Everyone remember Crush’s cameo in the credits of WALL-E? Where he and other animals suddenly appear after hundreds of years of being possibly extinct? What’s up with that? They may of kept animals aboard the Axiom. Although there wasn’t any mention.
Maybe they’re robot turtles.
I’ve always thought there was some sort of place on earth where there’s plants and everything and the animals live there, but nobody knows about it because it’s hidden. 
Perhaps they were stored on the ship in some sort of stasis?
Yeah, they could be cryogenically frozen on the Axiom some place.
Maybe they must have had a special ship for all the animals.
They used a Garden of Eden Creation Kit:
They do keep huge archives of DNA samples of animal species now, along with the Doomsday Vault in Norway for plant seeds. They could have used those.
I figure they probably have a DNA bank, but I think this answer is cooler. xD
They -DO- cryopreserve DNA samples from somatic cells, as well as store sperm, fertilised eggs etc. of endagered species today. It’s not a perfect process though and you do need surrogates in order to carry them to term anyway. Plus of course, it’s not the only conservation method we should rely on.
It’s possible in the last few centuries they perfected the process somehow. Hell, maybe they can cryopreserve animals a la futurama now (I do n’t know). There are other ways they are developing to prevent freeze-thaw damage occurring (which is why they need a lot of samples now), however it still results in solute damage (it’s called vitrification), I think.
In any case, have this adorable picture of an ocelot kitten who came from a fertilised egg which had been frozen for 7 years or something like that who was born from a surrogate mother:
dels-old.nas.edu/ilar_n/ilarjour … _312f3.jpg
The paper it came from:
I could say this:
Since the civilians aboard the Axiom had witnessed the first signs of life, we could assume that animal life had returned as well. When they went aboard the ship, and Wall-E and EVE reconciled, as well as during the credit roll, the robots aboard the axiom as well as Wall-E had helped in maintaining life on Earth somehow while the captain had gathered all the information he could about the anatomy of fishing, gardening through the Ships motherboard to the people, due to his intiqued curiousity about life on Earth. As the world started to improve, so did the radioactivity inside the natural waters in the oceans, thus maintaining the recurring fish life, which (in the credits) they used fishing techniques to capture and sell them for food. During this case, they were allowed healthier access to food other than the liquified food they once used in the Axiom (they used that food momentarily until they could harvest new food).
That’s my idea on how fish life came to be.
Maybe they built a ship like the Axiom that contained only animals, and it was sent back to earth as part of Operation Recolonize when one of the main fleet found a plant.
I just realized, there were other fleets who left earth other than the axiom, did THEY return back when the word came out from the axiom?
…whoa! You’re right! I don’t think so. The Axiom probably is programmed to send out messages to the other ships. I’m sure the Autopiolet of those ships got the message and deleted it ASAP.
I second that. 
How many people do you suppose were on the Axiom?