Dear brother, assalamualaikum. Is your objective to prepare pure isolate? If so, we  prepare pure isolate of a pathogen by single spore or hyphal tip method. Then  you can use that pure mycelia of a pathogen for inoculation.

Did you try stereo binocular microscope? It may help you put the single spore on root system.

Thanks

Mohammod Hossain 

Dear Hossaim, we have a methodology to develop a single conidium cultures.

The methodology is as follows:

Make the isolation and culture of normal form. After growth of the fungal culture, conidia are collected by means of fragments cut from the culture medium and transferred to test tubes containing 9 ml of sterile distilled water, followed by serial dilution to 10-4. Then, 1 ml of the suspension obtained is distributed in 3 Petri dishes containing water agar (AA), 2%. The plates are incubated under conditions favorable to the fungus germination. Single spore cultures is obtained by collecting the conidia of a light microscope. The conidium is collected by cutting a fragment in the focus corresponding to the microscope light with a piece developed at Embrapa. After the development of single culture, do a suspension of conidia and pulverize the leaves. In your case, you may need to let the spores start the mycelial growth and is transferred to the root. I hope I helped, if you have questions please contact us.