Early detection of harmful algal blooms remains challenging due to the low abundance of target microalgae and the limited sensitivity of conventional detection methods. Here, we present a high-throughput microfluidic cell concentrator that enables rapid and efficient pre-concentration of microalgae from large sample volumes. The system integrates a multiplexed inertial microfluidic device with a recirculation system, allowing repeated concentration cycles without manual sample transfer. Using the concentration system, we demonstrated the concentration of suspensions of a normal microalga (C. vulgaris) and a harmful cyanobacterium (M. aeruginosa). Starting from an initial density of 1 × 105 cells/mL and a volume of 1 L, three concentration cycles increased the cell density to the 107 cells/mL range within 90 min. The increased cell density resulted in more than a 100-fold enhancement in fluorescence signal measured using a plate reader. Excitation-emission matrix analysis further demonstrated that pre-concentration significantly improved species-specific fluorescence signatures. These results indicate that the proposed microfluidic concentrator enables rapid, scalable, and effective enrichment of microalgae and offers a promising platform for early detection and monitoring of harmful algal blooms.
One of the major subfields of chemical ecology is the study of toxins and how they mediate interactions between organisms. Toxins produced by harmful algae (phycotoxins) impact a wide variety of organisms connected to the marine food web. Significant research efforts have thus aimed to identify the ecological and evolutionary drivers behind harmful algal blooms (HABs) to facilitate their forecasting, mitigation, and management. Nutrient availability is a key factor controlling growth and toxin production. Additionally, recent evidence has shown that harmful algae can sense the presence of zooplankton grazers, primarily copepods, and respond by dramatically increasing toxin production. Phycotoxin production is consequently controlled by a combination of bottom-up and top-down drivers, but the relative importance of the two is not understood. We therefore conducted a meta-analysis of 113 control-treatment contrasts from 37 peer-reviewed experimental studies, comparing the effects of relative nitrogen enrichment (defined here as an increased nitrogen: phosphorus ratio relative to control) and elevated grazing risk (exposure to zooplankton grazers or their chemical cues) on phycotoxin induction. We focused on the two most studied marine HAB-forming genera, Alexandrium dinoflagellates and Pseudo-nitzschia diatoms. We show that phycotoxins are induced in response to both relative nitrogen enrichment and elevated grazing risk. Although both genera responded similarly to relative nitrogen enrichment, Pseudo-nitzschia toxins increased 10 times more than Alexandrium toxins in response to grazers. Grazing risk thus appears to rival, perhaps even supersede, the well-established phycotoxin-inducing effect of relative nitrogen enrichment in marine harmful algae. Although this analysis is limited to the two most-studied marine HAB genera, we conclude that future attempts to understand the evolution and variable production of phycotoxins require integration of bottom-up nutrient availability and top-down selective pressures to elucidate phycotoxin dynamics in marine HAB-forming species.
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Microalgae hold the potential to supply sustainable food, fuel, plastics, and chemicals at commercial scales. Cultivating microalgae at extreme pH (>10) and high alkalinity provides multiple benefits, including (1) reducing the risk of contamination by undesired organisms and (2) enabling direct air capture of CO2, which expands the land area suitable for algae farming compared to using CO2 point sources alone. However, we currently have a limited understanding of which algal taxa can grow under these conditions. Therefore, we conducted a high-throughput screening of 49 freshwater microalgae strains, comprising 40 species, for their ability to grow in moderate (pH 8.5, 25 mM alkalinity), high (pH 10, 75 mM alkalinity), and extreme (pH 10, 150 mM alkalinity) cultivation environments. Our results show that moderate alkalinity tends to significantly increase algae growth (including potentially harmful strains). However, higher levels inhibited all but a small subset of green algae and cyanobacteria. Effects of salinity and alkalinity differed, indicating that they are broadly decoupled. Our results identify new industrially relevant alkaline-tolerant strains, show that algae isolated from "normal" ecosystems can be extremophilic, and suggest that future bioprospecting efforts for alkaline-tolerant algae adapted to local climatic conditions could yield additional productivity gains for the algae industry.
Accurate species-level identification is essential for tracing toxin sources, understanding bloom dynamics, and improving monitoring. However, short-read metabarcoding often lacks resolution for closely related harmful microalgae. We applied PacBio HiFi long-read metabarcoding of ITS1-5.8S-ITS2 and partial LSU (D1-D2) rDNA to 600 eDNA samples from the China Sea, spanning ∼40° of latitude (2019-2024). Using a reproducible QIIME 2 workflow, a curated Amphidomataceae reference set, and species-resolution criteria (p-distance= 0.040 in Azadinium; 0.045 in Amphidoma), we resolved 44 Amphidomataceae lineages (17 named species, 27 putative new taxa) and mapped their fine-scale biogeography. The four azaspiracids (AZAs) producers exhibited distinct distributions: Az. dexteroporum occurred along warm saline shelves of the East and South China seas; Am. languida was restricted to temperate nearshore areas in the Yellow Sea and Yangtze estuary; Az. poporum was observed mainly nearshore with ribotype segregation (B and C widespread); and Az. spinosum was widespread in the East and South China seas, dominated by ribotype A and B. Niche metrics and clustering of sea-surface temperature (SST), salinity, and trophic index (TRIX) defined three ecological groups consistent with MaxEnt habitat suitability. Likely AZAs sources are Am. languida and Az. poporum in the Bohai/Yellow seas, and Az. dexteroporum, Az. poporum, and Az. spinosum in the East/South China seas. HiFi long-read metabarcoding resolves hidden diversity, strengthens risk assessment, and provides a reproducible, scalable framework for global species- and subspecies-level mapping of harmful microalgae.
The frequent occurrence of harmful algal blooms (HAB) poses severe threats to aquatic ecosystems, aquaculture industries and human health. Recently, algicidal bacteria have emerged as a promising biocontrol strategy. However, the precise mechanisms underlying their algicidal effects remain poorly understood, limiting their practical application in environmental management. This review systematically summarises the interactions between bacteria and algae, as well as the various algicidal modes employed by bacteria, with a particular focus on the mechanisms driving bacterial algicidal activity. Key bacterial behaviours such as chemotaxis, adhesion, quorum sensing and the release of extracellular vesicles have been identified as critical factors in the algicidal process, among which the role of bacterial extracellular vesicles warrants special attention. Furthermore, we elaborate on the death mechanisms of algal cells upon bacterial attack, including loss of cellular structural integrity, impairment of photosynthetic systems, oxidative stress responses and disruption of calcium ion homeostasis. Notably, advancements in detection technologies have increasingly highlighted the importance of calcium signalling regulation in algal cell death. This review not only elucidates the molecular mechanisms of bacterial algicidal activity, providing a theoretical foundation for the biocontrol of red tides, but also deepens our understanding of bacteria-algae interactions.
Human-driven activities related to diverse industries such as textiles, pharmaceuticals, plastics, leather, and agriculture contribute significantly to the discharge of pollutants into aquatic environments, thereby threatening the ecological balance and posing a risk to living organisms. Over the past few years, algae have been acknowledged as a cost-effective and sustainable resource for the detoxification of harmful pollutants, primarily through mechanisms such as intracellular biodegradation, bioaccumulation, and biosorption. Besides the direct involvement of algae in the removal of pollutants, they can be converted into carbon-rich materials such as hydrochar, biochar, and activated carbon. These materials possess high specific surface areas and different functional groups, which make them quite effective for the adsorption of organic pollutants in wastewater treatment. Algal-derived adsorbents exhibit high adsorption efficiency because of the synergistic effects of various interactions, including electrostatic forces, hydrogen bonding, π-π interactions, and pore filling effects, all of which depend on the engineered surface functional groups and porous structure of algae-derived carbon-rich materials. This review uniquely explores various algal species for the preparation of adsorbents and also examines the modification methods used to convert algae into adsorbents. It examines their effectiveness in the removal of organic contaminants from water systems. Future research needs to bridge the gap between laboratory-scale and real-world applications, especially through pilot-scale studies in real wastewater and comprehensive life-cycle assessments.
Harmful algal blooms (HABs) can be caused by dinoflagellates like Alexandrium minutum, which produces Paralytic Shellfish Poison toxins derived from saxitoxins. The abundance of these toxic algae is shaped not only by abiotic factors, but also by microbial interactions such as parasitism by the alveolate Parvilucifera infectans. These parasites can infect algal cells, inhibit growth, and induce death, thereby contributing to the termination of HABs. Salinity can affect algal physiology and may modulate host-parasite dynamics by altering the parasite's ability to infect and kill HAB-forming algae. Despite their ecological relevance, the interactions between algae and parasites, and the modulation of algal toxins during cell infection at varying salinity, remain poorly understood. Here, we investigated the impact of the parasite P. infectans, a well-recognized model organism that preys on A. minutum under different salinity conditions. We monitored infection success in cultures and recorded metabolome changes during parasite cell invasion using ultra-high-performance liquid chromatography-high-resolution mass spectrometry (UHPLCHRMS). P. infectans tolerated salinity from 20 PSU to 32 PSU and induced the death of whole algal cultures within 3 weeks in laboratory-controlled experiments. Comparative metabolomics revealed that parasite infection decreased the abundance of algal toxins in A. minutum. The parasite infection, rather than salinity, induced significant shifts in the host cell metabolome. Several polar metabolites and osmolytes, such as ectoine, dimethylsulfoniopropionate, glycine betaine, choline, and carnitine, were identified at elevated levels in parasite-infected cells, suggesting potential roles in parasite development and reproduction.
Allelopathy is increasingly recognized as a key driver of species interactions in aquatic ecosystems, yet its ecological scope and functional significance remain insufficiently integrated. This review synthesizes current knowledge on chemically mediated interactions, emphasizing their ecological importance and potential role in mitigating harmful algal blooms (HABs). Growing evidence suggests that allelochemicals may represent environmentally sustainable alternatives to synthetic algicides, while the influence of allelopathy extends far beyond bloom control to encompass complex interactions among vascular plants, algae, cyanobacteria, diatoms, macroalgae, and corals. Aquatic allelopathy remains far less explored than its terrestrial counterpart, revealing substantial knowledge gaps and the need for ecologically realistic research frameworks. Both abiotic factors (e.g., light, temperature, nutrient availability) and biotic interactions strongly modulate allelopathic outcomes, highlighting the context-dependent nature of these processes. Particular attention is given to bloom-forming taxa such as Microcystis aeruginosa and Prymnesium parvum, which serve as model systems for understanding the relationship between toxicity and allelopathy. Evidence from dinoflagellates, diatoms, and other microalgae further underscores the mechanistic diversity of allelopathic interactions. By integrating findings across taxa and environments, this review advances a comparative framework for interpreting chemically mediated interactions in aquatic systems and identifies key priorities for future research. Collectively, the evidence positions allelopathy as both a fundamental ecological process and a promising avenue for the development of sustainable HAB management strategies.
Offensive odor issues caused by harmful algae are a long-term challenge impacting freshwater and water supply systems worldwide, while the key odor-causing compounds and algae responsible for these issues are not fully understood. A multifactorial water quality dataset, including information on odor characteristics, algae species, natural organic matter composition, and basic water quality (∼20000 measurements), was generated in Huangpu River watershed over a year to identify the major odorants and algal sources for odor issues caused by harmful algae. By integrating analytical tools, three predominant odor profiles were systematically characterized: (i) earthy/musty odor associated with 2-methylisoborneol (n.d.-74.1 ng/L); (ii) swampy/septic odor mainly linked to thioethers (n.d.-355 ng/L), and (iii) fishy odor from heptanal and dimethyl sulfide. Correlation network showed Cyanophyta's distinct spatiotemporal distribution compared to Bacillariophyta, Euglenophyta, and Chlorophyta, and they are self-generated sources of newly produced organic matter. Data analysis by Structural Equation Modeling and Principal Component Analysis delineated the odorant-algae associations: (1) Oscillatoria sp. and Pseudanabaena sp. as potential 2-methylisoborneol producers; (2) Cryptomonas sp. positively correlated with dimethyl sulfide concentrations, which might also be contributed by biological methylation of SO42-; (3) Phytoplankton belonging to Chlorophyta, Bacillariophyta, and Cryptophyta associated with heptanal synthesis. These algae were mainly from the input of Taihu Lake or the tributary at sampling point S13. The study first employs multiple data analytical tools to provide an operational paradigm for identifying the collective odor contributors and major odor-producing algae, which will benefit the management of algal-derived odor problems in drinking water.
Barley straw bales are commonly used to control cyanobacterial growth in lakes, but the method is time-consuming, labor-intensive, and its effectiveness requires deployment of bales prior to bloom formation. This study investigates brewer's spent grain (BSG), a byproduct of the brewing process, as an alternative source of allelopathic chemicals shown to negatively impact toxic microalgae. Water extracts of BSG, barley straw, and Sargassum natans were tested for their ability to inhibit the growth of toxin-producing (Microcystis aeruginosa and Karenia brevis) as well as non-toxin-producing (Tetradesmus obliquus and Phaeodactylum tricornutum) algal species. BSG extracts at concentrations above 250 mg/L effectively inhibited the growth of both freshwater and marine toxin-producing species (M. aeruginosa and K. brevis), while exhibiting no significant effect on the diatom and chlorophyte species tested (T. obliquus and P. tricornutum). Additional experiments using antibiotics with K. brevis suggest that growth inhibition may be mediated by changes in the bacterial community, though the specific mechanism of M. aeruginosa death remains unresolved. A microcosm experiment further evaluated the impact of BSG extract on a natural bloom of cyanobacteria (Raphidiopsis raciborskii) in lake water. Application of 250 mg/L BSG extract to natural lake water shifted the community composition from cyanobacteria to chlorophyte dominance. These findings highlight the potential use for a brewery's waste product as a cost-effective tool for managing harmful algal blooms. However, the high concentrations required, excess nutrient content in BSG, and impact on bacterial communities indicate limitations for large-scale application.
Algal blooms, carbon emission hotspots in aquatic ecosystems, typically are accompanied by high microplastics (MPs) levels. However, the role of MPs in algae-driven carbon cycling remains elusive. Here, Microcystis aeruginosa(M. aeruginosa) was used to investigate the responses of CO2 and CH4 emissions to MPs during cyanobacterial harmful algal blooms (cHABs, a predominant algal bloom type), integrating physicochemical analysis and high-resolution chemical and microbial approaches to elucidate the role of MPs in carbon emissions throughout growth-decline phases of algal blooms. The results exhibited three phases. In phase I, MPs facilitated M. aeruginosa growth, thereby stimulating aerobic CH4 production through photosynthesis-coupled reactive oxygen species mechanisms. As aggregate settling dynamics varied with heteroaggregation, the survival patterns of M. aeruginosa changed, reducing CO2 and CH4 production through decreasing carbon substrates in phase II. However, M. aeruginosa decay, accelerated by MPs, not only enhanced anaerobic organic matter utilization in water, but also elevated the nominal oxidation state of carbon in sediment, promoting hydrogenation and altering the balance between methanogenesis and methanotrophy, subsequently increasing CO2 and CH4 production in phase III. Ultimately, MPs exacerbated cumulative carbon emissions of cHABs, suggesting MPs as facilitators behind algal blooms being foci of carbon emissions.
Urea inputs to aquatic ecosystems have increased rapidly due to intensified fertilizer use, wastewater discharge, and aquaculture expansion, altering nitrogen composition and accelerating eutrophication. However, the physiological, ecological, and evolutionary mechanisms linking urea enrichment to harmful algal blooms (HABs) remain incompletely synthesized. Here, we integrate a bibliometric survey of 818 papers from 2003 to 2024 with a quantitative analysis of 32 physiological studies and a comparative genomic assessment of urea metabolic pathways. Urea concentrations range from the nanomolar scale in open oceans to >20 μM in eutrophic rivers and estuaries-levels sufficient to stimulate urea-preferring taxa. Many HAB-forming dinoflagellates and cyanobacteria exhibit enhanced growth, photosynthetic efficiency, and in some cases, increased toxin production when supplied with urea. Comparative pathway analysis shows that bloom-forming taxa predominantly utilize the energy-efficient urease pathway, whereas non-blooming taxa more commonly rely on the ATP-consuming urea amidolyase (UAL) pathway. Several bloom-forming species are capable of using both pathways, suggesting metabolic flexibility under fluctuating nitrogen regimes. These findings support the hypothesis that anthropogenic urea enrichment acts as a selective pressure favoring taxa capable of rapid and energetically economical nitrogen assimilation. We identify key research gaps-including evolutionary origins of UAL, regulatory divergence between pathways, and interactions with warming and stratification-and provide recommendations for monitoring and management. This synthesis highlights urea as a critical yet underappreciated component of global nitrogen pollution and HAB dynamics.
The development of green and high-efficiency flocculants for controlling harmful algal blooms (HABs) is currently a critical research focus in the field of water treatment. Plant tannins have garnered significant attention as a sustainable biomass resource; however, their application in high-salinity environments, such as seawater, remains relatively underexplored. In this study, four plant tannins were systematically investigated to select black wattle tannin (BWT) as the optimal precursor due to its superior comprehensive performance. A formaldehyde-free alkaline amination modification route was established, with synthesis parameters optimized via response surface methodology (RSM). The results indicated that the modified tannin prepared under optimal conditions (25 g/L BWT, ammonia-to-tannin molar ratio of 5.656, aerobic conditions, 20°C, and stirring at 100 rpm for 4 h) achieved a stable removal efficiency of over 85% for Heterosigma akashiwo. Furthermore, this modification effectively overcame the application bottlenecks of high residual color and turbidity associated with natural tannin treatment. Mechanism analysis revealed that the performance enhancement was attributed to the synergistic effect of oxidation, polymerization, and amination reactions, resulting in the formation of a high-efficiency flocculant with enhanced bridging capabilities.
The Zhe-Min coastal region of China, a principal fisheries area, frequently experiences harmful algal blooms (HABs) driven by the nutrient-rich southward current of the Zhe-Min Coastal Current (ZMCC). In spring 2025, however, routine monitoring (since 2001) recorded an unprecedented absence of large-scale HABs. This study investigates the dynamical mechanisms underpinning this suppression. Our analysis indicates that a persistent, record-breaking anomalous northeastward sea surface current inhibited southward nutrient transport to the Fuzhou-Wenzhou coast. Dynamical decomposition shows that this anomalous current resulted from distinct regional processes: off Fuzhou it manifested as a barotropic response to an anomalous cross-shelf sea-level gradient associated with an extremely weak northeasterly monsoon, while off Wenzhou it was predominantly baroclinic, driven by cross-shelf temperature gradients linked to frequent marine heatwaves. The observed thermal extremes are largely attributable to the record-breaking northward shift of the subtropical high-pressure system during the spring of 2025. Moreover, the interaction between a coastal marine cold spell and offshore heatwaves in March promoted cross-shelf transport that exported coastal nutrients offshore. These findings indicate that climate-related shifts-notably weakened monsoonal forcing and increased frequency of extreme thermal events-can act synergistically to form a compound hazard chain that substantially alters coastal physical-biological coupling, however, in this instance, suppressed large-scale HABs outbreak. Future research should pay more attention to the impacts generated by the coupling processes among such extreme events.
This study investigated the bioremediation effects of Ulva lactuca (U. lactuca) on aquaculture pollution in integrated multi-trophic aquaculture (IMTA) systems, with a focus on environmental quality improvement, microbial community dynamics, harmful pathogens, and ARGs mitigation. We performed a comparative analysis of key environmental factors and harmful pathogens in IMTA ponds with U. lactuca, using algae-free ponds as controls. Additionally, 16S rRNA sequencing was employed to analyze water and sediment microbial communities, and quantitative real-time PCR (qPCR) to quantify the abundance of 12 common aquaculture ARGs. The results showed U. lactuca markedly improved water and sediment environmental indicators in the IMTA system, elevating dissolved oxygen (DO) and pH while reducing total nitrogen (TN)/total phosphorus (TP). Microbial analysis revealed reduced harmful bacteria (e.g., Vibrio) in U. lactuca ponds; U. lactuca enhanced microbial diversity and richness in water and sediment via photosynthetic oxygen release and pH regulation, creating a high-DO, alkaline microenvironment that inhibits facultative anaerobic pathogens and promotes pollutant-degrading microbes. Water Bacteroidetes/Firmicutes and sediment Bacteroidetes/Chloroflexi were enriched, and U. lactuca ponds had significantly lower ARG abundances (total reduction up to 34.11%). Network analysis indicated U. lactuca-mediated ARG removal was driven by microbial and environmental shifts. This work verifies U. lactuca's potential to reduce harmful environmental indicators, pathogens and ARGs in IMTA systems, establishes a more systematic framework for elucidating its ecological functions in IMTA, and provides a scientific basis for optimizing IMTA design and enhancing environmental sustainability.
Harmful algal blooms have occurred more frequently in recent decades and threaten aquaculture, tourism and human health. As a promising control method, most studies on allelopathic mechanisms have focused on the physiological effects on harmful algae. This study employed a multiomics approach to investigate the allelopathic response of the dinoflagellate Scrippsiella acuminata to the allelochemical protocatechuic acid, a phenolic compound known for its inhibitory effects on algal growth. Using transcriptomic, proteomic, and metabolomic analyses, we identified significant changes in gene expression (5247 upregulated and 81 downregulated), protein expression (56 upregulated and 49 downregulated), and metabolite profiles (320 upregulated and 168 downregulated) in response to allelochemical stress. Transcriptomic data revealed an upregulation of genes associated with antioxidant systems and energy metabolism, suggesting a potential antioxidant response to protocatechuic acid exposure. Proteomic analysis highlighted the impact on photosynthesis, energy metabolism, and genetic information processing, with a particular emphasis on the modulation of lipid and carbohydrate metabolism to adapt to stress. Metabolomic profiling corroborated these findings, demonstrating shifts in lipid and amino acid metabolism indicative of an adaptive strategy for energy storage and maintenance of cellular homeostasis under allelochemical stress. Notably, alterations in photosynthesis-related proteins and metabolites indicated a direct effect of protocatechuic acid on the photosynthetic machinery, potentially impairing algal growth and energy production. In conclusion, our multiomics analysis provides a comprehensive view of the complex response of S. acuminata to allelochemical stress, revealing the intricate interplay among genetic, proteomic, and metabolic adjustments. These insights contribute to the understanding of allelopathic interactions and offer potential avenues for the development of novel strategies to manage harmful algal blooms.
Chlorophyll a is an important pigment used by algae to absorb solar energy for photosynthesis. Because chlorophyll a is used by all algae (including cyanobacteria) for photosynthesis, it is often measured as an index of algal abundance. Although chlorophyll a is an imperfect representation of algal abundance, other methods for quantifying algal abundance are time consuming, expensive, and still imperfect. Chlorophyll a can be quantified using a probe that can be deployed for weeks or months at a time, generating high frequency chlorophyll a data alongside other water quality data collected with deployed sensors. These other water quality metrics include measurements of several variables that could represent hypothesized drivers of variation in algae abundance. Here, we used water quality and chlorophyll a data compiled for the purpose of predicting harmful algal blooms in the Illinois River to identify the strength of relationships between chlorophyll a concentration in the water column and other water quality variables that may have a mechanistic link to algal abundance. We used statistical models and causal modeling to evaluate the relationships between environmental data and chlorophyll a concentration. We found the highest concentrations of chlorophyll a occurred when discharge was low and temperature was high. Relationships were weak to moderate in all modeling approaches that related environmental data to chlorophyll a concentration, even when accounting for optimized lag times. The direction and magnitude of statistical associations between chlorophyll a and environmental data also varied by site. From a causal modeling perspective, the available data may poorly represent the hypothesized mechanisms, or we may be missing causal drivers of variation in chlorophyll a concentration.
Harmful algal blooms (HABs) driven by excess nitrogen and phosphorus threaten water security worldwide. Conventional treatments face challenges in achieving simultaneous algae demolition, phosphorus recovery, and nitrogen stripping, often leading to secondary pollution. This study introduces a novel plasma-electrosorption triplex system (PETS) that enables synergistic, one-step algae demolition, phosphorus recovery, and nitrate removal within an integrated unit without the need for externally supplied chemical additives. The system couples a dielectric barrier discharge (DBD) plasma reactor with pulsed electrosorption using a single power source. Plasma-generated reactive oxygen species (ROS) disrupt algal cells and oxidize organic phosphorus, while triggering an autocatalytic Fe(II/III) cycle for phosphate precipitation. Subsequent pulsed electrosorption achieves selective nitrate capture through modulated electric double layers. Under optimal laboratory conditions using synthetic water, PETS achieved high removal efficiencies of 99.9% for algae, 99.9% for phosphorus, and 85.1% for nitrate. Mechanistic studies revealed that ROS-induced membrane damage and Fe(OH)3-mediated adsorption are crucial for algal inactivation and phosphorus recovery, while pulsed electric fields enhance ion migration. The system exhibited excellent stability over multiple cycles and in various real water matrices, offering a transformative and sustainable framework for managing eutrophic waters.
Harmful cyanobacterial blooms pose increasing threats to aquatic ecosystems and human health; yet, the role of zooplankton grazing in regulating blooms remains understudied. We investigated the seasonal feeding behaviour and fitness consequences of feeding preferences in natural zooplankton communities for toxic (microcystin-producing) versus non-toxic cyanobacteria across temperature gradients in eutrophic Lake Greifen, Switzerland. We conducted monthly experiments from April to October 2023 to test the grazing behaviour of four zooplankton groups (daphnids, calanoid copepods, cyclopoid copepods, and microzooplankton) exposed to mixed diets of green algae and either toxic or non-toxic Microcystis strains at 15 °C and 25 °C. Contrary to expectations of cyanobacteria avoidance, zooplankton exhibited predominantly non-selective grazing throughout the seasonal succession, consuming both toxic and non-toxic cyanobacteria at similar rates, regardless of temperature. Notably, during the peaks of phytoplankton abundance (April and September), mesozooplankton demonstrated a selective preference for cyanobacteria over green algae, particularly non-toxic strains. Temperature effects were subtle but revealed metabolic constraints: elevated temperatures occasionally triggered selective consumption of cyanobacteria in copepods, while fitness costs (survival) from exposure to toxic species were mostly restricted to transitional bloom periods and high-temperature conditions. These findings suggest that toxic cyanobacteria may not always evade grazing pressure through secondary metabolite deterrent effects. Our results suggest that zooplankton communities can adapt and graze on cyanobacteria regardless of toxicity under the tested conditions, even during bloom conditions. These observations highlight the potential for zooplankton to interact with cyanobacterial populations, which may have implications for bloom prediction and management strategies, particularly under climate warming scenarios.