Itumeleng Moroenyane

Institut National de la Recherche Scientifique
Plant microbiome succession and assembly modulated by endogenous signal peptides in soybean (Glycine max)

Moroenyane, I., Laliberté, C., Tremblay, J and Yergeau, É

Managed agricultural ecosystems are unique systems where crops and microbes are intrinsically linked and selected to promote crop health and increase production. This study focuses on the successional development of the plant microbiome and assembly processes that delimit them, and aims to 1) tests for evidence of niche differentiation and to what extend signal peptides influence community assembly and 2) create a successional model that can predict these niche shifts as they occur. Soybean plants were grown in an environmental chamber. Microbiome and xylem sap samples were collected at the various developmental stages: emergence, growth, flowering, and seed maturation. Microbial community structure and abundance were assessed with amplicon sequencing. Sap was purified and signal peptides were identified using nano-LC-MS/MS. Abundance was highest in the epiphytic and rhizosphere communities, and community structure varied according to- plant organ, plant developmental stage, and life history (epiphytic or endophytic). Machine learning models correctly predicted the abundance and distribution of key taxa. Niche shifts were detectable across plant organs and developmental stages. Interestingly, these niche shifts were in part related to turnover in signal peptide diversity and abundance. Lastly, niche-based processes delimited distribution and assembly of endosphere and rhizosphere communities. This demonstrates that by understanding the mechanistic processes that assemble microbiome communities, it becomes possible to identify key microbes that are essential for promoting plant growth and health, but also key intervention points where the microbiome community can be engineered to be composed of microbes that can mitigate plant stresses and influence long-term management practices.