I would doubt this is the case (the fungi would die if it was the case). Just a guess - likely if you use the Trizol method you have some aromatic hydrocarbons acting as reverse transcriptase or PCR inhibitors. 

My problem is not at RT or PCR level.. I m blocked at the point of mRNA isolation (by polyA fishing); maybe the hydrocarbon inhibits the affinity of the polyA to the baits.On the other hand my sample has been washed twice after been filter out from the liquid culture...

Barbara Blasi just to follow up on the question, have you eventually solved the problem? We recently are trying to fish out mRNA and also showed that nothing seemed to bind to the oligo(dT)-cellulose beads, instead just found in the flow through