Is the identification to species level using PCR done by sequencing the amplicon (of 18S or ITS)? In that case it is neccesary to have DNA from only the target organism, otherwise the obtained sequence results will be contaminated with other species and useless (no clean signal, a lot of background noise).

Isolating fungal mycelium on agar before DNA extraction for PCR is essential because it ensures the purity of the fungal sample and eliminates potential contaminants. Agar plates allow for the selective growth of the target fungus, providing a controlled environment to obtain a pure mycelial culture. This is crucial for accurate PCR analysis, as contaminants could introduce foreign DNA into the PCR reaction, leading to erroneous results. By isolating mycelium on agar, researchers can obtain a clean and well-defined fungal sample, enhancing the specificity and reliability of subsequent DNA extraction and PCR processes.

Becouse the nucleous was increased in the hayphae for mycelium so that give more DNA yelid

Dear Scarlet Maguire,

Fungal colonies form on the surface of the agar as molds. This is the main distinction between colonies of bacteria and fungi. Colony morphologies are helpful in bacterial and fungal recognition and differentiation. Agar is necessary for the enrichment and growth of target organisms. If you take them directly to genotype without a proper understanding of it phenotype will always be a risky game. If you want to study of it is genome it is necessary to take the pure culture. Otherwise, you will be wasting a lot of money and time on the sequencing. If your target wants to detect in that case you might get an answer by doing species-specific PCR, but you would not get as promising results as you expected.