Decoding the DNA and RNA viromes of a tropical urban lagoon

Human and livestock sewage is one of the major causes of excess nutrients, leading to the eutrophication of aquatic ecosystems and potentially to the emergence or spread of pathogenic viruses. This study aimed to investigate the composition and diversity of aquatic viromes in a highly anthropized lagoon, to identify the presence of pathogenic taxa and to explore their use as possible viral indicators of faecal contamination. For this, water and sediment samples were collected in the Ebrié Lagoon (Ivory Coast) at seven stations with contrasting levels of eutrophication. The DNA viromes of the planktonic and the benthic compartments were highly divergent, but were not influenced by the level of eutrophication. Conversely, the RNA viromes in the water column were comparable to those found in sediment, but showed significant differences between the stations. We detected the presence of viral DNA and RNA sequences we had assigned as indicators of faecal contamination (smacovirus, pecovirus and pepper mild mottle virus) as well as human pathogens (human cyclovirus, coxsackie B virus and picobirnavirus), which were all enriched in the most eutrophicated sites. These findings suggest that the examination of viromes represents a promising tool for assessing the state of human‐induced contamination of aquatic ecosystems. This metagenomics‐based study explored viral communities in a polluted lagoon to identify pathogenic viruses and assess their role as indicators of faecal contamination. Results showed that DNA viruses differed between water and sediment compartments, while RNA viruses diverged significantly between stations according to eutrophication levels. Faecal contamination‐ and human disease‐related viruses were enriched in the most eutrophicated sites, highlighting the potential use of viral communities in evaluating human‐induced contamination in aquatic ecosystems.