The hidden genetic reservoir: structural variants as drivers of marine microbial and viral microdiversity

Intraspecific genetic diversity is fundamental to understanding microbial adaptation, evolution, and contributions to ecosystem stability. However, traditional short-read metagenomics often underrepresents this diversity, particularly structural variants (SVs), due to assembly limitations in complex natural populations. To overcome these constraints, we employed third-generation (long-read) metagenomics to investigate the eco-evolutionary role of SVs in microbial and viral marine populations. Our analysis focused on the cellular metagenome fraction (0.22–5 μm size range) across distinct ecological niches within the photic zone of the marine water column. Insertions and deletions emerged as the predominant SVs in the marine microbiome, occurring at similar frequencies across genomes. These SVs were not only found within the core genome but also in the flexible genome, serving as a source of genetic variability within genomic islands. Insertions were significantly larger, reaching more than 2 Kb, in streamlined microbes such as Pelagibacter (SAR11 clade) or the archaeon Nitrosopumilus. In contrast, SVs in viral populations were smaller and more uniform in size (~ 430 bp). Functionally, SVs were enriched in genes linked to nutrient uptake, amino acid metabolism, and regulatory networks due to the presence of non-coding RNAs. These SVs often encompassed entire genes or operons, acting as an important reservoir of niche-specific diversity that supports the emergence of ecological lineages better adapted to environmental gradients, such as rhodopsin-containing subpopulations in shallower waters. In viruses, SV-driven genetic plasticity facilitated host range adaptation and the evolution of mechanisms modulating host metabolism. We identified long-term genetically stable populations of cyanophages and pelagiphages, wherein SVs represented the primary source of genomic diversification. Notably, certain subpopulations of pelagimyophages carry SVs encoding a pstS gene, which enhances host phosphate uptake and increases viral replication efficiency—a beneficial adaptation in phosphate-depleted environments such as the oligotrophic Mediterranean Sea. By capturing SVs directly from natural populations, this study provides new insights into microbial evolution, phage-host interactions, and the broader implications of genomic plasticity for ecosystem resilience in marine environments. Furthermore, these results highlight the transformative potential of third-generation sequencing to unveil previously hidden layers of microbial and viral diversity.