Conversion from natural to agricultural soils increases network complexity and reshapes cross-kingdom microbial associations

Soil microbial communities are key drivers of ecosystem processes. While agricultural conversion is well known to homogenise soil microbial communities, it remains unclear whether this process regulates multi-kingdom interaction networks. Here, we used shotgun metagenomics to investigate paired natural and agricultural soils collected along a 900 km transect following the 550 mm annual precipitation isohyet in New South Wales, Australia. We profiled the diversity, community assembly processes, and cross-kingdom co-occurrence networks of bacteria, fungi, archaea, protists, and viruses in response to land-use change. Our results indicated that land-use change exerted a limited influence on microbial diversity across most kingdoms. However, agricultural conversion significantly reduced the stochasticity of viral community assembly. Notably, agricultural practices increased the complexity of microbial interaction networks. In particular, agricultural soils strengthened associations between bacterial and fungal communities while weakening bacterial–viral interactions. This integrated cross-kingdom analysis provides new insights into how land-use change reshapes microbial communities and their ecological networks across large spatial scales under constrained climatic conditions.