Objectives Viruses are an important component of soil microbial communities in paddy fields, and play a non-negligible role in regulating host communities and elemental biogeochemical cycles. Exploring the interaction mechanism between viruses and hosts and the expression of accessory metabolic genes (AMGs) in paddy fields under rice straw returning is helpful to reveal the far-reaching effects of viruses on soil nitrogen cycling in paddy fields, aiming to provide a new perspective for understanding the role of viruses in the process of soil element biogeochemical cycling.

Methods A long-term straw return positioning experiment, located in Huizhou of Guangdong Province, was started since 2015. Soil samples were collected in 2023 from five treatment plots: no straw returning (CK), total straw returning (S, the amount of straw returned to the field in a single season is 6400 kg/hm²), and 1.1, 1.2, and 1.3 times of the whole straw return amount (S1, S2, and S3, the amount of straw returned to the field in a single season are 7075 kg/hm², 7750 kg/hm², 8425 kg/hm², respectively). The community composition of soil viruses and bacteria, and the relative abundances of viruses, bacteria, and AMGs involved in the nitrogen cycle process were analyzed by metagenomic and metavirome sequencing technology.

Results The dominant families of soil viruses in paddy fields were Circoviridae, Microviridae, Geminiviridae and Genomoviridae, but 84.62%−93.92% of the viridae were still unclassified or unknown. S treatment increased the abundance of Circoviridae significantly, while S1, S2 and S3 treatments decreased the abundance of Genomoviridae but increased the relative abundances of unclassified or unknown viridae significantly (P<0.05). The dominant bacterial phylum in paddy field were Proteobacteria, Chloroflexi and Acidobacteria, and the straw return amount and the growth period of rice had no significant effect on the dominant bacterial phylum. A total of 8 viral contigs carrying the organic nitrogen transformation genes glnA, gltD, gdhA and ncd2/npd, were identified, and the abundance of these viral contigs in the straw returning treatment was almost all higher than that of CK. The results of host prediction showed that the hosts of two virus contigs carrying nitrogen cycle genes were Pseudomonas and Actinomycetota, while the hosts for the other virus contigs were unable to predict. The abundance of bacterial ncd2/npd gene was positively correlated with microbial biomass nitrogen content (P=0.015, n=10), but not with total ammonium nitrogen and nitrate nitrogen (P=0.108, n=10). The partial least squares path model showed that straw return significantly affected the alpha diversity of soil bacteria (P<0.0007). The organic nitrogen transformation gene ncd2/npd carried by bacteria significantly affected the content of soil microbial biomass nitrogen (P<0.0039).

Conclusions Straw returning significantly affected the relative abundance of virus taxa in paddy field, which could promote the expression of more AMGs encoded by viruses and play an important role in soil nitrogen cycling. By affecting the alpha diversity of soil viruses and bacteria, the amount of rice straw returned to the field indirectly affects the relative abundance of ncd2/npd genes carried by bacteria, and ultimately has an important impact on the organic nitrogen transformation process.