I agree with Jon Richfield. To start analysis it is necessary to have a collection of the evident examples of the advanced cases of physiological substitutions in the symbiosis systems. In the Host-Parasite systems I would propose two:

Cestoda (P) - Birds or mammals (H) - worm use the enzymaticsystem of the host

Root-knot nematode (Meloidogyne) (P) - Arabidopsis plant (H) (a nematode uses the former bacterial genes recieved in LGT to plant parasitic feeding). (NK WhiTeman & A D. GLOSS 2010 Nematode debt to bacteria Nature 488:641-642)

But probably Arno Germond is interested in the mutualistic physiological substitution examples.

Examples with fungi are excellent for mutualistic physiological interactions

Dear Arno

Population genetic theory suggests that when a mutation is preserved in a population in terms of its incidence at high frequencies, it probably bestows some advantage to its possessor. What could be the advantage of carrying a gene that causes one (in a symbiotic relationship) to lose the functionality of an enzyme (unlike its non-symbiotic ancestors) that is of a crucial benefit (in line with your example)? For instance, trees need the nutrients that are available deep into the earth. To obtain those, the trees could have evolved much efficient root systems -- indeed, several trees have. However, this may take many-many years and might not turn out by any means. It just so happens that fungi already have this ability. When the two species find themselves in close proximity, it is much faster to evolve a way to incorporate the "tool" already available to the other organism than to reinvent the trait (http://science.howstuffworks.com/life/evolution/symbiosis2.htm). Thus it seems that losing of an enzyme (say for example that helps in obtaining nutrients by the tree) that was of importance to a generation is of no issue provided the present generation is equipped with the ‘tool’ (for the same function), already available to the other organism (its symbiont). Recent studies have shown that this kind of interaction spur on diversification as well (http://www.nature.com/nature/journal/v494/n7436/full/494151c.html#access). To be remembered that traits that allow an organism to take advantage of the other life forms in its environment are just as successful as the traits that allow it to escape (or eat) them (http://science.howstuffworks.com/life/evolution/symbiosis2.htm).

Best

Dola

Its a good question indeed!