Endophytic Microbiome of Biofuel PlantMiscanthus sinensis(Poaceae) Interacts with Environmental Gradients

Miscanthusin Taiwan occupies a cline along altitude and adapts to diverse environments, e.g., habitats of high salinity and volcanoes. Rhizospheric and endophytic bacteria may helpMiscanthusacclimate to those stresses. The relative contributions of rhizosphere vs. endosphere compartments to the adaptation remain unknown. Here, we used targeted metagenomics to compare the microbial communities in the rhizosphere and endosphere among ecotypes ofM. sinensisthat dwell habitats under different stresses.ProteobacteriaandActinobacteriapredominated in the endosphere. Diverse phyla constituted the rhizosphere microbiome, including a core microbiome found consistently across habitats. In endosphere, the predominance of the bacteria colonizing from the surrounding soil suggests that soil recruitment must have subsequently determined the endophytic microbiome inMiscanthusroots. In endosphere, the bacterial diversity decreased with the altitude, likely corresponding to rising limitation to microorganisms according to the species-energy theory. Specific endophytes were associated with different environmental stresses, e.g.,Pseudomonasspp. for alpine andAgrobacteriumspp. for coastal habitats. This suggestsMiscanthusactively recruits an endosphere microbiome from the rhizosphere it influences.