Benefit and risk: Keystone biomes in maize rhizosphere associated with crop yield under different fertilizations

The highly diverse beneficial and deleterious microbes in the rhizosphere influence plant growth and crop production in agricultural ecosystems. However, our understanding of the relationships between beneficial and risky phylotypes in the rhizosphere, and plant growth, in addition to their potentially varied response to different fertilization treatments in black soils, remains poor. Here, we investigated variations in multitrophic (e.g., bacteria, fungi, invertebrates, and protists) community composition and diversity under different five-year fertilization treatments, and identified the potential beneficial and potential risky keystone multitrophic biota in maize rhizosphere and bulk soils based on ecological networks and soil food web structure. Bacteria and protist community compositions exhibited greater variations under different fertilization regimes when compared with those of fungi and invertebrates. In addition, two keystone phylotype groups associated with crop yield and soil function were detected, and the potential beneficial keystone phylotypes exhibited higher relative abundances in C-fixation, N-fixation, and P-mineralization genes; conversely, the potential risky keystone phylotypes were associated with denitrification and nitrate reduction genes, and included more potential fungal pathogens. Furthermore, structural equation modeling results indicated that organic amendments, particularly cow manure, could improve crop yield by enriching beneficial keystone phylotypes and suppressing risky keystone phylotypes. Altogether, the results of the present study highlight the critical roles of rhizosphere biota in food production, and identify keystone phylotypes that are beneficial or harmful to crop production and soil function, which could facilitate the conservation of beneficial biota and the early detection of potential pathogens, as well as the exploitation of beneficial biota to increase crop yield.