Bacterial diversity of lowland soils under cocoa cultivation in Amazon

This study investigated bacterial diversity in soils from six cacao-producing islands in Mocajuba, Pará, Brazil. Using next generation sequencing shotgun metagenomic DNA, we characterized the microbial composition and ecological structure of floodplain soils cultivated with Theobroma cacao. Taxonomic classification revealed a rich bacterial community encompassing 21 phyla, 54 classes, 121 orders, 240 families, 604 genera, and 2,289 species. The dominant phyla, Actinomycetota and Pseudomonadota, are known for their ecological roles in organic matter decomposition, antibiotic production, nitrogen cycling, and plant growth promotion. Alpha diversity metrics varied among samples, with P3 showing the highest species richness and P5 exhibiting the highest Shannon, Simpson, and evenness indices, suggesting a more balanced community. Beta diversity analysis based on Bray-Curtis dissimilarity under Total Sum Scaling (TSS) normalization revealed ecological gradients ranging from 0.228 to 0.527. Spatial ordination and hierarchical clustering indicated gradual shifts in community composition, supporting the concept of a compositional continuum shaped by environmental gradients. Functionally, Burkholderia lata was dominant in P1, reflecting its role in potassium solubilization, while Streptomyces species-detected in five of the six samples-contribute to biogeochemical cycling and pathogen suppression. Bradyrhizobium and Paraburkholderia, identified in P3, P5, and P6, are associated with nitrogen fixation and plant hormone regulation. These findings reveal the ecological complexity and functional potential of cacao soil microbiomes, providing insights for sustainable management of Amazonian floodplain agroecosystems.