At the end of the movie Passengers, the 2 main characters have grown a garden. That's understandable; earlier we saw plants growing on one part of the ship. But where did the birds in the garden come from?
The Avalon is a ship part of an ongoing colonization of various planets. The ship has entire storage of equipment, tractors, prefab housing, submarines. In the original script, there was a gene bank. In the final film, there is also the entire garden of specimens of plants used for transplantation. (Like was explained in The Martian, you don't official colonize until you plant crops).
It's completely realistic that they would also take any number of animals in suspended animation for companionship, work, food or other reasons. They are colonizing, and want familiar species of animals around. Song birds are just the animal version of taking roses to a new planet.
Now that we have that out of the way I have to disagree that a metal spaceship is going to turn into the garden of Eden like they showed without serious reconfiguring. As I recall they planted a tree into the deck of the space ship. That doesn't seem reasonable to me. Trees require dirt to grow, and the space below the deck is going to be filled with all kinds of conduit and mechanical gizmos. They would have to replace the floor with dirt of sufficient depth to allow the plants to have a stable root system. Furthermore the crew is shown walking out to the central concourse from the elevator door so it isn't like the lower level of the concourse was filled with dirt to accommodate the roots. They created the garden to be level with the old floor.
While it is possible in theory for them to rip out the deck of the ship, fill it with enough dirt, and plant their garden it would be a tremendous project both in terms of scale and risk.
DIRT. They would not have been transporting enough dirt on that ship to sustain the tree. Let lone the rest of the plants. I would argue that the ship would have not brought any dirt. As they are going to a planet made of it.