Virome characterization of a highly anthropized aquatic ecosystem : the Ebrié lagoon in Ivory Coast

Dans cette thèse, nous avons choisi d’étudier la composante virale d’un site lagunaire exposé aux rejets domestiques, agricoles et industriels : la Lagune Ebrié bordée par la ville d’Abidjan, en Côte d’Ivoire. Les objectifs de cette thèse visaient (1) à caractériser les viromes benthiqes et planctoniques dans 7 sites de cette lagune présentant des niveaux d'eutrophisation contrastés, en distinguant les viromes ADN et ARN, et (2) à examiner les stratégies de reproduction virale. Pour cela, une approche métagénomique shotgun combinée à des analyses bioinformatiques a été utilisée. Nous avons montré que la composition des viromes ADN était spécifique à chaque compartiment (plancton/benthos). À l’inverse, la composition des viromes ARN était plus influencée par le niveau d’eutrophisation du milieu. Les viromes des sites les plus eutrophisés présentaient des séquences associées aux pathogènes humains d'origine fécale et aux indicateurs de pollution fécale humaine. L’étude des interactions entre les virus et leurs hôtes bactériens, a permis de montrer que cette lagune tropicale était plus propice aux stratégies lytiques de reproduction virale dans les stations les plus eutrophes. Enfin, en utilisant une approche basée sur la prédiction théorique des hôtes bactériens, nous avons pu montrer la fiabilité de l’approche choisie générant des profils taxonomiques bactériens comparables à ceux obtenus par l’approche classique basée sur le métabarcoding ciblant le gène ARN 16S. Ce travail de thèse a donc permis d’apporter un jeu de données unique, mais aussi de nouvelles connaissances fondamentales sur la composition du virome de sites aquatiques soumis à de forts niveaux de pollution.uIn this thesis, we chose to study the viral community in a tropical lagoon exposed to domestic, agricultural and industrial discharge : the Ébrié Lagoon bordering the city of Abidjan in the Ivory Coast. The objectives of this study were (1) to characterize the benthic and planktonic viromes in seven sites in the lagoon with contrasting levels of eutrophication, distinguishing between DNA and RNA viromes, and (2) to examine the reproductive strategies of viruses. To this end, we used shotgun metagenomic sequencing combined with bioinformatics analysis. The key findings showed that the composition of DNA viromes was specific to each compartment (plankton/benthos). Conversely, the composition of RNA viromes was more influenced by the level of eutrophication than by the compartment. Viromes of the most eutrophicated sites contained sequences associated with human pathogens of faecal origin and with indicators of human faecal pollution. The study of interactions between the viruses and their bacterial hosts showed that the most eutrophic sites in this tropical lagoon were more conducive to lytic viral reproductive strategies, while lysogeny was more common in the most oligotrophic sites. Lastly, the results of an approach based on the theoretical prediction of bacterial hosts via the Prokaryotic virus Host Predictor indicated the reliability of this tool in generating taxonomic profiles of bacterial hosts comparable to those obtained by the classical approach based on metabarcoding targeting the 16S rRNA gene. This study provided not only a unique dataset, but new fundamental knowledge on the composition of the virome of aquatic sites subjected to high levels of pollution

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

WOS:000998532700001The 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

Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing

Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage–host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages’ bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data

Viral life strategies in a heavily anthropized tropical lagoon

International audienceAbstract Ecological traits of aquatic microorganisms have been poorly investigated in tropical latitudes, especially in lagoons, which are often subjected to strong anthropogenic influence, conducive to microbial development. In this study, we examined the abundance of both viral and bacterial communities, as well as their interactions (lytic and lysogenic infections) in the water and sediment of seven main stations of the Ebrié Lagoon (Ivory Coast) with contrasting levels of eutrophication. The highest bacterial and viral concentrations in both planktonic and benthic samples were found in the most eutrophicated stations, where viral lytic infections also exhibited their highest values. Conversely, the highest fractions of inducible lysogens were measured in the most oligotrophic stations, suggesting that these two main viral life strategies are mutually exclusive in this lagoon. Our findings also revealed the importance that nutrients (especially ammonium) play as drivers of the interactions between viruses and their bacterial hosts in tropical lagoons

Viral life strategies in a heavily anthropized tropical lagoon

Ecological traits of aquatic microorganisms have been poorly investigated in tropical latitudes, especially in lagoons, which are often subjected to strong anthropogenic influence, conducive to microbial development. In this study, we examined the abundance of both viral and bacterial communities, as well as their interactions (lytic and lysogenic infections) in the water and sediment of seven main stations of the Ebrié Lagoon (Ivory Coast) with contrasting levels of eutrophication. The highest bacterial and viral concentrations in both planktonic and benthic samples were found in the most eutrophicated stations, where viral lytic infections also exhibited their highest values. Conversely, the highest fractions of inducible lysogens were measured in the most oligotrophic stations, suggesting that these two main viral life strategies are mutually exclusive in this lagoon. Our findings also revealed the importance that nutrients (especially ammonium) play as drivers of the interactions between viruses and their bacterial hosts in tropical lagoons

Decoding the DNA and RNA viromes of a tropical urban lagoon

\ₑprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1462-2920.16463Human 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

Could Sterile Aedes albopictus Male Releases Interfere with Aedes aegypti Population in Reunion Island?

International audienceIn Reunion Island, the feasibility of an Aedes albopictus control program using the Sterile Insect Technique (SIT) is studied. Because, in some regions, Ae. albopictus is living in sympatry with Aedes aegypti, the impact of releasing millions of sterile male Ae. albopictus on female Ae. aegypti reproduction needs to be assessed. Thus, to study the potential heterospecific matings, a marking technique using rhodamine B has been used. Rhodamine is given in solution to male mosquitoes to be incorporated into the male body and seminal fluid and transferred during mating into the bursa inseminalis and spermathecae of females. The presence of rhodamine in females occurred in 15% of cases when Ae. aegypti females were offered non-irradiated Ae. albopictus males, 5% when offered irradiated Ae. albopictus males and 18% of cases in the inverse heterospecific matings. Moreover, our results also showed that these matings gave few eggs but were not viable. Finally, the results showed that whatever the type of mating crosses, females in cages previously crossed with males of another species can re-mate with males of their species and produce an equivalent amount of egg compared to females only mated with conspecific males. Despite the promiscuity of the males and females in small cages for three days, heterospecific mating between sterile male Ae. albopictus and female Ae aegypti, 95% of the females have not been inseminated suggesting that in the field the frequency satyrization would be very low

A global metagenomic map of urban microbiomes and antimicrobial resistance

We present a global atlas of 4,728 metagenomic samples from mass-transit systems in 60 cities over 3 years, representing the first systematic, worldwide catalog of the urban microbial ecosystem. This atlas provides an annotated, geospatial profile of microbial strains, functional characteristics, antimicrobial resistance (AMR) markers, and genetic elements, including 10,928 viruses, 1,302 bacteria, 2 archaea, and 838,532 CRISPR arrays not found in reference databases. We identified 4,246 known species of urban microorganisms and a consistent set of 31 species found in 97% of samples that were distinct from human commensal organisms. Profiles of AMR genes varied widely in type and density across cities. Cities showed distinct microbial taxonomic signatures that were driven by climate and geographic differences. These results constitute a high-resolution global metagenomic atlas that enables discovery of organisms and genes, highlights potential public health and forensic applications, and provides a culture-independent view of AMR burden in cities.Funding: the Tri-I Program in Computational Biology and Medicine (CBM) funded by NIH grant 1T32GM083937; GitHub; Philip Blood and the Extreme Science and Engineering Discovery Environment (XSEDE), supported by NSF grant number ACI-1548562 and NSF award number ACI-1445606; NASA (NNX14AH50G, NNX17AB26G), the NIH (R01AI151059, R25EB020393, R21AI129851, R35GM138152, U01DA053941); STARR Foundation (I13- 0052); LLS (MCL7001-18, LLS 9238-16, LLS-MCL7001-18); the NSF (1840275); the Bill and Melinda Gates Foundation (OPP1151054); the Alfred P. Sloan Foundation (G-2015-13964); Swiss National Science Foundation grant number 407540_167331; NIH award number UL1TR000457; the US Department of Energy Joint Genome Institute under contract number DE-AC02-05CH11231; the National Energy Research Scientific Computing Center, supported by the Office of Science of the US Department of Energy; Stockholm Health Authority grant SLL 20160933; the Institut Pasteur Korea; an NRF Korea grant (NRF-2014K1A4A7A01074645, 2017M3A9G6068246); the CONICYT Fondecyt Iniciación grants 11140666 and 11160905; Keio University Funds for Individual Research; funds from the Yamagata prefectural government and the city of Tsuruoka; JSPS KAKENHI grant number 20K10436; the bilateral AT-UA collaboration fund (WTZ:UA 02/2019; Ministry of Education and Science of Ukraine, UA:M/84-2019, M/126-2020); Kyiv Academic Univeristy; Ministry of Education and Science of Ukraine project numbers 0118U100290 and 0120U101734; Centro de Excelencia Severo Ochoa 2013–2017; the CERCA Programme / Generalitat de Catalunya; the CRG-Novartis-Africa mobility program 2016; research funds from National Cheng Kung University and the Ministry of Science and Technology; Taiwan (MOST grant number 106-2321-B-006-016); we thank all the volunteers who made sampling NYC possible, Minciencias (project no. 639677758300), CNPq (EDN - 309973/2015-5), the Open Research Fund of Key Laboratory of Advanced Theory and Application in Statistics and Data Science – MOE, ECNU, the Research Grants Council of Hong Kong through project 11215017, National Key RD Project of China (2018YFE0201603), and Shanghai Municipal Science and Technology Major Project (2017SHZDZX01) (L.S.