Only fungal migration runs through the biotopes of soil, phyllosphere and faeces

Abstract Background: Understanding the microbial linkages among the soil, plants and animals is crucial for maintaining the balance of thet ecosystem in grazed grasslands. However, previous study always focused on the biotopes of soil, phyllosphere and faeces respectively and little has been known about the microbial distribution and migration among these biotopes. Here, a systematic survey to investigate the alteration and overlap among the various microbiotas of biotopes and how the microbial cycle served for the ecosystem was conducted on the molecular ecological level. Results: Our findings revealed that the biotopes drived the distinct microbial community assemblages with various richness, β-diversity and composition. The substantial overlaps between soil and phyllosphere in fungi, bacteria and archaea indicated that soil played the role of the microbial source for phyllosphere. Nevertheless, Ascomycota were the only microorganisms definitely migrating among all the biotopes. After the long-term impact of faeces via grazing, the soil and phyllosphere microbiota were altered significantly. Conclusions: Biotopes driving leads the discrepancy of microbiota distribution among soil, phyllosphere and faeces. Soil could potentially perform as the microbial reservoir for phyllosphere. However, there was only fungal migration running through the ecosystem to link all the biotopes. These findings improved our understanding of microbial linkages among the biotopes in the grazed grassland ecosystem and better managing the soil, plants and animals for the pasture ecosystem service.