Bacterial ecology in confined and spatially structured in vitro habitats

Bacteria commonly coexist within communities where they compete for limited space and resources. These communities play an essential role in supporting a diversity of critical ecosystems from regulating metabolism within the gut to cycling nutrients within Earth's atmosphere. Mechanical forces have long been recognized as critical regulators of cell function within eukaryotic systems. Microbiology, however, has largely focused on the influence of the chemical environment with most studies of bacterial populations performed in well-mixed cultures. An important aspect of bacteria living in confined and spatially structured communities is that the environment significantly increases the amount of physical interaction between cells. Advances in microfluidics and quantitative microscopy now provide powerful methods for probing the effects of these interactions. These techniques have revealed that mechanical interactions may often be a critical driver of the evolution and ecological dynamics of bacterial populations. Here we provide an overview of recent findings related to bacterial competition within confined and spatially structured habitats.