If the deck is no more than 2 to 3 feet off the ground, you can plant a tree or shrub directly into the ground with the foliage showing above the decking. Design the framing of the deck so a joist runs where you want one side of the opening to be. Position another joist to frame the other side of the opening. Close the frame with two crossbraces cut from a joist. Then add the decking.
If the deck is too high to plant in the soil, make a built-in planter. Follow the method just described, but use wood treated with preservative that is rated for ground contact. Use 2x10 joists to make the frame (even if using another size joist elsewhere in the framing). Cut a piece of 3/4-inch plywood the size of the frame and drill several 1/2-inch drain holes in it. Screw the plywood into place from below to form a bottom for the planter. Line with landscape-grade plastic, poke holes aligned with the drilled holes, and fill with soil.