Long term? The ecosystem. If we don’t change course, at some point the species that goes extinct is us, and nature is going to recover. Life has survived much worse than what we can do.
Realistically I think if humanity decided altogether to go for the genocide ending to life on earth we’d be able to kill all life on earth. We can’t directly kill all of the bacteria but if we were dogged enough we could induce the Venus ending (we will long be dead before victory is claimed though).