A Versatile Glass Jar System for Semihydroponic Root Exudate Profiling

Our intensive agricultural systems are based on high inputs of fertilizers and pesticides. This is harmful to the environment and also not sustainable. Thus, key questions in research are how to lower these inputs while maintaining yield of our crops.

One promising avenue to do that is to supply plants with beneficial microbes in the field. However, to be able to do that successfully, we need to understand the complex chemical crosstalk between the partners. We study this interaction by looking at root exudates in our lab.

We find that root exudation is very dynamic. It differs between plant species, developmental stages, and also diurnal time points. Plants also react to the presence of different kind of microbes by changing their metabolic profile.

Because root exudates are nutrients and signals to the microbial community, studying exudation profiles is crucial to understand how plants interact with microbes in their environment. Developments in metabolomics, but also in next generation sequencing technologies really push the field of plant microbiome interaction forward. Obviously, you need a metabolomics workflow to detect the compound or the compounds of interest in a given system.

And next generation sequencing technologies are really essential in understanding the structure, but also the function of plant microbiomes. Also, it is very helpful to use specialized growth systems or simplified growth systems like the one we present here to understand the molecular mechanisms of plant microbe interactions. Our system can be kept sterile, but we can also inoculate it with target microorganisms.

One challenge we have is to detect metabolites in low concentration in exudates. If the background is low, then it's easy to do it. If we have a much more complex environment such as soil, then it's more difficult.

Another challenge that is unresolved is when we add microbes to the picture. Then it's not possible to distinguish between the compound produced by plants or by the microbes. We developed a system that is low cost and reasonably easy.

Its sterile designs allows for consecutive experiments. First plant metabolites are discarded. Then plants are inoculated with microbes, and here the changes in the metabolite profile are evaluated.

It also allows for the growth of different plant species for an extended period of time. So in summary, this system is well-suited for many applications.