In each Grade area there are actually 4-5 trees that can appear in multiple locations. One you deplete a tree (it stops sparkling) it will move to a different location. However if you don't completely deplete it it will continue to sparkle but you can't harvest it. To harvest different nodes you have to run a circut of different spots to refresh the one you just used. The amount on times a tree can be harvested depends on your rank compared to the grade. Your stats affect how many attempts you have at a tree
So essentially you need to set up a circut of 3 nodes (they can be primary or secondary types) to harvest. EG Oak Tree -> Clump of grass -> Ash Tree -> Oak Tree -> Clump of Grass etc
If a primary node is depleted when you finish with it, it will move to a different location. so you could go: Oak Tree (stops sparkling), Oak Tree (fresh respawn) -> clump of grass -> Ash Tree -> Oak tree