First, the proper time to investigate the root infection with mycorrhizal fungi is the flowering stage of plant growth; in this stage the infection process is very active. After flowering stage, degradation of some roots begins.
Secondly, For collecting a reasonable quantity of mycorrhizal fungi spores, you must wait up to the maturity stage of plant growth, at this stage the mycorrhizal spores will release from the degraded roots to the soil.
It also depends on which climate you are in. If there is strong seasonal variation on temperature and precipitation. It also depends on what is the purpose of study: seasonal variation study, diversity study, or just a "take a look to see what is in there". For diversity based on spore collection, I would suggest to set up trap cultures with field soil and roots. Cheers. Sidney
Plant host for trap culture must be one that first adapt well under you greenhouse or growth chamber conditions. I prefer to use a C4 plant, that produce a lot of roots. In our Culture Collection we put around 40-60 Brachiaria (or Sorghum) seeds per 1,5 Kg pot, so there are a lot of roots to fungi get in, growth and sporulate and plants do not grow to high at this density. Let it go for about 4 months and check for spores.