Setting a baseline for global urban virome surveillance in sewage

The rapid development of megacities, and their growing connectedness across the world is becoming a distinct driver for emerging disease outbreaks. Early detection of unusual disease emergence and spread should therefore include such cities as part of risk-based surveillance. A catch-all metagenomic sequencing approach of urban sewage could potentially provide an unbiased insight into the dynamics of viral pathogens circulating in a community irrespective of access to care, a potential which already has been proven for the surveillance of poliovirus. Here, we present a detailed characterization of sewage viromes from a snapshot of 81 high density urban areas across the globe, including in-depth assessment of potential biases, as a proof of concept for catch-all viral pathogen surveillance. We show the ability to detect a wide range of viruses and geographical and seasonal differences for specific viral groups. Our findings offer a cross-sectional baseline for further research in viral surveillance from urban sewage samples and place previous studies in a global perspective

Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance

The field of eDNA is growing exponentially in response to the need for detecting rare and invasive species for management and conservation decisions. Developing technologies and standard protocols within the biosecurity sector must address myriad challenges associated with marine environments, including salinity, temperature, advective and deposition processes, hydrochemistry and pH, and contaminating agents. These approaches must also provide a robust framework that meets the need for biosecurity management decisions regarding threats to human health, environmental resources, and economic interests, especially in areas with limited clean-laboratory resources and experienced personnel. This contribution aims to facilitate dialogue and innovation within this sector by reviewing current approaches for sample collection, post-sampling capture and concentration of eDNA, preservation, and extraction, all through a biosecurity monitoring lens.</jats:p

Response of top shell assemblages to cyclogenesis disturbances. A case study in the Bay of Biscay

M. Munoz-Colmenero holds a National ~ Spanish Grant (reference AP-2010-5211). This study has been supported by the Regional Government of Asturias (grant number SV-PA-13-ECOEMP-41; GRUPIN14-093) and the Spanish National Project MINECO CGL2013-42415-R. This is a contribution from the Marine Observatory of Asturias (Spain).Cyclones and other climate disturbances profoundly affect coastal ecosystems, promoting changes in the benthic communities that require time, sometimes even years, for a complete recovery. In this study we have analysed the morphological and genetic changes occurred in top shell (Gibbula umbilicalis and Phorcus lineatus) assemblages from the Bay of Biscay following explosive cyclogenesis events in 2014. Comparison with previous samples at short (three years before the cyclogenesis) and long (Upper Pleistocene) temporal scales served to better evaluate the extent of change induced by these disturbances in a more global dimension. A significant increase in mean size after the cyclogenesis was found for the two species, suggesting selective sweeping of small individuals weakly adhered to substrata. Loss of haplotype variants at the cytochrome oxidase subunit I gene suggests a population bottleneck, although it was not intense enough to produce significant changes in haplotype frequencies. The high population connectivity and metapopulation structuring of the two species in the area likely help the populations to recover from disturbances. At a wider temporal scale, cyclogenesis effects seemed to compensate the apparent decreasing trends in size for P. lineatus occurred after the Pleistocene eHolocene transition. Considering disturbance regimes for population baselines is recommended when the long-term effects of climate and anthropogenic pressures are evaluated.Depto. de Genética, Fisiología y MicrobiologíaFac. de Ciencias BiológicasTRUEpu

The impact of DNA extract homogenization and replication on marine sediment metabarcoding diversity and heterogeneity

Metabarcoding of environmental DNA (eDNA) is an attractive complement to morphological methods for surveys and routine monitoring of marine sediment benthic communities. However, metabarcoding and other genetic techniques are heavily affected by choices made during sampling, processing, and analysis. Here, we investigated the effect of different eDNA extraction protocols on observed alpha- and beta diversity of replicates from the same grab. Specifically, we compared (A) homogenization intensity during sediment DNA extraction, (B) extraction replicates vs larger sediment extraction volume, and (C) pre- and post-PCR extract pooling. Using the 18S V1-V2 region marker, we show that a Precellys homogenizer protocol during DNA extraction can significantly improve sediment metabarcoding results in terms of captured diversity and inter-replicate homogeneity compared to vortexing only. This effect superseded that of increased sediment extract volume. Pre-PCR pooling of DNA extraction replicates increased observed rarefied richness compared to data from single extracts only, but not to the extent of sample extract replicates amplified individually before pooling. We argue that this discrepancy was due to a reduction both in recovered sample diversity, but also the number of PCR artifacts and PCR drift. Our results demonstrate that extraction replicates of smaller sediment volumes, in combination with moderate Precellys homogenization and pre-PCR pooling, are a cost-effective way to increase the amount of organism diversity that is recovered from sediment eDNA metabarcoding samples