The second site is one much closer to home, Shinji Shumeikai. This organizations headquarters are in Shiga Prefecture, just west over the mountains from here. Sounds like a must-visit spot. Their statement on the environment at their web site says:
The greatest expression of Shumei's deep concern for the health of our Earth is its commitment to the practice of the Natural Agriculture method of growing food, a method that emphasizes the integrity of nature and the purity of soil, water, and air.
They have also made a partnership with The Rodale Institute to cooperate in developing natural farming practices.