Metatranscriptomics reveals system-specific viral adaptive strategies and prokaryotic defense trade-offs across...

Viruses are increasingly recognized as critical modulators of microbial community dynamics in anaerobic digestion (AD) systems, yet their ecological roles across distinct AD process types remain poorly understood. Here, we investigated viral ecology in three full-scale food waste treatment systems representing three predominant process types-dry AD (Dry-AD), wet AD (Wet-AD), and two-stage wet AD (2St-wet-AD)-through integrated metatranscriptomics and metagenomics. We recovered 4404 viral operational taxonomic units (vOTUs) and 206 metagenome-assembled genomes (MAGs). Dry-AD exhibited unique viral-prokaryotic diversity decoupling, elevated lysogeny (48.7% vs. 22.1%-26.5% in wet systems), and reduced transcriptionally active communities (viruses: 65.5% vs. 89.4% and 80.7% in wet systems; prokaryotes: 76.9% vs. 94.5% and 86.3% in wet systems). Comparative analyses revealed stronger viral endemism (55.4% system-specific vOTUs) than prokaryotes (30.6% MAGs). Virus-host networks demonstrated highly centralized infection patterns in Dry-AD with uneven transcript-based virus-host ratios (VHR) (Clostridia: 18.28 vs. Methanomicrobia: 0.15) compared to more uniform ratios (≈1.0) in wet systems. Transcriptomic profiling provided the first quantitative evidence of system-specific antiviral defense strategies: Wet-AD exhibited the highest defense gene transcriptional activity (3833 TPM), Dry-AD reduced defenses transcription (2614 TPM), while 2St-wet-AD displayed the lowest defense transcriptional activity (2455 TPM). Functional annotation revealed viral auxiliary metabolic genes exhibited distinct transcriptional patterns: enhancing host stress resilience in Dry-AD, promoting nutrient acquisition in Wet-AD, and improving metabolic efficiency in 2St-wet-AD. These findings reveal that viruses adopt distinct ecological roles across different AD process types, providing mechanistic insights for developing system-specific strategies to optimize stability and efficiency.