Near real-time long-read eDNA sequencing reveals harmful algal bloom dynamics in the Indian River Lagoon

Harmful algal blooms (HABs) are increasingly impacting estuarine ecosystems, yet current microbial surveillance methods often focus on prokaryotic 16S rRNA profiles and overlook eukaryotic bloom-forming species. Here, we applied Oxford Nanopore Technologies (ONT) MinION long-read sequencing targeting the 18S rRNA gene to characterize spatial and seasonal patterns of eukaryotic microbial communities in the Indian River Lagoon (IRL), a biologically diverse 251 km long estuary along Florida’s Atlantic coast. Water samples were collected across 20 sites during wet and dry seasons spanning subtropical and temperate subregions. Sequencing yielded high-resolution community profiles, detecting over 200 unique species and highlighting clear differences in community composition by season, region, and environmental gradients including salinity, temperature, and nutrient ratios. Eleven harmful algal bloom taxa were detected, including Aureoumbra lagunensis , Karlodinium veneficum , and Pyrodinium bahamense , with A. lagunensis reaching >50% relative abundance in some sites. Our results show that long-read sequencing of the 18S rRNA gene can capture eukaryotic diversity and resolve potentially harmful taxa. This approach offers a promising tool for rapid, field-deployable, detection of HAB species and improves our understanding of how environmental drivers shape bloom risk across complex estuarine systems like the IRL.