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A field site in the Coachella Valley of California was selected as an ideal experimental location to study the effect of organic amendments on soil ecology and crop productivity. The high temperatures, low rainfall, and frequent irrigation of low desert agriculture leads to rapid breakdown of organic residue and soils naturally low in organic matter. Because organic carbon is relatively scarce in desert soils, amending with compost or cover crops may have a more dramatic and easily detectable effect than in temperate regions. Our experimental treatments included all possible combinations of summer cover crops and vegetable crop management systems. Summer cover crops were dry fallow or sudangrass or cowpea. Fall lettuce was followed by spring cantaloupe. Both crops were continuously managed as either conventional, organic, or an integrated system that reduced insecticide applications. The experimental design allowed direct comparisons of many combinations of organic or conventional fertility and pest management regimes. Yields in the first year of study were lower in the organic plots. However, yields for the following year for conventional and organic systems were equal despite less effective insect control in the organic system. Soil organic matter content was correlated with soil structure and lettuce yield. However, the range of organic carbon was very narrow (0.5-1%) and it was correlated with the clay percentage of the soils. The negative charges of the surface of the clays act as an absorbent interface where the organic molecules attach. Attachment to the clay surfaces protected organic matter from microbial degradation so that it could accumulate in the soil, but the amount of organic carbon accumulated was restricted to the limited amount of colloidal or clay particles present in these sandy desert soils. Soil microbial respiration was related to the amount of organic carbon added as either cover crop or compost, indicating that microbes were degrading and using the organic residues as an energy source.