We [Heart] Actinobacteria

Every ecosystem has a top dog, a species that out-evolves and outcompetes everything else to survive and thrive under a wide range of conditions. In freshwater lakes, that champion is a special group of actinobacteria, small microbes—like, really, really tiny —that make up a superabundant group of bacteria that’s involved in most of what goes on in the freshwater universe.

Nobody knows more about freshwater actinobacteria than University of Wisconsin-Madison professor of environmental engineering Trina McMahon. With the support of Wisconsin Sea Grant, McMahon’s laboratory members have spent the last five years studying the little critters from every imaginable angle—and in the process have become the pre-eminent experts on the topic. What they’ve found has enlarged our understanding of how freshwater lakes function and exist.

“If you think of the lake as an entity, a living breathing thing that cycles nutrients, these bacteria are responsible for half of it,” said McMahon. “They’re very, very tiny, but because of their numbers and their level of activity, they’re driving huge amounts of the carbon cycling and nutrient regeneration,” said McMahon. “We’ve had a special place in our heart for a long time for the freshwater actinobacteria.”

The relationship began back in 2007, with Ryan Newton, one of McMahon’s first Ph.D. students. Newton, who’s now an assistant professor with the UW-Milwaukee School of Freshwater Sciences, developed a baseline bar code of actinobacterial RNA sequences that allows researchers to track, classify and enumerate bacteria in lakes. Using that code, Newton and McMahon demonstrated that actinobacteria are the predominant species in inland lakes.

In 2012, McMahon’s lab used a cutting-edge method to take a single cell of the actinobacteria and sequence its genome. What they found was that the actinobacteria have a rhodopsin protein similar to the protein in the human eye that allows it to sense light. In the actinobacteria, however, the rhodopsin almost certainly does more—converting the light into energy. (Those findings were recently published in the International Society for Microbial Ecology Journal.)

In a 2014-16 funded project with Wisconsin Sea Grant, McMahon and UW-Madison structural biologist Katrina Forest took it further, revealing something even more surprising about freshwater actinobacteria.

“Actinobacteria have the retinal found in most opsin proteins that allows them to harvest light, but we think they also have another light-harvesting structural molecule that allows harvesting of a different wavelength of light, amplifying the energy that gets harvested in a way that not many other bacteria have.”

That extra method of acquiring energy helps explain why they’ve shot to the top of the ecosystem ladder like a supercharged bullet. Currently, a graduate student in Forest’s lab is charting the actinobacterial cell’s biochemical machinery to definitively identify the structure of this second light-capturing molecule. McMahon suggests it might be possible that different groups of actinobacteria harvest different wavelengths of light.

In addition to the light-harvesting mechanism, McMahon’s lab has noted that the actinobacteria also interact extensively with the gunky-green cyanobacteria and algae that often overtake freshwater lakes during the summer months.

“They have in their cell wall/membrane all this machinery to suck up other dead organisms’ parts,” McMahon explained. “We think of them as vultures or scavengers—they wait for other organisms to die and then they eat up their parts. Then they recycle the atoms into carbon dioxide and also into new cell material. They are the foundational recyclers of the lake.”

McMahon said the interactions take a variety of forms—everything from the actinobacteria eating the dead cyanobacteria to sucking up molecules excreted by the cyanobacteria during periods of rapid growth.

“They’re super in one sense but they’re also crippled in another in that they depend on being able to scavenge what they can’t make themselves,” she said. “What’s fascinating is that we haven’t figured out if the actinobacteria help fuel the cyanobacteria blooms or keep them in check,” said McMahon. “There’s some early evidence that maybe they’re actually partners with the cyanobacteria in certain roles, which would mean that understanding actinobacteria might help us control cyanobacteria blooms better.”

McMahon’s well aware that she faces a strong ewwww factor associated with her research—who wants to talk about gross bacteria and smelly, potentially poisonous blue-green algae in our lakes? To get around that, McMahon has begun talking about actinobacteria using the same language people use to talk about the bacteria that live in humans’ guts, performing helpful tasks like digesting our food and bolstering our immune systems.

“People start to feel a little less scared about the bacteria when they think about it that way,” she said. “If we can understand how the actinobacteria function, and all the different ways they get energy and support the ecosystem, then we have that much deeper an understanding of the lake system. Then we can either do some kind of intervention to improve lake quality or at least make a prediction about what’s going to happen if we do make an intervention.”

McMahon’s research focus will now shift to determining how special each of the strains of actinobacteria are. Armed with genome sequences from the Great Lakes, Lake Mendota, lakes in Sweden and other countries around the world, McMahon’s working to determine whether the bacterial strain she’s studied in Madison’s Lake Mendota is endemic to all lakes or has adapted to its specific environments.

“Maybe the cell in Lake Mendota gets carried to a lake in northern Wisconsin, but maybe it can’t live there because it depends on its friends who are in Lake Mendota,” she said. “We would actually prefer if they weren’t too endemic, because we’d like to take what we’ve learned and apply it to all lakes.”