Once a micro-organism starts to grow on a single food source it immediately starts to adapt so as to more efficiently use that food - it is driven to do so via natural selection as any strains that develop to grow faster or more efficiently will quickly overgrow less well developed strains.
Of course man has probably offered a helping hand along the way by actively choosing the best strains for his purposes. After 9000 years of this the only strain left is highly adapted to that one food source.
Scientists have now taken a close look at the genome of 'tame' A. oryzae in an attempt to discover how it differs from the wild species it is descended from (A. flavus) and what changes have happened to optimise its use of starch and how efficiently it produces sugars. This may well give us clues on how to best alter other similar fungi to perform better in other industrial processes.