Tracing the Molecular Roots of Harmful Algal Toxins
Sampling location at the Jackson Estuarine Laboratory in Durham, NH, where water samples were collected to monitor environmental conditions and Alexandrium abundance throughout bloom development.
On some days along the New Hampshire coast, the ocean looks deceptively ordinary. The water is calm, the sky is clear, and shellfish beds appear undisturbed beneath the surface. Yet during these moments, shellfish harvesting can be quietly suspended—not because of storms or visible pollution, but because of organisms too small to see. Microscopic algae drifting in the water column may be producing a powerful neurotoxin capable of accumulating in shellfish and causing serious illness in humans.7,10 When this happens, coastal economies pause, monitoring programs intensify, and scientists work to understand what triggered the change.
These events are part of a broader phenomenon known as harmful algal blooms (HABs).7 While many algal blooms are harmless, certain species can produce toxins under specific environmental conditions.7,10 My research addresses a central question underlying HAB dynamics: What causes some algae to become toxic, and why does this occur only under certain circumstances? Supported through a Summer Undergraduate Research Fellowship (SURF) at the University of New Hampshire, this project explores how environmental conditions shape toxin production at the molecular level to better understand the mechanisms driving bloom toxicity in coastal ecosystems.
Alexandrium: Tiny, Ancient, and Potent
Phytoplankton are microscopic algae that drift in the water column and are among the ocean’s most important—and often overlooked—organisms.6 These single-celled photosynthetic microbes form the base of marine food webs and are responsible for approximately half of the oxygen produced on Earth.6 Most phytoplankton species are harmless and essential to ecosystem function. Some are even visually striking under the microscope, exhibiting complex shapes or bioluminescent properties.
However, a small subset of phytoplankton species can become harmful under particular conditions such as changes in temperature, salinity, or nutrient availability that influence toxin production.7,11 Among them is the dinoflagellate genus Alexandrium, which is well documented in New England waters for producing saxitoxin, the compound responsible for paralytic shellfish poisoning.10 Saxitoxin interferes with nerve signaling by blocking sodium channels in nerve cells. In humans, ingestion of contaminated shellfish can lead to symptoms ranging from tingling and numbness to paralysis and, in severe cases, respiratory failure.10
What makes Alexandrium especially intriguing is that toxin production is not constant. Even when blooms appear similar in size or location, toxin concentrations can vary widely.9,10 This variability raises important questions about what environmental and biological factors regulate toxin production.
Not All Blooms Are Created Equal
A common misconception about harmful algal blooms is that toxin production is inevitable once a bloom forms. In reality, toxin concentrations fluctuate, depending on environmental conditions such as temperature, salinity, and nutrient availability.7,11 Two blooms of the same species can therefore have dramatically different ecological and public health consequences.
For many years, algal toxins were considered metabolic accidents—chemical by-products with little functional significance. More recent research challenges this interpretation. Emerging evidence suggests that algal toxins may play adaptive roles, such as mediating competition among microorganisms,5 deterring animals that feed on them, or helping cells respond to environmental stress.12 If toxin production represents a regulated response rather than an accidental process, understanding when and why toxins are produced requires looking beyond bloom presence and into the molecular biology of the cells themselves.
Figure 1. Cultures of Alexandrium spp. maintained in the cold room at 15°C in Rudman Hall, University of New Hampshire. These cultures were grown under controlled environmental conditions to investigate how factors such as temperature and salinity influence toxin production.
Research Approach and Methods
To investigate how environmental conditions influence toxin production, I studied Alexandrium spp. samples grown under controlled laboratory conditions in Rudman and Spaulding Hall as well as samples collected during natural bloom events along the New Hampshire coast. Rather than focusing solely on toxin concentrations, this project examined the genetic potential for toxin production. Specifically, I investigated a gene known as sxtA, which is essential to the saxitoxin biosynthesis pathway.4,8 Genes can be thought of as instructions in a cookbook; however, the presence of a recipe does not mean it is actively being used. This study aimed to determine whether the presence and abundance of toxin-related genes corresponded to measurable toxin production under different environmental conditions.
Culture Experiments. I maintained laboratory cultures of Alexandrium spp. under controlled temperature and salinity treatments to mimic environmental variation observed during coastal bloom events.11 Cultures were grown in sterile seawater media under a 12:12 light-dark photoperiod and monitored for cell growth using a flow cytometer. At predetermined time points, I harvested cells by gentle filtration and stored filters at ?80°C for later DNA extraction and toxin analysis.
Figure 2. Agarose gel showing PCR amplification of the sxtA gene from environmental samples collected during an Alexandrium bloom at Hampton Beach, NH. Bright bands indicate successful amplification of the saxitoxin biosynthesis gene, confirming its presence in bloom samples.
Field Sampling. I collected field samples during naturally occurring Alexandrium bloom events in May 2025 at Hampton Beach State Park along the New Hampshire coast. Surface seawater was collected using sterile sampling bottles and processed similarly to laboratory cultures. Water was pre-filtered to remove large debris, and the phytoplankton were concentrated onto 0.2 ?m polycarbonate filters (47 mm) for subsequent DNA and toxin extraction.
DNA Extraction and Molecular Screening. I extracted DNA from both cultured and field samples using the ZymoBIOMICS DNA Miniprep Kit. I then screened extracted DNA for the presence of the saxitoxin biosynthesis gene sxtA using conventional polymerase chain reaction (PCR), a method used to make many copies of a specific DNA sequence.8 PCR products were visualized on agarose gels to confirm successful amplification.
Quantitative PCR (qPCR). Samples that tested positive for sxtA were analyzed by quantitative PCR (qPCR) to estimate gene copy number.8,9 This method allowed me to compare toxin-related gene abundance across environmental treatments. Standard curves constructed from known template concentrations were used to convert threshold cycles values (Cq) to estimated copy numbers.
Toxin Quantification (ELISA). To quantify saxitoxin directly I performed enzyme-linked immunosorbent assays (ELISA) on matching samples.2 ELISA is a biochemical technique that uses antibodies—proteins designed to recognize specific molecules—to detect and measure compounds such as toxins. In this case, antibodies in the assay bind specifically to saxitoxin present in the samples.
Figure 3. The author performing gel electrophoresis to visualize PCR-amplified DNA fragments. This step confirms successful amplification of target genes and allows for verification of product size prior to downstream analyses.
When the toxin binds to the antibody, a chemical reaction produces a color change, however, in this assay, color intensity is inversely related to toxin concentration, meaning that lower absorbance corresponds to higher toxin levels. The intensity of this color is measured using a plate reader at a wavelength of 450 nanometers, which allows the instrument to quantify how much toxin is present. Toxin concentrations were then calculated by comparing sample readings with a standard curve generated from known saxitoxin concentrations.
By pairing qPCR results with ELISA measurements, I compared genetic potential for toxin production with measured saxitoxin levels. By linking molecular techniques with toxin assays, this approach enabled me to investigate whether environmental conditions that influence toxin-related gene abundance also affect toxin production at the cellular level.
Results and Current Findings
Analysis of this project revealed substantial variability in both toxin-related gene abundance and saxitoxin concentration across samples. PCR screening confirmed the presence of the sxtA gene in multiple samples, indicating that many Alexandrium populations possess the genetic capacity for toxin production.8,9 However, qPCR analyses showed that sxtA gene copy number varied widely across environmental conditions, ranging from low to high copy numbers even within similar treatments.
Despite this variability in gene abundance, there was no consistent relationship between sxtA gene copy number and measured saxitoxin concentration. Samples with similar gene copy numbers often exhibited different toxin levels, and conversely, samples with relatively low gene abundance sometimes showed elevated toxicity. These results indicate that gene presence and abundance alone do not regulate toxin production.9,10
Figure 4. Quantitative PCR (qPCR) amplification curves showing fluorescence intensity (RFU) across PCR cycles for samples containing the sxtA gene, a key component of the saxitoxin biosynthesis pathway in Alexandrium. Variation in amplification profiles reflects differences in gene abundance across samples, which were used to estimate relative gene copy number and assess potential links to toxin production.
Comparisons across environmental conditions suggest that salinity may play a more influential role in driving saxitoxin production than temperature. While temperature treatments showed variability among replicates, no clear trend in toxicity was observed across the temperature range tested. In contrast, shifts in salinity were more consistently associated with changes in toxin concentration.11
Together, these findings suggest that toxin production in Alexandrium is not directly controlled by sxtA gene copy number, but is instead regulated by additional environmental or physiological factors.10,12 This highlights the complexity of toxin production and suggests that predicting bloom toxicity requires a more integrated understanding of both molecular potential and environmental context.
Why This Matters Beyond the Lab
Although this research takes place at the molecular scale, its implications extend far beyond individual cells. Harmful algal blooms disrupt fisheries, affect tourism, and pose serious public health risks to coastal communities.7,10 In New England, shellfish closures have both economic and cultural consequences, highlighting the importance of effective harmful algal bloom monitoring and prediction.
As climate change continues to alter coastal environments through warming waters, shifting salinity patterns, and changing nutrient dynamics, understanding how these factors influence toxin production becomes increasingly important.7,11 Research that links environmental conditions to molecular mechanisms of toxin regulation may ultimately help improve monitoring strategies and inform management decisions.9,10
This project also highlights the role undergraduate researchers can play in addressing complex scientific questions. With access to mentorship, funding, and research infrastructure, undergraduate students can contribute meaningful insights into issues that affect ecosystems and human communities alike.
Conclusion and Personal Reflection
This study represents an early step toward understanding how environmental conditions influence toxin production in harmful algal bloom species. By examining both genetic potential and toxin concentration, this research contributes to a more mechanistic view of saxitoxin production in Alexandrium spp. Studying organisms invisible to the naked eye revealed how processes occurring at the smallest scales can have far-reaching impacts. As coastal systems continue to change, understanding these microscopic drivers will remain essential for protecting ocean health.
On a personal level, conducting this research deepened my appreciation for the interdisciplinary nature of marine science. Working with molecular tools alongside ecological questions reinforced the importance of integrating multiple approaches when studying complex environmental problems. This project strengthened my interest in phytoplankton physiology and harmful algal bloom research and shaped my trajectory as a developing marine scientist.
This research was conducted as part of an independent project funded by a Summer Undergraduate Research Fellowship (SURF) from the Hamel Center for Undergraduate Research at the University of New Hampshire. I would like to thank Mr. Dana Hamel, the Class of 1959 Fund for Excellence, and the UNH Parents Association Undergraduate Research Fund for their financial support. I would also like to thank my faculty mentor, Dr. Elizabeth Harvey, and the members of the UNH Phyto Lab for their guidance and support.
References
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Cornett, J. C., Cates, R. J., Ledger, K. J., Pinger, C. W., Hart, C. E., Laboda, K. R., ... and Hollarsmith, J. A. 2024. “Assessing Methods for Detecting Alexandrium catenella Dinophyceae and Paralytic Shellfish Toxins in Southeast Alaska.” Integrated Environmental Assessment and Management.
Detree, C., Nù?ez-Acu?a, G., Roberts, S., and Gallardo-Escárate, C. 2016. “Uncovering the Complex Transcriptome Response of Mytilus chilensis against Saxitoxin: Implications of Harmful Algal Blooms on Mussel Populations.” PLoS ONE 11 (10): e0165231. doi:10.1371/journal.pone.0165231
Kim, H. S., Bui, Q. T. N., Wang, H. et al. 2023. “Molecular Cloning, Origin, and Expression of Saxitoxin Biosynthesis Gene sxtB from the Toxic Dinoflagellate Alexandrium catenella.” Journal of Applied Phycology 35, 673–685. https://doi.org/10.1007/s10811-022-02862-4
Fistarol, G., Legrand, C., Selander, E., Hummert, C., Stolte, W., and Granéli, E. 2004. “Allelopathy in Alexandrium spp.: Effect on a Natural Plankton Community and on Algal Monocultures. Aquatic Microbial Ecology 35, 45–56. https://doi.org/10.3354/ame035045
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Murray, S. A., Wiese, M., Stüken, A., Brett, S., Kellmann, R., Hallegraeff, G., and Neilan, B. A. 2011. “sxtA-based Quantitative Molecular Assay to Identify Saxitoxin-Producing Harmful Algal Blooms in Marine Waters.” Applied and Environmental Microbiology 77 (19), 7050–7057.
Murray, S. A., Ruvindy, R., Kohli, G. S. et al. 2019. “Evaluation of sxtA and rDNA qPCR Assays Through Monitoring of an Inshore Bloom of Alexandrium catenella Group 1. Scientific Reports 9, 14532. https://doi.org/10.1038/s41598-019-51074-3
Murray, S., John, U., Savela, H., and Kremp, A. 2021. “4 Alexandrium spp.: Genetic and Ecological Factors Influencing Saxitoxin Production and Proliferation.” Climate Change and Marine and Freshwater Toxins, edited by Luis M. Botana, M. Carmen Louzao, and Natalia Vilarino, Berlin, Boston: De Gruyter, pp. 133–166. https://doi.org/10.1515/9783110625738-004
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Author and Mentor Bios
Olivia Lucia is a marine, estuarine, and freshwater biology major from Suffern, New York, who will graduate from the University of New Hampshire (UNH) in May 2026. She received a Summer Undergraduate Research Fellowship (SURF) in 2025 to conduct the research described in this article in Dr. Elizabeth Harvey’s Phytoplankton Ecology Lab, where she studies harmful algal blooms and toxin production in Alexandrium spp. In addition to her research, Olivia serves as a COLSA ambassador and a Hamel Center for Undergraduate Research ambassador. Following graduation, she plans to pursue a master’s degree in marine biology at UNH and continue research focused on phytoplankton physiology and harmful algal bloom ecology.
Elizabeth Harvey is associate professor and chair of the Department of Biological Sciences at the University of New Hampshire. The UNH Phyto Lab focuses on elucidating the mechanisms that mediate associations between marine microbes, with a focus on understanding interactions that result in microbial mortality.
Copyright 2026 ? Olivia Lucia
