Microbial DNA extraction and 16S rRNA gene sequencing
To characterize the microbial community composition of native locations, we collected samples of rhizosphere and root from eight haphazardly selected hallii individuals growing at Austin (WFC) and ninefilipes individuals growing at Corpus Christi (CCBG) – we note that in this natural sampling scheme location and ecotype are confounded. Additionally, five bulk soil samples (all plant material removed) from each site were collected in areas adjacent to livinghallii plants (44 samples total) and DNA was obtained with the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany). 16S ribosomal RNA gene regions were amplified using the 515F-806R primer pair, barcoded and sequenced on the Illumina Novaseq platform on the SP flowcell using 250x250 reads. To characterize treatments in the greenhouse experiment, this procedure was repeated on rhizosphere, root and soil samples taken at harvest from seven replicates of each parent in each treatment (four treatments x 14 parents x three compartments = 168 samples).