This is the sort of question that should be considered from more
than one direction. Clearly this is a speculative scenario, so
take it as a given that there is a lot of 'what if' here. I
doubt we can do entirely without bacteria - as you say most of
the essential nutrients come from bacteria, who fix nitrogen. If
only plants were left on earth, eventually the plants would use
up all the nitrogen and they would have to find a way to fix
more. Can bacteria emerge from just a world of plants? I don't
think viruses arise spontaneously, but since genomes often have
viruses embedded in them, over the course of a billion years or
so, its possible since bacteria and viruses continue to be
impressed upon our genomes. Would it happen in time? Most would
be skeptical whether that timing could work out. In practice it
would be hard to create a world like this. I would be interested
to see whether you could sterilize the microorganisms off of
seeds without killing the plant for instance. If you're asking
about a small st