Salk Institute scientists reveal plants supercharge their immune systems after drought, pointing to genetic strategies for hardier crops.
For plants, growth is usually the top priority. Sunlight, nutrients, and water fuel that process — but when drought strikes, growth comes to a standstill. Surprisingly, when the water returns, plants don’t immediately resume growing. Instead, they shift focus.
Using advanced single-cell and spatial transcriptomic techniques, Salk biologists studied how the model plant Arabidopsis thaliana recovers after drought. They found that immune-boosting genes switch on almost instantly across the plant’s leaves. This response, called Drought Recovery-Induced Immunity (DRII), gives plants a temporary immune surge during recovery.
Importantly, DRII isn’t unique to Arabidopsis. The team observed the same response in both wild and domesticated tomatoes, suggesting this recovery strategy is evolutionarily conserved — and may occur in other key crops. The findings highlight potential genetic pathways for engineering plants that are not only drought-tolerant, but also better equipped to fight off disease when water becomes scarce.
The findings, published in Nature Communications on Aug. 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
For more than 50 years, Arabidopsis thaliana has been a cornerstone model for plant biology. It grows quickly, is easy to study, and has a simpler genome than many other plants. Yet the genes it carries are widely shared across crops such as tomatoes, wheat, and rice — making it a powerful stand-in for understanding how plants function, according to a press release.
Like all plants, Arabidopsis depends on water. It absorbs moisture through microscopic pores on its leaf surfaces — but these same pores also create an open doorway for pathogens. The plant must constantly balance the need to take in water with the need to defend itself.
That balancing act becomes even more critical after drought. In dry conditions, Arabidopsis closes its pores, halts growth, and conserves resources. Once water returns, the pores snap open to rehydrate the plant — leaving its internal tissues suddenly exposed to the outside world. The question researchers set out to answer: how does a plant protect itself during this vulnerable moment of drought recovery?
“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 team rehydrated drought-stressed Arabidopsis plants and tracked how their leaves responded at the genetic level. Starting just 15 minutes after watering and continuing through 260 minutes, they monitored shifts in gene expression. This rapid, high-resolution timeline sets the study apart — plant biologists rarely capture changes 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.”
Although every cell in an Arabidopsis leaf carries the same genetic code, each cell activates different sets of genes that shape its identity and role. To capture these fine-scale differences, researchers turned to advanced sequencing technologies: single-cell and spatial transcriptomics.
Traditional approaches involved grinding up an entire leaf and measuring only the average gene activity — a method that masked the diversity of individual cells. Single-cell transcriptomics, by contrast, reveals gene expression in each cell, offering a much sharper view of cellular dynamics. Spatial transcriptomics adds another layer, mapping that expression back onto the intact tissue. Together, these methods let scientists see not only what each cell is doing, but also how neighboring cells interact during drought and recovery.
Drought Recovery-Induced Immunity (DRII)
Within just 15 minutes of rewatering, dormant genes in Arabidopsis leaves began firing up. Gene activity surged cell by cell until thousands were switched on, launching a powerful immune response. The researchers call this defense surge Drought Recovery-Induced Immunity (DRII). During the vulnerable window of rehydration, DRII shields the plant from pathogens, buying it critical time to recover and resume growth.
After observing DRII in Arabidopsis, the team wondered whether tomatoes — both wild and cultivated — showed the same response. They did. Like in Arabidopsis, DRII boosted pathogen resistance in tomatoes, suggesting this rapid immune surge may be conserved across many crop species.
Still, key questions remain. Rehydration begins in the roots, yet gene activity in the leaves changes within just 15 minutes. How does the signal move so quickly from belowground to aboveground — and what exactly is that signal?
The researchers also propose that DRII challenges how we think about plant stress. Instead of merely toggling between survival and growth, plants may be preparing for the critical recovery phase once water returns. The balance between short-term survival and long-term resilience could depend on a system that gauges the severity of stress and anticipates what comes next.
“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.