Ultra-high throughput droplet microfluidics for cultivation and functional screening of environmental microbial strains and consortia.

Screening microbial diversity is critical for discovering novel strains with enhanced biocatalytic capabilities. Traditional cultivation techniques often miss rare or slow-growing microorganisms, limiting our understanding of microbial biodiversity and its practical applications. Droplet-based microfluidics has emerged as a powerful platform for ultra-high- throughput screening of single cells or microbial consortia, encapsulated within microscale droplets that act as precisely controlled bioreactors. This tutorial review focuses on the application of droplet microfluidics for microbial cultivation and isolation, emphasizing advantages such as rapid throughput and the ability to isolate and analyze individual cells. Unlike previous reviews that broadly address microfluidic technologies or target specific applications like antibiotic resistance or enzyme discovery, we concentrate on protocols specifically designed for the clonal and parallel cultivation of microorganisms from environmental samples. Droplet microfluidics has already shown significant promise in environmental biotechnology, bioremediation, and microbial ecology. Its broader adoption dramatically reduces assay volumes and costs while enhancing screening efficiency, positioning droplet microfluidics as a key technology for the future of environmental microbiology research.