This is one of the contrast that Alice Walker made in the story. See the comparison between the colors? Black and white, right?
The white bubbles represent the white american while the black soil represents the black people. The bubbles flow freely while the black soil is fixed in the ground never moving.
This is similar to the situation back then when the blacks were moved to slavery.
Relating it to Alice Walker. She is a black writer, a social activist and was on the womanist group (which I think was kind of like the feminist group). I think she wants to reach out something to the readers as she wrote this contrast.
The sentence, "the white bubbles disrupt the thin black scale of soil" basically completes the description the author writes of the spring near Myop's home.
As far as a literal description goes, Myop is by the edge of the water. At the edge of the water is where little, white, foamy bubbles form. There is soil around the edge of the water. As the water made waves, the white bubbles rose up against the soil. Hence, the white bubbles disrupt the soil.