Global climate changes include more intense and concentrated rainy seasons and severe and longer-lasting dry seasons. In this context, the benefits carried out within agroforestry systems (AFS) have played a significant role, especially for tropical crops such as cocoa. The present study evaluated the changes in photosynthetic traits and the physical, chemical, and microbiological soil properties in response to variations in the shading tree species. Three cocoa genotypes (CCN51, TCS01, and TCS19) were cultivated under three AFS designs, differing in the accompanying shade tree species ( Cariniana pyriformis , Tabebuia rosea, and Terminalia superba ). No significant differences in CO 2 assimilation rates among the different cocoa genotypes were observed. However, TCS01 exhibited a 20% higher leaf water use efficiency (WUEl) than the TCS19 genotype, associated with decreased stomatal conductance. The designs combining C. pyriformis with CCN51 and TCS01, as well as the design associating CCN51 with T. rosea, exhibited significantly higher WUEl for cocoa plants as compared to the systems involving T. superba combined with TCS19. In addition, the cocoa genotype TCS01 exhibited the highest potential for carbon storage when combined with C. pyriformis , whereas TCS19 exhibited the lowest potential for this feature under the T. superba association. The chemical, physical and biological properties of soils were evaluated, and an orthoPLS-DA multivariate analysis was performed to contrast the differences between TCS01 associated with C. pyriformis (higher WUEl and C sequestration) with the combination of TCS19 with T. superba (lower WUEl and carbon sequestration). The results highlight the importance of soil pH, [Al], [Mn], and [Mg] for a better physiological performance exhibited by TCS01 under C. pyriformis AFS as compared to TCS19 under T. superba . Thus, taken together the data obtained here suggest that species-genotype-dependent interactions in AFS-cocoa may determine soil characteristics, which may indirectly affect important physiological traits, such as leaf water use efficiency and long-term carbon storage of cocoa plants. • Advantageous interspecific interactions can generate improve leaf-level water use efficiency and carbon storage in cocoa. • Cocoa TCS01 associated with C pyriformis shows better leaf-level water use efficiency and carbon storage as compared with TCS19 associated with T. superba . • The evaluated shade tree species contrasted regarding their effects on the chemical features of adjacent soils. • Soil acidity, aluminium, manganese and magnesium concentrations were the soil features most correlated with the contrasts observed in the cocoa genotypes.
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