"I was surprised that such a large portion of the bacterial community was undergoing this type of change," said Robin Rohwer, a postdoctoral researcher at The University of Texas at Austin and lead author of the study. "I was hoping to observe just a couple of cool examples, but there were literally hundreds."
Rohwer conducted the research during her doctoral studies at the University of Wisconsin-Madison and later at UT Austin. Lake Mendota undergoes stark seasonal transformations, with ice covering the lake in winter and algae dominating in summer. These shifts favor different bacterial strains at various times, creating a continuous cycle of competitive adaptation.
The study utilized a 20-year archive of 471 water samples from Lake Mendota, collected as part of a National Science Foundation-funded project. Researchers assembled metagenomes - comprehensive genetic blueprints - by analyzing fragments of DNA left by bacteria and other organisms. This represents the longest metagenomic time series from a natural environment to date.
"This study is a total game changer in our understanding of how microbial communities change over time," said Brett Baker, a co-author and Rohwer's postdoctoral mentor. "This is just the beginning of what these data will tell us about microbial ecology and evolution in nature."
The study also uncovered longer-term evolutionary shifts triggered by extreme environmental events. For example, during an anomalous 2012 summer - marked by early ice melt, hot and dry conditions, and reduced algae - a significant number of bacteria exhibited lasting genetic changes related to nitrogen metabolism.
"I thought, out of hundreds of bacteria, I might find one or two with a long-term shift," Rohwer said. "But instead, 1 in 5 had big sequence changes that played out over years. We were only able to dig deep into one species, but some of those other species probably also had major gene changes."
With climate change expected to bring more extreme weather events to the Midwest, the findings carry important implications for understanding microbial responses to environmental stresses. "Our study suggests microbes will evolve in response to both gradual climate shifts and abrupt changes," Rohwer added.
Reconstructing bacterial genomes required supercomputing resources from the Texas Advanced Computing Center (TACC). Rohwer explained that this computational effort, which took months at TACC, would have required 34 years on a standard laptop due to the complexity of assembling over 30,000 genomes from about 2,800 species.
"Imagine each species' genome is a book, and each little DNA fragment is a sentence," she said. "Each sample has hundreds of books, all cut up into these sentences. To reassemble each book, you have to figure out which book each sentence came from and put them back together in order."
The study included contributions from researchers Mark Kirkpatrick at UT, Sarahi Garcia of Carl von Ossietzky University of Oldenburg and Stockholm University, and Matthew Kellom of the U.S. Department of Energy's Joint Genome Institute. A related paper in the journal explores the ecology and evolution of viruses in the same lake samples.
Research Report:Twenty years of bacterial ecology and evolution in a freshwater lake
Related Links
Long-Term Evolution Experiment
Darwin Today At TerraDaily.com
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