If you are going to do amplification from DNA, then it will be better to isolate the fungi first, normally this is what we do when isolating fungi from plant parts:

1) surface sterilize the plant parts with 70% ethanol

2) Cut the plant parts that is needed

3) Shake the plant part in 10% clorox 160rpm 10m

4) Transfer and shake in sterilized distilled water 10m

5) Repeat step 4

6) Take out the plant parts and dap dry with tissue

7) Cut the plant part into smaller pieces

8) Put them on agar plate (You can use suitable selective media base on what type of fungi you expect to isolate)

9) Once you have pure culture of the fungi you can proceed DNA extraction

@ Vikki Wong, thank you for your answers. Actually, I have to do qPCR so need to do direct DNA extraction.

Do you have suggestions about it too?

Bhawana