Soil bacterial communities associated with stony soils influence the tuber size of Tetrastigma hemsleyanum

Abstract Background Plants grown in stony soils have better-developed root systems and higher crop yields than those grown in non-stony soils. The roles of various physical and chemical effects of stony soils on plant growth have been published, but the roles of soil microbiota and rhizosphere microbiota have not been investigated. Methods Tetrastigma hemsleyanum plants were cultivated for two years in stony soils and in the same soil from which rock-fragments had been removed. The microbiome and the tuber transcriptome were analyzed, using multiple bioinformatics methods. Results The soil microbiota of these two soils were markedly different, and the stony soils contained high abundances of bacterial taxa belonging to the Actinobacteria, Rokubacteria, Rhizobiales, Desulfarculaceae, and Chthoniobacteraceae. These discriminatory taxa in soils may promote the tuber growth of T. hemsleyanum, through releasing nutrients from rocks and colonizing the rhizosphere and tuber surface of T. hemsleyanum. In addition, stony soils induced a dramatic change in the tuber’s transcriptome, particularly with respect to the pathways of phytohormone biosynthesis, photosynthesis, and biotic stress resistance, expression levels of which showed strong correlations with the aforementioned bacterial taxa. Conclusions These results indicated that beneficial effects of stony soils on plant growth may be closely correlated with their specific microbiota, which can, in turn, influence multiple biological processes of host. This is the first study to reveal the role of stony soils-driven microbiota in tuber growth, and stony soils can represent a microbial repository for the screening of microbial isolates to increase plant yield.