Scientists seek more microbial might on the farm

Nov 18, 2013

In a lab on the Iowa State University campus in Ames, Chiliang Chen loads tiny vials containing soil samples into a machine called a Powerlyzer. It will smash soil samples to homogenize the tissue and tease out the DNA of the microorganisms within. Chen works with Gwyn Beattie, the Robert Earle Buchanan Distinguished Professor of Bacteriology at Iowa State. Beattie and about two dozen other scientists recently published a report called How Microbes Can Help Feed the World. It’s a recognition that bacteria, viruses and fungi may have much more to offer than anyone is currently exploiting.

Farmers and scientists have long understood that what lives beneath the soil affects how crops grow. That spurred the field of plant pathology, which in turn brought novel ways for fighting plant diseases—warding off infectious viruses and damaging fungi, for example. But now these microbiologists are focused on how to harness the good things microbes can do, with the goal of increasing farmers’ yields and diminishing their dependence on chemical inputs.

“The idea is if you sequence the genome of a microbe that’s beneficial, there are clues in there as to how it’s doing its good deeds,” Beattie said.

Researchers have known for over a century that the bacteria rhizobia helps soybeans get nitrogen from the soil. Now, they can describe the complexities of that relationship.

“Once they both recognize the presence of each other, it’s like a key has been put in the door and this unlocks a process that unfolds that even involves the plant literally laying down cell wall material in a tunnel for the bacterium to come into the plant,” Beattie said. “It’s that sophisticated.”

Beattie says understanding at that level of detail could lead eventually to specific suggestions for farmers. The big question is: how do you grow your beneficial bacterial garden?

She’s hoping that the microbes themselves may eventually lead her to recommendations for farmers seeking to nurture soil health and gain productivity through crop rotation. Those discoveries are likely to be well-received. At a recent agriculture conference in Des Moines, Rick Bednarek, Iowa’s state soil conservationist, urged farmers and landowners to do more to recognize and respect their microbes.

To illustrate the relationship between soil particles and a fungus, he asked volunteers to squirt silly string at different size Styrofoam balls. The balls represented different size particles in the soil and the silly string held them together in an odd-shaped, delicate sculpture.

“What happens when you start tilling?” Bednarek asked, as he whacked the precarious pile of foam balls.

The balls fell down around the people and colorful strips of silly string broke into small pieces as they dropped off the balls. Bednarek’s message: the soil environment is fragile—and vital.

Some agricultural science companies already bring microbes to market. BASF, which calls itself “the chemical company,” makes bacteria based products that exploit the soybean-rhizobia connection. Mark Howieson, BASF’s applications and analytics team leader in Ames, Iowa, says as academic researchers advance the study of microbes, companies like his can push new tools onto the landscape. 

“If you think about what they’re very good at, it’s discovery and finding new ideas and being very close to farmers and understanding what the challenges are,” Howieson said. “And if you look at a company like BASF, we’re very good at development and commercialization.”

The more farmers can make use of good microbes, the less they’ll need fertilizers and other chemicals. But it could take a while. Although Beattie is thrilled that her Powerlyzer can run 24 samples at once, that’s just a very small piece of the puzzle.

“This is the poster child for Big Data in many ways because every single sample has billions of different organisms present in it,” she said, “and you need to have a lot of samples to answer any kind of question about agriculture.”

As she and her colleagues seek those answers, they are striving to reach the American Academy of Microbiology’s goal of reducing chemical inputs by 20 percent and increasing yields by 20 percent in the next 20 years…a tall order for those tiny critters.