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Maize Plant Genetics Shape Root Microorganism Communities

Maize growing in a field.
Credit: Markus Spiske / Unsplash.
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Tiny organisms such as bacteria and fungi help to promote the health and function of plant roots. It is commonly assumed that the composition of these microbes is dependent on the properties of the soil. However, an international team of researchers led by the University of Bonn has now discovered when studying different local varieties of maize that the genetic makeup of the plants also helps to influence which microorganisms cluster around the roots. The results, which have now been published in the prestigious journal Nature Plants, could help to breed future varieties of maize that are better suited to drought and limited nutrients.

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In order to grow properly, plants take in water and nutrients through their roots. But they have the assistance of some tiny helpers: A layer of bacteria and fungi, just a few millimeters thick, can be found directly around the roots. “These microorganisms are essential for the health and fitness of the plants,” says Dr. Peng Yu, head of the junior research group “Root Functional Biology” at the Institute of Crop Science and Resource Conservation (INRES) at the University of Bonn. The microbes help with the absorption of water and nutrients and protect the plants against harmful organisms – similar to how the “microbiome” in the intestines of humans helps to determine whether we become ill or stay healthy.

The traditional view is that the composition of the microbiome – the totality of all microorganisms – is mainly determined by the properties of the soil. This includes things such as the type of soil and whether it is more acidic or alkaline. However, an international team of researchers led by the University of Bonn has now demonstrated in maize plants that the genetic makeup of the host plants has a significant influence on the composition of the root microbes.

“Our study also showed that the microbiome around the roots has a crucial influence on how resilient the maize plants are when faced with stressful conditions such as a nutrient deficits or lack of water,” says Prof. Dr. Frank Hochholdinger from the Crop Functional Genomics department in INRES at the University of Bonn. In view of global climate change and the limited supply of the nutrient phosphorous, resilience of these plants to drought and a lack of nutrients could play an even greater role in the future.

Adapting regional varieties of maize to environmental conditions

The various varieties of maize have very different genetic composition. Regional varieties have adapted themselves to very different environmental conditions depending on whether they are cultivated, for example, in cooler highland or the warmer lowland areas of South America. “The fact that farmers have continued to select those varieties of maize suited to the local climate over many centuries has led to very different genotypes that we were able to utilize for our study,” says Dr. Yu, who is head of an Emmy Noether junior research group funded by the German Research Foundation and also a member of the PhenoRob Cluster of Excellence and the transdisciplinary research area “Sustainable Futures” at the University of Bonn.

In cooperation with scientists from Southwest University in Chongqing (China), the researchers studied a total of 129 different varieties of maize. Some of these were cultivated under “normal” conditions while others experienced deficiencies in phosphorus, nitrogen, or water. Additionally, the team sequenced the DNA of the microbes from 3168 samples taken from the layer found directly around the roots that is just a few millimeters thick.

The role played by the genetic makeup of the roots became apparent in those plants grown under stressful conditions. Interestingly, the lack of nutrients and water had a significant influence on the composition of the microbes. Furthermore, the team discovered important characteristic differences in the microbiome between different varieties of maize under the same stressful conditions. “We were able to prove that certain maize genes are able to interact with certain bacteria,” says Dr. Yu to explain on the most important results. Using data on the growth conditions at the place of origin of a certain variety of maize and on its genetic composition, the researchers were even able to predict which key organisms would be found in the microbiome around the roots.

The bacterium Massilia promotes the growth of lateral roots

The results for bacteria of the genus Massilia especially stood out: “It was very noticeable that very few specimens of this microbe were found when there was a sufficient supply of nitrogen,” says Prof. Dr. Gabriel Schaaf from the Ecophysiology of Plant Nutrition department at INRES and member of the PhenoRob Cluster of Excellence. If there was a lack of nitrogen, however, lots of Massilia could be found clustering around the roots. The team then inoculated maize roots with this bacterium. The plants grew a lot more lateral roots as a result and were therefore able to significantly improve their uptake of nutrients and water.

But how do maize plants manage to harness the tiny Massilia bacterium for this type of root growth? Following further studies, the researchers discovered that the roots actually attracted the Massilia bacteria using flavones. This substance is one of many secondary metabolites in the plant and stimulates the growth of lateral roots with the aid of the bacteria. “However, this was dependent on whether the maize plant had a microtubule-binding gene,” says Dr. Peng Yu. If this gene was missing, the plant did not produce more lateral roots.

The varieties of maize with the missing gene come from a huge database of maize mutations that has been set up by the researchers headed by Dr. Caroline Marcon at INRES. This database helps researchers explain the functions of maize genes.

Maize varieties better adapted to drought and a lack of nutrients

The international team of researchers hopes that they will also be able to predict yield in the medium term. “We are carrying out basic research,” says Hochholdinger. “However, these results could act as the basis for cultivation of maize varieties better suited to drought and a lack of phosphorous by using genome and microbiome data.”

Reference: He X, Wang D, Jiang Y, et al. Heritable microbiome variation is correlated with source environment in locally adapted maize varieties. Nat Plants. 2024. doi: 10.1038/s41477-024-01654-7

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