Phyllosphere Keystone Beneficial Specialists Enhance Yield in Nutrient Deficiency-Resistant Sorghum Cultivars

The phyllosphere, the aboveground interface between plant leaves and their microbial residents, plays a vital yet underappreciated role in crop productivity. While root- and soil-associated microbiomes are well-studied, the ecological assembly and yield-related effects of host-mediated phyllosphere microbial communities remain largely understudied, particularly under field conditions. This study investigates the phyllosphere microbiomes of sorghum cultivars resistant and susceptible to nutrient deficiency, focusing on how host genotype mediates microbial community assembly, keystone enrichment, and yield outcomes. The β-diversity of phyllosphere microbiomes differs significantly between resistant and susceptible cultivars, with resistant lines also showing more modular co-occurrence networks enriched in keystone taxa. These cultivars supported a higher abundance of keystone beneficial specialists (KBS), predominantly affiliated with Bacteroidia and Bacilli, and their abundance was positively correlated with yield. In contrast, susceptible cultivars exhibited lower and more taxonomically dispersed KBS, with a negative correlation between KBS and yield. Structural equation modeling suggested that while soil properties consistently promoted yield across cultivars, the impact of KBS on yield was genotype-dependent. These findings reveal a host-driven microbial mechanism linking phyllosphere composition to yield performance and highlight KBS as potential targets for microbiome-informed breeding or foliar microbial applications to improve crop productivity in sustainable systems.