Plant-associated microorganisms during the reproductive period best predict sorghum yield and quality

Crop plants are intimately associated with an enormous diversity of microbiota that profoundly influence their productivity, but the contribution of plant-microbiome interactions to grain yield and quality of sorghum during different developmental stages remains unclear. The aim of this study was to evaluate the relative importance of sorghum-associated bacterial and fungal communities in different compartments in predicting sorghum grain yield and quality. We collected soil and sorghum plant samples from various compartments during the vegetative (jointing and heading stages) and reproductive (filling and maturity stages) periods of a long-term field experiment with multiple fertilization regimes. The sorghum-microbiomes in different compartments, including phyllosphere, leaf endosphere, stem endosphere, root endosphere and rhizosphere, were characterized using bacterial 16 S rRNA gene and fungal ITS region sequencing. Microbial diversity at the filling and maturity stages was higher than that at the heading and jointing stages. Microbial community composition during the reproductive period was distinct from that during the vegetative period, and the microbial co-occurrence network was more stable and complex during the reproductive period. Random forest analysis revealed that the microbiome during the reproductive period had a greater impact on grain yield and protein content than during the vegetative period. In predicting sorghum grain yield and protein content, the microbiomes in the root endosphere and rhizosphere were more important than other compartments. Both bacterial and fungal community in these compartments played an equal role. These findings highlight the importance of bacterial and fungal communities during the reproductive period for grain yield and quality formation in sorghum, with profound implications for developing new microbiome-based strategies to promote plant performance and sustainable agriculture.