From Soil to Leaves: Decoding the Microbiome of Oil Palm in Colombia.
6 affiliations
- 1Colombian Oil Palm Research Center - Cenipalma, Oil Palm Agronomy Research Program, Bogotá, 11121, Colombia. [email protected].
- 2Graduate Program in Agricultural and Livestock Microbiology, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
- 3Department of Agricultural, Livestock and Environmental Biotechnology, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
- 4Colombian Oil Palm Research Center - Cenipalma, Oil Palm Biology and Breeding Research Program, Bogotá, 11121, Colombia.
- 5Aquaculture Center of UNESP, São Paulo State University (UNESP), SP, Jaboticabal, Brazil.
- 6Colombian Oil Palm Research Center - Cenipalma, Oil Palm Agronomy Research Program, Bogotá, 11121, Colombia.
Abstract
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.
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BibTeX
@article{teheransierra2026from,
title = {{From Soil to Leaves: Decoding the Microbiome of Oil Palm in Colombia.}},
author = {Luis Guillermo Teheran-Sierra and Lucas Amoroso Lopes de Carvalho and Fernan Santiago Mejia-Alvarado and Catalina Chaves-Sierra and Daniel Guariz Pinheiro and Nolver Atanacio Arias Arias},
journal = {Microbial ecology},
year = {2026},
month = aug,
doi = {10.1007/s00248-026-02844-w},
url = {https://europepmc.org/article/MED/42957855},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - From Soil to Leaves: Decoding the Microbiome of Oil Palm in Colombia.
AU - Luis Guillermo Teheran-Sierra
AU - Lucas Amoroso Lopes de Carvalho
AU - Fernan Santiago Mejia-Alvarado
AU - Catalina Chaves-Sierra
AU - Daniel Guariz Pinheiro
AU - Nolver Atanacio Arias Arias
PY - 2026
DA - 2026/08/03
JO - Microbial ecology
DO - 10.1007/s00248-026-02844-w
UR - https://europepmc.org/article/MED/42957855
AB - 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.
SN - 0095-3628
SN - 1432-184X
ER -