An automated two-level system for size-based enrichment of soil microbiomes

Extracting microorganisms from soil for metagenomic analysis is challenging because of the structural heterogeneity of the soil matrix. Conventional methods such as differential centrifugation often compromise cell viability through shear stress, while static filtration suffers from rapid clogging. Here, we present the automated two-level enrichment system (ATLES), which can be used to automate and standardize this process. Unlike traditional setups, ATLES uses a hydrodynamic recirculation mechanism to maintain tangential flow across the membrane, thereby preventing pore blockage. Experimental results demonstrate that the system successfully isolates larger fungal biomass (>3 μm) while removing smaller bacteria (<2 μm) from soil suspensions. A consistent recovery rate of ∼30% was maintained, verifying the stability of the system against matrix interference. This study demonstrates the feasibility of using macroscale fluidic control to achieve precise, automated microbial fractionation in environmental samples.