Antibiotics Off the Beaten Path

As more antibiotic-resistant “superbugs” emerge, it’s clear that we desperately need new antimicrobial drugs. Yet, over the past couple of decades, antibiotic discovery has largely been stagnant.

“The reality is there’s almost no new antibiotics that are developed. And that’s because pharmaceutical companies have decreased their investment—in part because of the rediscovery issue,” explains bacteriology professor Cameron Currie.

The “rediscovery issue” refers to the fact that soil has historically been the prime source of new antibiotics—but it seems to be tapped out. When scientists screen soil microbes for new antibiotics, they keep finding the same compounds over and over again.

Currie is part of a team that is looking elsewhere.

Currie and his colleagues have been focusing their efforts on microbes that are associated with insects, plants and marine life from all around the United States, funded by a $16 million grant from the National Institutes of Health that was awarded in 2014.

“One of the major hurdles is finding new compounds, and that’s where we’re really excelling,” says Currie, a co-principal investigator on the grant. His partner is David Andes in the UW–Madison School of Medicine and Public Health.

At the front end, the work involves some good old-fashioned bioprospecting. Currie’s group, which is in charge of the terrestrial sphere, has gathered more than 2,000 flies, aphids, caterpillars, bees, ants and other insects, as well as mushrooms and plants, from locales near and far, including Alaska, Hawaii and Wisconsin’s Devil’s Lake.

Back at the lab, things get high-tech pretty quickly. Microbes are isolated from the samples and tested for antimicrobial activity. Promising strains undergo genetic sequencing that allows Currie’s group to determine how likely they are to produce novel antibiotic compounds. From there, other scientists involved in the grant go on to test the most promising compounds in a mouse model of infection. This approach has already yielded some exciting drug candidates.

“We have 9,000 strains to screen, and we have already found some new compounds that are effective at combating infections in mice and have low toxicity,” says Currie.

With so many samples to process, Currie’s group adopted bar code technology to help them keep track. They have a bar code reader—like you’d find in a grocery store— connected to a lab computer that they use to scan petri dishes, look up samples and add new data. For each microbial strain they’ve isolated, the database has photos of the “host” insect or plant, GPS coordinates for the collection site, assay results, genetic sequence and much more.

At this point, Currie feels confident that the project will pay off, and he’s eager to see one of the group’s compounds go into human clinical trials.

“If you find one new antibiotic that gets used in treatment, it’s a major success. You’re saving people’s lives,” Currie says.

Protecting our Pollinators

People and bees have a long shared history. Honeybees, natives of Europe, were carried to the United States by early settlers to provide honey and wax for candles. As agriculture spread, bees became increasingly important to farmers as pollinators, inadvertently fertilizing plants by moving pollen from male to female plant parts as they collected nectar and pollen for food. Today, more than two-thirds of the world’s crop plants—including many nuts, fruits and vegetables—depend on animal pollination, with bees carrying the bulk of that load.

It’s no surprise that beekeeping has become a big business in the farm-rich Midwest. Wisconsin is one of the top honey-producing states in the country, with more than 60,000 commercial hives. The 2012 state honey crop was valued at $8.87 million, a 31 percent increase over the previous year, likely due in part to the mild winter of 2011–2012.

But other numbers are more troubling. Nationwide, honeybee populations have dropped precipitously in the past decade even as demand for pollination-dependent crops has risen. The unexplained deaths have been attributed to colony collapse disorder (CCD), a mysterious condition in which bees abandon their hives and simply disappear, leaving behind queens, broods and untouched stores of honey and pollen. Annual overwintering losses now average around 30 percent of managed colonies, hitting 31.1 percent this past winter; a decade ago losses were around 15 percent. Native bee species are more challenging to document, but there is some evidence that they are declining as well.

Despite extensive research, CCD has not been linked to any specific trigger. Parasitic mites, fungal infections and other diseases, poor nutrition, pesticide exposure and even climate change all have been implicated, but attempts to elucidate the roles of individual factors have failed to yield conclusive or satisfying answers. Even less is known about native bees and the factors that influence their health.

Poised at the interface of ecology and economy, bees highlight the complexity of human interactions with natural systems. As reports of disappearing pollinators fill the news, researchers at CALS are investigating the many factors at play—biological, environmental, social—to figure out what is happening to our bees, the impacts of our choices as farmers and consumers, and where we can go from here.

Where Are We Now?

TIM DONOHUE HAS SPENT THE LAST FOUR YEARS BUILDING A PIPELINE—but not the kind that springs to mind when we think of fuel.

The professor of bacteriology heads the CALS-led Great Lakes Bioenergy Research Center (GLBRC), founded with $142 million from the U.S. Department of Energy and a groundbreaking charge—to create the next generation of biofuels by harnessing renewable energy from the nonfood plants that are so plentiful all around us: grasses, trees and crop residues.

“We need to create liquid transportation fuels that are more cost-effective, more sustainable and won’t compromise the Earth or our quality of life,” says Donohue. “We’re in the middle of developing ways to generate these new fuels that are essential for powering our daily lives.”

With Michigan State University (MSU) as UW–Madison’s major partner, Donohue has assembled a team that now includes more than 400 researchers and staff and an additional nine member institutions. The effort spans two countries, 11 states and more than 60 individual lab and field facilities.

That’s a lot of brainpower. But the magnitude of the effort is commensurate with the task at hand, Donohue notes.

“We need to be considering everything from roots in the ground to what’s coming out of the nozzle,” Donohue says. “Without such a holistic approach, we won’t be able to demonstrate that this technology is feasible or see the weak spots where we can make improvements.”

What GLBRC has built is a research pipeline, a process that considers all factors that go into developing and implementing cellulosic biofuels—from creating sustainable agricultural landscapes and building better bioenergy crops to innovations in plant biomass processing and converting plant sugars into fuels.

While the promise of creating sustainable plant-based fuels isn’t new, the level of public investment needed to tackle this challenge has only recently emerged. According to the International Energy Agency, the United States leads world spending on biofuels public research, development and demonstration projects, investing $189 million in 2010 alone.

“By relying on fossils fuels, we’re living on energy that arrived on Earth many millions of years ago,” says Steve Slater, GLBRC’s scientific programs manager. “In order to reach a sustainable energy economy, we need to learn to live on the energy that arrives from the sun today. There’s a lot of that solar energy held within plant biomass, if we can figure out how to sustainably convert it to liquid fuels.”

Four years into its five-year grant, GLBRC has made some significant breakthroughs along the research pipeline. Here are some major points of interest.

First Stop: PLANTS

At agricultural research stations in Wisconsin and Michigan, GLBRC researchers tend to tall stands of such biofuel crops as switchgrass and miscanthus, measuring above-ground traits like crop yield and digging down in the dirt to monitor soil microbes and water movement. Sophisticated instruments measure greenhouse gases such as carbon dioxide and nitrous oxide. Researchers count birds and insects to measure biodiversity and use satellite data to capture a watershed-level view of land use patterns.

It’s a lot of information, but each measurement plays a role in determining how these crop contenders would fare as large-scale bioenergy crops.

The leaves and stalks of these potential bioenergy plants are comprised of large quantities of cellulose, the most abundant organic compound on the planet. Cellulose is a polysaccharide, a long chain of tightly linked sugar subunits that must be broken down into simple sugars before they can be processed into biofuel. That alone is difficult—but to make the process even harder, much of a plant’s cellulose is locked within cell walls that form a tough, protective barrier. Breaking past the walls, using enzymes or chemicals to do so, is one of the biggest challenges in creating economically viable cellulosic biofuels.

Plant cell wall structures have evolved over time to fight off pests and disease. The more scientists understand about how the walls are created, the easier it will be to break them apart. DNA sequencing capacity provided by the Department of Energy (DOE) Joint Genome Institute allows plant breeders access to genetic and genomic data that provide clues about how those cell wall layers are built.

While determining the best genetic traits for bioenergy crops is a long-range goal, GLBRC plant researchers already have made important headway when it comes to tackling lignin, one of the toughest compounds that make up plant cell walls. Researchers hope to take it apart to get at the cellulose locked inside and convert small pieces of lignin into valuable co-products. CALS biochemistry professor John Ralph and his team have identified a gene that would allow easily breakable bonds to be incorporated into plant cell walls. They’re calling this new technology Zip-Lignin™ for its ability to break apart—or unzip—the lignin within. By getting lignin out of the way, biomass processing could be completed at lower temperatures. And lower temperatures mean lower overall costs.

And on another track, GLBRC researchers at MSU have located an enzyme that creates a plant oil with unique biodiesel-like properties. Now they’re working to encourage plants to produce more of that oil, which could be used directly as a “drop-in” or ready-to-use diesel replacement.