Spatiotemporal establishment of dense bacterial colonies growing on hard agar

Abstract

The physical interactions of growing bacterial cells with each other and with their surroundings significantly affect the structure and dynamics of biofilms. Here a 3D agent-based model is formulated to describe the establishment of simple bacterial colonies expanding by the physical force of their growth. With a single set of parameters, the model captures key dynamical features of colony growth by non-motile, non EPS-producing E. coli cells on hard agar. The model, supported by experiment on colony growth in different types and concentrations of nutrients, suggests that radial colony expansion is not limited by nutrients as commonly believed, but by mechanical forces. Nutrient penetration instead governs vertical colony growth, through thin layers of vertically oriented cells lifting up their ancestors from the bottom. Overall, the model provides a versatile platform to investigate the influences of metabolic and environmental factors on the growth and morphology of bacterial colonies.

Mechanics of biofilms formed of bacteria with fimbriae appendages

“…We have demonstrated that varying local interaction between individual cells, such as the total fimbriae number and EPS growth rate, can lead to qualitative change in the structural form of the bacterial colony. The overall shape of the bacterial colony observed in our simulations is similar to that noted in a number of other experimental studies [43,49] and numerical analyses [34,37,42].…”

“…Discrete models treat biofilms as a collection of individual ‘agents’ (or particles) that interact with each other, with the surface to which the biofilm is attached, and with other surrounding biofilm components (such as EPS and water). With discrete models, it is a simple matter to assign properties, shapes, and behaviors to individual bacteria and then allow the model to determine how these characteristics lead to different collective (emergent) behavior of the biofilm system [ 31 – 34 , 38 , 42 , 43 ]. However, most continuum models do not account for the numerous forces acting between individual bacterial cells, whereas most discrete models (also known as individual based models ) do not account for the separate flow fields of water and EPS past the cells.…”

“…The continuum model is based on an extension of that of Cogan and Keener [ 39 ], with an improved model for the water-EPS interfacial force. The discrete model is based on an extension of an accurate discrete element method (DEM) for adhesive particle flows [ 45 – 47 ], and includes a wide range of cell-EPS and cell-cell forces and torques for both spherical [ 31 ] and spherocylindrical cell shapes [ 34 , 42 , 43 , 48 , 49 ].…”

Environmental heterogeneity can tip the population genetics of range expansions

“…The neutral diversity and adaptation in spatially expanding populations has been studied in computer simulations (Edmonds et al, 2004; Klopfstein et al, 2006; Kuhr et al, 2011; Kuhr and Stark, 2015; Lavrentovich and Nelson, 2014; Otwinowski and Krug, 2014), in the field (Ramachandran et al, 2005; White et al, 2013; Louppe et al, 2017), and in microbial colonies (Hallatschek et al, 2007; Fusco et al, 2016; Gralka et al, 2016b; Korolev et al, 2011), which can serve as a useful model system because short generation times and ease of handling allow for quantitative investigations of the evolutionary dynamics of range expansions. In microbial colonies, nutrient gradients and mechanical effects limit the number of proliferating individuals to a small region close to the colony perimeter called the growth layer (Grant et al, 2014; Gralka et al, 2016b; Warren et al, 2019). For mutations occurring inside the growth layer, most mutant offspring are concentrated in a relatively small number of enormously successful lineages that manage to remain at the front and 'surf’ on the expanding population wave (Excoffier and Ray, 2008).…”

Correlation between the Spatial Distribution and Colony size Was Common for Monogenetic Bacteria in Laboratory Conditions.

“…Pattern formation of a single colony is known to be mediated by mechanical interactions [12]. In particular, recent studies have demonstrated that mechanical interaction plays an important role in determining the sizes of monogenetic colonies [13] and the patterns of polygenetic colonies [14].…”