The natural world plays a very important role in Okami. All of the powers that you gain throughout the game are those of the natural world. From restoring life to withered trees, to controlling the flow of water, air, and creating fire and ice. All of which you must employ to overcome the obstacles on your path.
The forces which you go up against have deteriorated the natural world in Okami to the point where no life can exist. This is why you have come down to the mortal world, or samsara, as the goddess Amaterasu. You take the form of a white wolf, an animal, and your task is to bring back life to the trees, rivers, and mountains of Japan.
This scenario equates the prosperity of humans with the prosperity of the natural environment. When the wells and rivers dry out, and the crops and tress wither, the people can no longer live off the land. When the water is poisoned and the mountains frozen, the people begin to die. The game emphasizes that the downfall of the environment is also the downfall of the people.
The natural world must be respected, and in Okami this is portrayed quite simply. As per Shinto tradition, everything in nature possesses a spirit, or kami. The river has a kami, and the mountain has a kami just as each tree and flower has its own kami. Destroying the land, hurts and angers these kami, thereby creating chaos within the natural world. By appreciating nature, and caring for it, we please the kami. In turn we also create a world which allows us to live in it and prosper.
The importance of the natural world is thus continually brought to the foreground. By granting the player powers of nature, Okami shows us that natural forces are strong enough to effect change in the world. This importance is further emphasized by demonstrating the detrimental effects of the natural world's decay on all living things, and especially the people. Yet all of this culminates in the notion that all things in nature posses kami which must also be harmonized with—taking a final step from an impersonal view of the natural machine to that of a living and spiritual entity with which we coexist.