When scientists from the Minnesota DNR and U.S. Geological Survey looked back on several years of phytoplankton data from Lake Pepin, one detail stood out: a common diatom named Stephanodiscus hantzschii was missing entirely in 2012. That is unusual. This tiny alga is one of the most common species worldwide in high-nutrient systems like the Mississippi River. In Lake Pepin, it typically plays a key role at the base of the aquatic food web.

The study could not pinpoint a single cause, but the conditions that spring were far from typical. Water temperatures in April 2012 were about 18°F warmer than other study years, and the lake’s supply of soluble reactive phosphorus, the readily available form of phosphorus that fuels algal growth, dropped to unusually low levels for several weeks. While the exact mechanism is not certain, that season’s combination of heat and low SRP occurred alongside the unusual patterns seen in the phytoplankton community.

The research suggests that S. hantzschii’s absence may have been linked to that unusual spring. This species is known from earlier research to be one of the first diatoms to slow or stop growth when phosphorus runs short. In Lake Pepin, the brief nutrient shortage and early warmth may simply have closed its usual spring window to bloom.

While that might sound like a small mystery, it hints at something bigger. Even short-term shifts in temperature or nutrients can ripple through the river’s entire food web, changing which species thrive, which vanish, and how energy moves through the system. When the foundation shifts, so does everything above it, from microscopic communities to the lake’s overall condition.

It is a reminder that the health of the river begins at the smallest scales, where changes in timing, warmth, and nutrients can set the course for everything that follows.

Read the full study here.

Study: Burdis, Ward and Manier (2025), “Phytoplankton assemblage dynamics in relation to environmental conditions in a riverine lake,” Aquatic Ecology.