Some bacteria evolve like clockwork with the seasons, researchers report.
The researchers found that through the course of a year, most individual species of bacteria in Wisconsin’s Lake Mendota rapidly evolved, apparently in response to dramatically changing seasons.
Gene variants would rise and fall over generations, yet hundreds of separate species would return, almost fully, to near copies of what they had been genetically prior to a thousand or so generations of evolutionary pressures. (Individual microbes have lifespans of only a few days—not whole seasons—so the scientists’ work involved comparing bacterial genomes to examine changes in species over time.)
This same seasonal change played out year after year, as if evolution was a movie run back to the beginning each time and played over again, seemingly getting nowhere.
“I was surprised that such a large portion of the bacterial community was undergoing this type of change,” says Robin Rohwer, a postdoctoral researcher at the University of Texas at Austin in the lab of coauthor Brett Baker.
“I was hoping to observe just a couple of cool examples, but there were literally hundreds.”
Rohwer led the research, first as a doctoral student working with Trina McMahon at the University of Wisconsin-Madison and then at UT.
Lake Mendota changes greatly from season to season—during the winter, it’s covered in ice, and during the summer, it’s covered in algae. Within the same bacterial species, strains that are better adapted to one set of environmental conditions will outcompete other strains for a season, while other strains will get their chance to shine during different seasons.
The team used a one-of-a-kind archive of 471 water samples collected over 20 years from Lake Mendota by McMahon, Rohwer, and other UW-Madison researchers as part of National Science Foundation-funded long-term monitoring projects.
For each water sample, they assembled a metagenome, all of the genetic sequences from fragments of DNA left behind by bacteria and other organisms. This resulted in the longest metagenome time series ever collected from a natural system.
“This study is a total game changer in our understanding of how microbial communities change over time,” Baker says. “This is just the beginning of what these data will tell us about microbial ecology and evolution in nature.”
This archive also revealed longer-lasting genetic changes.
In 2012, the lake experienced unusual conditions: The ice cover melted early, the summer was hotter and drier than usual, the flow of water from a river that feeds into the lake dwindled, and algae, which are an important source of organic nitrogen for bacteria, were more scarce than usual. As Rohwer and the team discovered, many of the bacteria in the lake that year experienced a major shift in genes related to nitrogen metabolism, possibly due to the scarcity of algae.
“I thought, out of hundreds of bacteria, I might find one or two with a long-term shift,” Rohwer says. “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.”
Climate scientists predict more extreme weather events—like the hot, dry summer experienced at Lake Mendota in 2012—for the midwestern US during the coming years.
“Climate change is slowly shifting the seasons and average temperatures, but also causing more abrupt, extreme weather events,” Rohwer says.
“We don’t know exactly how microbes will respond to climate change, but our study suggests they will evolve in response to both these gradual and abrupt changes.”
Unlike another famous bacterial evolution experiment at UT, the Long-Term Evolution Experiment, Rohwer and Baker’s study involved bacterial evolution under complex and constantly changing conditions in nature. The researchers used the supercomputing resources at the Texas Advanced Computing Center (TACC) to reconstruct bacterial genomes from short sequences of DNA in the water samples. The same work that took a couple of months to complete at TACC would have taken 34 years with a laptop computer, Rohwer estimates, involving over 30,000 genomes from about 2,800 different species.
“Imagine each species’ genome is a book, and each little DNA fragment is a sentence,” Rohwer says. “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 appears in Nature Microbiology.
Other coauthors of the new study are from UT, Carl von Ossietzky University of Oldenburg (Germany), Stockholm University, and the US Department of Energy’s Joint Genome Institute.
This is one of two related papers in the journal; the companion paper focuses on the ecology and evolution of viruses from the same lake samples.
Support for this research was provided in part by the US National Science Foundation, US National Institutes of Health, the Office of Science of the US Department of Energy, US Department of Agriculture, the Simons Foundation and the E. Michael and Winona Foster-WARF Wisconsin Idea Graduate Fellowship in Microbiology.
Source: UT Austin
