation of any specific pattern were analyzed.Results showed that the chemotactic behavior of the bacteria leads to non-trivial population patterns even in the absence of environmental heterogeneities. The presence of structural pore scale heterogeneities had also an impact on bacterial distributions. For a range of chemotactic sensitivities, microorganisms tend to migrate preferably from larger pores toward smaller pores and the resulting distribution patterns thus resembled the heterogeneity of the pore space. The results clearly indicated that in a porous medium like soil the distribution of bacteria may not only be related to the external constraints but also to the chemotactic behavior of the bacterial cells