amplicon sequencing of soil
Library preparation was carried out using a Nextera DNA Sample Preparation Index Kit (96 Indices, 384 samples; Illumina, Inc.) with the following alterations to the recommended protocol. Indexing PCR reactions were set up using the KAPA HiFi HotStart ReadyMix PCR Kit (Kapa Biosystems) with 5 L of the purified PCR products as template and 5 L each of index primers 1 and 2 (i7 & i5, respectively) and amplified for 12 cycles (details in supplementary materials). The indexed PCR product was purified as above. The concentration of the indexed PCR product was measured spectrophotometrically and standardized to a concentration of 10 ng/mL using the elution buffer as diluent. To allow inclusion of more samples, pools of 16S amplicons were indexed together with 18S and ITS samples for each sample