To tame lake-fouling algal blooms, try an ecosystem approach | Science

Every summer, surges of toxic green muck plague lakes worldwide, sickening hikers who fail to purify drinking water, closing favorite swimming holes, and killing fish. The most feared—and studied—cause of these freshwater “algal” blooms is a genus of cyanobacterium called Microcystis. Its explosive summer growth is thought to be spurred by rising levels of phosphorus, nitrogen, and other nutrients, perhaps from fertilizer run off or other pollution sources. But new research, driven by advances in DNA sequencing, suggests other types of microbes also play key roles in these massive overgrowths.

According to one study, viruses killing off a main competitor of toxic Microcystis may help pave the way for blooms; another indicates nitrogen fixation by other bacteria may provide the needed boost. The results suggest that reducing nutrients may not be enough to stop these slimy explosions, some scientists say. That doesn’t mean curbing pollution is unimportant, they stress, but ecological factors must be considered.

“Interspecies biological interactions help determine blooms,” says Kevin Johnson, a marine scientist at the Florida Institute of Technology who was not involved in the work. “The more details we understand of bloom creation, the better our knowledge of how they might be prevented or controlled.”

With the warming climate and continuing inflows of pollution, harmful algal blooms are on the rise, becoming more frequent and longer lasting in ever more places across the globe. They are “a pretty wicked problem,” says Ariane Peralta, a microbial ecologist at Eastern Carolina University.

In some lakes, reducing fertilizer runoff at first seemed to thwart blooms—then they came back. Similar plans for bloom-choked Lake Erie might backfire, a team of academic microbiologists and water quality experts funded by the National Science Foundation and other US agencies reported in May. A 2014 bloom there caused such severe shortages of drinking water in the nearby city of Toledo, Ohio, that Canada and the United States have agreed to cut phosphorus going into the lake by 40%.

But a simulation of that strategy, along with an analysis of more than 100 related scientific papers, led the team to conclude that although limiting phosphorus might shrink Lake Erie blooms, they could also grow more toxic: with lower overall growth of microbes, any photosynthetic Microcystis left would receive more sunlight and have more nitrogen available, two conditions that favor an increase in their production of microcystin, a substance that makes the blooms toxic. They suggested the lake’s nitrogen should also be curtailed.

That simuation hinted that other microbes can indirectly influence the impact of Microcystis. But researchers studying blooms have tended to overlook lakes’ many microbial inhabitants, which can include huge numbers of diatoms and other eukaryotes, as well as viruses and various types of bacteria, including smaller than average ones called picocyanobacteria. “Everyone glosses over them as not of managerial concern,” says Cody Sheik, a microbial ecologist at the University of Minnesota, Duluth.

Part of the problem has been that it’s been difficult to sort out which microbes are doing what in a lake. But Lauren Krausfeldt, a microbiologist at Nova Southeastern University, recently turned to metagenomics, a strategy of sequencing all the DNA in samples of water and other environments, to reconstruct the microbial ecosystem in Florida’s Lake Okeechobee. The largest lake in the US southeast, Okeechobee’s annual summer blooms have begun to spread down rivers and spill into the Gulf of Mexico and Atlantic Ocean, forcing beaches to close. Between April and September in 2019, the bloom season, Krausfeldt and her colleagues collected multiple water samples at 21 places across the lake. From the fragments of DNA isolated from the samples and sequenced, they pieced together whole genomes belonging to specific species.

The analysis uncovered 30 kinds of cyanobacteria never before detected in the lake, and in some cases new to science, including 13 that could potentially cause blooms, she reported last month at Microbe 2022, the annual meeting of the American Society for Microbiology. “I was surprised at the diversity,” Krausfeldt says.

When there was no bloom, the most common organisms were the picocyanobacteria. But as the season progressed, DNA belonging to bacterial viruses, known as phages, that infects the picocyanobacteria rose steeply. Shortly thereafter, the concentration of toxic Microcystis began to skyrocket. An analysis of its genome suggested why: Microcystis contains several antiviral defenses, such as the system that spawned the genome editor CRISPR, that picocyanobacterial lack. In addition, the bloom-forming cyanobacterium has genes that enable it to store nitrogen, a key nutrient, which may provide another competitive advantage over the many lake microbes that did not.

Krausfeldt suspects the phages lie dormant until some unknown environmental cue activates them. Then, after the viruses start slaying more and more picocyanobacteria, newly available nitrogen, phosphorus, and more light fuel a Microcystis bloom, Krausfeldt suggests. The phages’ destruction of its hosts’ cells may release even more nutrients, playing a key role in enabling algal blooms, she concludes.

Sheik, who says he had not considered phages as a factor in blooms but now wants to explore such viral dynamics, embraces Krausfeldt’s ecosystem mindset. “By taking a holistic approach, we can better understand how supporting organisms can help sustain blooms,” he says.

Sheik and his colleagues have also added metagenomics, as well as gene activity assessments, to his studies of several small lakes in Minnesota. Those lakes, he reported at the meeting, contain not only some Microcystisbut also another bloom-forming cyanobacterium called Dolichospermum. In 2020 and 2021, when he and colleagues tracked the microbial dynamics in one lake throughout the summer, they saw Dolichospermum become the most abundant microbe only to have its population crash by July. Nitrogen levels in the lake rose and fell in parallel with the microbe, suggesting it was fixing nitrogen and boosting its concentration in the water.

Nitrogen is usually quite scarce in these relatively pristine lakes, yet the nutrient is essential for the production of microcystin. That might explain why Sheik and his colleagues saw levels of Microcystis and its toxin rise after the bloom in nitrogen-fixing Dolichospermum. Microcystis must rely on other members of the freshwater ecosystem to fix nitrogen or to recycle it by breaking down other life forms, Sheik says.

“I’m blown away” by the metagenomic work, says Benjamin Wolfe, a microbiologist at Tufts University, because it can illuminate in great detail the lake’s microbial interactions.

The case of Dolichospermum illustrates how complicated algal blooms can be. The good news, however, is that causes unlike in Europe, where this bacterium toxic blooms, Dolichospermum species in the United States lack the genes to make toxins—at least for now, says Sheik, who plans to keep watching for them in his metagenomic studies.

How the microbial dynamics that drive blooms can be interrupted is still unknown, and the picture is getting more complicated all the time. “We are grappling with understanding what parts of complex microbial communities are changing and what we can change to produce a different outcome,” Peralta says. But she’s optimistic that in time, “we can figure out what levers we can move.”