Most in the seed industry are well-familiar with the concept of biologicals: a broad category of microorganisms, plant extracts, biochemical compounds and other products derived from natural sources that are used to protect plants, enhance growth or combat pests. Biological additives, whether in the form of seed treatments, soil additives or foliar sprays, are only one component of a much bigger story about how seeds and plants interact with the microbiome. Researchers are currently just scratching the surface of how critically important bacterial populations are to plant health, resilience to various stresses and ultimate productivity.
“We are at the very tip top of an iceberg. The microbiome is just as important to plant health as it is to human health, and we’re only just starting to understand it even in human health,” says Jeffrey L. Dangl, the John N. Couch distinguished professor of biology and an investigator of the Howard Hughes Medical Institute at the University of North Carolina at Chapel Hill. A leading authority on plant immune systems and microbial interactions, Dangl heads a lab that investigates how plants recruit beneficial microbes from their environment and how these interactions influence plant health and growth.
The Challenge
Leveraging the microbiome is an extremely exciting frontier that could have huge ramifications to plant resilience and productivity, especially around climate change / extreme weather resilience and fungal disease resistance. However, there are big challenges that need to be overcome to achieve those gains. Currently, adding a biological to the growing environment typically translates to short-term gain. Much more could be possible if researchers can first overcome some major hurdles, Dangl says.
“The key issue in anything adding to the microbiome, whether you apply them or you build a plant to recruit them, is that they have to be able to invade into a pre-existing community, and they have to be able to persist there,” he explains. “Those two things — invasion and persistence — are extremely difficult to do. That, at least in my view, is the nub of the problem and the rate-limiting step of designing microbials or the plants that recruit them.”
The most direct way to engage a plant’s microbiome is via a biological that impacts the plant root or leaf microbiome. A typical bacterial community on plant roots consists of between 100 and 300 bacterial species. On leaves, the bacterial population is typically made up of between about 30 and 150 species and their associated strains. There is large strain variation within any one of these species, making the combined metagenome of leaves or roots on a given plant cultivar extremely complex. The challenge is that these microbial communities operate in balance. Unless a major event occurs that interrupts the balance, the community’s natural balance makes it extremely resilient to invaders.
“It’s no different than your gut. So long as your gut is in balance, that balance is extremely hard to disrupt,” Dangl says.
Interestingly, it’s not just foreign bacterial species that have trouble making inroads into an existing community. Even species of bacteria that are ultra-common in soil — so common that one would think their population should be easy to support and establish — are, in fact, difficult to manipulate.
For example, the most widely known beneficial bacteria in the soil microbiome is rhizobia. Much work has been conducted on finding supernodulators: rhizobia mutants that produce more nodules on legume roots and, correspondingly, fix more nitrogen. Strains of supernodulators have been isolated and introduced, yet even they — despite rhizobia already being a key player in the microbiome’s balance — have a very difficult time finding a long-term foothold in the bacterial community.
“There was a study done in North Africa some time ago,” Dangl says. “The researchers dipped seeds in various strains of rhizobia, then dug up the resulting mature plants to look at the nodules. The oldest nodules are closest to the top of the root. As they went down the root looking at the nodules, they could tell the difference via PCR of the rhizobia. They found the inoculant in usually about the first four to six nodules — the ones the plant produced earliest — but, after that, it was all a natural strain of rhizobia. That means the inoculant strain had been pushed out of the community. So even though you’re dunking these seeds in your strain of interest, that strain is horribly inefficient in maintaining itself in the environment.”
The rhizobia example is evidence that even a common species may be inefficient in colonization because selection is more specific than species.
“There are certain families of bacteria that are always recruited. But if you drill down through any bacterial genus from species to the specific strains, the variation is huge,” Dangl says.
Current Benefits
What this currently means is that, while some biologicals offer proven efficacy in theory, they may lack return on investment in practice, he says.
“If you think about biologicals for things like fungal control, you may end up adding spray 10 times a season because the bacteria — even if they’re very effective at enhancing fungal resistance — simply don’t make it long enough to give you protection that you need.”
This doesn’t mean conventional biologicals can’t be effective in some instances, Dangl says.
In some cases, a short-term biological gain is itself sufficient benefit. For example, coating a seed with the soil bacteria that are associated with the primary plant growth regulators auxin, ethylene and cytokinin could get that seed off to a stronger start, potentially helping the resulting plant survive its most vulnerable germination and emergence stage.
“In some cases, it’s about giving the seed a huge head start. In my rhizobia example, instead of having to recruit those rhizobia naturally in the soil and then have them proliferate to form a module, you’re flooding the seed and, once it emerges, the root with the bacteria,” Dangl says. “So, you’re just upping the frequency of some event that you know needs to happen with or without you. Even if it’s a short-term gain, that’s a critical gain. But that’s a very different goal than applying a rescue biological to save a crop from drought after it hasn’t rained in a month. In the latter case, we’re not there yet.”
In other cases, a particular biological solution might align with the unique bacterial community that already exists with a specific cultivar in a specific field. Dangl says farmers should absolutely try new options but should do so with their eyes wide open and their scientist hats firmly in place.
“Farmers are great experimenters. They need to verify [strip trial] for their soils, their bacterial communities, their cultivars,” Dangl says.
Engineered Solutions
One work around of the challenge of invasion and persistence is to attack the challenge as an engineering problem: essentially ‘gluing’ a specific microbe to a root biochemically. That concept has been proven for decades. Beginning in the 1990s, French researcher Yves Dessaux and his colleagues designed plants that secreted specific sugars, then engineered a bacterium that depended on those sugars but couldn’t produce them on its own. This created a symbiotic relationship where the bacterium had to colonize the plant roots to survive, showcasing a sophisticated example of how plants and microbes can be engineered to cooperate.
In the three decades since then, significant work has been done on microbial engineering to customize microbial communities to create ‘designer’ seed microbiomes. By identifying specific microbes that perform critical functions like nutrient solubilization or pathogen suppression, researchers are finding ways to engineer seeds to recruit these beneficial microorganisms in a targeted manner. This approach could lead to crops that are naturally more resilient to environmental stresses, including drought and salinity.
Dangl sees big opportunity for engineered solutions ahead.
“I think eventually we’re going to see a lot more of driving a microbe to a host biochemically. And we’re in a GMO world now, which I’m a firm believer in. There are challenges — we have to engineer in fail-safes if we’re releasing engineered bacteria into the environment, but that’s possible because they can be made to be biochemically dependent on the host plant,” he says.
Companies like Pivot Bio are leading the charge in another type of bacterial engineering. Pivot Bio has successfully altered the DNA of a strain of bacteria to enable that bacteria to convert atmospheric nitrogen to ammonia at corn plant roots. Within five years of the technology’s introduction as a seed treatment, it is already being used on 5% of U.S. corn seed. The company says the product’s use in the last two years alone has prevented the release of 932,500 metric tons of carbon dioxide equivalent.
Bacterial Recruitment
While biologicals are generally formulated products of selected microorganisms or compounds that are applied to the soil, foliage or seed with the intention of changing the existing microbiome, another stream of related research focuses on harnessing and leveraging naturally occurring microbial communities.
Instead of trying to force-fit bacteria to new environments or engineer plant-bacteria relationships, Dangl’s team is focused on this kind of ‘natural’ recruitment of microbes. He and his team are searching for specific strains of naturally occurring bacteria that offer drought resistance and, rather than being a foreign introduction, already exist in conjunction with individual crop cultivars.
Using researchers’ favorite R&D plant, Arabadopsis, on agar plates in the lab, they start by mimicking a drought environment.
“The drought-stricken plants look terrible,” Dangl says. “They’re about one third the size of control plants. Then we take our collection of bacteria – maybe 20 or 30 strains, all of which are isolated from various soils but are the same genotype [of bacteria] and from the same [crop cultivar] — and we treat the sick plants with the microbes. Our goal is to find a specific strain that rescues these terrible, ugly plants back to a quasi-normal plant. We’re trying to find effective strains that are already adapted to the host.”
He says finding effective strains for individual cultivars is “absolutely do-able”. That’s the good news.
The not so good news is that a strain that proves a game-changer in one cultivar may fall entirely flat in another cultivar. He admits it’s a daunting challenge.
“So now imagine you’re a wheat farmer and you want a biological to control fungal infection, drought or another issue. You may need a particular strain for your cultivar. And it’s more than that, because the endogenous community is different from field to field. So, what works in one field may fail in another under certain conditions.”
What’s Ahead
One thing is certain in plant microbiome research: the future is coming fast. While big unknowns currently remain, Dangl has confidence that manipulating bacteria will play a rapidly increasing role in agricultural production.
“When we started this lab about 15 years ago, we — and I mean the research community — really didn’t know anything [about the microbiome’s interaction with plants],” Dangl says. “The amount of new, truly fundamental knowledge is incredible, and that is just going to increase. We’re on a steep, steep upward climb in knowledge.”
