Recent studies have discovered that there are likely many plant virus species that have mutualistic relationships with their hosts. Whereas some viruses are essential for the survival of their hosts, others simply give their hosts a fighting edge in the highly competitive natural world. It is noteworthy that several studies have shown that either cryptic harmless plant viruses or acute plant viruses can reduce the impact of abiotic stress on their host plant. In addition, viruses, such as bacteriophage can play a key-role in the control of plant bacterial outbreaks. Hence, it is now widely accepted that the composition, the community structure and the activity of the host microbiome is a crucial parameter of the host health. On the other hand, the surrounding environments and especially the plant community structure may influence the host microbiome composition. We plan to test during my PhD study the hypothesis that modification of the plant microbiome (bacteriome and virome) may significantly have an impact on the plant pathogen dynamics, and further on the pathogen emergence or non-emergence. Therefore, we here aim at characterizing the endophyte microbiome of pilot rice agrosystems from the Yunnan Province of China. Areas with different rice cultural practices (traditional agriculture vs conventional agriculture) will be surveyed for 2-3 years. In addition, the effect of the very recent increasing use of modern rice varieties in the Yuanyang terraces where mix of traditional rice varieties have been used for centuries will also be studied. Metagenomics-based analyses of both the microbial and the virus communities inhabiting the plant endosphere of three compartments (roots, stems and leafs) will be carried out. Culturomics, 16S rRNA barcoding and virion-associated nucleic acid meatgenomics-based approaches will be used in this study.