Coleridge's Rime of the Ancient Mariner seems to fit this description. The mariner kills an albatross, the bird that brought him and his fellow sailors good luck. For the murder of one of God's innocent creatures, the mariner suffers greatly--having to wear the dead albatross around his neck, the death of his fellow mariners, hot and windless weather, among other torments. It is not until he blesses the snakes in the sea that the hell he is suffering begins to lessen. After he confesses his deed to the hermit, and receives forgiveness, the mariner realizes that
He prayeth best, who loveth best
All things both great and small;
For the dear God who loveth us,
He made and loveth all.
This is the story that is his to tell. His lifelong penance is to teach others the lesson he has learned.
I immediately thought of The Rime of the Ancient Mariner where, at the end, there is even a line about how humans should love nature because God created all things. As the mariner comes to an appreciation of his guilt in killing the albatross, he comes to a better understanding of nature and God.
The first poem that comes to mind for me is "The Chambered Nautilus" by Oliver Wendell Holmes--one of America's Fireside Poets. While the poem's goal (like many Romantic poems) is to teach the reader a moral lesson from nature, Holmes also uses the small seashell to demonstrate God's care in designing such a creature, one that can diligently work on its shelter even when storms would destroy it.
You might also consider some of Aesop's Fables, many of which focus on tiny creatures or ones that would be considered underdogs becoming the victor.