Soil microbial spatial interactome by single soil particle sequencing

Soil-seq is a droplet microfluidics-based single soil particle sequencing method. Soil-seq begins with encapsulating filtered soil particles within a specific size range into hydrogel spheres. The hydrogel locks cells with their associated soil particles, enables effective cell lysis while retaining genomic DNA molecules, and aids in PCR inhibitor removal. Utilizing droplet microfluidics, the hydrogel microspheres with soil and cell genomic DNA molecules are processed using droplet PCR, generating barcoded 16S rRNA amplicon sequencing libraries. The reads from a single soil particle are grouped by barcode sequences, enabling single particle community taxonomic abundance estimation.