Author: Darío Sánchez, PhDIt’s easy to forget that plants are living, breathing beings too. They are alien from us humans, but they share many traits, good and bad. One of those is stress.
Plants, just like you, can get stressed about their living situation, environment, and quality of life. And just like you, they can respond to it. They do so by communicating with their neighbours and crying for help. And their closest neighbours? Underground microbes.
The Rhizobiome, a Collection of Root Microbes
What is the Rhizobiome? Simply put, it is the microbial community around a plant’s roots. Think of it as the plant’s underground support network. Much like the human microbiota, the rhizobiome works closely with plants, helping them absorb nutrients, protect them from infection, and benefit in a symbiotic relationship of the existence of the plant. Research reveals just how essential this relationship is, particularly when plants face environmental challenges.
Plants don’t fight stress alone. They actively recruit specific microbial communities through chemical signals sent via their root exudates, essentially “calling” for backup when drought, heat, cold, or salt stress arrives. The rhizobiome responds, providing multiple layers of defence that turn a stressed plant into a resilient one.
How Does the Rizhobiome Help Plants Survive Stress?
Three mechanisms explain how the rhizobiome enhances plant stress tolerance. Understanding these reveals why nurturing soil health is as important as managing above-ground growth.
Extracellular polysaccharides
Bacteria within the rhizobiome produce extracellular polysaccharides (EPS), which are highly hydrated polymers composed primarily of polysaccharides (sugars) and proteins. Common EPS-producing bacteria include Pseudomonas, Bacillus, and Paenibacillus. Under stress conditions, these EPS polymers become critical infrastructure.
In the soil, EPS functions like a porous matrix that absorbs and holds water, much like the mucilage naturally produced by plant roots. During drought, this creates zones of moisture around the root, buffering against water loss and maintaining soil water availability even as conditions dry out. The matrix also becomes a hotspot for microbial activity, where root exudates and organic matter are more efficiently degraded, releasing nutrients the plant can readily access. By coating soil particles and root surfaces, EPS stabilises the rhizosphere osmotically, allowing the plant to maintain cellular function even as external water stress intensifies.
Interestingly, bacteria increase EPS production in response to stress itself. Under heat, desiccation, or salt stress, microbes synthesize even more of these protective polymers, suggesting that individual bacteria sense plant stress signals and adjust their chemistry accordingly. Essentially, EPS helps create a buffer zone where plants can hold water and easily access nutrients, all thanks to microbes and the rhizobiome.
Osmo-protectants
Osmo-protectants are small molecules that act as cellular sponges, allowing water molecules to move into plant cells and preventing protein denaturation when stress strikes. Some osmo-protectants are synthesised directly by rhizobiome microbes, while others are made by plants after microbes stimulate that through chemical signals.
Common osmo-protectants include proline, glycine betaine, and trehalose. However, microorganisms adapted to extreme environments (hot springs, salt lakes, frozen tundra) produce unusual alternatives like mannosylglycerate and mannosylglyceramide that outperform common osmolytes in both osmotic adjustment and protein protection. By engineering soil microbes to carry genetic traits from these extremophiles, researchers could boost modern agriculture.
Enzymes and extremozymes
The rhizobiome produces a sophisticated toolkit of enzymes that plants cannot make, but still benefit from. Hydrolases (such as amylases, cellulases, and glucosidases) break down carbon substrates in soil organic matter. Peptidases (including proteases and nitrate reductases) decompose nitrogen-containing compounds, releasing bioavailable nutrients.
These enzyme activities directly correlate with soil health and crop productivity. Soil enzyme activity serves as a key biological indicator of soil wellbeing, responding rapidly to environmental changes and abiotic stress. When microbial enzyme activity declines, so does the plant’s access to nutrients, even if those nutrients technically exist in the soil.
Under stress, plants with robust rhizobiomes maintain higher enzyme activity in their root zone, meaning continued nutrient availability even as conditions deteriorate. Studies tracking wheat and maize roots show that beneficial microbes upregulate proteins related to glutathione metabolism and protein degradation, allowing roots to adapt their cellular machinery to stress conditions.
Extremozymes, enzymes used to extreme environments, stay active even during heavy stress from drought, heat, cold, or high salt conditions. Studying how extremozymes can be added and expressed in rhizobiomes could boost crop production and plant health under stress.
Engineering the Rhizobiome to Accelerate Plant Stress Resilience
The understanding of how microbes support plants under stress has evolved from observation to intervention. Rather than waiting for soil microbes to naturally assemble, researchers now look to engineer microbial communities specifically designed for stress tolerance.
TOLERATE and similar initiatives represent this shift towards applied microbiome science. Instead of assuming microbes will adapt to future conditions (which would happen slowly), teams are taking a proactive approach. At TOLERATE, we want to select and modify bacteria to improve the rhizobiome.
Bioaugmentation, the addition of beneficial microbes to soil, has traditionally been used for environmental remediation. Now TOLERATE and researchers worldwide are repurposing it to enhance crop resilience during drought, heat, and salinity stress.
The approach requires caution. Introducing engineered strains must maintain harmony with native soil communities rather than disrupting them. Field trials in controlled environments test whether inoculant microbes can establish themselves, function as intended, and persist in real agricultural soils without ecological backlash.
Microbe engineering and the TOLERATE project
At TOLERATE, we want to find genetic sequences that microbes once used to make more stress-resistant systems to make osmo-protectants, EPS, and extremozymes. These microbes might now be extinct, but they once helped plants with climate change, drought, heat, cold, or salt resistance.
We can mine the sequences to the genes that made them survive once and engineer current rhizobiome microbes to carry these enhanced proteins and systems. The aim is simple: boosting climate change resilience in crops.
Climate change is intensifying drought events globally, with major food crop yields declining in regions already experiencing water scarcity. The prospect of harnessing beneficial rhizobiomes offers a pathway toward sustainable agriculture that doesn’t require additional fertilisers, pesticides, or irrigation infrastructure. Instead, it works with soil biology, and you do not need to plant new crops, it works on existing ones.
If you want to stay updated on our latest news and scientific breakthroughs on rhizobiome use to fight climate change, microbe engineering, and bioaugmentation, check our ‘News’ page!