By Kanika Chowdhary and Mayurika Goel from TERI (The Energy and Resources Institute)
06 July 2026, New Delhi: Climate change is often understood through what we can measure i.e. rising temperatures, melting glaciers, changing rainfall patterns, and declining crop yields. Yet some of its most significant impacts may be unfolding beyond the reach of conventional metrics, within the microscopic communities living inside plants. Among them are endophytes, the hidden microbial partners that help medicinal plants produce many of the compounds on which human health depends.
These hidden inhabitants are known as endophytes such as bacteria and fungi that live within plant tissues without causing disease. For decades, they were largely overlooked by scientists and conservationists alike. However, research is revealing that these microscopic partners are far more than passive residents. They are active participants in plant survival, adaptation, and medicinal chemistry. In many cases, the therapeutic value of medicinal plants depends not only on the plant itself but also on the microbial communities it hosts.
Climate change is not only altering ecosystems and species distributions; it is also reshaping the intricate relationships between plants and their associated microbiomes. For medicinal plants, whose value lies in their ability to produce bioactive compounds, such disruptions may have consequences that extend far beyond ecology.
The healing power of medicinal plants does not arise from the plant alone. It is increasingly understood to be the product of an intimate partnership between plants and the endophytic microbes that inhabit them. These microscopic allies can trigger, regulate, and sometimes directly contribute to the production of secondary metabolites such as alkaloids, flavonoids, terpenoids, and phenolics that protect plants from environmental stress and form the basis of many traditional medicines and modern drugs. In many ways, nature’s pharmacy is not built by plants alone, but by millions of years of co-evolution between plants and their microbial partners.”
At TERI, this emerging field is already translating into actionable science. Researchers at the TERI–Deakin Nano Biotechnology Centre have been actively bioprospecting endophytic fungi associated with medicinal plants to uncover novel bioactive compounds with applications across pharmaceuticals, agriculture, food systems, and sustainable manufacturing. Studies on endophytic fungi such as Talaromyces assiutensis and Monascus purpureus have revealed their ability to produce natural pigments, antioxidants, antimicrobial molecules, and other high-value metabolites with potential use as pharmaceutical leads, functional food ingredients, biocontrol agents, and natural alternatives to synthetic chemicals. These investigations demonstrate that medicinal plants are host to rich microbial communities capable of generating an untapped diversity of bioactive molecules.
As climate change threatens both plant biodiversity and their associated microbiomes, conserving these hidden microbial resources becomes increasingly important for safeguarding future innovations in healthcare, sustainable agriculture, food security, and the bioeconomy. Research suggests that environmental stress can modify both the diversity and metabolic activity of microbial communities within plants, influencing the production of secondary metabolites that determine medicinal quality and efficacy.
The concern is no longer just whether medicinal plants can survive climate change, but whether their microbial partners can continue supporting the production of medicinal compounds. If climate stress disrupts these plant–microbe relationships, the quantity and quality of bioactive compounds may change. As a result, medicinal plants known for specific therapeutic properties today may not retain the same potency, effectiveness, or chemical profile under future environmental conditions.
Such changes would have consequences not only for traditional medicine systems such as Ayurveda, Traditional Chinese Medicine, and indigenous healing practices, but also for modern pharmaceutical research that depends heavily on nature as a source of novel bioactive compounds.
Paradoxically, the very environmental pressures that threaten these delicate plant–microbe relationships may also create new opportunities for innovation. Climate change acts as a powerful selective force, favouring microbial communities that can withstand extreme conditions and support plant survival under stress. Understanding these adaptive endophytes could open new avenues for conserving medicinal plants, enhancing metabolite production, and developing climate-resilient solutions for agriculture, healthcare, and biotechnology.
Such findings suggest that endophytes could become valuable tools for conserving medicinal plants in a changing climate. By harnessing naturally adapted microbial communities, scientists may be able to improve plant resilience, sustain metabolite production, and develop more sustainable cultivation systems.
Beyond their role in plant health, endophytes contribute directly to climate mitigation. By improving plant productivity, photosynthetic performance, and root biomass, they enhance the ability of vegetation to capture atmospheric carbon dioxide and store it in plant tissues and soils. Their capacity to improve plant survival under environmental stress also helps maintain ecosystem carbon stocks, making endophytes valuable allies in strengthening nature-based solutions for climate change.
In other words, conserving endophytes will help preserve not only medicinal value but also the ecological processes that regulate Earth’s climate. Despite these far-reaching benefits, microbial endophytes remain largely absent from climate adaptation policies and biodiversity conservation strategies. Most conservation programs focus on protecting plant species and habitats, while the microbial communities associated with those plants receive little attention. This plant-centric approach overlooks a fundamental reality: preserving a medicinal plant without preserving its microbiome may not fully conserve its ecological function or therapeutic potential.
The challenge before us is therefore conceptual as much as scientific. We must move beyond viewing plants as isolated organisms and begin recognizing them as part of a larger biological partnership. Scientists increasingly describe this integrated unit as a holobiont a host and its associated microbiome functioning together as a single ecological entity.
Adopting this perspective has important implications for research and policy. Future studies must employ integrative approaches that combine genomics, metabolomics, transcriptomics, and proteomics to understand how climate stress influences plant–microbe interactions and secondary metabolite production. Conservation programs should include microbial diversity as a measurable indicator of ecosystem health. Sustainable cultivation systems should incorporate beneficial endophytes to enhance resilience and reduce dependence on chemical inputs.
At the same time, ethical and regulatory frameworks must evolve alongside advances in microbial biotechnology. As industries increasingly explore the commercial potential of endophyte-derived compounds and microbial bioinoculants, issues such as biosafety, equitable benefit sharing, indigenous knowledge rights, and responsible bioprospecting will become increasingly important.
Perhaps the most important lesson emerging from this research is that resilience often resides in relationships we cannot see. The future of medicinal plants may depend as much on the microbes living within them as on the plants themselves. These microscopic partners help shape the chemistry, adaptability, and survival of some of nature’s most valuable species.
As climate change continues to transform ecosystems across the globe, understanding and conserving medicinal plant microbiomes may become one of the defining challenges and opportunities of the coming decades. Protecting nature’s pharmacy will require more than conserving plants alone. It will require safeguarding the invisible microbial alliances that have quietly sustained plant health, medicinal value, and ecological resilience for millions of years.
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