The Secret Lives of Bacteria

CONSIDERING HOW WELL STUDIED THEY ARE, SOME LARGE GAPS remain in our scientific understanding of bacteria. For instance, we don’t yet know how bacterial chromosomes are separated into daughter cells during cell division or how their complicated chemical language really works. Using techniques from a broad spectrum of fields—including biochemistry, genetics, materials science and engineering—biochemistry professor Doug Weibel is designing advanced microtools and novel experimental setups to answer, for the first time, persisting questions about these surprisingly complex microorganisms. Through this basic work, he’s finding novel antibiotics and other interesting drug candidates.

Why are there still so many major unknowns about bacteria? How can that be?

The issue with bacteria is they are so small. By comparison, eukaryotic cells are enormous! For a calibration point, a human hair is about 100 microns in diameter. That’s about the thickness of a piece of scotch tape. And a eukaryote—when it’s spread on a surface—is maybe 40 microns in diameter. But the bacteria we look at are about one micron long, and their short axis is just several hundred nanometers. Until recently it was very difficult to look at them under a microscope and see anything useful going on inside the cell. Fortunately, there’s been a revolution in optical microscopy techniques over the last five years, and now we can see inside them with pretty good resolution.

How has our understanding about these microorganisms grown in recent years?

Historically, bacteria have always been thought of in the context of the way that we studied them: as individuals. They were always freely suspended in liquid nutrients and were dilute enough so that they never made physical contact with each other. But it’s pretty clear now that many bacteria in the ecosystem exist in tight-knit communities.

And during certain developmental stages, bacterial cells will display collective dynamics, where they are no longer acting as individual cells—as little one-bit processors—but are actually making collective decisions. In these cases, they are communicating and acting more like a multicellular organism—as something a lot more sophisticated than we’ve ever really appreciated.

Tell me more about this collective behavior.

A lot of people know that bacteria swim in solution, but they also swim in groups on surfaces. This collective movement on surfaces is called swarming.

As the bacterial community moves across a surface, the cells mix—and this mixing ensures that all of the cells get nutrients and growth factors to continue replicating. Swarming allows the cells to grow explosively and to colonize whatever niche they’re provided with.

What are you trying to learn about swarming in your lab?

We’re trying to figure out two things. One has to do with behavior: How does the motion of individual cells on a small scale lead to the pattern formation—the continuous mixing—of the swarm on a large scale? The other question is really the biochemistry of how it works. How do cells sense the surface and then change their morphology to interact with it?

This work should tell us some basic rules about how cells sense things outside of themselves—from fluids to surfaces to other cells. I think this is super interesting.

Many bacteria in the ecosystem exist in tight-knit communities.

Can you describe one of the microtools you’ve developed to study bacteria?

Sure, but let me give you some more context first. In addition to studying the physical interactions between bacteria during swarming, we’re also interested in the role that chemical communication plays in the development of swarms. And swarming is just an early stage of biofilm development, so we are also interested in biofilms, which are basically bacterial communities that are firmly attached to surfaces.
One question that’s been in the field for a long time is, what is the length scale over which these chemical signals can be propagated? That is, if you have a swarm or a small early-stage biofilm that’s secreting signals, how far away does another biofilm have to be before it can no longer eavesdrop? To answer this question we created a microtool that we call the waffle.

The Infection Eaters

Bacteriologist Marcin Filutowicz specializes in developing antimicrobial technologies that one day may help replace antibiotics—and save lives—as the power of our antibiotics arsenal wanes. But he doesn’t stop there. Filutowicz has founded or co-founded three biotech companies to help ensure that his technologies actually make it into the world’s hospitals. The idea for his newest venture, Amebagone, founded this year, sprung from his work investigating a collection of soil-borne amoebas assembled decades ago by UW bacteriologist Kenneth Raper, who is best known for helping ramp up penicillin production in time to save thousands of soldiers wounded during World War II.

Grow Magazine: Let’s start with the basics. What’s an amoeba?

Amoebas are unicellular organisms. They are not animals or plants or bacteria. They are protists, which is a whole separate group. And what they do, their sole purpose in life—as much as we can say—is to feed on bacteria. So this is their primary source of sustenance, and once they eat all of the bacteria in their environment they yell at each other—using chemical signals—and gather together.

On the Petri dish, you can see them swarming when they decide to aggregate. Initially, they form something that looks like a slug. It’s a community of a million or so amoebas that are packed together into a sack. The slug moves around looking for more food. If it can’t find anything to eat, the slug transforms into stalks and spores that get distributed by the wind. When the spores land on moist soil, they germinate and start eating the bacteria in the soil, and the process repeats itself.

How did you start working with these organisms?

For one of my companies, PlasmiGon, we needed access to libraries of small molecules to be successful. After screening a few libraries that were available to me, I started thinking about other potential sources of small molecules, and I realized that Ken Raper, who established the whole field of amoeba studies, had left a huge collection of amoebas in our department. This collection involves over 1,000 different amoebas gathered from five continents and several island nations. So it’s extremely diverse in terms of the geographical locations. It represents a huge resource of diversity of small molecules.

So my take was, why don’t we start reviving these amoebas and come up with techniques to look for useful small molecules produced by them? So we started opening those samples, some of them 70 years old. And then the issue was, well, how do you propagate them? Because, to be honest, I knew nothing about amoebas.

I went to a colleague and asked, “How do you grow these beasts? Do you grow them like bacteria?” And he said, “You feed them with bacteria.” The moment he said that—“You feed them with bacteria”—I went back to my office and I quickly computed all of the information I had learned over the past few days. I realized that this could be a new biotherapy because the particular amoeba we wanted to grow, Dictyostelium discoideum, is benign. There was no single report of it having adverse effects on humans, animals or plants. It’s an organism that you simply put alongside bacteria, and they do nothing else but eat it. I disclosed this to WARF in 2009, but they turned my disclosure down.

That’s surprising.

Not really. At the time, we didn’t have any proof-of-principle, no data, nothing. It was just an idea. But I decided that I could not let it die. I decided to form Amebagone and let that company patent the technology.

How do you picture amoebas being used in medicine?

Right now we’re focused on methicillin-resistant Staphylococcus aureus (MRSA). This MRSA is a major agent of nosocomial infections in hospitals. It kills a lot of people. And it happens that two billion people on this planet carry staph in their nostrils. It is part of our natural biota. They inhabit a very narrow area in our nostrils that has just the right temperature and salinity, so they are not all over. They are compartmentalized in a band or section of the nostrils.

And we all touch our noses. We can’t help it. As we touch, there’s moisture in there, and so we contaminate our fingertips. And after surgery, it’s natural to want to see the wound, and in many cases people accidentally self-contaminate the surgery site just by lifting up the dressing to look at it.

But if we can deliver amoebas to the nostrils pre-surgery, we can essentially decontaminate the nostrils of undesirable microbes. We did proof-of-principle experiments with MRSA, and amoebas eat MRSA like crazy. So even though antibiotics cannot kill MRSA, amoebas can.

How Bacteria Move

FOR SUCH TINY ORGANISMS, BACTERIA lay a big footprint on our lives. And one reason why is that they can really get around. Most bacteria are able to navigate nimbly in a host of environments—including our bodies—to find food or a host, and the results can be both helpful (such as when bacteria boost our immune system or aid with digestion) or terribly destructive. But how does a brainless, single-celled organism plan its peregrinations? Doug Weibel, assistant professor of biochemistry, explains:

  • Whip it: One of the most common methods of transport for bacteria is with the aid of flagella, thin, whip-like structures that extend from the cell walls of many kinds of bacteria. Some bacteria have a single, tail-like flagellum or a small cluster of flagella, which rotate in coordinated fashion, much like the propeller on a boat engine, to push the organism forward.
  • The hook: Many bacteria also use appendages called pilli to move along a surface. These pilli, which can cover the surface of a bacterium like tiny hairs, bind receptors and pull a bacterium forward when retracted. Pathogenic bacteria such as Salmonella deploy this method of mobility when moving along the surface of a human cell in search of a place to dig in.
  • Getting warmer: With no brain to supply motivation, a bacterium instead must rely on chemical cues from its environment to provide an impetus to move. This process, known as chemotaxis, is completely involuntary. Bacteria simply respond to the tugs and pulls of their environment to take them to useful places. A bacterium tracking down a chemical stimulant (such as a nutrient) moves in a way known as “random walking.” About once every three seconds, a moving bacterium will suddenly “tumble,” a brief pause that allows the organism to reorient itself. If the chemical cues are right to continue, the bacterium will begin moving on the same path. If not, it will change course, creating a jagged path toward its destination.
  • Joining the crowd: Some bacteria don’t just seek out nutrients—they also seek out each other. Like dancers in a performance, these strains cluster together to create swirling patterns of coordinated motion. Congregating bacteria also can join to form a biofilm—a thin matrix of bacteria stuck together on a surface. Bacterial cells in a biofilm can have characteristics that aren’t present when they develop on their own, and it’s believed that biofilm formation may play a role in many bacterial infections that affect humans. The discovery and exploration of these forms of bacterial collaboration has changed how scientists regard these organisms, which the more we learn about them seem anything but simple.

Turning Dirty Bombs into Clean Silage

When the Soviet Union was dissolved in 1991, a group of microbiologists in Kazakhstan lost their jobs. And that’s a good thing, because they’d been employed to develop biological weapons.

But if you’re interested in world security, it’s probably not a bad idea to keep people with this kind of expertise off the job market, which is why the U.S. Department of Agriculture retrains former weapons makers to do agricultural research. Sponsored by the state department, the program teams U.S. researchers with colleagues in former Soviet republics to redirect their microbiological talents on problems that will lift the economies of their home countries.

“The goal is to help them develop production of commodities that could be used commercially, either domestically or for export,” says Paul Weimer MS’75 PhD’78, a bacteriologist who participates in the program.

Weimer and Richard Muck, scientists with the USDA’s Agricultural Research Service who hold appointments on the CALS faculty, have traveled to Kazakhstan twice and will return this year. Kazakh scientists have also visited the UW-Madison campus, where Weimer and Muck have demonstrated improved techniques for making silage.

Although Kazakhstan is in the middle of an oil boom, it’s still largely an agrarian country with extensive grasslands. Thanks to oil, incomes have improved, creating interest in new foods and ways of eating. This has led to a “mini dairy boom,” says Weimer. “But they don’t have strong dairy production system in terms of feed analysis and the technology to grow high-quality forages. We’re helping them develop enzyme preparations that will help them upgrade their grasses to make better silage.”

In the course of the Kazakh scientists’ former line of work, they had researched countless native bacteria and fungi and discovered some that produce an effective cellulase, an enzyme that breaks down cell walls and release sugars. Weimer and Muck helped them find ways to put these native microbes to work making silage.

“Their results look pretty promising,” Weimer reports. In fact, quantities of the Kazakh enzymes may soon be on their way to Wisconsin, where Muck and Weimer will use them to make silage and feed cows.