Evaluating Plankton Assemblages in the Hudson River: Microscopy and Molecular Methods

The Hudson River Estuary (HRE) is a tidal freshwater-to-saline system and is one of the most complex estuaries in the northeastern United States. Due to its proximity to a large metropolitan area, the HRE is heavily impacted by anthropogenic stressors which intensify over time, stressing the need for high-resolution plankton monitoring as a tool managing estuarine resilience in a changing environment. This study used a combination of microscopy and gene sequencing of 18S and 23S rRNA regions to explore the plankton community of the HRE over a four-week period. Across all three methods, a total of 27 phytoplankton genera and 15 zooplankton genera were identified in the samples. The Simpson Index and the Shannon–Weaver Index were consistently higher for the 18S sequencing data compared to microscopy counts or 23S sequencing data. Across samples, 18S rRNA recovered higher diversity values and captured key taxa in agreement with microscopy, suggesting that 18S is the most effective molecular marker for broad eukaryotic plankton monitoring in the HRE. There was substantial variation in community composition, which reflects the dynamic nature of the HRE, where short-term shifts in freshwater discharge, nutrient input, and turbidity may influence local plankton structure in narrow temporal windows. Continued paired sampling will be critical for detecting long-term ecological trends, guiding management strategies, and advancing our understanding of estuarine health in urbanized environments.