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Hidden Secrets of the Soil

08:13AM Jan 03, 2015

Ag revolution rolling in the microbial world

Maren Friesen is digging in the dirt, armed with a shovel and Ziploc bag. She’s using primitive tools to search for primitive bacteria—and hoping for a high-tech outcome. Friesen, assistant professor of plant biology, Michigan State University, is searching for a tiny microbe that holds tremendous promise for agriculture and offers a gateway to nitrogen fixing.

If Friesen can track down the elusive bacterium Streptomyces thermoautotrophicus, it might open the door to crop growth without the use of synthetic fertilizers. Earth’s atmosphere is composed of 78% nitrogen—but in a form most crops can’t harness. Bacteria fills the gap for some crops. Soybeans and peanuts have special root structures (nodules) that protect bacteria from oxygen—a nitrogen-fixing killer. However, corn, wheat and rice primarily lack the symbiotic relationship with bacteria and get their 
nitrogen meals through fertilizer.

Michigan State researcher Maren Friesen is on the search for a nitrogen-fixing bacterium.

In the early 1990s, at the edge of a charcoal burning pit, German researchers discovered S. thermoautotrophicus bacterium. This strain  appeared to have a special knack for converting nitrogen from the air to a form plants can use—even in the presence of oxygen, which normally poisons the reaction. Yet, on the cusp of a breakthrough, the bacterium was lost—gone, disappeared. 

“We believe it may have been lost by the lab that was working on it,” Friesen says. “That seems a little strange given how exciting the possibilities were. We don’t know what happened in the lab, but we know the strain is no longer available.”

Whether contamination, mislabeling or a maintenance accident, it was a blow to agriculture research. Friesen is attempting to pick up the trail, sampling soils across the world. If she is able to locate S. thermoautotrophicus or a similarly functioning bacterium, the potential for advances would be immense. 

“The first green revolution was due to a number of factors—and the commercialization of synthetic nitrogen fertilizers was one of those,” Friesen says. “By harnessing beneficial microbes, the hope would be to transfer the same ability that legume crops already have to cereal crops such as corn.”

If Friesen finds a possible strain, she’ll immediately test it to confirm nitrogen fixation. “It’s impossible to know what’s actually in a particular soil until you get it back to the lab to culture it or use DNA sequencing,” she says. “We’ve been targeting habitat, looking for soils close to 60°C—warm soils with levels of carbon monoxide present.”

Would there be a yield reduction for nitrogen-fixing plants? Genetic testing and protein determination will follow, and later, transference to other organisms. Friesen’s ultimate goal is transference to plants. How long might the research chain take? “Time is difficult to gauge for the downstream process, but it would probably take no less than five to 10 years,” Friesen says. “Nitrogen fixation is a complicated process with dozens of genes involved in producing the enzymes.” 

A significant concern for nitrogen fixation centers on a reduction in yield. A plant diverting photosyn-thesis energy to nitrogen fixation might yield less. “Even if there is a yield penalty, it could be far less than the cost of degraded soil or synthetic fertilizer inputs. Certainly, the economics would be a determining factor,” she adds.

Early bacterial technology might be coated on seed, applied as crops grow or engineered into the plant genome. Friesen believes once researchers understand more about plants and microbial communities, the applied information will continue to help farming systems become more resilient. In terms of using microbial diversity, she emphasizes science has only scratched the surface regarding what makes soil healthy for particular plants.

“There are almost no attributes or functions of plants that can’t be altered by the microbes they associate with,” Friesen explains. “Bacteria offer a fantastic opportunity to production agriculture.”

Despite scientific advances, many soil functions remain unknown, particularly at the microbial level. Bacterial soil science in agriculture is still in its infancy, but in the past decade, researchers have developed novel technologies enabling genome sequencing of microorganisms (bacteria, fungi and viruses) to help 
unlock the mechanisms of survival.

When it comes to bacteria and fungi, soil is often a black box, an incredibly complex, invisible world filled with inaccessible nooks. The ability for researchers to look at soil from a microbial perspective constantly demands new technologies to understand microbe-scale life. In the past, researchers had a no-parts list of soil—literally what’s contained inside and what are the related functions—but that has changed and scientists are on the cusp of extracting even more secrets from the dirt. 

“I think we’re going to discover extraordinary adaptability and versatility of microbial partnerships with animals and plants. We’re going to find out why some parts of a field have disease-tolerance and other parts don’t,” says Jack Gilbert, an environmental microbiologist who manages the Earth Microbiome Project (EMP). 

Gilbert’s EMP coordinates scientific projects from across the globe and focuses on all environments, including soil. He picks out specific relationships between microbes and plants, essentially collating science to unlock soil secrets. “The information and data lead directly to heartier plants. When we understandbacteria in soil and plants, we also understand the ability to survive drought, cold temperatures, nutrient-poor environments and diseases,” Gilbert says.

“There are more bacterial cells, viral and fungal, in the soil, than stars in the universe,” he adds. “The diversity is incredible. If I take two soil cores on either side of a crop plant, I’ll find different microbial populations—as different as societies in New York and Tokyo. There are similar roles you can see, but different players and genetic languages being spoken.”

Agriculture is only just beginning to realize the intricate associations of the microbial world. As medicine continues to identify the bacterial roles of human disease, agriculture is keeping pace by investigating bacteria related to crop tolerances and productivity in general. Agriculture and medicine—two of the oldest professions on the planet—have always advanced in tandem, a relationship visible through microbial discoveries. 

“We’re witnessing a renaissance of microbial biology in agriculture and medicine,” Gilbert says. “It’s been a rocket ship of discovery over the past decade, and we’re running to keep up with our own discoveries. The fields of agriculture and medicine are the fuel that’s driving the rocket ship of innovation.”

The more information scientists pull from the recesses of soil, the better positioned farmers are to understand the engines driving crop environments. The bacterial world hides a host of surprises for farmers, and as each layer of knowledge is peeled back, the ability for producers to care for their crops and land increases.

“I like to think of agriculture as sitting on the constant—never too excited about a good year; never too down about a bad year,” Gilbert says.

“Farmers are willing to wait, see and observe over much longer time frames than other professions,” he explains. “By acting on data and long-term trends, maybe farmers are the original scientists.”

To learn more about how technology will advance production agriculture in the next 10 years, visit