Protist Diversity in La Union, Philippines Revealed by Metabarcoding: Ecosystem‐ and Database‐Dependent Lineage Patterns

ABSTRACT Protists are widely distributed, single‐celled eukaryotes whose hidden diversity has increasingly been revealed through molecular techniques. Despite this progress, global studies remain uneven, with Southeast Asia, particularly the Philippines, understudied. This research investigates protist community diversity, including Amoebozoa as a focal subgroup, across freshwater and marine ecosystems using a metabarcoding approach supported by two reference databases. Environmental DNA was collected from sites, and the V4 region of the 18S rRNA gene was amplified and sequenced using Oxford Nanopore Technologies. Results showed that the Telonemia, Stramenopiles, Alveolata, and Rhizaria (TSAR) supergroup consistently dominated protist communities across ecosystems. Richness curves approached saturation, with freshwater habitats exhibiting broader family level diversity and generally higher taxonomic richness. While community composition differed between freshwater and marine environments, multivariate analyses revealed partial overlap, with patterns influenced by the choice of reference database. Marine communities were more compositionally heterogeneous, whereas Amoebozoa displayed relatively stable but low abundance distributions. Although database selection strongly affected inferred taxonomic composition and reduced overlap between datasets, the ecological gradient between ecosystems remained consistent. These findings demonstrate that metabarcoding captures broad ecological patterns in protist biogeography while highlighting the need for improved reference databases and further exploration of microbial diversity in the Philippines.