Much of this whole thread was kinda strange for me. The movie clearly shows a thunderstorm, as in rain, as in water. Also, the pictures of the earth showed oceans and the Great Lakes, altho these might have been dead to visible life. And several posters talked about an initiative which is already well underway: seed collection. There is also another recent initiative involving DNA sample storage, which includes animals (insects are animals, but you will never see them on the front of an ‘Animal Crackers’ box), so given another 100 years of this, it could be quite considerable, wherever they are storing the samples, in a lab, bunker or spaceship.
Chesnut trees are unable to reproduce and have been unable to grow beyond small shoots for most of a century now. But they aren’t dead, just waiting for a cure. So roots and ungerminated, hardened seeds are always a source of renewal.
I would imagine that the evolution process would take some time for mammals to reproduce in a still nearly uninhabitable earth, so a Noah’s ark of the Axiom would make sense too, since Wall-E does show some religious themes, and the trash is like the great flood while the humans needed to be saved from it with the ‘big ark’, the Axiom. The only reason we haven’t seen this was that it wasn’t important in the original story until we could come to a speculation at the epilogue that they were able to introduce animal life back into the planet when the weather had improved as well as the surface beneath it.