The Individual Microbe: Single-Cell Analysis and Agent-Based Modelling

Individuality of microbes is increasingly recognized as crucial in many biological systems. The interplay of individual heterogeneity, local interactions and adaptive behavior determine their dynamics. A bottom-up approach using agent- or individual-based modelling has advanced our understanding of such systems, but it has in the past been limited by the lack of reliable observations at the single cell level. In fact, until very recently we have not been able to identify microbes and record their mostly invisible activities, such as nutrient consumption or toxin production on the level of the single cell, not even in the laboratory. Recent technological advances in single-cell microbiology, using flow cytometry, microfluidics, x-ray fluorescence microprobes, and single-cell -omics, allow for the observation of individuals within populations. In addition, the spectacular increase in capacity of standard PCs and the proliferation of high performance computing facilities currently makes the simulation of big populations with non-trivial models feasible.
The combination of agent-based modelling and single-cell analysis has been dubbed microbial individual-based ecology or individual-based microbiology. It has been increasingly used in environmental and food microbiology, among others, for the understanding of the systems behavior and the study of emergent patterns at the population level. Individual-based microbiology has particularly succeeded in describing microbial systems as varied as biofilms, phytoplankton communities or soils. One of its strengths is that it also allows for the incorporation of both lower and higher levels of organization into the individual-based framework. Integrating lower levels of organization enables a more mechanistic approach for simulating single cell behavior based on systems microbiology models for intracellular structure and dynamics. By integrating higher levels of organization, feedbacks between multiple levels in multiple species communities systems can also be tackled, grouping them into functional groups where necessary.
This Research Topic will solicit contributions advancing the connection between individual microbes with intracellular and/or population levels including (but not limited to) heterogeneity, diversity and structure in microbial populations, interactions of microbes within the population and with their environment, and intracellular biochemical mechanisms and networks, among others. Both modelling and experimental approaches are solicited in each area, either together or separately.