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Chemical communication in the rhizosphere of plants

Periodic Reporting for period 4 - CHEMCOMRHIZO (Chemical communication in the rhizosphere of plants)

Reporting period: 2019-10-01 to 2021-11-30

In CHEMCOMRHIZO we studied the use by plants of metabolites to communicate with other organisms in their rhizosphere, strigolactones and solanoeclepin A. The strigolactones are used by the friends of plants, the arbuscular mycorrhizal fungi, for host detection but also by their enemies, root parasitic plants. I postulated that this dual role is the result of a paradigm: enemies of plants recruit molecules that are essential to the plant as cues. This paradigm has two implications: 1) other plant-produced signalling molecules known to be abused by plant enemies likely have another, beneficial function in plants and 2) the involvement of multiple biological functions exerts a selective pressure on these signalling molecules resulting in the evolution of structural diversity and biological specificity. For the strigolactones we investigated implication 2): what is the biological relevance of the large structural diversity in the strigolactones. For implication 1) we studied another rhizosphere signaling molecule that is abused by the plant enemy, cyst nematode, solanoeclepin A. Together, the work was supposed to shed light on the significance of structural diversity in signalling molecules and the co-evolution of perception and to result in the discovery of a new class of signalling molecules in plants. It could also provide the basis for applications to optimise colonisation by beneficial AM fungi, and control parasitation by root parasitic plants and nematodes.
After setting up the PI’s new lab in Amsterdam, purchasing a new ultra-sensitive mass spectrometer and hiring the people on the project we set up a method called aeroponics to be able to collect root exudates of plants in high amounts and a targeted analytical method for the detection of the rhizosphere signaling molecules that we investigate, strigolactones and solanoeclepin A. In parallel, we set up untargeted metabolomics to allow for discovery work on the role of the root exudate, for example in shaping the microbiome. This analytical chemistry was also used to support our molecular biological work: identifying genes involved in the biosynthesis of rhizosphere signaling molecules, which is especially supported by RNAseq on roots and gene co-expression analysis. These candidate genes were subsequently tested through a variety of approaches such as through transient over expression in N. benthamiana, transient silencing and with mutants/transgenic lines. Our analytical chemistry was also used to support our work on the perception of the rhizosphere signals by parasitic weeds and nematodes. Finally we studied how plants use strigolactones and other compounds to attract beneficial micro-organisms to their roots. These micro-organisms can help the plant to withstand stressful conditions and we showed that strigolactones play a role in this microbe recruitment by plants.
The most important results and their dissemination
- We have further elucidated the structural diversity in the strigolactones in maize, have elucidated the entire strigolactone biosynthetic pathway of maize and showed that natural variation in the strigolactone blend in maize correlates with differences in Striga resistance. This will be published in a paper we will submit to Science and was disseminated to a scientific audience in seminars for the GLS plant science groups at UVA as well our institute, SILS
- We have identified the recruitment of two additional cytochrome P450 families that facilitate the biosynthesis of the strigolactone structural diversity. This shows that the evolution of different strigolactone structures is indeed under selective pressure. The work was disseminated in scientific meetings and will be published in in scientific papers
- We developed a method to analyse the production of the nematode hatching stimulant, solanoeclepin A, using LC-MS/MS in the exudate of a single tomato and potato plant (published in Planta); using this method we demonstrated that solanoeclepin A production is regulated by several environmental conditions; it will form the basis for high-impact follow up work that will be disseminated to the scientific community and published.
- We have made it likely that the classical dauer pathway is involved in the release from hatching upon perception of the hatching stimulant, solanoeclepin A. This work is partially published as review and will be submitted for publication soon. It also forms the basis for follow-up work to try to identify the solanoeclepin receptor which could have important practical consequences
- The combination of Striga strigolactone receptors and triple-quad LC-MS/MS analysis is a useful strategy to unravel receptor ligand specificity and will be published
- We developed a transient silencing method, Virus Induced Gene Silencing, that effectively silences gene expression in the roots of tomato, and used that method to alter the root exudate composition, which in return resulted in changes in the rhizosphere microbioom; we will publish this in several scientific papers and disseminate it in scientific meetings
- The development of rhizosphere metabolomics and its combination with other phenotyping methods, including metabarcoding of the microbial community, allowed us to pinpoint relationships between plant rhizosphere signalling molecules, including strigolactones and solanoeclepin A, and microbe recruitment. These ideas were disseminated at scientific meetings and we have several papers in prep on this of which one is virtually accepted.
We have elucidated an additional step in the strigolactone biosynthetic pathway of tomato and have completely resolved the biosynthesis of all 8 maize strigolactones. We have shown that the production of solanoeclepin A is prone to environmental conditions which should help to unravel its complicated biosynthesis. With our transient silencing method, VIGS, but also with stable transformation we are able to manipulate these pathways and show what the beneficial role is of all these different molecules that are secreted by plants into the soil. This will also allow us to study how important these signaling molecules are for the enemies of plants and how they perceive these. With that knowledge we can optimize plants to not attract enemies (but to do attract their friends) and to develop agrochemicals that can be used to control these enemies..