Nitrogen’s Underestimated Role in Fueling Cyanobacteria Blooms in Lake Ecosystems

For decades, most conversations about harmful cyanobacteria blooms have focused almost entirely on phosphorus. It has long been the nutrient blamed for feeding algae explosions that discolor shorelines, close beaches, and threaten drinking water. But new research from the University of Vermont (UVM) shows that nitrogen, even in surprisingly small amounts, can play an equally powerful role in driving these blooms—especially in shallow, nutrient-rich waters like the northern bays of Lake Champlain.

This study adds an important layer to our understanding of what actually fuels cyanobacteria growth. It suggests that managing phosphorus alone may not be enough to protect waterways. Even trace amounts of nitrogen entering a lake system can influence bloom size, composition, toxicity, and duration. The findings come from a detailed field investigation conducted in 2021 in two bays—St. Albans Bay and Missisquoi Bay—that regularly experience cyanobacteria issues. The research used both traditional weekly sampling and advanced high-frequency buoy sensors to capture fine-scale changes in water conditions.

Below is a clear, comprehensive look at the findings, the methods, and why nitrogen deserves far more attention in water-quality management.

How the Study Was Conducted

Researchers monitored two shallow bays on Lake Champlain that are known hotspots for summertime cyanobacteria blooms. Both bays are connected to different watersheds, making them ideal for studying how nutrient differences affect bloom behavior.

Fieldwork involved:

Weekly water sampling for phytoplankton, cyanotoxins, and nutrient measurements
High-frequency buoy sensors recording complete water-column data every 15 minutes
Measurements including dissolved oxygen, pH, temperature, turbidity, and meteorological factors like wind speed and air temperature

These high-resolution sensors allowed scientists to see conditions that traditional weekly sampling often misses—short-term changes that can influence bloom formation or collapse.

Two cyanobacteria genera were the main focus: Microcystis and Dolichospermum, both commonly found in Lake Champlain. The team also screened for various cyanotoxins to understand how nutrient levels corresponded with toxin production.

What the Researchers Found

Despite phosphorus being the historical culprit behind Lake Champlain’s water-quality challenges, the study uncovered important new evidence:

Small increases in nitrogen strongly influenced bloom biomass.
In Missisquoi Bay, nitrogen levels were sometimes twice as high as in St. Albans Bay. Even these relatively small differences were linked to stronger cyanobacteria growth.
Nitrogen appeared to impact bloom composition and potential toxicity.
Not all cyanobacteria respond the same way to nitrogen availability, and nitrogen can shift which species become dominant.
Toxin levels were low during major blooms, but this doesn’t guarantee safety.
The study found that high biomass did not necessarily mean high toxin concentration during initial bloom phases.
Nitrogen levels in the lake’s northeast arm have risen since 2009, with the largest increases occurring in recent years.
Floods and storm-driven runoff are likely contributors.

This last point is particularly important: climate change, which brings more extreme rainfall events, may increase the frequency of nitrogen pulses entering lake systems. When these nitrogen bursts combine with warm, calm water, cyanobacteria can grow extremely rapidly.

Why Nitrogen Matters More Than Most People Realize

The traditional focus on phosphorus made sense for many years. It was easier to track, easier to model, and widely understood to be a key driver of freshwater eutrophication. But cyanobacteria are highly adaptable organisms. Some can:

Fix atmospheric nitrogen, storing it for later use
Shift nutrient uptake strategies depending on availability
Respond quickly to nitrogen pulses, even when phosphorus levels are unchanged

Nitrogen also exists in many different forms—such as nitrate, ammonium, urea, and various organic nitrogen compounds. Cyanobacteria can use several of these forms efficiently. That versatility means nitrogen can influence bloom dynamics in ways that are harder to predict than phosphorus alone.

Some cyanobacteria species need external nitrogen because they cannot fix it from the atmosphere. For these species, even a small external nitrogen input can dramatically increase their growth rate.

This makes nitrogen a critical but often overlooked part of the story.

Understanding How Physical Conditions Amplify Blooms

Nutrient levels are only one piece of the puzzle. Lake conditions interact with nutrient availability in ways that can either strengthen or weaken cyanobacteria dominance.

Key environmental factors include:

Temperature – warm water encourages rapid cyanobacteria reproduction
Wind – calm conditions help cyanobacteria float to the surface and form thick mats
Mixing events – storms or strong winds can stir up sediment, releasing stored nutrients
Water column stability – stable, stratified water favors bloom formation

Shallow areas like Missisquoi Bay are especially vulnerable because they mix easily. A single storm can churn up sediment-bound nutrients—especially phosphorus and nitrogen—feeding a bloom that was already developing.

Heatwaves and extreme precipitation events—both expected to increase with climate change—are likely to make cyanobacteria blooms more frequent and more intense in the coming years.

The Complexity of Toxin Production

One of the most interesting aspects of the study was that toxin levels remained low during major bloom events. However, once a bloom collapsed, researchers detected toxins during a secondary bloom.

Several possibilities could explain this:

A different cyanobacteria species may have risen to dominance after the main bloom crashed.
Environmental stress may trigger toxin production in certain strains.
Some strains possess toxin-producing genes, while others do not, even if they look identical under a microscope.

Identifying which species carry toxin-producing genes requires genetic analysis, which is part of the next phase of research planned by the UVM team.

Future Research Directions

Lead researcher Katelynn Warner will continue investigating cyanobacteria dynamics during her postdoctoral work at UVM. Her plans include:

Using both high-frequency and biweekly sampling across four Lake Champlain sites
Studying how nitrogen influences cyanobacteria growth and toxin potential
Conducting laboratory experiments to see how increases in temperature and nutrient loads affect bloom behavior
Performing genetic testing to identify toxin-producing strains

These findings could help determine whether the cyanobacteria dominating Lake Champlain blooms are even capable of producing harmful toxins—and under which environmental conditions they do so.

Why This Matters for Lake Management

The takeaway is clear: focusing solely on phosphorus will not fully address harmful cyanobacteria blooms. Nitrogen management needs to be part of the strategy.

This means:

Improving agricultural practices to reduce nitrogen runoff
Enhancing wastewater treatment
Monitoring stormwater flows more carefully
Conducting more frequent and detailed water testing
Considering both nutrients—not just one—when developing regulations

Because nitrogen is chemically diverse and more mobile in the environment than phosphorus, managing it will be challenging. But the consequences of ignoring it could be significant, especially under changing climate conditions.

Research Paper:
Interactive effects of stoichiometry and environmental variability regulate cyanobacteria toxicity in two eutrophic bays