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.

Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments.

The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.