Eukaryotic Microalgae Communities from Tropical Karstic Freshwater Lagoons in an Anthropic Disturbance Gradient Microscopic and Metagenomic Analysis

The Yucatan aquifer sustains the people living in the Mayan forest and its associated fauna. Human activities threaten water quality and the environmental services associated with it. To assess the eukaryotic microalgae community structure as a bioindicator of water quality, we employed a combined approach of microscopic and shotgun metagenomics to identify specific genera associated with shifts in physicochemical parameters in three permanent lagoons located in Campeche, Mexico. We could identify highly complex and diverse communities independent of human activity intensity, harboring an average of 362 genera at each lagoon. Of those, 85 were affected by alkalinity, carbonates, water hardness, and cyanuric acid levels. Some genera, like <i>Nannochloropsis</i> and <i>Thraustotheca</i>, showed significant negative correlations with lead concentration. The functional annotation of genes revealed these communities' highly diverse metabolic capabilities and the pending work for extensive genomic characterization of rare clades.