Liliana Quiza Moreno

Metagenomics of the wheat rhizosphere to engineerthe microbiome for healthier, more productive crop under low fertilization regimes.

Liliana Quiza Moreno, Marc St- Arnaud, Etienne Yergeau

The plant microbiome can both enhance or deteriorate the health of plants, and have enormous implications in food production systems. Engineering the plant-associated microbiome could improve beneficial microbes increasing nutrient availability, promote plant growth, inhibit pathogens and may help plants withstand heat and drought. Although it is known for decades that the microbiome of plants is key to its health, we are just beginning to understand the complex interactions occurring within this system. Here, we applied shotgun metagenomics and amplicon sequencing to observe the interactions between wheat (Triticum aestivum) and its rhizosphere microbiome, across three years (2013, 2014, 2015), two time points (spring and late summer) and 10 different varieties. grown under low fertilization regimes. Our hypothesis was that differences in the capacity of each variety to recruit a microbiome would result in different capacity to thrive under low fertilization. The bacterial 16S rRNA gene and the fungal ITS region were sequenced for all samples, while shotgun metagenomics was performed for samples from a single time point. Large differences in fungal and bacterial communities were observed between sampling dates, while subtler, but significant differences were observed between wheat varieties. Shotgun metagenomic analyses revealed several genes that were differentially abundant between the varieties. These taxonomic and functional differences between varieties showed significant links with yields under low fertilization. In the longer term, the microbial taxa and functions identified as positively linked to productive wheat varieties could be used to promote wheat adaptation to sub-optimal fertilization conditions.