You remove mushrooms and bushes by using a shovel on them. You do not get anything from it.
To produce grain, you need to:
1)Cut down wild (green) patches of cereal with a scythe or a sickle.
2)Make a thresher and put the gathered cereal in there. That will get you some straw and some seed.
3)Put fertilizer onto weeded soil to prevent more weeds from growing on it. You can also use shovel to remove weed to free more space.
4)Use a hoe to till it
5)Put seeds into tilled soil. It will grow into golden wheat, which you gather for same cereal.
6)Thresher it into more seeds, replant them, and so on in cycle. You do not need to repeat fertilizng the soil, only tilling, planting and cutting.