Top-heavy trophic structure within benthic viral dark matter

Viruses exert considerable influence on microbial population dynamics and community structure, with cascading effects on ecosystem-scale biogeochemical cycling and functional trajectories. Creating broadly generalizable theory on viral trophic ecology requires further inquiry into historically unexplored microbial systems that currently lack empirically demonstrated patterns in viral infectivity, such as structurally complex benthic communities. This becomes increasingly relevant considering recently proposed revisions to the fundamental mechanisms that modulate the strength and direction viral trophic linkages. Here, we employed deep longitudinal multiomic sequencing to characterize the viral assemblage (including ssDNA, dsDNA, and dsRNA viruses) and profile lineage-specific host-virus interactions within benthic cyanobacterial mats sampled from Bonaire, Caribbean Netherlands, over a complete diel time-series, and reconstruct patterns in intra-mat trophic structure. We recovered 11,020 unique viral populations spanning at least 10 viral families across the orders Caudovirales, Petitvirales, and Mindivirales, with evidence for extensive genomic novelty from reference and environmental viral sequences. Analysis of coverage ratios of viral sequences and computationally predicted hosts spanning 15 phyla and 21 classes revealed virus:host abundance and activity ratios consistently exceeding 1:1, with overall power-law scaling indicating an increasingly top-heavy intra-mat trophic structure with significant top-down pressure. Diel activity of cyanophages showed clear temporal patterns that seem to follow host physiological condition. These data generate important hypotheses concerning taxon-dependent variation in the relative contribution of top-down vs. bottom-up forcing in driving mat community dynamics, and establish a useful database of viral sequences from this previously unexplored system toward the generation of generalizable trans-system theory on viral trophic ecology. SIGNIFICANCE STATEMENTRecent advances in viral ecological theory suggest a better understanding of system-specific viral ecology is needed from diverse environments to create generalizable theory that accurately predicts patterns of trophic interaction strengths across systems, especially in the Anthropocene. This study characterized viral-host trophic structure within coral reef benthic cyanobacterial mats - a globally proliferating cause and consequence of coral reef degradation - using paired multiomic sequencing. Recovered viral sequences displayed remarkable genomic novelty from other well-characterized viruses and spanned diverse viral taxa. Unexpectedly, lineage-resolved trophic linkages displayed a strongly active top-heavy trophic structure, suggesting extensive top-down forcing. These results highlight the context-dependence of viral trophic interaction strengths and suggest that viruses strongly influence reef cyanobacterial mat and reef ecosystem functional trajectories.