Aarhus University Seal

A new study reveals key role of plant-bacteria communication for the assembly of a healthy plant microbiome supporting sustainable plant nutrition

In an interdisciplinary study, researchers discovered that symbiotic bacteria communicate with legume plants through specific molecules and that this communication influences which bacteria grow near the plant roots. The findings provide insights into how plants and soil bacteria form beneficial partnerships for nutrient uptake and resilience. These results are a step towards understanding how communication between plants and soil bacteria can lead to specific beneficial associations providing plants with nutrients.

Nitrogen nutrition and signaling during root nodule symbiosis impact the community assemblies. Lotus plants grown in the presence of inorganic nitrogen secrete specific metabolites and assemble a microbial community with low connectivity. Lotus plants grown in symbiosis-permissive conditions secrete metabolites such as flavonoids (1) that induce Nod factor production in compatible nitrogen-fixing Rhizobiumisolates (2). Nod factors are recognized by the Lotus host which initiates a signaling pathway (3) to accommodate the symbiont. Symbiotically active roots have an exudate profile (4) and associated microbial communities that differ from plants grown in the presence of inorganic nitrogen. It remains to be determined how bacterial communities associated with symbiotically active plants impact the host to promote the symbiotic association and plant growth (5). Figeure: from Ke Tao et al. 2024)

The results in Nature Communications find that symbiotic, nitrogen-fixing bacteria can ensure dominance among soil microbes due to its signalling-based communication with the legume plant host. Researchers discovered that when legumes need nitrogen, they will send out from the roots and into the soil specific molecules that are in turn recognized by the symbiotic bacteria to produce another molecule, the Nod factor which is recognized back by the legume plant. When this mutual recognition was established, the plant will modify the panel of root secreted molecules and by this will affect which soil bacteria can grow in the vicinity of their roots.

Plants like legumes have a special relationship with certain bacteria in the soil. These bacteria help the plants grow in soil that does not have much nitrogen by converting nitrogen from the air into a usable form. Depending on the nitrogen available in the soil, legume plants can be in different states: lacking nitrogen, in a partnership with the bacteria, or using nitrogen from inorganic sources like nitrate.

The symbiosis with nitrogen-fixing bacteria was shown before to affect the rest of microorganisms living around the plant roots. However, it is not always clear how this partnership affects other microbes, and whether it depends on how much nitrogen the plant has.

In the new study, the team found that the communities of bacteria around the roots and in the surrounding soil differ depending on and have predictive power of the plant's nitrogen status. Moreover, it was found that signalling exchange between legume and its symbiont plays a critical role in modulating the profile of root secreted molecules, influencing the assembly of a symbiotic root microbiome.

The results provide valuable insights into the complex interplay between nitrogen nutrition, Nod factor signaling, and root microbiome assembly. The findings emphasize the importance of symbiosis and nitrogen nutrition in shaping plant-bacteria interactions, offering potential applications in agriculture and sustainable plant growth.

This is a clear example of interdisciplinary research, where the expertise in chemistry from Associate Prof. Dr. Marianne Glasius to analyze root exudates, in mathematics from Prof. Dr. Rasmus Waagepetersen to develop predictive models, and plant genetics and microbiome from Prof. Dr. Simona Radutoiu enabled complex causational studies of root-associated bacterial communities. By integrating these diverse fields, the researchers were able to answer key questions about how nitrogen nutrition and symbiosis influence plant-bacteria interactions, providing valuable insights for sustainable agriculture.


We strive to ensure that all our articles live up to the Danish universities' principles for good research communication. Against this background, the article is supplemented with the following information:

Study type:


External funding:

This work was supported by the Bill and Melinda Gates Foundation and the UK’s Foreign, Commonwealth and Development Office (FCDO) through the Engineering Nitrogen Symbiosis for Africa project (ENSA; OPP11772165), the Danish Council for Independent Research (9041-00236B), the Molecular Mechanisms and Dynamics of Plant-microbe interactions at the Root-Soil Interface project (InRoot), supported by the Novo Nordisk Foundation grant NNF19SA0059362. The China Scholarship Council supported K.T. and S.Z. for their Ph.D. study.

Conflicts of interest:


The scientific article:

Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly

Ke Tao1,5, Ib T. Jensen1,6, Sha Zhang1, Eber Villa-Rodríguez1, Zuzana Blahovska1, Camilla Lind Salomonsen2, Anna Martyn1,7, Þuríður Nótt Björgvinsdóttir2, Simon Kelly1,8, Luc Janss3, Marianne Glasius2, Rasmus Waagepetersen4 & Simona Radutoiu1

1Department of Molecular Biology and Genetics, Aarhus University, Denmark.
2Department of Chemistry, Aarhus University, Denmark.
3Center for Quantitative Genetics and Genomics, Aarhus University, Denmark.
4Department of Mathematical Sciences, Aalborg University, Denmark.
5Present address: Department of Biology, University of Copenhagen, Denmark.
6Present address: Department of Mathematical Sciences, Aalborg University, Denmark.
7Present address: Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany.
8Present address: Biotechnology, Lincoln Agritech, Canterbury, New Zealand.

Nature Communicationshttps://www.nature.com/articles/s41467-024-47752-0

More information

Simona Radutoiu
Department of Molecular Biology and Genetics
Aarhus University, Denmark