It is apparently canon that there are animals and plants on the Earth's surface in Neo's day.
However, in the first movie, The Matrix, Morpheus tells Neo that one of the things known for certain is that humans "burned the sky" in order to deny solar engery to the machines, which in turn led to the humans who survived the War being plugged into the Matrix to provide bioelectric energy to supply the machines.
If there's not enough sunlight for solar power, how can there be enough to grow plants to serve as food for animals? Low levels I can understand -- house plants, at least, thrive in conditions too dim for solar panels to produce cost-effective power -- but every surface scene we see in the trilogy is as dark as a cloudy night; light coming only from the machines. That wouldn't begin to support photosynthesis, which means all animal life would starve in, at most, a matter of a few years.




