This study examines diatom assemblages in the Matsu Archipelago, influenced by Minjiang River runoff, and focuses on harmful algal blooms (HABs) from August 2021 to July 2022. Utilizing 18S rRNA gene metabarcoding and microscopic analysis, we observed a significant diatom bloom during early summer runoff, peaking at 5×10⁵ cells L^-1. The research highlights the diatom bloom and reveals dynamic community changes during the runoff season, with dominant genera including: Pseudo-nitzschia, Chaetoceros, and Skeletonema. Skeletonema abundance correlated with NO₃ levels, Chaetoceros had a slight PO₄ affinity, and Pseudo-nitzschia showed a negative correlation with Skeletonema. Notably, high concentrations of potential toxin-producing Pseudo-nitzschia species like P. multistriata, P. pungens, and an autumn peak of P. cuspidata were observed, preferring high light and pH conditions. These findings highlight the intricate relationship between diatom dynamics and environmental factors, offering essential insights for managing HABs, especially Pseudo-nitzschia species, amidst environmental changes.

18S rRNA gene metabarcoding, terrestrial runoff, microscopic analysis, time-series variation

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