Despite the fact that microbes, such as root-associated fungi and bacteria, played crucial roles in the origin and diversification of land plants, we still have limited knowledge of how plants’ performance in the environment is determined by microbial communities (microbiomes). Although high-throughput sequencing studies have allowed us to reveal the structure of plant-associated microbiomes, we are at an early stage of understanding the ecological processes organizing plant–microbiome linkages. In recent studies on complex webs of plant–microbe (Nature Communications 5:5273; Science Advances 1:e1500291; Nature Ecology & Evolution 1:0024) and microbe–microbe associations (Journal of the Royal Society Interface 13:20151097), I have explored “core microbes”, which potentially have great impacts on community- or ecosystem-scale dynamics of terrestrial ecosystems. In light of findings in those “bird’s-eye view” analyses, I will discuss how we can build an interdisciplinary research basis for understanding and managing plant–microbiome linkages in both natural and agricultural ecosystems.