From Soil to Leaves: Decoding the Microbiome of Oil Palm in Colombia

Plant microbiomes are shaped by hierarchical ecological filters in which compartmentalization through the progressive selection of microbial communities along the soil-root-leaf continuum, emerges as the strongest structuring force. Despite the agronomic importance of oil palm (Elaeis guineensis Jacq.) as an important oil crop, compartment-resolved characterizations of its microbiome remain scarce, and the microbiome of the interspecific hybrid OxG (E. oleifera × E. guineensis), widely planted in Latin America to sustain production in disease-affected areas, had not been previously described. Here, we used 16S rRNA (V3-V4) and ITS (ITS2) metabarcoding to survey bacterial, archaeal, and fungal communities across bulk soil, rhizosphere, roots, and leaves of productive plots of E. guineensis and OxG hybrid palms under two soil consociations in Colombia. Sequencing produced 10,298,116 raw reads, of which 79.83% were assigned to amplicon sequence variants (ASVs). Compartment was the dominant force structuring both prokaryotic and fungal communities (PERMANOVA p < 0.01), with alpha diversity decreasing along the bulk soil-rhizosphere-roots-leaves continuum and the leaf compartment being the most distinct and least diverse. Compartment-specific biomarkers included Acidobacteriota and Saitozyma in soil, Bradyrhizobium and Pseudomonas in roots, and Methylocella and Pseudocladosporium in leaves. Predicted functional potential inferred with PICRUSt2 closely tracked the taxonomic gradient, with compartment explaining 85.87% of the variance in KEGG composition. Additionally, we found that OxG hybrid exhibited recurrent enrichment of Acidobacteriota and Ascomycota, along with more fragmented co-occurrence networks than E. guineensis. However, palm species effects were consistently weaker than compartment effects and varied with locality.