Single-Cell Insights into Virus–Microbe Interactions in Emerging Contaminant Degradation

Abstract

Viruses are increasingly recognized as critical regulators of microbial ecology, yet their roles in pollutant degradation remain largely unexplored. Here, we integrate Raman-activated cell sorting–stable isotope probing (RACS-SIP) and single-cell genomics to elucidate virus–microbe interactions underlying methylnaphthalene biodegradation in petroleum-contaminated soils. Microcosm experiments demonstrated up to 80% removal of methylnaphthalene within 36 days, accompanied by pronounced shifts in microbial and viral communities. Correlation analyses suggested potential virus–host associations, with Ochrobactrum and an unclassified Caudoviricetes phage emerging as key contributors to degradation. RACS-SIP enabled in situ identification and isolation of active degraders, and single-cell genomic analysis indicated that viral auxiliary metabolic genes, including methyltransferases, aldehyde dehydrogenases, and decarboxylases, may complement host pathways for the multistep conversion of methylnaphthalene to naphthalene. Subsequent mineralization occurs through canonical catechol and gentisate pathways encoded by the host genome. This study provides preliminary evidence that viruses may act as metabolic collaborators rather than passive parasites in pollutant degradation, potentially enhancing host metabolic capacity and influencing biodegradation outcomes. Beyond revealing a virus-inclusive metabolic network, the RACS-SIP framework overcomes key limitations of traditional metagenomic methods by resolving virus–host linkages at the single-cell level. These findings broaden our understanding of viral ecological functions and highlight novel leverage points for bioremediation technologies targeting emerging contaminants.