Microeukaryotic Diversity and Habitat Structuring in a Desiccating Alkaline Maar Lake (Central Mexico)

Microeukaryotes are important components of microbial food webs in saline and alkaline lakes, yet their diversity and distribution across distinct microhabitats remain poorly understood. We characterized microeukaryotic communities associated with microbialites, microbial mats, hypersaline waters, and sediments in the desiccating maar lake Rincón de Parangueo (central Mexico) using 18S rRNA gene amplicon sequencing. After quality filtering and rarefaction, 417 amplicon sequence variants (ASVs) belonging to 17 eukaryotic phyla were identified. Community composition differed among microhabitats, with mats harboring the highest number of exclusive genera and water containing the fewest. No genus was shared across all four microhabitats. The greatest taxonomic overlap occurred between mats and water, suggesting ecological connectivity between benthic and planktonic environments. Ordination analyses and environmental data indicated strong habitat filtering associated primarily with salinity and conductivity. Co-occurrence network analysis revealed a highly modular community structure (Q = 0.789), with distinct habitat-associated modules and limited connectivity among them. Chlorophyta dominated assemblages, particularly in microbialites and water, whereas Bacillariophyta, Amoebozoa, Discoba, Aphelidiomycota, and Rotifera were present. Recurrent taxa such as Dunaliella and Picocystis occupied central network positions. These results demonstrate strong microhabitat-scale structuring and highlight the importance of fine-scale environmental heterogeneity in shaping diversity within alkaline maar lakes.