Mathematical modeling of intercellular interactions within the biofilm

Biofilm engineering to improve succinic acid production in Escherichia coli by enhancing extracellular polysaccharide synthesis

Biofilms play crucial roles in enhancing microbial tolerance to environmental stress. Biofilm engineering in industrial microorganisms has been a promising and efficient approach to improve the production of metabolites. In this study, the psl gene cluster from Pseudomonas aeruginosa, for extracellular polysaccharide synthesis, was first introduced in a succinic acid (SA) producing Escherichia coli strain to enhance the biofilm formation ability. The engineered strain Suc260 (pslA-J) showed the improved tolerance to harsh environments and improved SA synthesis capability. Compared to the control, strain Suc260 (pslA-J) produced 70.54 g/L of SA from glucose in a 5 L bioreactor, representing an increase of 13.41 %. To further enhance the synthesis efficiency of SA, a cell immobilization fermentation system based on biofilms on alginate beads was designed. Finally, 62.66 g/L of SA with a yield of 0.76 g/g was produced from wheat straw hydrolysate in a 5 L bioreactor at the optimal pH of 6.8. When the pH was adjusted to a lower value (pH 6.0), the SA production and yield still reached 57.67 g/L and 0.75 g/g, respectively, representing 28.96 % and 42.15 % higher than those of the control strain. This study provides an efficient platform technology for the production of bio-based SA in large scale.

Mass transfer in heterogeneous biofilms: Key issues in biofilm reactors and AI-driven performance prediction

Biofilm reactors, known for utilizing biofilm formation for cell immobilization, offer enhanced biomass concentration and operational stability over traditional planktonic systems. However, the dense nature of biofilms poses challenges for substrate accessibility to cells and the efficient release of products, making mass transfer efficiency a critical issue in these systems. Recent advancements have unveiled the intricate, heterogeneous architecture of biofilms, contradicting the earlier view of them as uniform, porous structures with consistent mass transfer properties. In this review, we explore six biofilm reactor configurations and their potential combinations, emphasizing how the spatial arrangement of biofilms within reactors influences mass transfer efficiency and overall reactor performance. Furthermore, we discuss how to apply artificial intelligence in processing biofilm measurement data and predicting reactor performance. This review highlights the role of biofilm reactors in environmental and energy sectors, paving the way for future innovations in biofilm-based technologies and their broader applications.

Morphological instability and roughening of growing 3D bacterial colonies

The morphogenesis of two-dimensional bacterial colonies has been well studied. However, little is known about the colony morphologies of bacteria growing in three dimensions, despite the prevalence of three-dimensional environments (e.g., soil, inside hosts) as natural bacterial habitats. Using experiments on bacteria in granular hydrogel matrices, we find that dense multicellular colonies growing in three dimensions undergo a common morphological instability and roughen, adopting a characteristic broccoli-like morphology when they exceed a critical size. Analysis of a continuum “active fluid” model of the expanding colony reveals that this behavior originates from an interplay of competition for nutrients with growth-driven colony expansion, both of which vary spatially. These results shed light on the fundamental biophysical principles underlying growth in three dimensions.

How do growing bacterial colonies get their shapes? While colony morphogenesis is well studied in two dimensions, many bacteria grow as large colonies in three-dimensional (3D) environments, such as gels and tissues in the body or subsurface soils and sediments. Here, we describe the morphodynamics of large colonies of bacteria growing in three dimensions. Using experiments in transparent 3D granular hydrogel matrices, we show that dense colonies of four different species of bacteria generically become morphologically unstable and roughen as they consume nutrients and grow beyond a critical size—eventually adopting a characteristic branched, broccoli-like morphology independent of variations in the cell type and environmental conditions. This behavior reflects a key difference between two-dimensional (2D) and 3D colonies; while a 2D colony may access the nutrients needed for growth from the third dimension, a 3D colony inevitably becomes nutrient limited in its interior, driving a transition to unstable growth at its surface. We elucidate the onset of the instability using linear stability analysis and numerical simulations of a continuum model that treats the colony as an “active fluid” whose dynamics are driven by nutrient-dependent cellular growth. We find that when all dimensions of the colony substantially exceed the nutrient penetration length, nutrient-limited growth drives a 3D morphological instability that recapitulates essential features of the experimental observations. Our work thus provides a framework to predict and control the organization of growing colonies—as well as other forms of growing active matter, such as tumors and engineered living materials—in 3D environments.