Chemical structure of plant-derived molecules drive changes in microbial communities and their effects on plant health

Yian Gu, Xiaofang Wang, Tianjie Yang, Ville-Petri Friman, Stefan Geisen, Zhong Wei, Yangchun Xu, Alexandre Jousset, Qirong Shen

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Soil microbes form a major line of defense against plant pathogens. When effective, they can provide plants with an extensive and flexible immunity against a range of diseases. However, intensive farming can rapidly lead to reduction in this natural immunity by favouring low diversity microbial communities in the rhizosphere (the soil zone immediately surrounding the roots), calling for strategies to restore the functioning of microbial communities. Root exudates form a major input of labile carbon in the rhizosphere and play a key role in recruiting and activating beneficial microbes. Here we studied if plant-derived compounds can be used to modulate microbial communities to enhance plant health, and if these effects can be predicted by the chemical properties of the added compounds.

To this end, we inoculated individual compounds and mixtures of plant-derived low molecular weight molecules – sugars, amino acids, organic acids and phenolic acids – into soils and evaluated their influence on microbial community composition. In a follow-up experiment, we further examined how these molecules affected the suppression of bacterial wilt of tomato plants.

We found that while each compound triggered a unique effect on the soil microbial community, chemical classes had also predictable effects, and organic and amino acids generally decreased the microbial community diversity compared to sugars and phenolic acids. We could further connect these changes with microbiome functioning, where less diverse communities became more susceptible to bacterial wilt disease caused by the bacterial pathogen Ralstonia solanacearum. Particularly, amino acids and high-nitrogen compound mixtures induced more severe disease symptoms by clearly reducing microbial diversity.

Together, our results suggest that the chemical structure of plant-derived low molecular weight compounds can predictably drive changes in the soil microbial community, which are sometimes associated with elevated risk of disease outbreaks.

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