Integrating natural gradients and controlled assays to reveal bacterial responses to cadmium in Theobroma cacao L., soils

Cadmium (Cd), a toxic heavy metal found in agricultural landscapes worldwide, has been pointed out in cropped soils with Theobroma cacao L., as one of the main contaminants that translocate into plant tissues. Among the factors linked to cadmium translocation into plants, the role of soil bacterial communities in chemical transformation in soils has been poorly investigated. Overall, soil bacterial communities are shaped by diverse environmental and anthropogenic factors that influence crop yield and health. Cadmium alters soil microbial communities and increases the risk to human health through plant uptake. Although the impacts of cadmium on soil bacteria have been studied in other crops, there is limited information on cacao. Thus, this study aimed to assess the responses of soil bacterial communities in cacao farms to cadmium exposure, both natural and spiked. A total of 225 rhizosphere soil samples were collected from 16 plots across five cacao farms in two Colombian departments. The complementary approaches used were: (i) 16S rDNA amplicon sequencing to assess the composition of the bacterial community in soils with natural Cd concentrations, and (ii) isothermal microcalorimetry (IMC) to measure the temporal metabolic responses of bacteria to Cd in closed systems for 80 hours at 25 °C. The findings suggest that nearly 28% of the bacterial community responds to high cadmium concentrations in soils, both in natural and experimental conditions. Field-based observations revealed that Cd-responsive taxa detected under natural soil conditions included several unculturable bacterial groups, whereas laboratory experiments with Cd spiking predominantly selected for previously characterized cadmium-tolerant bacteria (CdtB). Significant variation in natural Cd-bacterial community composition and Cd-related metabolic activity was observed across the farms. Moreover, Cd-responsive bacterial taxa exhibited increased abundance during Cd spikes. As expected, contrasting patterns were revealed by the activity-response measured by IMC and taxonomic analyses of 16S rRNA gene sequences.