Identification of the major capsid gene (g23) of T4-type bacteriophages that assimilate substrates from root cap cells under aerobic and anaerobic soil conditions using a DNA–SIP approach

• Rice callus cells were used as a model material of root cap cells of rice plant.
• DNA–SIP approach was employed to trace the carbon flow of 13C-labelled callus cells.
• Carbon flow from callus cells to phages via bacterial hosts was identified.
• Phages mediated carbon cycles of root cap cells in microbial loop in aerobic soil.

As the most abundant biological entities, viruses are increasingly recognised as a major driving force of global biogeochemical nutrient cycles. This study demonstrated that T4-type bacteriophages drive the microbial loop of carbon from root cap cells in rice rhizospheres based on an analysis of the major capsid gene (g23). Rice callus cells were used as a model for root cap cells, and 13C-labelled callus cells were allowed to decompose. DNA extracted from the soils after incubation under aerobic and anaerobic soil conditions was subjected to PCR–DGGE after density gradient centrifugation. Although 13C-labelled g23 fragments were not detected in soil incubated under anaerobic conditions, many 13C-labelled g23 fragments belonging to Paddy Groups V, VIII and IX were obtained from the soil incubated under aerobic conditions. Some g23 fragments were detected throughout the incubation period, and others were obtained only during the early or late incubation period. This study demonstrated that the level of infection of soil bacteria by T4-type phages was very different between aerobic and anaerobic soil conditions. Based on the results of this study, the roles of phages in the decomposition of the root cap cells of rice plants in rice fields are discussed.