Using biological forms of fertilizer such as compost, animal manures, and legume cover crops, builds soil organic matter, even when routine tillage is used for weed control. Building soil organic matter increases soil water retention and nurtures more active soil microbial communities that retain nitrogen in the soil longer and transform it into non-reachable gaseous forms. There is a small but telling body of research in the US that suggests that improved soil quality influences the ability of crops to withstand or repel insect attack and plant disease.

Organic biological fertilizer sources release their nutrients slowly over time, providing more opportunity for the nitrogen to be digested by soil organisms and taken up by crops before leaching below the root zone. Increased soil organic matter in the soil leads to tighter nutrient cycling and greater water holding capability in organically managed soils, with the result that nitrate leaching from groundwater is about half that of conventionally farmed soils. Recent data from a 12-year study shows that fields under organic management had half the annual nitrate leaching losses than fields under conventional management.

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