Prophage induction drives soybean rhizobacterial community differentiation and nutrient cycling benefiting root development.

Bacteriophages, lytic or lysogenic, play critical roles in structuring different soil bacteriomes and driving their functionality. Lysogeny is favored in the plant rhizosphere and may play a major role in plant-rhizobacteria assembly and function. However, the ecological footprint and consequence of prophage activity in the rhizosphere are poorly understood. Here, we conducted a 35-day pot experiment to examine how prophage induction influences soybean rhizosphere viromes and bacterial communities, along with associated changes in nutrient cycling and plant development. The results showed that mitomycin C-induced prophage induction triggered immense viral production, altering virome structure-with more observed species richness in the rhizosphere. We observed a greater impact on the rhizosphere virome than on the bulk soil virome. The resulting lysis decreased the soil organic matter content but significantly increased dissolved organic carbon and nitrate contents in the soil, which improved soil nutrient conditions and stimulated soybean root development. Prophage induction markedly influenced the rhizobacterial community structure, resulting in reduced community diversity. The enrichment of fast-growing bacterial populations was stimulated, suggesting that viral lysis increased microbial activities and accelerated nutrient turnover. The bacterial interaction network was drastically shifted, with complexity being decreased in the bulk soil and increased in the rhizosphere, potentially stimulating the differentiation of the bacterial communities. Together, our results demonstrated that induction of prophages can cause extensive nutrient turnover and variations in plant-rhizobacteria interactions, driving the rhizobacterial community assembly process. This study provides novel insights into the mechanisms of phages controlling microbial function in primary production and soil carbon storage by modulating microbial traits (e.g., carbon use efficiency, growth rate, death, and community assembly) and via processes like the viral shunt.