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Global soil carbon cycling plays a key role in regulating and stabilizing the earth's climate change because of soils with amounts of carbon at least three times greater than those of other ecological systems. Soil minerals have also been shown to underlie the persistence of soil organic matter (SOM) through both adsorption and occlusion, but the microscopic mechanisms that control the latter process are poorly understood. Here, using time-resolved in situ atomic force microscopy (AFM) to observe how calcite, a representative mineral in alkaline soils, interacts with humic substances, we show that following adsorption, humic substances are gradually occluded by the advancing steps of spirals on the calcite (10 (1) over bar4) face grown in relatively high supersaturated solutions, through the embedment, compression, and closure of humic substance particles into cavities. This occlusion progress is inhibited by phytate at high concentrations (10-100 mu M) due to the formation of phytate-Ca precipitates on step edges to prevent the step advancement, whereas phytate at relatively low concentrations (<= 1 mu M) and oxalate at high concentrations (100 mu M) have little effect on this process. These in situ observations may provide new insights into the organo-mineral interaction, resulting in the incorporation of humic substances into minerals with a longer storage time to delay degradation in soils. This will improve our understanding of carbon cycling and immobilization in soil ecological systems.