Abundant non-canonical DNA viruses in seawater revealed by high-throughput single particle sequencing

Viruses and other extracellular genetic elements play essential roles in marine ecology and evolution, yet their composition remains elusive. In this study, we compartmentalized a coastal seawater sample into picoliter-sized semi-permeable capsules for in-capsule amplification and barcoding of DNA from individual particles. We obtained genomic sequences of 2,037 particles from a 300 nanoliter sample, capturing a broad range of cellular and extracellular entities. The ratio of viruses to cells (9:1), the predominance of Caudoviricetes viruses, and the taxonomy of cellular genomes indicated quantitative genome recovery. The virus-like genomes included an abundant population of Naomiviridae that lacked metagenomic representation and were linked to several abundant cellular host lineages, suggesting their use of non-canonical DNA and a potentially overlooked ecological significance. The reported Environment Micro-Compartment Genomics (EMCG) technology provides a new opportunity for high-throughput, quantitative, and cost-effective genome analyses of extracellular genetic elements at the resolution of individual particles.