ena-STUDY-CNRS and university of Rennes 1-19-09-2021-17:40:11:234-1805
Intra- and inter-annual changes in root endospheric microbial communities of Vitis vinifera are mainly determinist
Microbial communities provide essential services to plants and are therefore crucial for crop production, including grapevine. Understanding how microorganisms assemble is one of the main challenges in microbial ecology today. While many studies have assessed spatial microbial assembly, temporal dynamics are still overlooked. Depending on the plant development stage, temporal changes in microbiota are expected through changes in plant needs and in root architecture, and environmental pressures. We analyzed the composition of microbiota in two cultivars in a single vineyard at three dates over a period of  two growing years to investigate microbial temporal variability (intra- and inter-annual variations). Highly conserved temporal patterns were found in the two cultivars. Intra-annual changes in microbial community composition were recorded between June (i.e. flower set) and September (i.e. mature grapes) whereas convergent microbial communities were observed on the two September dates. In particular, the increase in Actinobacteria and decrease in Glomeromycota in September were interpreted as shifts in the microbiota community patterns related to plant physiological requirements. We also demonstrated a high proportion of non-random assembly of root endosphere bacteria, underlining the deterministic influence of the plant or the environment in microbial recruitment over time. Our study suggests an intra-annual rhythm of microbiota shifts, marginally random, hence a succession within the root-microbiota endosphere governed by active plant filtering. A better knowledge of the  microorganisms reservoir, from which plants draw and organize their microbiota, will be important for future viticulture and for a broader view of agriculture in the context of global warming.
Microbial communities provide essential services to plants and are therefore crucial for crop production, including grapevine. Understanding how microorganisms assemble is one of the main challenges in microbial ecology today. While many studies have assessed spatial microbial assembly, temporal dynamics are still overlooked. Depending on the plant development stage, temporal changes in microbiota are expected through changes in plant needs and in root architecture, and environmental pressures. We analyzed the composition of microbiota in two cultivars in a single vineyard at three dates over a period of  two growing years to investigate microbial temporal variability (intra- and inter-annual variations). Highly conserved temporal patterns were found in the two cultivars. Intra-annual changes in microbial community composition were recorded between June (i.e. flower set) and September (i.e. mature grapes) whereas convergent microbial communities were observed on the two September dates. In particular, the increase in Actinobacteria and decrease in Glomeromycota in September were interpreted as shifts in the microbiota community patterns related to plant physiological requirements. We also demonstrated a high proportion of non-random assembly of root endosphere bacteria, underlining the deterministic influence of the plant or the environment in microbial recruitment over time. Our study suggests an intra-annual rhythm of microbiota shifts, marginally random, hence a succession within the root-microbiota endosphere governed by active plant filtering. A better knowledge of the  microorganisms reservoir, from which plants draw and organize their microbiota, will be important for future viticulture and for a broader view of agriculture in the context of global warming.