In a world grappling with climate change and water scarcity, scientists are exploring plant mycobiomes – microscopic fungi that can boost crop resilience to drought and diseases. These fungi shape a plant’s water-saving or water-spending strategies, offering a promising avenue for sustainable agriculture in an uncertain future.
A warming climate with water at a premium sparks tremendous demand for crop plants that will be resilient to drought and other stressful conditions.
According to Christine Hawkes, a Professor at North Carolina State University in the United States, the next frontier for agricultural science is the plant mycobiome. Just as humans have rich communities of microbes in our gut and on our skin, plants do too – woven into their roots, squatting in the pores of their leaves and even inside their cells.
Recent research suggests that we could manipulate the microscopic fungi that interact with plants to make crops more resistant to drought and disease. A new article, published in December in PLOS Pathogens, details the opportunities and potential pitfalls of this emerging field.
“People have been taking advantage of these relationships between microbes and plants for a long time,” says co-author Christine Hawkes, who studies plant and soil microbiomes. “But that does not mean that we know how it works.”
Savers, spenders and a dimmer switch
Right now, “we just do not know enough about microbes” to understand the full potential of this technique, says co-author Xavious Allen, a PhD student at North Carolina State University who studies the interactions between plant pathogens and endophytes – organisms that live among the host plants’ cells and have a beneficial or neutral relationship.
These microscopic fungi that hang out with plants can help the hosts, hurt them or simply coexist. But Hawkes and Allen are most interested in the fungi that change a plant’s survival strategies.
In weathering a drought, plants have two main camps, Hawkes explains – the water savers and the water spenders. “Some plants essentially hunker down and reduce their activity and water use to very low levels,” she says. “Others try to use as much water as possible and hurry up and reproduce before they die.”
Plants achieve both strategies by opening and closing the gates. Water enters a plant through the roots and exits through the leaves – tiny pores called stomata that the plant can open and close to enable the exchange of gases with the environment. The plant needs CO2 from the air to grow, but when the stomata are open for the plant to breathe, the water escapes.
However, recent research indicates that these strategies “are not necessarily intrinsic to the plant but can be modified by fungi,” she adds.
“We do not always know the exact mechanisms,” she says, but certain fungi seem to be able to make plants double down as water savers or spenders – or even switch strategies altogether. “We have seen fungi that will sit in the stoma and stimulate it to close and not open or vice versa.”
Other fungi can help host plants to access resources they cannot reach on their own. “There are also fungi that live in roots that have filaments much finer than the roots,” Hawkes explains. These hair-like filaments can wind their way through dense soil and deliver water back to the plant. “There are multiple ways these fungi can change how a plant perceives drought.”
So how can we manipulate the manipulator and get the fungi to do our bidding? It is not as simple as slathering seedlings with fungal spores, Allen and Hawkes explain.
In short, “not everything in the microbiome lives happily together,” Allen says. “Everything seems to affect everything else – making one small change in a very specific area of function in the microbiome can often have widespread effects on the microbiome itself, either to the functions of microbes that are already there or to the overall structure of the community.”
If your desired microbe is not naturally part of the soil ecosystem where you are cultivating, “it may very well be outcompeted by what is already there,” and the effort and expense of fungal inoculation is wasted, Allen says. At the opposite end of the spectrum, an introduced fungus could overperform and escape into the broader ecosystem, with unpredictable consequences.
And since fungi are incredibly adaptable, you cannot always trust them to follow your instructions – the very same species that can form a beneficial relationship with a plant can flip a switch and devour it if conditions change and the partnership no longer benefits the microbe.
Mycobiome: past and future
Although this new generation of mycobiome manipulation is years away, it is far from science fiction – “people have been manipulating microbes for a long time without realising it,” Hawkes says.
Ancient crop rotation techniques that create disease-suppressive soil actually manipulate the mycobiome, Hawkes says. And legumes, famous for their ability to fix nitrogen and thereby improve soil quality, only get that superpower through a relationship with a microbe called rhizobia that lives on its roots.
In the last several years, fungal microbes have been deployed to help to save endangered plants in Hawaii from disease. Hawkes says there are numerous examples of successful inoculations using Trichoderma fungi, which encourage root growth. “They do a million things,” she says. “They have a very broad niche, which I think enables them to be successful almost anywhere.”
Although mycobiome manipulation is not ready for agricultural prime time yet, Hawkes and Allen see a payoff on the horizon. Hawkes says she is most excited about people working to directly manipulate the genetics of host plants and microbes.
Some groups that study bacterial microbes are “using really novel molecular tools to try and do in situ manipulation in the microbial community, which really gets around a lot of the community ecology problems and the local adaptation problems,” she says. “Right now, what they are doing is things like trying to get horizontal gene transfer from plasmids into bacteria, in real time, to change function.”
Since bacteria do this on their own, “you are taking advantage of a natural process,” Hawkes explains. “I think that this kind of thing will come around to fungi – so you can manipulate the full community instead of having to go through all these tortuous pathways to do it.”