Dylan , very thoughtful  question indeed. Please explore  different kinds of substrates being used for variety of orchids   for studies on mycorrhiza specific microbiome , since microbiome of orchid might not able to replicate under micro- biomes of non-orchid substrates. And , this is where , we have to be very particular. There is now international  Plant Microbiome Consortium to address such issues.

Hi, identifying fungi from root interactions nowadays is done by DNA sequencing. It is not simple but very reliable. There are many ways to do this. It depends on your access to molecular biology facilities and money. Sanger sequencing of DNA extracted from single pelotons is cheap and laborious VS sequencing the whole fungal community in your samples by next gen sequencing is more expensive

Hi, 

Sequencing DNA is crucial for an acute identification. I usually do a phylogenetic analysis of ITS sequence. But to know what you have in the roots is also a good idea doing microscopical observation.   

Regards

Molecular methods....