An experimental test of the keystone species concept in microbial food webs using a synthetic soil pore space system
Genomic DNA was extracted using PowerSoil Pro Kits (Qiagen, Hilden, Germany) following the manufacturers protocol. Microbial community structure was characterized by high throughput sequencing (Illumina MiSeq, v3 chemistry) of taxonomic barcode markers from bacteria (16S V4 region using 515F806R), fungi (ITS2 region using 5.8S-Fun/ITS4-Fun), and protists (18S rRNA gene using 616*f1132r) from chip samples and non-inoculated chip controls. Sequencing reads were processed using the DADA2 pipeline in R, including quality filtering, chimera removal, and OTU clustering at 97% similarity, and taxonomic assignment using the SILVA, UNITE, and PR2 databases, with additional filtering to remove contaminants and nontarget sequences.