Preparation of environmental samples
For Field-Samples-1 data, white clover (Trifolium repens ) root nodules were collected from two locations: Store Heddinge, Denmark (6 plots) and Aarhus University Science Park, Aarhus, Denmark (2 plots) (Supplementary Figure S4 ). The clover varieties sampled were Klondike (Store Heddinge) and wild white clover, (Aarhus). 100 large pink nodules were collected from 4 points on each plot, making a total of 32 samples. Nodules were stored at -20°C until DNA extraction. Nodule samples were thawed at room temperature and crushed using a sterile homogeniser stick. Crushed nodules were mixed with 750µl Bead Solution from the DNeasy PowerLyzer PowerSoil DNA isolation kit (QIAGEN, USA) and DNA was extracted following the manufacturer’s instructions. DNA sample concentrations were measured using a Nanodrop 3300 instrument (Thermofisher Scientific Inc., USA).
For Field-Samples-2 data, root nodules were additionally sampled from 13 white clover conventionally-managed field trial plots at Store Heddinge, Denmark (Sample 1A-13A, Additional File 2 ). All plots were sown under the same conditions in 2017. Three to ten clover plants were sampled from one point in each plot and the 100 largest nodules collected. Nodules were stored at -20°C, and DNA was extracted for each sample using the Qiagen DNeasy PowerLyzer PowerSoil DNA isolation kit, as above. Samples were processed independently with Platinum (non-proofreading) and Phusion (proofreading) polymerases to evaluate the method dependency on polymerase choice, as described in the following sections.