Throughout Prisoners, different shots of different trees are shown (including the famous tree shot at the beginning) and after searching for some time about what do they really mean I only found this article which is based on one of director's interviews.
They’re kind of like ghost characters.
They’re always there, at least in the background. Each scene you can feel their presence. And they are linked with this idea of necessary violence.
However, the scene that raises my curiosity is the scene with a tree that looks a lot like "tree of life" and given the many uses of symbolism in this movie and having Roger Deakins at there hands, I wonder if there are other meanings/symbols behind the trees.