The best you can do with the light microscope without staining really is the Ingham system – you can see clamps on hyphae to identify basidiomycetes and her system of color and width. You guess wide clear hyphae are zygomycetes. But without the sporulating sexual phase determining fungi is a nightmare. (By the way I lost the conversion factor she uses for hyphal length to biomass somwhere in my paperpile – if someone has it at hand, I would appreciate be filled in!)

Once you see the interaction on the root, you know what is going on – but hyphae only. No chance.

With bacteria same story – you can identify some species on educated guess base (bristle-like lactobacilli, corkscrews…) but the rest is metabolical typing (or in both cases nowadays DNA sequencing).

So the question is, are we catching organisms only – or are we catching a quorum sensing state? Maybe it is more essential to catch a smaller group interacting well to convince the rest of the guys to do so too. Like a dancing cheerleader troup of influencers.

Protozoans do a great deal of microbiome shaping by their food preferences.

So I sometimes think it is rather a question of diversity offered to a structure/foodsource – or lithobiont system if you want to be independent of a foodsource – and a couple of influencers to start the system.