LA JOLLA (August 29, 2025)—A plant's number one priority is to grow—a feat that demands sunlight, nutrients, and water. If just one of these three inputs is missing, like water in a drought, growth halts. You might then think that at the end of that drought, the plant would jump right back into growing. Instead, its priorities shift.
Salk plant biologists used advanced single-cell and spatial transcriptomic techniques to look closely at how a small, flowering plant called Arabidopsis thaliana recovers after drought. They discovered that immunity became the plant's number one priority during this post-drought period, as they watched immune-boosting genes light up rapidly throughout the Arabidopsis leaves. This supercharged immune response, dubbed "Drought Recovery-Induced Immunity" (DRII), also occurred in wild and domesticated tomatoes, suggesting that prioritizing immunity is conserved evolutionarily and likely takes place in other important crops.
The findings, published in Nature Communications on August 29, 2025, plant the seed for growing more resilient crops and protecting the global food supply in years to come.
"Drought poses a major challenge for plants, but what is less understood is how they recover once water returns," says senior author Joseph Ecker, professor, Salk International Council Chair in Genetics, and Howard Hughes Medical Institute investigator. "We found that, rather than accelerating growth to compensate for lost time, Arabidopsis rapidly activates a coordinated immune response. This discovery highlights recovery as a critical window of genetic reprogramming and points to new strategies for engineering crops that can rebound more effectively after environmental stress."
Thirsty plant, dry soil
Arabidopsis has served as an important laboratory model for plant biologists for half a century. The plant is quick and easy to grow, and it has a relatively simple genome compared to other plants. But crucially, many of the individual genes within the Arabidopsis genome are shared across many plant species—including agriculturally relevant crops like tomatoes, wheat, and rice.
One feature Arabidopsis shares with every plant is its need for water. The little plant sucks up water through microscopic pores on its "skin"—but these little pores can also put the plant at risk, as they directly expose its vulnerable insides to the outside world. This challenges the plant to find a balance between taking in water and defending itself against harmful environmental intruders like pathogens.
This balance becomes even more challenging during drought recovery. Without water, the plant closes its pores and enters a stressed state, arresting its growth and rationing its stores. When water returns, the pores quickly reopen to quench the thirsty plant, exposing it suddenly once more to the hazards of the outside world. So, how do plants protect themselves from this sudden onslaught in the drought recovery process?
"We know a lot about what's happening in plants during drought, yet we know next to nothing about what happens during that critical recovery period," says first author Natanella Illouz-Eliaz, a postdoctoral researcher in Ecker's lab. "This recovery period is incredibly genetically active and complex, as we've already discovered processes we had no idea—or even assumed—would be a part of recovery. Now we know definitively that recovery is worth studying more moving forward."
A speedy, single-cell, spatially aware study
The researchers took Arabidopsis plants that had been living in a drought state and reintroduced the parched plants to water. They surveyed the plants' leaves for changes in gene expression starting at 15 minutes and incrementally worked all the way up to 260 minutes. This speedy surveillance sets the study apart, as plant biologists often don't capture data so soon after rehydration.
"What's really incredible here," adds Illouz-Eliaz, "is we would have entirely missed this discovery had we not decided to capture data at these early time points."
While all the cells in an Arabidopsis leaf share the same genetic code, the expression of each gene in that code varies from cell to cell. The pattern of genes expressed by each unique cell determines that cell's identity and function. Effectively capturing gene expression patterns that differ between microscopic cells means recruiting sophisticated gene-sequencing technology like single-cell and spatial transcriptomics.
Older methods required scientists to take a leaf, grind it up, and measure general expression patterns from there. Single-cell transcriptomics allows scientists to capture gene expression within a cellular context, which in turn more accurately represents cellular dynamics within plant tissues. In addition to this impressive single-cell precision, spatial transcriptomics analyzes those single cells within the physical context of the intact plant. With this method, scientists can process the leaf (or a section of that leaf) as a whole to see how expression differs between neighboring cells throughout drought or recovery.
Drought Recovery-Induced Immunity (DRII)
Just 15 minutes after rewatering, the team watched dormant genes sprout to life. Expression patterns shifted significantly across the many leaf cells, turning on gene after gene until thousands of new genes were active. These many genes kick-started an immune response that the researchers call "Drought Recovery-Induced Immunity" (DRII). In the vulnerable rehydration period, DRII came to Arabidopsis' defense, protecting the plant against pathogens.
After witnessing DRII in Arabidopsis, the team was curious whether wild and farmed tomato plants experience DRII, too. Both tomato types did experience DRII, which, like in Arabidopsis, increased their pathogen resistance. These tomato findings also suggest the immune response may be shared across many other plant and crop species.
There's more left to understand about this rapid immune response. For starters, the rehydration process starts in the roots, so how does the signal travel so quickly from the roots to the leaf, enacting gene expression changes in only 15 minutes? And what is that signal?
The researchers also believe the findings can help shift the field's perspective on plant stress. Perhaps plants aren't just focusing on survival and growth, but rather on preparing for what comes next after water returns. And maybe weighing survival versus longevity depends on a system that senses stress severity.
"Our results reveal that drought recovery is not a passive process but a highly dynamic reprogramming of the plant's immune system," says Ecker. "By defining the early genetic events that occur within minutes of rehydration, we can begin to uncover the molecular signals that coordinate stress recovery and explore how these mechanisms might be harnessed to improve crop resilience."
Other authors include Jingting Yu, Joseph Swift, Kathryn Lande, Bruce Jow, Lia Partida-Garcia, Travis Lee, Rosa Gomez Castanon, William Owens, Chynna Bowman, Emma Osgood, Joseph Nery, and Tatsuya Nobori of Salk; and Za Khai Tuang, Adi Yaaran, Yotam Zait, and Saul Burdman of the Hebrew University of Jerusalem.
The work was supported by the United States–Israel Binational Agricultural Research and Development Fund (FI-601-2020), George E. Hewitt Foundation for Medical Research, Weizmann Institute of Science, Howard Hughes Medical Institute, National Institutes of Health (K99GM154136, NCI CSSG P30 CA014195, NIA P30 AG068635), Henry L. Guenther Foundation, and Waitt Foundation.
About the Salk Institute for Biological Studies:
Unlocking the secrets of life itself is the driving force behind the Salk Institute. Our team of world-class, award-winning scientists pushes the boundaries of knowledge in areas such as neuroscience, cancer research, aging, immunobiology, plant biology, computational biology, and more. Founded by Jonas Salk, developer of the first safe and effective polio vaccine, the Institute is an independent, nonprofit research organization and architectural landmark: small by choice, intimate by nature, and fearless in the face of any challenge. Learn more at www.salk.edu .
