Definitely it is possible.In every stage of the plant root fungal endophytes are present. With different treatment the concentration may vary and it could be a parameter for study the fungal endophytes of a specific crop.
but my question is: can we sampled treatments at the end of growing season? (because tension effect on some of treatment to grows earlier than others ) or it must be in a same time ( one time, not end of the each growing season)