Effects of conventional and organic management on viral communities in a non-experimental agroecosystem In Hong Kong, China

Soil viral communities are affected by factors such as agricultural management, crop type and soil compartment. In this study, metagenomics analysis was used to investigate the characteristics of viral communities in farmland under conventional and organic management in Hong Kong, China, in order to assess the effects of land management, crop type, and rhizosphere on soil viral communities and identify specific viruses they affect. We hypothesized that agricultural management had the greatest impact on viral communities. Genome annotation revealed double-stranded DNA viruses were dominant viruses, with Siphoviridae being the most prevalent viral family (account for 42.4%). Hierarchical clustering, principal coordinate analysis and redundancy analysis demonstrated significant distinctions in viral communities between organic and conventional farming systems. Organic management was associated with reduced viral diversity as indicated by lower Shannon, Simpson, and Chao diversity indices, alongside a notable increase in viral abundance. Specifically, Siphoviridae exhibited an 84.5% increase, while Marseilleviridae and Baculoviridae surged by approximately 99% and 93.8%, respectively. The structure of viral communities was primarily influenced by management mode, followed by crop type. Viral structure was mainly affected by soil pH, available phosphorus and available potassium. Organic agricultural management could significantly increase soil pH, organic matter content and available nitrogen, which may help to maintain the health of plants and soil. Our findings suggest that organic management practices have a large effect on increasing viral diversity, promoting healthier soils via viral taxa and functions.