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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 theglobe. 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 U.S. 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  make the blooms toxic (Science, 26 May,  p. 1001). 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 U.S. 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 infect 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 Microcystis,  but 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 unlike in Europe, where this bacterium causes 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.”