Root-associated bacterial and fungal communities of the endangered páramo bromeliad Puya goudotiana

Páramo, a tropical high-altitude ecosystem, is threatened by climate change and land-use change. This ecosystem hosts unique biodiversity like the endangered bromeliad Puya goudotiana. While root-associated microbiomes are essential for plant survival and stress tolerance, the microbial communities associated with this species remain uncharacterized. Oxford Nanopore amplicon sequencing was used on root endosphere and bulk soil samples of P. goudotiana, targeting the 16S rRNA gene to evaluate bacterial communities, and the 18S rRNA gene as an exploratory marker for fungal communities. We assessed the taxonomic composition, diversity, functional profiles and co-occurrence networks. Microbial communities were highly differentiated by sample type, with roots exhibiting lower alpha diversity than bulk soil. The root microbiome showed higher prevalence of acidophilic taxa such as Granulicella and Acidipila and symbionts like Bradyrhizobium, whereas bulk soils were dominated by typical páramo taxa, including Candidatus Solibacter, Candidatus Koribacter and Bryobacter. Both bulk soil and roots were characterized by a high abundance of saprotrophic fungi (e.g., Psilocybe) and potential pathogens such as Fusarium, Botrytis and Puccinia. Functional predictions indicated higher prevalence of chemoheterotrophic functions in the roots, while nitrogen and sulfur cycling functions were enriched in bulk soil. Notably, and contrary to prior expectations, co-occurrence networks were more complex in the root endosphere than in bulk soil, suggesting that rhizosphere filtering promotes structured microbial assemblages despite reducing overall diversity. These findings provide a first microbial baseline for P. goudotiana and open new perspectives for understanding plant-microbe interactions and enhancing páramo vegetation resilience under climate change.