Acknowledgements
We thank David Sherlock for his experimental expertise in developing this method, the University of York Technology Facility for sequencing, Simon Kelly for DADA2 expertise, Asger Bachmann, Terry Mun, M. Izabel A. Cavassim, and Marni Tausen for preliminary data analysis and script development, and DLF for access to their clover field trials. This work was funded by grant no. 4105-00007A from Innovation Fund Denmark (S.U.A.). Initial development of the method was funded by the EU FP7-KBBE project LEGATO (J.P.W.Y).