Seasonal Symphony: How Lake Bacteria Adapt in Perfect Harmony


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Some bacteria evolve like clockwork with the seasons
The researchers examined genetic data from microorganisms in a unique collection of water samples gathered over 20 years from Lake Mendota in Wisconsin. Credit: Robin Rohwer/University of Texas at Austin.

Similar to Bill Murray in the film “Groundhog Day,” bacterial types in a Wisconsin lake seem to be trapped in an endless cycle they cannot escape. In this instance, it resembles Groundhog Year.

As noted in a research article in Nature Microbiology, scientists discovered that throughout a yearly cycle, the majority of distinct bacterial species in Lake Mendota swiftly evolve, seemingly in reaction to drastically changing seasons.

Gene variations would rise and decline over generations; nevertheless, hundreds of individual species would revert almost entirely to near duplicates of their genetic state prior to approximately a thousand generations of evolutionary influences. (Each bacterium has a lifespan of only a few days—not entire seasons—thus the researchers’ effort involved contrasting bacterial genomes to study alterations in species through time.)

This identical seasonal transformation recurred each year, as if evolution were a film rewound to the start each time and replayed, evidently going in circles.

“I was astonished that such a considerable segment of the bacterial community was experiencing this type of change,” remarked Robin Rohwer, a postdoctoral researcher at The University of Texas at Austin in Brett Baker’s lab. “I was anticipating merely a few fascinating instances, but there were genuinely hundreds.”

Rohwer spearheaded the investigation, initially as a doctoral candidate collaborating with Trina McMahon at the University of Wisconsin-Madison and subsequently at UT.






Lake Mendota undergoes significant changes from season to season—during winter, it is blanketed in ice, and in summer, it becomes covered in algae. Within the same bacterial species, strains that are better suited to particular environmental conditions will outpace other strains for a period, while other strains will have their opportunity to thrive in various seasons.

The team utilized an extraordinary collection of 471 water samples procured over 20 years from Lake Mendota by McMahon, Rohwer, and other UW-Madison researchers as part of extensive monitoring initiatives.

For each water sample, they compiled a metagenome, encompassing all the genetic sequences from fragments of DNA left behind by bacteria and other organisms. This resulted in the longest metagenome temporal series ever assembled from a natural environment.

“This research is a complete game changer in our insight into how microbial communities transform over time,” stated Baker. “This is merely the beginning of what this information will reveal about microbial ecology and evolution in nature.”






This archive also unveiled more persistent genetic transformations.

In 2012, the lake faced unusual circumstances: the ice cover melted prematurely, the summer was hotter and drier than typical, the river feeding into the lake experienced diminished flow, and algae, a vital source of organic nitrogen for bacteria, were more limited than usual.

As Rohwer and the team uncovered, numerous bacteria in the lake that year saw a significant shift in genes associated with nitrogen metabolism, likely due to the lack of algae.

“I anticipated that out of hundreds of bacteria, I would discover one or two exhibiting a long-term shift,” Rohwer explained. “But unexpectedly, one in five had substantial sequence alterations that unfolded over several years. We managed to delve deeply into just one species, but many of those other species likely also experienced considerable gene changes.”

Some bacteria evolve like clockwork with the seasons
Numerous types of bacteria in Lake Mendota evolved swiftly with the seasonal transitions, reverting to a comparable condition each year, for two decades. The azure dots illustrate the extent to which individual species within the genus Nanopelagicus altered genetically throughout time. The ebony line signifies a 6-month rolling average. Credit: University of Texas at Austin

Climate researchers anticipate an increase in extreme weather incidents—similar to the hot, arid summer witnessed at Lake Mendota in 2012—in the midwestern United States in the upcoming years.

“Climate change is gradually altering the seasons and average temperatures, while also prompting more sudden, extreme weather occurrences,” Rohwer stated. “We’re uncertain about the specific responses of microbes to climate change, but our research indicates they will adapt in reaction to both these gradual and abrupt shifts.”

Differing from another notable bacterial evolution study at UT, the Long-Term Evolution Experiment, Rohwer and Baker’s research examined bacterial evolution under intricate and perpetually changing conditions found in nature. The researchers employed the supercomputing facilities at the Texas Advanced Computing Center (TACC) to reconstruct bacterial genomes from brief DNA sequences obtained from water samples.

The same analysis that required a few months to finalize at TACC would have taken 34 years using a personal laptop, as estimated by Rohwer, incorporating over 30,000 genomes from approximately 2,800 different species.

Some bacteria evolve like clockwork with the seasons
The team examined genetic material from microbes in a unique collection of water samples gathered over two decades from Lake Mendota in Wisconsin. Credit: Robin Rohwer/University of Texas at Austin.

“Think of each species’ genome as a book, with each tiny DNA fragment representing a sentence,” Rohwer remarked. “Every sample consists of hundreds of books, all fragmented into these sentences. To reconstruct each book, you must determine which book each sentence originated from and piece them back together in the correct sequence.”

Other co-authors of the recent study include Mark Kirkpatrick from UT; Sarahi Garcia of Carl von Ossietzky University of Oldenburg (Germany) and Stockholm University; and Matthew Kellom from the U.S. Department of Energy’s Joint Genome Institute.

This is one of two interconnected papers released in the journal; the companion paper delves into the ecology and evolution of viruses sourced from the same lake samples.

Further details:
Robin R. Rohwer et al, Two decades of bacterial ecology and evolution in a freshwater lake, Nature Microbiology (2025). DOI: 10.1038/s41564-024-01888-3

Zhichao Zhou et al, Unraveling viral ecology and evolution over 20 years in a freshwater lake, Nature Microbiology (2025). DOI: 10.1038/s41564-024-01876-7

Courtesy of
University of Texas at Austin


Reference:
Lake bacteria evolve like clockwork with the seasons, research shows (2025, January 3)
retrieved 3 January 2025
from

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