Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms

作者：Jing Dai, Yang Ouyang, Rohit Gupte, Xiao‐Jun Allen Liu, Yuwen Li, Fang Yang, Shaorong Chen, Tony Provin, Erin J. van Schaik, James E. Samuel, Arul Jayaraman, Aifen Zhou, Paul de Figueiredo, Jizhong Zhou, Arum Han · 发表于：Applied and Environmental Microbiology · 年份：2025 · DOI：10.1128/aem.01794-24 · 被引用次数：11 · 研究领域：Innovative Microfluidic and Catalytic Techniques Innovation、Microbial Community Ecology and Physiology、3D Printing in Biomedical Research

ABSTRACT Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well as for bioremediation. However, cultivating soil microorganisms while maintaining a broad microorganism diversity to enable phenotyping and functional analysis of as diverse individual isolates as possible remains challenging. In this study, we developed and tested the ability of several culture media formulations that contain defined soil metabolites or soil extracts to maintain microorganism diversity during culture. We also assessed their performance in microfluidic droplet cultivation where single-soil microorganism isolates were encapsulated and cultivated in picoliter-volume water-in-oil emulsion droplets to enable clonal growth needed for downstream functional analyses. Our results show that droplet cultivation with media supplemented by soil extract or soil metabolites enables the recovery of soil microorganisms with higher diversity (up to 1.5-fold higher richness) compared to bulk cultivation methods. Importantly, 1.7-fold more of less abundant (<1%) phyla and 11-fold more of unique genera were recovered, demonstrating the utility of this method for interrogating highly diverse soil microorganisms for broad ranges of applications. IMPORTANCE Although soil microorganisms hold a significant value in bioproduction and bioremediation, only a small fraction—less than 1%—can be cultured under specific media and cultivation conditions. T...