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Cocoa (Theobroma cacao L.) is an important crop in Peru. International regulations require products derived from cocoa to be free of heavy metals (HMs), such as cadmium. Arbuscular mycorrhizae (AM) contribute to reduced HM content in the plant, preventing its accumulation in the fruit and facilitating the rhizodeposition of HMs through glomalin-related soil proteins (GRSP). We studied the presence of mycorrhizal symbiosis in cocoa plants and cadmium in three plantations in San Martín, Peru. The maximum Cd content detected in soils was 1.09 (mg/kg), an amount below the tolerable limit for agricultural soil (≥1.4 mg/kg). Cocoa roots showed 68–86% active mycorrhizal colonization; agronomic management did not cause differences between plantations. Levels of GRSP were between 7.67 (GRSP-EE) and 13.75 (GRSP-T) mg protein g soil−1. Morphological and molecular analysis of Glomeromycota fungi showed the presence of families Claroideoglomeraceae, Paraglomeraceae, Gigasporaceae, Glomeraceae, Acaulosporaceae, Archaeosporaceae, and Diversisporaceae. Our results show the presence of arbuscular mycorrhizal symbiosis in cocoa plantations and suggest that T. cacao may phytostabilize HM in its rhizosphere through the production of GRSP. The presence of mycorrhizal symbiosis indicates the potential for the preparation of biofertilizers for cocoa since the production of GRSP is promissory for the biostabilization of soil HMs.

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