It was a silly question, so Trina McMahon laughed. What’s more important: a lab coat or a Twitter handle? “Twitter handle, for sure. We don’t do anything anymore in the lab,” she says. “Probably a pair of muck boots is even more important. You’ve got to get dirty in the field and get your samples, and then maybe spend a day in the lab, but then you spend the rest of your time in front of a computer.”
Microbial ecologists like McMahon use computers as their eyes. The bacterial communities they study — microbiomes in the human gut, in a Yellowstone geyser, in Lake Mendota — are almost entirely invisible. How, then, to see? “What we’re spending so much of our time doing in microbiome research is natural history, what the plant ecologists were doing 120 years ago, running around with their field notebooks,” says the Vilas Distinguished Achievement Professor with appointments in both bacteriology and civil and environmental engineering. “Only our field notebooks are our sequencers.”
It’s the first golden age of microbiome discovery, and this generation of microbiologists has little need for a microscope. Instead they use increasingly sophisticated techniques to read the genetic code of entire ecosystems, running complex statistics on powerful computers to sketch their specimens. It’s undoubtedly a paradigm shift — in humans, for example, it’s been suggested that the human microbiome is so important to human health that it’s like discovering a new organ system.
Could the next breakthrough come from Lake Mendota?
Lake Mendota is often called the most studied lake in the world. That’s in part because Edward Birge and Chancey Juday helped launch the science of limnology at the University of Wisconsin. The Center for Limnology has been a locus of world-class ecological research for decades, developing some of the most complex ecological models in the world.
It now also happens to be the lake with the world’s most amassed microbial data thanks to 18 years of methodical sampling now overseen by McMahon’s lab. This shared focus on Lake Mendota implies a certain kinship of purpose, but it also stokes a friendly intellectual rivalry.
McMahon knows all about Lake Mendota’s fabled scholarship, but she has her critique: those models ignore microbes. The limnologists say that the microbes are always there, in pretty much the same numbers, and they always do pretty much the same thing: turn dead things back into their constituent nutrients and carbon dioxide. Why worry about them?
“I think Trina has been very bold in being willing to do the Birge and Juday thing, the pure descriptive phase of it,” says recently retired UW Center for Limnology director Stephen Carpenter. “As a basic science enterprise, I totally support it.”
At the same time, he acknowledges it wouldn’t be hard to find ecologists who would question the return on investment so far. “That kind of modeling is very important,” McMahon acknowledges in return. “But it glosses over all of the mechanism. I want to understand the mechanism.”
Just one example: over the last decade, microbial breakthroughs have rewritten our understanding of the nitrogen cycle, the natural processes that convert nitrogen in the environment into different chemical forms. “Because there may be something in the mechanism that fundamentally changes the coarser scale models in a way that you can’t predict.”
Robin Rohwer winces as she opens her laptop to launch R Studio, an interface used for statistical programming. Her left middle finger is broken and bruised, the result of an epic race-day capsize in Lake Mendota. It was so windy the race was canceled, and five of the six sailboats dumped on their way back in.
A lifelong lake junkie, Rohwer knows lakes, the look and feel of them. If you told her what microbes were present, she could probably tell you the color of the water. But if you broke out mugshots of Lake Mendota’s most common bacterial species, she wouldn’t recognize a single one. For a fish biologist or a botanist, that would be unthinkable.
Rohwer uses R Studio as her X-ray spectacles. She wasn’t a programmer when she started in McMahon’s lab in 2011, but now she has a library of personal code. “I just make a loop and look at it in a ton of different ways,” she says. By season, by week, by top 10, by temperature, depth, and light intensity.
The resulting kaleidoscope of graphs are exploratory plots that guide her toward a more intuitive understanding of the data. “When I visualize them, what I see in my head is the curve over time,” she says. “Is it spiky? Is it smooth? That’s how I think. Even if you don’t see a pattern, it gives you an idea of something to start with.”
It’s a necessary perspective given the crazy diversity of microbes. Rohwer’s been trying to decode 11 years’ worth of bacterial samples collected from the deepest point in Lake Mendota between 2000 and 2011. The mission: identify everything in these 95 samples.
During this time, as many as 29 fish species were found in the lake alongside 18 species of zooplankton and 16 species of aquatic plants. For microbes, the magic number might be 17,437. That’s not 17,437 species, but 17,437 OTUs, or operational taxonomic units. “We can’t use the word species because that’s taken by the microbiologists,” she says. They have very strict definitions of a microbial species. “But we need to call it something in order to work with it.”
Microbes facilitate the cycling of almost every nutrient through the lake ecosystem, and their DNA contains signatures of these chemical reactions. Rohwer uses these signatures and other genetic fingerprints to sort the microbes into OTUs. What emerges is a rough picture of “who” is probably doing what.
While the majority of bacteria survive using fairly basic life chemistry, bacteria are so prolific and diverse that you can’t rule out the possibility of something really funky, something you couldn’t even imagine. It’s microbes, after all, that have evolved to survive temperatures above boiling and to tolerate toxic heavy metals. “Microbes are crazy diverse,” McMahon says. “We don’t know if 17,437 actually means that there are truly 17,437 different ways of making a living in the lake, or 25. That’s one of the things that we’re trying to figure out.” Those 25 OTUs are the most common threads, present most of the time, and clearly the workhorses of the lake.
Then there’s the remainder, making up the majority, called the “long tail” because that’s what their frequency of occurrence looks like when plotted on a graph. Most of these 17,437 OTUs occurred only once, on one day, but this rare biosphere makes up a huge proportion of the data set. “What is this deep diversity doing in the ecosystem?” Rohwer asks. This is a primal question driving microbial ecologists, but she just shrugs: not enough data.
Realistically, they have little idea of what even the common bacteria do. Consider AC1, by a long shot the most prosperous family of bacteria in Lake Mendota. “AC1 is just so abundant and nobody knows what it does,” Rohwer says. But here’s the kicker: Twenty-five years ago, nobody even knew that AC1 even existed.
Continue reading this story in the Fall 2017 issue of Grow magazine.