Droplet-Based Microfluidics Platform for Ultra-High-Throughput Bioprospecting of Cellulolytic Microorganisms

Discovery of microorganisms producing enzymes that can efficiently hydrolyze cellulosic biomass is of great importance for biofuel production. To date, however, only a miniscule fraction of natural biodiversity has been tested because of the relatively low throughput of screening systems and their limitation to screening only culturable microorganisms. Here, we describe an ultra-high-throughput droplet-based microfluidic system that allowed the screening of over 100,000 cells in less than 20 min. Uncultured bacteria from a wheat stubble field were screened directly by compartmentalization of single bacteria in 20 pl droplets containing a fluorogenic cellobiohydrolase substrate. Sorting of droplets based on cellobiohydrolase activity resulted in a bacterial population with 17- and 7-fold higher cellobiohydrolase and endogluconase activity, respectively, and very different taxonomic diversity than when selected for growth on medium containing starch and carboxymethylcellulose as carbon source. [Display omitted] •Droplet-based microfluidics was used for bioprospection of cellulolytic bacteria•Over 100,000 cells from a wheat stubble field were screened in less than 20 min•The enriched population exhibited high endoglucanases and exogluconase activity•Very different taxonomic diversity was found compared to growth-based selection Najah et al. develop a microfluidic system that enables screening of 105 uncultured cellulolytic microorganisms from wheat stubble in less than 20 min and using only 20 μl of reagents. This represents a ∼240-fold increase in throughput and a ∼250,000-fold decrease in reagent volume compared to conventional systems.