Introduction： Climate change is increasingly transforming aquatic ecosystems. The increasing utilization of coastal waters for mariculture and coastal development, decadal anthropogenic nutrient input loading, and a warming acidifying ocean are major forces associated with trends of increasing occurrence and cell densities of phytoplankton and micro- eukaryotic species over the past decades (Gobler, 2020; Hablützel et al., 2021). Phytoplankton are not only important primary producers but also drivers of biogeochemical and nutrient cycling services; they are ecosystem services, but also public health safety in the context of global climate change and anthropogenic stressors. Specifically, harmful algal blooms (HABs) refer to the massive occurrence of algae species which are either toxin and/or high-biomass producers, of which their rapid proliferation can result in severe envi- ronmental consequences. These include but are not limited to hypoxia, direct fish kills, and seafood contamination by phytotoxin such as ciguatoxin (Wang et al., 2018; Yan et al., 2020), leading to acute sick- ness and chronic poisoning in human consumers (Tan et al., 2023). The frequent occurrence of HABs in coastal waters also has a detrimental effect on the ecosystems and economies (Jacobs-Palmer et al., 2021). HABs and associated massive fish mortality events are particularly costly in developing countries with limited monitoring infrastructure and high reliance of coastal production and industries, devastating many livelihoods. The National Oceanic and Atmospheric Administration estimated an annual loss of $82 million in the United States due to HABs (NOAA, 2024). Furthermore, harmful algae species and associated HABs are not only increasingly prevalent in aquatic environments reportedly due to anthropogenic activities and eutrophication, increased rainfall, and warming temperatures (Zhou et al., 2022), but their geographical range of impact have also expanded polewards since the 1980s (Gobler, 2020). Facilitated by more anthropogenic factors such as globalization, maritime activities, and climate change, migrating harmful algae and HABs are new environmental exposures bound to pose new risks to now a wider range of unsuspecting aquatic ecosystems that humans inhabit nearby and utilize resources from. This necessitates improved high- throughput phytoplankton and harmful algae monitoring efforts on a global scale to prevent damage to food security, production, economies and public health. Study that can better our understanding of HAB- inducing agents and their underlying mechanisms, alongside effective measures to monitor, predict, and prevent harmful algae and bloom occurrences are therefore direly sought after within corresponding regional and global contexts (Hallegraeff et al., 2021). Currently, many state-of-the-art, high-throughput biomonitoring platforms are improving baseline information through visual identifi- cation approaches for real-time plankton detection. However, they require high investment to implement and may not be viable for many monitoring programs to incorporate, while manual identifications are often labor and time-intensive, and incomprehensive to reveal signifi- cant community-level insights. In this light, molecular approaches employing increasingly accessible sequencing tools for broad range surveillance, such as environmental DNA biomonitoring, can facilitate a deeper understanding of phytoplankton response to critical natural environmental changes and human impacts (Ugya et al., 2025). How- ever, sequencing-based surveillance that furthers harmful algae moni- toring applications has seen relatively few research. To this end, the effectiveness of such monitoring not only relies on available genome references but also updated knowledge and criteria for downstream functional screening to enable a unified and globally comparable iden- tification and interpretation of phytoplankton and harmful algae sta- tuses at the users' end. Currently, relatively few databases comprehensively summarize the expanding collection of harmful algae for practical applications. Foun- dational databases, such as Lundholm et al. (2009), have significantly contributed to compiling toxin-producing harmful algae, while other efforts documenting blooming and high-biomass producing algae tend be regionally focused, exemplified by decade-long monitoring programs in Chinese waters (Chen et al., 2023). This underscores the critical need for a synthetic, global knowledge platform that consolidates information on potent harmful algae worldwide. Moreover, the diversity of phyto- plankton and the spectrum of ‘harmful algae’ requiring monitoring are continually expanding alongside frequently taxonomic revisions. In parallel with the growth of genomic reference databases, ongoing curation and streamlining of functional databases are essential to sup- port effective screening and monitoring applications. This will be highly beneficial to offer a more unified and standardizable approach to foundational to aquatic food webs and often utilized as health indicators of aquatic ecosystems (Hutchins and Tagliabue, 2024). The fundamental environmental mechanisms that govern and support a healthy phyto- plankton community have been frequently studied. In addition to gen- eral temperature gradients and seasonality, phytoplankton dynamics can also be shifted by nitrate enrichment (Cheung et al., 2021) and tidal currents (Lo et al., 2025). However, the dynamic species co-interactions and taxon-specific responses within the phytoplankton community context are still limitedly studied despite its underpinning importances. This has further implications for not only trophodynamics and systematic coastal phytoplankton monitoring to take advantage of bio- informatics with potentially higher taxonomic resolution results, sup- plementing the established traditional visual surveys and monitoring platforms targeting plankton (Jacobs-Palmer et al., 2021; Manaff et al., 2023). In this study, we compiled an updated harmful algae database as a shared knowledge platform to pave way for effective functional screening applicable to aquatic systems. We further employed molecular approaches to investigate phytoplankton and harmful algae distribution and occurrence mechanisms in the context of a typical urbanized coastal ecosystem historically suffering from frequent red tides. At the time of our study, notable blooms in the study zone of Hong Kong were reportedly caused by species including Guinardia delicatula, Polykrikos geminatus, Karenia longicanalis, Takayama tuberculata, and Noctiluca scintillans. Subsequently, we screened DNA metabarcoding data from sampled seawater to investigate its role as an informative complement to the traditional visual red tide monitoring efforts established. The ob- jectives of the study are to (1) characterize spatial patterns of phyto- plankton communities as the important functional component of the ecosystem and their response to environmental conditions and anthro- pogenic impact; (2) conduct screening with the updated harmful algae database, utilizing high-throughput strengths of DNA metabarcoding to reveal potentially hidden assemblies of harmful algae; and (3) review and assess the potent overlapping in detection between visual and mo- lecular methods and the effectiveness of eDNA metabarcoding as a supplementary monitoring and risk detection tool. We anticipate that with refined reference databases, molecular-based harmful algae screening and monitoring will not only provide valuable baseline with better coverage of exotic and rare hidden species but also provide important community patterns of harmful algae distribution in relation to water quality and human influence, benefitting future efforts to un- derstand, manage, and prevent bloom outbreaks and maintain a sus- tainable coastal ecosystem.
