Multi-omics DNA Extraction and Sequencing

DNA extracted with a kit was processed with the Qiagen DNeasy PowerSoil Pro Kit according to the manufacturer’s instructions (cat number 47014). DNA extracted by boiling was processed by thawing community samples, transferring 100 μL to a PCR plate, and heating the plate in a PCR machine at 100°C for 10 min. 5 μL of undiluted sample was used as the DNA input for the 16S rRNA gene amplicon library protocol. The 16S libraries for the cryopreservation, adjusted community ratios, PMA, and boil-extraction comparison experiments were prepared using 515F-806R primers according to the Earth Microbiome Project protocol (67 (link)) and were sequenced on an Illumina MiSeq platform with a paired-end 150 V2 kit as previously described (68 (link), 69 (link)). 16S libraries for the community dynamics experiment were prepared using 341F-805R primers (F 5′-CCTACGGGNGGCWGCAG-3′ R 5′-GACTACHVGGGTATCTAATCC-3′) and were sequenced on an Illumina MiSeq platform with a paired-end 150 V2 kit. The 16S libraries for the plant experiments were prepared using 515F-806R primers and were sequenced on an Illumina NovaSeq platform with a paired-end 250 V2 kit. Shotgun metagenomics libraries for the human-assembled/machine-assembled experiment were prepared using 1 ng of DNA input and Nextera XT indexes and were sequenced on an Illumina MiSeq platform with a paired-end 150 V2 kit.