Lough Neagh is the largest and one of the most economically important freshwater lakes in the British Isles. We performed a yearlong analysis of the structural and dynamical changes of virio- and bacterioplankton communities using a metagenomic approach: whole-genome shotgun sequencing for viral population and amplicon-based 16S rDNA sequencing for bacterioplankton. The 12 viral metagenomes obtained were functionally and taxonomically annotated. The separate assembly of 12 viral libraries yielded 8,249 contigs longer than 7 kb with the two largest being 140,745 and 140,522 bp in length. After that we performed nucleotide blast search of contigs longer than 7 kb against all contigs from 12 libraries to generate clusters consisting of closely related and/or identical contigs. These related contigs were additionally reassembled within the cluster limits and 2,949 individual viral genomes (complete or partial) were identified. Here we present the first study of dynamics and succession of the individual viral species. To analyse temporal dynamics of virioplankton, we mapped reads of each of the 12 libraries onto the assembled individual viral genomes and calculated their abundances. This helped to identify viruses persisting in the Lough Neagh water column throughout the year as well as those appearing in only some time points.
The knowledge of dynamics of viral and bacterial populations and changes in environmental parameters allowed us to classify identified viral genomes into three groups: with the single peak of abundance in the summer-autumn period, most abundant in the winter-spring period, and a group of persisting viruses with other patterns of abundance. The differences in taxonomic composition and functional potential of Lough Neagh viral population in different seasons were identified. Finally, we clustered orthologous viral genomes and performed novel analysis of the succession of related viral species in the real freshwater ecosystem and factors driving it.