In a weird way, I hope this goes horribly wrong, and the super trees become an invasive species that results in an apocolypse of unstoppable forests that dominate the globe.
I assume not (at least for the majority of readers); it's instructive to consider why one feels trees are more in tune with nature than some lowly bacteria, or as the original implication made, more in tune than humans too.
Can trees destroy humanity? No, they move pretty slowly and we can defeat them with axes and fire. And we've been doing just that and show no signs of stopping. If trees take over the world again, that can only happen in a world already devoid of humans. With climate change upon us, this is a "good" future for our planet -- intelligent life may arise again in a planet full of tall trees. It's a much better future to picture, than a planet like venus or mars.
Can bacteria destroy humanity? Yes, we've bred them to be immune to antibacterials -- imagine some ancient bacterium which wiped itself out by being too lethal, gaining antibacterial resistance through cross-contamination in a lab. But it wiped itself out before the invention of airplanes, and suddenly it's capable of spreading faster and further than before. It's a stretch, but almost plausible. CRISPR might help somebody make it a reality.
But, I think your bacteria comparison is rather poor, given that nobody ever said anything about trees wiping out all life.
Maybe it is related to that episode you mention?
https://theinfosphere.org/The_Futurama_Holiday_Spectacular#A...