By Ashley Stender | July 23, 2026

Plants respond to stress through chemistry. When they experience heat, drought, nutrient limitation, or other environmental challenges, their metabolism can shift rapidly, offering clues about how they are growing, adapting, or protecting themselves.

For C-SPIRIT, those chemical clues are central to the search for bioactive compounds that can support plant resilience. Led by Miyako Kusano at the University of Tsukuba in Japan, the Kusano Lab brings expertise in plant metabolism and metabolic networks, helping researchers understand what those chemical changes reveal. The lab studies how plants respond to their surroundings, from environmental stress and developmental change to interactions with other organisms.

Kusano is a member of C-SPIRIT’s Aim 1, focused on metabolite discovery, and Aim 3, focused on gene and pathway discovery. Her expertise supports C-SPIRIT researchers working across crops, stress responses, compounds, and field systems.

Reading Plants Through Metabolic Signatures

The Kusano Lab focuses on the enormous diversity of metabolites produced by plants and the patterns those compounds create under different conditions.

“Our lab uses metabolomics, other omics approaches, and network biology to interpret this chemical information,” Kusano says. “In simple terms, we try to understand plants by reading their metabolic signatures.”

Rather than studying compounds as molecules alone, the lab examines how metabolites connect with genes, traits, and environmental conditions. These connections can reveal how plants regulate their metabolism and how that regulation contributes to agriculture, crop quality, and plant resilience.

For C-SPIRIT, this perspective is especially valuable because the Center’s work depends on more than identifying promising compounds. Researchers also need to understand what those compounds may mean biologically.

What Metabolites Reveal About Stress

When plants are under stress, metabolite profiles can change quickly. Those shifts offer a close view of what is happening inside the plant as it responds to heat, drought, nutrient limitation, or intense light.

“Metabolites are very close to the actual physiological state of a plant,” Kusano says. “While genes and transcripts can tell us what a plant may be preparing to do, metabolites often reflect what is actually happening inside the plant at a given moment.”

These shifts may reflect changes in carbon and nitrogen metabolism, cellular homeostasis, redox balance, or the production of defense-related compounds. Kusano emphasizes that metabolites should not be viewed only as end products. Some function as protective molecules, some act as signals, and others reflect larger changes in metabolic networks.

By studying those changes, the lab can help C-SPIRIT researchers better understand which compounds may be associated with resilience and why.

Finding the Biological Meaning of Compounds

C-SPIRIT’s Aim 1 focuses on metabolite discovery, including the identification of bioactive compounds that may improve plant resilience. The Kusano Lab contributes to that goal through metabolomics-based analysis and biological interpretation.

The lab can help identify compounds associated with stress tolerance, recovery, or improved plant performance. Those compounds may act as protective metabolites, signaling molecules, metabolic precursors, or markers of resilient physiological states. Understanding those roles is an important step in deciding which compounds may be most useful to pursue.

“Because plant metabolomes are highly complex, it is important not only to detect compounds but also to understand their biological meaning,” Kusano says.

The Kusano Lab is also developing methods to improve the accuracy of metabolite annotation and enable quantification without authentic standards. Within C-SPIRIT, that expertise helps move metabolite discovery beyond measurement by connecting chemical data to testable hypotheses about plant resilience.

Linking Metabolites, Genes, and Pathways

C-SPIRIT’s Aim 3 focuses on gene and pathway discovery, making data integration central to the Kusano Lab’s role. A metabolomics experiment can produce a long list of compounds or mass spectral features, but for the Kusano Lab, that list is just the starting point. The larger goal is to organize those data into patterns that can point toward pathways, networks, and biological hypotheses.

“The greatest opportunity is that data integration allows us to move from lists of changing compounds toward biological interpretation,” Kusano says.

Metabolomics can show which compounds change under certain conditions. When those changes are connected with gene expression, pathways, phenotypes, stress conditions, and field performance, researchers can begin to understand why they change and what they may mean for plant function.

The challenge is that metabolites are chemically diverse, highly dynamic, and often difficult to annotate. Their levels can be shaped by tissue type, developmental stage, environmental conditions, sampling time, and stress intensity. Metabolite levels and gene expression also do not always correspond directly because metabolism is regulated at many levels.

For this reason, careful experimental design, high-quality data processing, compound annotation, and biological validation are essential. Sharing metabolomics data within C-SPIRIT can also help researchers compare metabolic responses across crops, stress conditions, and experimental systems.

“For our lab, C-SPIRIT provides an opportunity to make metabolomics more connected, more interpretable, and more useful for plant resilience research,” Kusano says.

From Chemical Clues to Actionable Knowledge

The Kusano Lab is especially interested in crops and plant systems where metabolism is closely linked to stress resilience, productivity, and quality. Within C-SPIRIT, the lab’s target crops are soybean and tomato, with particular interest in how metabolites shape responses to environmental stresses such as heat, drought, and nutrient imbalance.

Kusano says the lab has recently started tomato abiotic stress experiments using heat-sensitive and heat-resistant lines. At the University of Tsukuba, the team can conduct greenhouse and field experiments at the same time and location, allowing researchers to compare controlled and field conditions more directly.

“I would like our contributions to help transform metabolomics data into actionable biological knowledge,” Kusano says.

For the Kusano Lab, this means identifying compounds, metabolic pathways, and network signatures that help explain why some plants are more resilient than others. It also means supporting a more predictive understanding of plant metabolism, so researchers can better anticipate which compounds or pathways may improve plant performance.

“Metabolomics is not simply a technology for measuring many compounds,” Kusano says. “It is a way to understand plant life through chemistry.”

Through C-SPIRIT, the Kusano Lab is helping connect that chemistry to the Center’s broader mission of identifying bioactive compounds and understanding how they can support resilient crops and sustainable agricultural systems.