Potatoes contain something about which most people are entirely unaware: endophytes, which means “within plants.” Endophytes can also be found in other vegetables, fruits, and grains. In fact, all plants harbor endophytes in the form of bacteria, fungi, and other microbes.
Endophytes eat plant-derived nutrients but typically don’t cause disease. Instead, they bolster plant growth, disease resistance, antioxidant status, or tolerance to stressors such as drought, heat, and cold. Endophytes enable plants to respond quickly to such stressors by expanding their genetic repertoire, according to a review by ecologist Christine Hawkes and colleagues. To improve crop health and sustainability, Hawkes studies how plants, their fungal residents, and such stressors interact.
Given climate-related drought and temperature extremes, declining soil quality, and a decrease in arable land, endophytes, argue Pankaj Trivedi, Chakradhar Mattupalli, Kellye Eversole, and Jan E. Leach, might undergird a sustainable “green revolution” to improve agricultural productivity while lessening reliance on environmentally damaging and health-threatening agricultural chemicals. Endophytes can have an impact, says plant biotechnologist Julissa Ek-Ramos, on “climate change, recovering the soil, and having more healthy food to eat.”
In 1809, German botanist Heinrich Friedrich Link first spotted microbes within plants with the help of a microscope. He dubbed the parasitic fungi he saw “endophytae,” which German botanist Heinrich Anton de Bary updated to “endophyte” in 1866. Until then, the prevailing view, originating with French microbiologist Louis Pasteur, was that diseased plants contain microbes and healthy plants do not. But as microbial ecologist Stéphane Compant and coauthors write, it was another Frenchman, microbiologist Marie Louis Victor Galippe, who in 1887 spotted microbes in healthy potato, lettuce, carrot, and beet plants. Galippe also found them in healthy grains and cauliflower, leading him to propose that they originate from soil and benefit plants. His revolutionary findings earned him criticism.
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“To this work, we must contrast the research of several experimenters accustomed to the difficulties of microbe technique,” wrote Émile Laurent in 1889 (author’s translation), implying that microbial contamination from sloppy lab technique explained Galippe’s findings.
Yet Galippe was correct. In the next two years, work from several researchers converged to show that endophytes can be beneficial to plants. They discovered endophytes, now called “rhizobia,” that live compartmentalized in legume roots, “fixing” nitrogen from air into forms that plants can use while also replenishing the nitrogen in soil. This explained the benefits of crop rotation with legumes. The turn of the century saw the advent of rhizobial soil inoculants for improving legume growth, with the FDA promoting such applications. However, rhizobia associate only with legumes and not with other crops, so researchers began investigating the role of other endophytes in the important staple, potatoes.
Scientists now know that endophytes indeed migrate from soil but also from above-ground sources, entering via leaves, stalks, and flowers, or inherited via seed. In fact, some seeds won’t germinate without endophytes, observe chemists Noel L. Owen and Nicholas Hundley. In 1915, British botanist and mycologist Mabel Cheveley Rayner coined the term “obligate symbiosis” to describe a similar requirement for seed endophytes, having identified one necessary for heather seedlings to develop roots. And similar to our various microbiomes in the gut, on the skin, and elsewhere, different plant tissues host distinct endophyte communities, according to a review by population biologist Maren Friesen and co-authors. Friesen, who studies the coevolution of plants and rhizobia, writes that just one gram of plant tissue harbors between 10 million and 10 billion endophytic bacteria alone.
“I try not to freak people out that there’s microbial communities all around us all the time,” plant pathologist and mycologist Lindsey Becker told me. She notes that people are often aware of pathogenic (disease-causing) microbes like E. coli but are less aware that living things normally carry a microbial zoo. Becker studies interactions among wheat, its resident fungi, and drought tolerance, with the goal of improving crop resilience. Wheat, after all, is one of four crops that, together, supply a majority of the world’s plant-derived calories and protein.
Interest in endophytes as crop “probiotics” has accelerated, stemming from new research technologies, climate change, and the impact of modern crop derivation on plant microbiomes.
“They’ve definitely broken the native microbiome relationship to some extent,” says Christine Hawkes. In addition, Ek-Ramos points out, decades of intensive herbicide, fungicide, antibiotic, and fertilizer use have altered both soil and plant microbial communities; by way of example she points to endophytes of modern corn compared to those of its wild ancestors. Modern corn crops, Ek-Ramos says, “are losing the ones that are helpful for nutrient acquisition, and they are losing the ones for disease control.” Scientists are similarly investigating endophytes of ancient wheat varieties, which, like corn’s ancestors, are more disease-resistant than modern varieties.
Scientists are also examining endophytes from sources unrelated to the target plant. For example, phytopathologist Zoulikha Krimi and team inhibited tomato pathogens and improved tomato germination and growth using endophytes from nettles and other wild plants. Using soil fungi that are also endophytic, Ek-Ramos and collaborators improved drought tolerance and pest resistance of corn, pest resistance of peppers, and pest resistance and growth of sweet sorghum. A different soil-derived endophyte promoted rice growth despite predation by weevils in a study by ecologist Marco Cosme and collaborators.
Meanwhile, microbiologist Sharon Doty and collaborators look to endophytes of wild poplars and willows from harsh environments.
“It’s really amazing how strongly these endophytes can combat the fungal pathogens of crops,” Doty says. And she notes regarding their growth-promoting effects, “It works in maize, in rice, in tomatoes, in bell peppers, and strawberries.” Her team has also isolated endophytes from sweet potatoes that improve the rooting of poplars, a promising biofuels crop.
Endophytes confer additional traits useful for a changing planet. For example, those from geothermal habitats can confer heat tolerance, based on studies led by geneticist Regina Redman. And crop physiologist K. M. Manasa demonstrated salt-tolerance in rice plants inoculated with an endophyte from seaside plants. Rice is salt-sensitive and one of the world’s main food crops. But increasing soil salinity is impacting a fifth of farmable land globally due to climate change and human water and land use practices.
How exactly do endophytes do what they do? Friesen and coauthors share some general explanations. Many endophytes produce compounds that inhibit plant pathogens or are protective antioxidants, for example. Others influence plant hormones that control growth, reproduction, and defense. Some even produce plant hormones. Still others improve access to nutrients such as phosphorus, potassium, and nitrogen.
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Nitrogen is often the most limiting soil nutrient for crops, something nineteenth-century farmers recognized. Agronomist and Nobel Prize nominee Johanna Döbereiner discovered nitrogen-fixing endophytes in non-legume plants in the twentieth century that, like rhizobia, might reduce the need for financially and environmentally costly synthetic fertilizers. Many of the endophytes Doty has characterized over twenty-five years fix nitrogen and promote growth in lab, greenhouse, and field trials but have a much broader host range than rhizobia, extending from farm lands to forests.
While most endophyte studies are lab or greenhouse based, there have been field trials for multiple crops, including Doty’s work in poplars and corn. Biologist Moncef Mrabet led a trial in which a fava bean endophyte bested a commercial fungicide in protecting potatoes from disease, and other trials have focused on bananas, clover, lettuce, and other crops. Ek-Ramos was part of a team that bioprospected cottonfields throughout northern and central Texas for beneficial microbes. They isolated and characterized multiple endophytes that protected cotton from aphids and other insect pests in both greenhouse and field. “We had cotton next to another farm, and they had to apply insecticide,” she recalls.
Through their actions on plants, endophytes might expand what’s considered farmable land, according to a review from a team led by microbial biotechnologist Bita Zaferanloo. This is important given climate change and an expected human population of 9.7 billion by 2050 and includes lands with degraded soils or in inhospitable environments—possibly even off-planet.
“We are looking in space and thinking of the other planets,” says Zaferanloo, who studies endophytes from plants adapted to Australia’s harsh deserts that might render lunar and martian ground more hospitable to crops.
“The Moon is our interest,” says Doty, noting that endophytes might reduce the need for cost-prohibitive transport of nutrients and soil. “We’ve learned from microbes in plants that are growing in these really hostile environments, even lava fields in Hawaii,” she says.
Despite many compelling findings and goals for endophyte use, the mechanisms governing their interactions with plants remain poorly defined. Endophytes can be unpredictable; for example, increasing rather than decreasing aphid infestation of beans and wheat, as noted in research from Denmark, or switching from beneficial to parasitic depending on water availability, as Hawkes witnessed.
“It’s not just the function between the plant and the microbe, but the surrounding environment,” she says. “The complexity is what’s interesting and the complexity is also the hurdle.”
An endophyte might not even colonize the target plant—something Rayner noticed nearly a century ago. And Hawkes notes that endophytes benefitting one crop might be detrimental to another. Indeed, the line between endophyte and pathogen is blurry. This underscores the importance of lab and greenhouse study before moving outdoors, where the situation’s more complicated.
Spread to nontarget plants is a concern scientists debate. Hawkes has seen the reverse, with microbes from nearby vegetation likely colonizing crops, though she doubts all introduced endophytes will succeed in a new environment. Meanwhile, one of the risks Friesen sees is the spread of spores from fungal endophytes, but, she says, “probably the vast majority of the time adding these is not going to be a big deal.” She’d like more monitoring for spread. Accordingly, in a three-year field study by Doty and collaborators, endophytes from inoculated trees did not spread to adjacent uninoculated trees. And Doty notes that there are regulations on endophyte use. For example, species of endophytic bacteria can only be used in states where they already exist.
Safety assessment for people is also critical, note Zaferanloo and team. Humans have always ingested endophytes given that endophyte–plant cohabitation goes back hundreds of millions of years, and endophytes contribute to our gut microbiome. But not all endophytes are safe. For example, certain grasses contain compounds from endophytes that sicken grazing animals.
“Our regulatory systems are working to make sure that it’s safe,” says Doty, noting that species considered for use in the United States can’t be known human pathogens. But she’d like testing for known pathogenesis-related genes that, within a single species, can be present in one strain but not another. She offers the analogy that some people are murderers, but not everyone is despite being the same species.
Developing real-world endophyte applications is a complicated challenge, but a necessary one given the need for more productive and sustainable agriculture. In the meantime, skeptical farmers are getting onboard.
“There’s a lot of conversations going on between researchers and farmers,” says Friesen, to “move the needle on our understanding of these processes that are so important for soil health but also plant health and the stability and security of our food supply.”
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