Objectives Viruses can impact bacterial survival and reproduction in different environments by encoding auxiliary metabolism genes (AMGs), and then indirectly affect biogeochemical cycles such as carbon, nitrogen, and phosphorus. This study aimed to investigate the abundance of carbon cycle-related functional genes co-encoded by viruses and bacteria in long-term fertilized paddy soil. This will help explore the viral-bacterial interaction mechanisms and provide an efficient fertilization and management strategy for paddy soils in the red soil region.

Methods This study is based on a long-term fertilization positioning experiment established in Jiangxi Province in 1981. The soil samples were collected from four treatment plots, including no fertilizer control (CK), chemical fertilizer application (NPK), returning green manure Astragalus smicus to early rice (M1), and the combined application of Astragalus smicus to early rice and straw to late rice (M2). Metagenomic and virome sequencing technologies were utilized to analyze the structural composition of bacterial and viral communities. The KEGG carbon metabolism pathway was used to investigate the distribution of viral and bacterial functional genes related to the carbon cycle, and to elucidate their effects on carbon cycle in paddy soil.

Results The bacterial community was predominantly composed of Anaeromyxobacteraceae, Nitrospiraceae and Bradyrhizobiaceae, with no significant differences in bacterial community composition at the family level across fertilization treatments. The most abundant viral families were Microviridae, Circoviridae and Siphoviridae, with significant variations in viral community composition among fertilization treatments. The relative abundance of Siphoviridae was significantly higher in CK than in M2 and NPK (P<0.05), and higher in M1 than in NPK (P<0.05). The relative abundance of Siphoviridae, Mimiviridae and Podoviridae was higher in M1 treatment than in the others. The phage community was dominated by Siphoviridae in all the fertilization treatments, and no significant differences existed among the treatments. Network analysis indicated that Siphoviridae as a core viral taxon, negatively correlated with the bacterial core taxon Anaeromyxobacteraceae. Among the seven carbon metabolism genes co-encoded by bacteria and phages, it was found that the IDHI gene involved in the Reductive tricarboxylic acid cycle was encoded by Siphoviridae in viruses and Proteobacteria in bacteria. The Calvin cycle gene K00615 and hemicellulose hydrolysis gene pmm-pgm were linked to unclassified phages but predicted to involve Proteobacteria hosts. Bacterial carbon cycle genes showed no significant differences among treatments, while the relative abundance of the viral-encoded GAPDH gene was significantly higher in the CK treatment than in the NPK and M2 treatments (P<0.05). The relative abundance of IDH1, pmm-pgm and K00615 genes was significantly higher in M1 than in NPK and M2 (P<0.05). The bacterial-encoded IDH1 and pmm-pgm genes in soil demonstrated significant positive correlations with microbial biomass carbon content and soil organic carbon content (P<0.01 and P<0.05, respectively). However, the viral-encoded common carbon cycle genes exhibited a negative correlation with soil organic carbon content and microbial biomass carbon content.

Conclusions Long-term differential fertilization significantly affected the virus community composition. Viruses affected the survival and reproduction of bacteria and carbon cycling processes in paddy soil through the expression of various AMGs. Phages and bacteria had complex interactions with each other in different fertilization treatments and played an important role in the carbon cycling of paddy soil by affecting the relative abundance of the co-encoded carbon cycle genes (IDH1 and pmm-pgm).