Marine viruses play a major role in the energy and nutrient cycle and affect the evolution of their hosts. Despite their importance, there is still little knowledge about RNA viruses. Here, we have explored the Atlantic Ocean, from surface to deep (4.296 m), and used viromics and quantitative methods to unveil the genomics, biogeography, and the mass contribution of RNA viruses to the total viroplankton. A total of 2481 putative RNA viral contigs (>500 bp) and 107 larger bona fide RNA viral genomes (>2.5 kb) were identified; 88 of them representing novel viruses belonging mostly to two clades: Yangshan assemblage (sister clade to the class Alsuviricetes ) and Nodaviridae . These viruses were highly endemic and locally abundant, with little or no presence in other oceans since only ≈15% of them were found in at least one of the Tara sampling metatranscriptomes. Quantitative data indicated that the abundance of RNA viruses in the surface and deep chlorophyll maximum zone was within ≈10 ⁶ VLP/mL representing a potential contribution of 5.2%–24.4% to the total viroplankton community (DNA and RNA viruses), with DNA viruses being the predominant members (≈10 ⁷ VLP/mL). However, for the deep sample, the observed trend was the opposite, although as further discussed, several biases should be considered. Together these results contribute to our understanding of the diversity, abundance, and distribution of RNA viruses in the oceans and provide a basis for further investigation into their ecological roles and biogeography.

Wastewater treatment plants (WWTPs) effluents are considered as hotspots for the dispersion of antibiotic resistance genes (ARGS) into natural ecosystems. The bacterial resistome (ARG collection in a metagenome) analyses have provided clues on antibacterial resistance dynamics. However, viruses and vesicles are frequently ignored. Here, we addressed the bacterial, viral and vesicle resistomes from a representative wastewater effluent in natural conditions and amended with polymyxin, which is used as a last resort antibiotic. Metagenomics showed that the natural prokaryotic resistome was vast (≈9,000 ARG hits/Gb metagenome) and diverse, while viral resistome was 2 orders of magnitude lower (≈50 ARG hits/Gb metagenome) suggesting that viruses rarely encoded ARGs. After polymyxin amendment, data showed no ARG enrichment ‐including to polymyxin‐ in the microbiome. Remarkably, microbiomes responded to polymyxin with a vast release of putative vesicles (3‐fold increase compared to the control), which might be used as ‘traps’ to decrease the antibiotic concentration. Intriguingly, although polymyxin resistance genes (PRGs) were rare in the microbiome (0.018% of total ARG found), in the viral and vesicle fractions, PRGs were more abundant (0.5‐0.8% of total ARG found). Our data suggest that vesicles could have a more active role in the context of transmission of antibiotic resistances. This article is protected by copyright. All rights reserved.