Unlike monocultures, rotations offer a number of advantages to plant production and to the maintenance of soil quality. These include disease breaks, improvements to plant nutrition, improved levels of organic matter, diverse nutrient sources for the soil biota and benefits for soil structure. Breakcrops can reduce numbers of host specific organisms. This may prevent the development of crops with fibrous roots e.g. cereals, are thought to provide more sites for micro-organisms to colonise compared to those with a single tap root and relatively few lateral branches, such as lucerne and canola.
Rotations including legumes or pasture have a larger and more diverse pool of organisms.
Cereal residues support more fungi whilst legume residues support more bacteria. Therefore numbers are prone to rapid decline if soil erosion occurs. Crops such as canola and mustard cause a reduction in mycorrhizae in the following crop. Brassica crops have been found to be better Take-all disease breakcrops than legumes. Decomposing brassica roots release isothiocyanates.