【文献转载】PNAS | 抗生素环丙沙星对土壤病毒群落及N2O产生的影响机制

Significance: Viruses, the most abundant biological entities, have great potential in regulating nutrient biogeochemistry and influencing ecosystem functions. However, their contributions to biogeochemical cycling and greenhouse gas emissions, particularly under environmental stress, remain largely unexplored. We report that antibiotic stress increases viral  contributions to greenhouse gas N₂O production by 18 to 29%, thereby advancing our understanding of the vital roles of viruses in biogeochemical cycles. Our results also reveal that antibiotic stress induces synonymous mutations in viral genomes, facilitating viral adaptation to hosts and promoting interactions with denitrifiers, which in turn enhances their metabolic potential. This study opens avenues for understanding the role of viral evolution in biogeochemistry, particularly in the context of increasing environmental stress of the  Anthropocene.

Abstract: Viruses are ubiquitous regulators of microbial dynamics and may thus greatly influence global microbial-driven greenhouse gas emissions. Anthropogenic stressors, such as chemical contamination, are likely to amplify these viral contributions; however, their global significance and underlying mechanisms remain elusive. Utilizing ¹⁵N tracing, metagenomics, and laboratory assays, we explore soil viral communities and their evolutionary potential under the stress from antibiotic ciprofloxacin (CIP), focusing on their roles in regulating nitrogen cycling and N₂O production. Through isolation and reinoculation of soil viruses, we demonstrate that CIP stimulates soil denitrification-derived N₂O production, with 18 to 29% of the  increase attributed to viral activity. Under CIP stress, soil viruses shift toward a lysogenic lifestyle, promoting mutualism with denitrifiers by horizontally transferring viral denitrification-related auxiliary metabolic genes (AMGs). The observed synonymous mutations in these AMGs, driven by CIP, suggest enhanced purifying selection, likely optimizing codon usage to align with host preferences. This optimization likely enhances the expression of denitrifying AMGs and increases N₂O production. This study provides insights into the overlooked role of viral dynamics and genomic mutations in modulating N₂O production under stressful environments, highlighting their evolutionary significance and impact on biogeochemical cycles in the Anthropocene.

Fig. 6. VP extraction and validation. (A) Schematic diagram showing soil VP extraction, incubation, re-extraction, and reincubation experimental design. (B) Transmission electron microscope images of VP in soil extraction. (C) The cumulative N₂O production in soils inoculated with active or inactive VP on day 7. The top row shows the cumulative N₂O production during the first 7-d incubation following viral inoculation, while the bottom row depicts production during the second 7-d incubation after reinoculating the soil with extracted VP from the first incubation. Different letters indicate significant differences among treatments (P < 0.05). Con, control, no viral particles; −VP, inactive viral particles; +VP, active viral particles; +VPS, active viral particles + suspension.