AbstractAccurate assessment of the benefits of soil health building practices to soil function and crop performance requires region‐specific data and locally relevant indicators. In this study, we used a long‐term experiment to measure the effect of 25 yr of differing management on soil health and crop performance indicators in organic and conventionally farmed annual crops in a Mediterranean climate. We measured the strength and consistency of the relationships between several indicators and three functions of a healthy agroecosystem—C storage, net N mineralization, and yields—over two growing seasons and two crop types. Lastly, we used path analysis to test the hypothesis that healthier soils lead to healthier plants and higher yields. Organic plots had greater C stocks and net N mineralization compared with the conventional plots, but lower yields. The path analysis suggested that yields were limited by factors other than N deficiency. The relationships between soil health indicators and soil function were unaffected by crop type but were moderated by yearly changes in weather and operations timing. The indicators most strongly and consistently related to C stocks were permanganate oxidizable C and microbial biomass C, and to N mineralization were CO2 mineralized from rewet soil and fluorescein diacetate hydrolysis. Our results highlight that (a) different indicators are appropriate for assessing different aspects of soil health, (b) using several years of data in developing robust ranges for indicator interpretation is important, and (c) links between soil and crop health must be assessed mechanistically within a given system.

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