Within these plantations of God, a decorum and sanctity reign, a perennial festival is dressed, and the guest sees not how he should tire of them in a thousand years. In the woods, we return to reason and faith. There I feel that nothing can befall me in life,—no disgrace, no calamity, (leaving me my eyes,) which nature cannot repair. ("Nature")
Even though this question is a popular one, it's meaning is rather vague and ambiguous. Since the answer is derived from the opening paragraphs of "Nature," Chapter 1: Nature, the question is understood more correctly as in this rewording: "In what part of Nature does Emerson describe the most profound change taking place in the life of man [humankind]?" The answer to this is eloquently described in the quotation above, taken from a section following after Emerson's discourse on seeing the "sun" and the "delights" of "every hour" of every day: It is in the "plantations of God" that the most profound change takes place.
Emerson speaks of "plantations of God" in the quotation above, then defines these "plantations" as the natural woods, which are unaltered by civilization or technology. Emerson says "the guest" never tires of the woods, and he implies a universality mirrored in his own subjective experience, suggesting that no one would ever tire of woods. He attributes "sanctity" (i.e., holiness) to the woods. He associates the woods with an infinitely long, "perennial," festival or celebration.
Three profound changes Emerson asserts the woods produce in humankind are the return to reason; the return to faith; and the reparation of the catastrophes of life: "nothing can befall me in life,—no disgrace, no calamity, ... which nature cannot repair." Consequently, based on this early passage of Emerson's essay "Nature," the part of nature in which Emerson describes the most profound change taking place in the life of man [humankind] is the woods, the "plantations of God" that return us to "faith and reason" and that repair our lives when destroyed by the horrors of life and living.