Dataset: Lagrangian structure and stretching in bacterial turbulence

Culturing:

Wild-type Bacillus subtilis bacteria (strain OI1084) were taken from −80°C frozen stock and streaked onto 1.5% agar plates prepared with Terrific Broth (TB, Sigma). Plates were incubated at 25°C for 24 hours, after which time a single colony from the plate was used to inoculate an overnight liquid TB culture at 30°C with shaking (200 rpm). The bacterial suspension was then subcultured (1.5 ml of cell culture into 60 ml of pre-warmed TB) and grown at 35°C and 200 rpm for 6 hours to mid-log phase (OD600 ≈ 0.2). Immediately prior to experiments, dense cell suspensions (∼ 1010 cells.ml−1) were prepared by centrifugation at 5000 g for 5 minutes, and the pellet was resuspended with 2 μl of fresh TB media.

Microfluidics and image analysis

Polydimethlysiloxane (PDMS) microfluidic channels were fabricated through soft lithography and plasma bonded to No. 1 thickness glass coverslips. The PDMS channels were thinly cast to ensure ample diffusion of oxygen to the bacterial suspension and prolonged cell activity. Dense cell suspensions were gently loaded into the microfluidic devices via pipette, and the channel inlet and outlet were sealed with wax to prevent residual flows. For all experiments, bacterial suspensions were imaged with brightfield illumination on an inverted microscope (Nikon Ti-E) using a sCMOS camera (Zyla 5.5, Andor Technology) at 40x magnification. Time-resolved velocity fields, u(x, t), of the bacterial suspensions were measured by performing Particle Image Velocimetry (PIV) using PIVLab implemented in MATLAB. The subsequent velocity fields were then lightly smoothed using a Guassian kernel with a standard deviation of one PIV pixel in space and one frame in time.