Programmable, Pneumatically Actuated Microfluidic Device with an Integrated Nanochannel Array To Track Development of Individual Bacteria

We describe a microfluidic device with an integrated nanochannel array to trap individual bacteria and monitor growth and reproduction of lineages over multiple generations. Our poly­(dimethylsiloxane) device comprises a pneumatically actuated nanochannel array that includes 1280 channels with widths from 600 to 1000 nm to actively trap diverse bacteria. Integrated pumps and valves perform on-chip fluid and cell manipulations that provide dynamic control of cell loading and nutrient flow, permitting chemostatic growth for extended periods of time (typically 12 to 20 h). Nanochannels confine bacterial growth to a single dimension, facilitating high-resolution, time-lapse imaging and tracking of individual cells. We use the device to monitor the growth of single bacterial cells that undergo symmetric (Bacillus subtilis) and asymmetric (Caulobacter crescentus) division and reconstruct their lineages to correlate growth measurements through time and among related cells. Furthermore, we monitor the motility state of single B. subtilis cells across multiple generations by the expression of a fluorescent reporter protein and observe that the state of the epigenetic switch is correlated over five generations. Our device allows imaging of cellular lineages with high spatiotemporal resolution to facilitate the analysis of biological processes spanning multiple generations.