Viral diversity and auxiliary metabolic genes in rare earth element mine drainage in South China

In extreme environments, viruses play a crucial role in regulating the structure and metabolic activities of microbial communities, thereby impacting the overall biogeochemical cycles. Previous research found that rare earth element acid mine drainage (REE-AMD) harbors a wide array of microbial species. However, our understanding of the viruses that infect these microorganisms remains limited. In this study, we utilized metagenomic analysis to explore the viral diversity, interactions between viruses and their hosts, as well as the viruses encoded auxiliary metabolic genes (AMGs) within REE-AMD. The results demonstrated that viral communities showed increased diversity with REEs pollution. Furthermore, AMGs exhibited habitat and host specificity. Viruses in water samples contaminated with REEs tended to encode AMGs related to cellular metabolic processes and stress responses to protect their hosts. In contrast, viruses in sediment samples were more likely to encode AMGs associated with nutrient competition, thereby expanding the ecological niches of hosts and viruses. Viruses would carry more AMGs from the dominant prokaryotes. Additionally, under REEs stress, viruses encode a greater number of carbon- and sulfur-related AMGs, influencing the carbon and sulfur cycles of microorganisms in REE-AMD. Overall, our study provides a first systematic characterization of the viral community in REE-AMD, which is crucial for understanding the intricate interactions among viruses, their hosts, and the surrounding environment.