The New York Times, June 16, 2016
The world’s crops face a vast army of enemies, from fungi to bacteria to parasitic animals. Farmers have deployed pesticides to protect their plants, but diseases continue to ruin a sizable portion of our food supply.
Some scientists are now investigating another potential defense, one already lurking beneath our feet. The complex microbial world in the soil may protect plants much like our immune system protects our bodies.
Scientists have known about so-called “suppressive soils” for decades. In 1931, a Canadian scientist named A. W. Henry discovered the spores of the common root rot, a fungus that strikes wheat crops, in a range of soil samples. But try as he might, he could almost never get the spores to grow.
Dr. Henry eventually realized that he needed to sterilize the soil to permit the spores to develop. The microbiome in healthy soils keeps pathogens at bay.
But exactly how soil microbes defend plants was a puzzle Dr. Henry couldn’t solve.
Today scientists are cataloging a staggering number of diverse species that live underground, and they’ve discovered some of the ways in which these fungi, bacteria and other organisms fight pathogens. But they’re still a long way from learning how this environment operates, because life in the soil is so complex.
“We don’t have a firm grasp on what it is and what it’s doing,” said Mark Mazzola, a plant pathologist at the Department of Agriculture.
Writing on Thursday in the journal Science, Dr. Mazzola and Jos M. Raaijmakers of the Netherlands Institute of Ecology noted intriguing parallels between soil immunity and our own immune system.
Researchers divide our immune responses into two types: an all-purpose defense against invaders, and precise assaults on specific enemies. Soil microbes seem to rely on a similarly two-pronged strategy.
When soils are loaded with microbes, they use so many nutrients that it’s hard for a lethal blight or other pathogen to gain a foothold. Some may manage to survive, but they don’t flourish — or wreak havoc on plants.
When scientists heat up soil and kill its native microbes, pathogens begin to grow, feasting on the nutrients in the soil and eventually attacking plants.
Along with this general defense, soil microbes can also target individual species of pathogens. Scientists have found that a strain of Pseudomonas bacteria, for instance, can protect wheat from a fungal disease called take-all root rot.
The bacteria are drawn to the damaged roots of sick plants, where they feed on the nutrients leaking out. As they multiply, the bacteria produce a compound that is toxic to the fungus. That toxin, scientists have found, can bring a fungal outbreak to a halt.
Some of the precision weapons made by soil microbes already are appearing at your local garden store. You can buy spores of a fungus called Trichoderma, for example, that attack another fungus that causes Pythium root rot.
“There are some success stories, but they are very few,” said Dr. Mazzola.
One reason that most biological control measures fail, he suspects, is that microbes exist in a dense ecological web, depending on many other species for their well-being. Taking a disease-fighting microbe out of one ecosystem and dropping it into another may leave it struggling to survive among strangers.
Another reason for the low rate of success is that soil immunity is generally not the work of a single species. “As time goes by, we find there are more players,” said Dr. Mazzola.
Making matters even more complex, plants turn out not to be passive beneficiaries of soil immunity. They seem to be orchestrating it.
Recent experiments have shown that when pathogens attack a plant, it responds by releasing chemicals into the soil that attract a number of microbial species. As those microbes gather around the plant, they release compounds that can kill the pathogen.
“It’s a triangle that’s much more complex than we originally envisioned,” said Dr. Mazzola.
Rather than import a single microbe in the hopes that it’s a silver bullet, Dr. Mazzola said, it may be possible for farmers to foster plant-protecting microbes dwelling in their fields. “There are some viable approaches to manage what we have in the system already,” said Dr. Mazzola.
In their own research, Dr. Mazzola and his colleagues added seed meal — the mashed-up husks of mustard and canola seeds — to apple orchard soil. They found that the seed meal encouraged the growth of certain soil microbes, and they in turn protected the apple trees from disease-causing fungi and nematode worms.
Two years after adding the seed meal to the orchards, the scientists found that the ecology of the microbes had changed. New species of protective fungi and bacteria had taken over, and the original ones had become rare. But the soil still continued to defend the trees.
Another potential strategy would be to breed crops that do a better job of summoning the microbes they need.
Experiments have already revealed that various strains of wheat and apples attract different combinations of microbes to their roots. Dr. Mazzola thinks that it may be possible to breed plants that send out a call to bring the best defenders to their side.
“We’re breeding for yield or color, but we’re not breeding for resistance,” said Dr. Mazzola.
Copyright 2016 The New York Times Company. Reprinted with permission.