Humans are no different than any other organism in that we are "nature." We have a role in nature just as much as you see the birds flying and the plants growing, we just see ourselves (for a number of cultural and biochemical reasons) as separate. The following are a collection of organizations and resources that I think are doing the best work to use our role in "nature" to better the world.
Rich Earth Institute: A group in Brattleboro, VT working with the USDA on closing nutrient cycles by using urine as fertilizer. "Our “liquid gold” is an abundant source of sustainable fertilizer, but we currently flush it into sewers where it causes nutrient pollution that is costing municipalities billions to remediate. By collecting and recycling urine into fertilizer, we can more affordably protect the aquatic environment while replenishing the soils that support us."
Humanure Handbook: The definitive guide to turning human waste into compost. Mixing our waste with drinking water (as flush toilets do) is not only ridiculous, but polluting, expensive, and dangerous.
Green Wave: An amazing model using aquaculture to restore ocean ecosystems.
Human Food Project: We are what we eat, and the microbes that eat what we eat. Researcher Jeff Leach's project studying the Hadza microbiome.