Rapid inoculation of single bacteria into parallel picoliter fermentation chambers

Microfluidic single-cell cultivation devices have been successfully utilized in a variety of biological research fields. One major obstacle to the successful implementation of high throughput single-cell cultivation technology is the requirement for a simple, fast and reliable cell inoculation procedure. In the present report, an air-bubble-based cell loading methodology is described and validated for inoculating single bacteria into multiple picoliter sized growth chambers arranged in a highly parallel manner. It is shown that the application of the injected air bubble can serve as a reproducible mechanism to modify laminar flow conditions. In this way, convective flow was temporarily induced in more than 1000 cultivation chambers simultaneously, which under normal conditions operate exclusively under diffusive mass transport. Within an inoculation time of 100 s, Corynebacterium glutamicum cells were inoculated by convection at minimal stress level and single bacteria remain successfully trapped by cell-wall interactions. The procedure is easy, fast, gentle and requires only minimal fluidic control and equipment. The technique is well suited for microbial cell loading into commonly used microfluidic growth sites arranged in parallel intended for high throughput single-cell analysis.