As humans, we rely on the community of microbes in our gut to help us thrive. These microorganisms, collectively known as the gut microbiome, serve many purposes. Chief among them are helping us breakdown food into nutrients that our bodies can absorb and use and preventing harmful pathogens from taking hold.

So what is a poor plant to do without a gut? Use its root microbiome of course! The root microbiome is the collection of bacteria and fungi that live in the soil in and around the plant’s roots. The root microbiome is remarkably diverse and fluid in its composition. One gram of soil from the roots can contain up to one billion bacteria from as many as 10,000 different species. To compare, one millilitre of intestinal fluid from a human contains similar numbers of microbial cells but they represent only 500 to 1000 different species.¹

The relationship between a plant and its microbial co-dwellers is generally one of give and take—the plant secretes carbon-rich sugars through its roots to feed the microbes and the microbes help the plants take up more nutrients from the soil and prime its immune system. Beyond this, we know surprisingly little about just what and how exactly all those microbial partnerships are contributing to plant health.

Dr. Ian Baldwin leads a group of researchers in the department of molecular ecology at the Max Planck Institute for Chemical Ecology in Germany. His team uses the wild tobacco plant Nicotiana attenuata to study the complex interactions between plants and microbes. In a paper published last week in the Proceedings of the National Academy of Sciences, the researchers describe how the root microbiome rescued plants from sudden-wilt disease.

As part of their ongoing studies, the researchers had been planting tobacco plants continuously on the same plot of land for the past 15 years. Eight years ago, they started to observe that some of their plants would suddenly wilt and die. The disease also caused the plants’ roots to turn from white to black. Over the years, their plants started showing symptoms earlier and mortality increased. By 2012, more than half of the tobacco plants in their original plot died from sudden-wilt disease. The researchers had unintentionally recreated one of monoculture farming’s most common problems—pathogen accumulation.

When the same crop is planted again and again in the same soil, pathogens can accumulate in the soil leading to disease outbreaks. That’s (one of the reasons) why crop rotations are so important to maintaining healthy soil—alternating crops break the cycle of transmission and disease. Taking advantage of this natural experiment, the researchers set out to test different control methods to improve survival of their plants.

Before they started testing different strategies, the researchers first wanted to know what they were up against. They isolated 36 bacteria and 70 fungi species from the roots of diseased tobacco plants and identified several pathogenic fungi as the most likely candidates for causing the wilting epidemic.

In the first stage of testing, the researchers assessed the effectiveness of different biocontrol strategies. Biocontrols are beneficial organisms, such as bacteria or fungi, which protect plants from pathogens. The researchers chose four native fungal isolates and six native bacterial isolates that they had harvested from the roots of healthy tobacco plants grown in the same field as the diseased plants. They also tested a chemical strategy using a fungicide. Treating the seeds before planting with either the fungicide or a mixture of all six bacterial species significantly reduced mortality when the seedlings were exposed to the pathogenic fungi later on. Only two native fungal isolates had an effect on reducing seedling mortality in the lab.

One of the biggest challenges with studies like this is that results from the laboratory are often hard to replicate under field conditions. The researchers hoped that by choosing biocontrols that were native to the plant, they would increase their likelihood of success.

Indeed, when they repeated their experiment in the original field, the researchers found that only plants whose seeds were treated with the mixture of bacteria showed improved resistance to sudden-wilt disease. Approximately 2.5% of plants treated with the bacterial mixture succumbed to disease whereas roughly 11% of untreated control plants died. Plants that had been treated with either fungicide, a mix of the two fungal isolates, charcoal (which has been shown in other studies to mitigate disease symptoms) or a combination of fungicide and charcoal fared as poorly or worse than control plants. Furthermore, these treatments also reduced plant growth unlike the bacterial mixture treatment, which had no effect on the plant’s growth rate.

Having established that the mixture of six bacterial species was effective in protecting against sudden-wilt disease, the researchers next asked which specific bacterial strain, if any, was responsible. They examined this first in the lab by systematically creating bacterial mixtures that were missing a single strain. From this, they identified three strains, K1, A176 and E46, whose absence significantly reduced the protective effect of the bacterial treatment and two strains, B55 and A70, whose absence produced no effect. When the researchers repeated this experiment in the field, they found that treatment with a mixture of K1, A176 and E46 reduced mortality by 36% compared to the 52% reduction in mortality seen with a mixture of all strains. Even though the mixture of just B55 and A70 had no effect on plant mortality, they act synergistically with the other three strains to produce the largest reduction in plant mortality when all five were mixed together. These findings highlight the fact that like in the human gut microbiome, no single species in the root microbiome is responsible for its beneficial effects.

With more work, biocontrols could become a promising alternative to traditional chemical-based methods of disease prevention and control. However, given the diversity of root microbiomes and plant needs, there is unlikely to be a “one size fits all” solution that can be applied generically to all plants to protect against all diseases. To improve the chances of success, treatments will likely need to be tailored to individual plant species by selecting microbes that are native to those species and that provide protection against the specific disease.

References: 
1. Berendsen, R., Pieterse, C., & Bakker, P. (2012). The rhizosphere microbiome and plant health Trends in Plant Science, 17 (8), 478-486 DOI: 10.1016/j.tplants.2012.04.001

2. Santhanam R, Luu VT, Weinhold A, Goldberg J, Oh Y, & Baldwin IT (2015). Native root-associated bacteria rescue a plant from a sudden-wilt disease that emerged during continuous cropping. Proceedings of the National Academy of Sciences of the United States of America PMID: 26305938