PIF2025 - Unveiling the Unknown Eukaryotic Microbial Biosphere: Targeted Metagenomics and Functional Atlases in Plant-Soil Ecosystems - (PID2024-162390NB-I00)

Project Summary: This PhD thesis project focuses on exploring the "unknown microbial biosphere" (UMB) by developing high-resolution genomic tools for uncultivated eukaryotes and creating global reference resources. Bridging computational biology and microbial ecology, the project aims to overcome the resolution limits of standard metabarcoding to map the rare biosphere. Objectives and Work Plan: Development of Targeted Metagenomics (WP1):Designing and validating a multi-locus hybridisation capture panel by selecting conserved phylogenetic markers to detect low-abundance eukaryotic DNA, and creating a pipeline for phylogenomic placement of novel taxa. Creation of a Gene Family Atlas (WP2): Developing of a unified Microbial Gene Family Atlas by integrating global genomic and metagenomic data, clustering sequences into orthologous groups (OGs), and performing large-scale functional and ecological annotation of unknown genes. Ecological Monitoring at Real Jardín Botánico (RJB) (WP4): Applying these tools in a longitudinal study at the RJB to investigate the recruitment of specific host-microbiomes and the seasonal dynamics of the eukaryotic rare biosphere.