design: DNA was extracted from freeze-dried and homogenised samples containing roots from both the spring onion and lettuce experiments according to the instructions of the Qiagen DNeasy PowerSoil Pro Kit. Then, amplicon PCR reactions were carried out (16S: 1 cycle of 95C for 1 minute; 30 cycles of 95C for 30 seconds, 51C for 30 seconds, 72C for 30 seconds; 1 cycle of 72C for 10 minutes.), followed by library preparation for Illumina sequencing. The 16S primers used were F515 and R806 as described in Caporaso et al., (2010) for bacterial amplification. Bead cleaning is then carried out, followed by PCR2 to add unique identifier sequences, which is verified by running a Tapestation and quantified by fluorometry. Next, samples are pooled and the pools are purified by bead cleaning and Tapestation is run. Finally, qPCR is carried out on pools, and then pools are pooled.