Whenever the dirt is disturbed, it negatively affects the drainage and microbes, temporarily. Unless installing plants or removing unwanted ones, I try to not disturb the soil, even in dead spots where I've just pulled up grass. Without human intervention, organic matter (besides dead roots) would never be under the surface. The worms & microbes are best able to do their job when things are "normal" and undisturbed.
A 15 min vid that explains these things much better than I can.
http://permaculturenews.org/20...
