Drought changes rice root microbiome

Drought can have a lasting impact on the community of microbes that lives in and around the roots of rice plants, a team led by University of California, Davis, researchers has found. The finding could help in understanding how rice responds to dry spells and how it can be made more resilient to drought. The U.S. National Science Foundation-funded work is published in Nature Plants.

The root microbiome of irrigated rice plants goes through a sequence of changes as the plants grow, and stabilizes when they flower. The sequence is consistent for a particular rice strain and geographic location. Previous work has shown that when a growing rice plant is deprived of water, it hits pause on the succession of changes.

Venkatesan Sundaresan and colleagues looked at changes in rice root microbes over time when plants were deprived of water for 11, 21 or 33 days. That kind of intermittent drought condition is common in rain-fed crops, according to Sundaresan.

The microbe community changes when water is taken away. More surprising is that the changes persisted for weeks after plants were watered again.

"Rice plants carry a 'memory' of the drought episode in their root microbiota, so plants that have experienced drought can be distinguished solely on the basis of their microbiomes," Sundaresan said.

The team was able to culture and sequence the most abundant of these microbes. The bacteria's DNA includes genetic code similar to plant genes for the growth hormone auxin.

"The persistence of changes in the microbiome means that root elongation continues even after drought has ended, allowing the roots to be better prepared to tap deep water," Sundaresan said. For some drought-tolerant rice cultivars, after a drought episode, the roots continue to grow long enough to penetrate the hardpan.

The persistent changes also mean that the microbiome response will be more rapid the next time drought hits, because it is altered from the first drought.

As extreme climate events become more common, crops are likely to experience more intermittent droughts, the authors note. Understanding what makes plants more resilient to drought conditions could help reduce crop losses.

"This research nicely demonstrates the complexity of living systems," said Gerald Schoenknecht, a program director in NSF’s Division of Integrative Organismal Systems. "An extended drought period permanently alters the plant and causes persistent changes in the community of microbes that lives in and around the plants' roots."