Beneficial microbes living in and around a crop’s roots could be powerful allies in the fight to keep plants alive through droughts, especially as climate change worsens. But before scientists can harness these microbial partners to make crops more resilient, they first need to better understand how drought affects the long-term relationships between crops and the root microbiome.
Now, a team of scientists at the University of California, Davis has shown that prolonged drought causes lasting changes to the microbiome of rice roots. The findings, recently reported in Nature Plants, point to one microbe in particular that could help rice recover from one drought and prepare for another, perhaps highlighting a means for crop resistance in the decades to come.
The researchers began by planting rice—a crop especially susceptible to drought—in a greenhouse. When the seedlings were young, the researchers stressed the plants with drought lasting 11, 21, or 33 days, while continuously watering some plants as a control. Throughout the growing season, the team regularly sampled the microbial taxa within and near roots, and identified these microbes by sequencing a portion of the so-called 16s ribosomal RNA gene, which varies widely across microbes.
The researchers knew from their own previous work and others’ that the root microbiome of well-watered rice shifts predictably over time—so much so that the composition of the microbiome at any point can indicate the age of the plant. They also had learned previously that drought delays the typical progression of the root microbiome.
In the present study, as expected, the microbial communities began shifting from normal development the moment the water was cut off and continued to diverge for as long as the drought persisted.
After the two milder droughts ended, the root microbiomes quickly bounced back. But following the 33-day drought, a full 50 days passed before the overall microbial composition inside the roots looked similar to the microbiome of continuously-watered rice roots.
The team then homed in on a subset of microbial taxa that are especially tied to a rice plant’s age. For plants in the 21- and 33-day drought treatments, some microbes that typically colonize rice roots late in the growing season were delayed and never reached normal levels.
Meanwhile, other bacteria increased under drought treatments, and the overall diversity of the root microbiome actually remained fairly constant. Only the abundance of the individual players fluctuated with different drought severities.
Exactly how this overall shift in the microbial community affects the health of the plant is unclear, says study author Venkatesan Sundaresan, a plant geneticist at the University of California, Davis. But one microbe in particular, a taxon of Streptomyces, appears to play an important role in weathering a dry spell. This microbe was prevalent in rice roots during and after drought—making up, on average, 13.5% of all microbes within the roots by the end of the 21- and 33-day droughts.
By running a follow-up drought experiment, as well as reanalyzing data from previous studies, the team confirmed that this Streptomyces is consistently abundant during droughts in the root microbiomes of several rice cultivars grown in a range of soils. They wondered what, if any, function it could serve the rice. “For all we knew, it could make plants sick,” says Sundaresan.
To find out, the team cultured a Streptomyces strain whose stretch of the 16s ribosomal RNA gene closely matched that of the Streptomyces identified in the experiment. When they inoculated rice seeds with this microbe, the resulting plants grew longer roots in both wet and dry conditions. In dry conditions, the extra root length was modest because plants tend to limit growth to conserve resources during a drought, explains Sundaresan. “Once drought goes away, then the roots can continue to grow longer because of this bacterial strain that’s hanging around, and now it can make a difference, not for the former drought but for the next episode.”
“Microbiome management is a new area,” says ecologist Posy Busby of Oregon State University, who was not involved in the research. “This study is important because it shows that there are persistent compositional changes in the rice root microbiome following severe drought.”
It’s exciting that the Streptomyces remains prevalent even after the drought, says plant scientist and microbiologist Cara Haney of the University of British Columbia, who also was not involved in the study. “If we wanted to engineer a microbial community that could protect against drought,” she notes, “it suggests that that could persist over time.” And if farmers could deliver this Streptomyces to plants in large enough quantities, says Sundaresan, “maybe we’d give the plant a fighting chance against the very first drought episode.”
The team is now exploring whether this Streptomyces may similarly lengthen roots in response to drought in other crops. Indeed, there’s reason to hope that this microbe, or another Streptomyces, may prove useful. A separate research team similarly found that drought causes bacteria within the same family as Streptomyces to grow more abundant in the roots of a range of plants.
“The holy grail of plant microbiome research,” says Sundaresan, “is giving farmers the beneficial bugs that they can put in their field and have them benefit the plant directly.”