Tailor your root: chitin-based rhizobiome selection towards plant beneficials

In contrast to soil ecosystems, soilless growing media are rather poor in terms of microbial diversity and nutritional value. Stimulating plant growth and immunity by tailoring the rhizosphere’s microbial community, instead of applying high rates of mineral fertilizers and chemical crop protections, will therefore be beneficial for soilless cultivation.

The addition of chitin, the second most abundant biopolymer on Earth, results in crop (lettuce, strawberry) yield increases of up to two fold and an increased plant defense (Botrytis cinerea infection on strawberry). The growth promotion might be explained by the degradation of chitin in plant-available N. Shotgun metagenomics of the microbial community revealed increased amounts of chitin-catabolic enzymes and ammonium oxidizing genes, resulting in higher ammonium and nitrate concentrations in the growing media. Increased levels of NPK fertilizer in the growing medium did not diminish the growth promoting effects of chitin addition though, by which we predicted that these effects are rather mediated through the stimulation of the rhizobiome community, rather than a nutritional response. Already one week after incubation, one fungal genus, Mortierella, increased in relative abundance up to 10 to 20-fold in the bulk soil. These Mortierella species were rapidly drawn from the bulk towards the plant root, influencing the rhizosphere community. Four isolated strains of Mortierella were screened for growth-promoting effects on Arabidopsis thaliana. Growth increases of the shoot (up to 4-fold) and root (up to 10-fold) were noted for all strains, showing the capacity to induce plant growth promoting effects. These effects might be regulated through the auxin pathway, as genome analysis of the four strains indicate a role in auxin production. In addition, we showed that Mortierella is capable of degrading chitin into small chitin oligomers. The presence of these oligomers resulted in the upregulation of the plant’s defense mechanism and activation of the jasmonic acid pathway. A clear defense priming effect of chitin was noted, explaining the decrease in disease symptoms on the strawberry leaves.

To conclude, the positive effect of chitin on plant growth and plant defense is driven by the changes in the microbial community of the bulk soil and rhizosphere. The application of chitin in combination with Mortierella strains thus has the capacity to reduce the impact of soilless cultivation on the environment.