Yep, they're stumps. At the moment they're purely decorative, to give a feeling of the effect the player is having on the landscape, and are automatically dug up when you dig on the tile. We had a notion to grow mushrooms on them but that was dropped.
Thank you for that information. I can understand why you dropped the idea of automatically growing mushrooms on tree stumps. When I first started planting dug mushrooms in the current (and past) versions of Autonauts, I saw that planted mushrooms would spread to every available nearby empty space. I built my mushroom farm within an area completely enclosed by a brick wall, with enough bots inside the wall to dig up the mushrooms, store some of them, plant some of them, and one Steam bot to wind up the others. That way, the mushrooms would only grow in that area.