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So ideally the beneficial microbes out compete pathogenic species and form a protective layer on the surface of living plant roots, in short the good microbes usually fight the bad ones so they are lumped all together in the ecosystem that you created there is no way around it.
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Ideally, but not everything is ideal, and not every circumstance or situation is ideal ether. That's when knowing exactly what your dealing with is important (not ideal), and with all the billions of microbes that exist (both plant and animal), at best you would need a degree in microbiology to possibly have a chance of telling one from another (even under a microscope). Yes there will always be pathogens right along side the beneficial microbes. And absolutely, under the right conditions the beneficial microbe's will generally tend to keep the pathogens in check. But not always, and you cant just forget that pathogens being able to get a foothold is a possibility. If circumstances permit the pathogens to get a strong foothold, they will be difficult for any beneficial microbes to deal with (at least without help).
That is where my issue is. You cant just assume every situation is "ideal" and just lump all microorganisms together in order to call them all beneficial, thus pretending that pathogens don't even exist. That's exactly what I see in the video, they make no reference to pathogens, and just define "
ALL" microbes as beneficial life. There's a distinct difference between beneficial microbes and pathogens. And it is quite possible (and easy) for pathogens to be able take over if given half a chance too.