In recent years, new data on the diversity of genera and species in the phylum Glomeromycota continue to be added and rearranged. Arbuscular mycorrhizal fungi are key to plant nutrition and agriculture. Studies report different short- and long-term cultivation practices that influence the abundance and diversity of Glomeromycota. To the best of our knowledge, there are no known studies of the fungal communities in the fine aroma cocoa cultivars. In this context, our work aims to discover the diversity of arbuscular mycorrhizae associated with two cocoa cultivation practices (conservative and semi-conservative) through the isolation of spores using microscopy and metabarcoding of the internal transcribed spacer region (ITS). Morphological analysis showed that the density of Glomeromycota spores exhibited significant differences between production systems. Although the metabarcoding analysis showed that diversity indices showed a higher increase in the roots than in the cocoa soil, independently of the cultivation practice. An abundance of 348 and 114 taxa were observed, corresponding to the conservative and semi-conservative practices, respectively. Seven genera were observed for the first time in cocoa crop agroforestry systems, including P. scintillans, R. diaphanus, R. fasciculatus, R. custos, D. disticha, M. perpusilla, and D. bernensis.
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