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<p>The Hudson River Estuary (HRE) is a tidal freshwater-to-saline system and is heavily influenced by anthropogenic activity associated with its proximity to a large metropolitan area, making high-resolution plankton monitoring a valuable tool for assessing and managing estuarine resilience under changing environmental conditions. This study used a combination of light microscopy and gene sequencing of 18&#xa0;S and 23&#xa0;S 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 18&#xa0;S sequencing data compared to microscopy counts or 23&#xa0;S sequencing data. Across samples, 18&#xa0;S rRNA recovered higher diversity values and captured key taxa in agreement with microscopy, suggesting that 18&#xa0;S 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.</p>

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

  • 期刊论文

  • 发表日期：

    2026年3月19日

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  • Gabrielle L. Corradino,
  • Hannah J. Laufer,
  • Megan R. Rivera,
  • Thia J. Ostrander-Lê,
  • Margaret R. Ireland,
  • Savannah R. Eklund

摘要

The Hudson River Estuary (HRE) is a tidal freshwater-to-saline system and is heavily influenced by anthropogenic activity associated with its proximity to a large metropolitan area, making high-resolution plankton monitoring a valuable tool for assessing and managing estuarine resilience under changing environmental conditions. This study used a combination of light microscopy and gene sequencing of 18 S and 23 S 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 18 S sequencing data compared to microscopy counts or 23 S sequencing data. Across samples, 18 S rRNA recovered higher diversity values and captured key taxa in agreement with microscopy, suggesting that 18 S 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.