Public awareness about the importance of gut microbiome is on the rise, as new data and tools give increasingly tailored guidance for improved diets and nutrition with remarkable impacts on human and animal health.
And just as our gut microbiome influences our health and well-being, the microbiota of plants also plays a crucial role in their resilience and productivity, ultimately impacting the natural environments as well as crop health, production and food supplies.
Plants are habitats for communities of microbes, generally called the microbiota, and they can play a key role in plant resilience to stresses imposed by lack of nutrients or water, or outbreaks of pests and diseases. This is particularly important when it comes to food crops, as healthy, well-nourished crops produce higher yields, which in turn support nutritious and healthy diets for people.
Soil provides the nutrients needed for plant growth, and its properties have the largest impact on root microbiota. Synthetic fertiliser is often applied to crops around the world to compensate for degraded or poor soils and increase the available nutrients for plant growth to encourage greater productivity.
However, a growing volume of research (1) indicates that the use of nitrogen fertiliser alters the microbiota of plants, affecting the biological process of absorbing nutrients (2) as well as disease resistance (3) and overall plant health.
Only some of the nitrogen fertiliser applied to soil is absorbed by the plants, leaving the rest to be broken down by soil micro-organisms or leached into the environment. An estimated two-thirds (4) of nitrogen fertiliser – or 75 million tonnes a year – is wasted and enters the environment, potentially disrupting the microbiota of crops and other plants.
These findings underscore the importance of developing and enhancing ways for crops to source nutrients biologically, not only to reduce the reliance on emissions-intensive and polluting fertilisers, but also to improve microbial diversity and overall soil and plant health.
Some plants – namely legumes like beans, peas and lentils – are genetically equipped to enrich their microbiota with beneficial soil bacteria that convert or “fix” atmospheric nitrogen in their roots. They do this by forming root nodules, which provide a biological niche for developing an exchange with the nitrogen-fixing bacteria, which eliminates the need for synthetic fertiliser.
But when nitrogen fertiliser is present in the soil, legumes do not engage with these bacteria to preserve energy. My team found that the result of this not only impacted the process of nitrogen fixation but also negatively impacted microbial connectivity, reducing the diversity of microbial interactions in the soil around plant roots.
On the other hand, the interaction between legumes and nitrogen-fixing bacteria that happens when fertiliser is not present was found to contribute to a diverse and beneficial root-associated microbiota.
The plant and the bacteria use chemical signals to coordinate their one-to-one interaction and this impacts the remaining microbiota. For example, when the legume is starved of nitrogen, the plant sends out signals that are recognised by bacteria in the soil. This in turn activates the production of bacterial symbiotic signals. These signals are then detected by the legume plant and the plant rewires its entire metabolism in the root and changes the signals sent out into the soil. The rest of the microbes in the soils are affected by these changes, and consequently we observe changes in the microbial communities.
The plant host is thus in control of these interactions with the entire root-associated microbiota and the interactions with the bacteria contributing to changes that promote symbiotic nitrogen fixation. By contrast, these changes do not occur when the plant receives nitrogen fertilisers and therefore microbial communities are impacted.
The potential to improve plant and soil health through biological processes is the driver behind an international research project called Enabling Nutrient Symbioses in Agriculture (ENSA) (5).ENSA is seeking to optimise and engineer this ability to fix nitrogen through symbiosis with soil microbes in other crops that currently do not recognise the symbiotic signal of the nitrogen fixing bacteria.
While more research is needed to fully understand the assembly of plant microbiota, scientists see exciting opportunities to try to improve the ability of legumes to interact with soil microbes, reducing the need for fertiliser and contributing to healthier, more diverse soils.
And the more we uncover about these different microbial relationships, the better chance we have of recreating the ability to fix nitrogen in non-legume crops, such as cereals and tubers. This would have a transformative impact on global agriculture, making it more likely that crops could grow even in degraded land.
Ultimately, the long-term goal is to be able to make the most of plant biology to develop healthier, more productive crops that in turn contribute to healthier environments.
Understanding which microbial functions from the associated microbiota are beneficial for the plant and how the plant genes contribute to the enrichment of these functions is key for using the microbiota and soil microbes for sustainable agriculture.
By learning from the intricate relationships within plant microbiota, we could pave the way for a more sustainable agricultural future, in much the same way in which we strive to understand and maintain our gut health for overall well-being. This would close the circle to improve the health of plants, people and the planet.
(1) https://www.nature.com/articles/s41467-024-47752-0
(2) https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.721441/full
(3) https://pmc.ncbi.nlm.nih.gov/articles/PMC7472254/
(4) https://ourworldindata.org/excess-fertilizer
Image from Pixabay
Further reading
A historic call to action against a global food crisis by 2050
Will the EU put a super-plough before soil conservation goals?
“It is time to review the EU’s outdated rules on GMOs” (Interview)