Soil diversity metabarcoding from cacao crop wild relatives in a tropical biodiversity hot spot in Colombia

Theobroma cacao, the source for chocolate fabrication, is a high-value crop that faces challenges such as the impact of climate change, pathogens, and cadmium accumulation. Soil associated with T. cacao has been extensively studied, looking for bio-controllers and microorganisms capable of Cd accumulation. However, there is no information about the microbial structure and interactions occurring in soil associated with cacao wild relatives, which represent a repository for biological diversity and its potential for biotechnological applications. We performed an extracellular DNA metabarcoding on soil samples associated with Theobroma spp. and Herrania sp. plants in two localities of the Biogeographic Choco. We found microbial high diversity indexes and no correlation with plants or sampling locations. Potential cacao pathogens and bio-controllers and unexpected differences in the physicochemical soil properties from close locations were detected. Cadmium, an important economic factor for the commercialization of cacao products, showed significant differences between locations associated with a particular Theobroma species. We discuss some important relationships with soil physicochemical properties, the urgent need to complete the missing information on the diversity of bacterial, fungal and insect groups, and the potential of comprehensive analyses for decision-making regarding land-use and vocation. Also, we did not find the only T. hylaeum tree after three years, evincing the urgent need for conservation strategies in Colombia's Choco region.