Metagenomic Characterization of Microbial Pollutants and Antibiotic- and Metal-Resistance Genes in Sediments from the Canals of Venice

The spread of fecal pollutants and antibiotic resistance in the aquatic environmentrepresents a major public health concern and is predicted to increase in light of climate changeconsequences and the increasing human population pressure on the lagoon and coastal areas. Thecity of Venice (Italy) is affected by diverse microbial pollution sources, including domesticwastewaters that, due to the lack of modern sewage treatment infrastructure in the historical citycenter, are released into canals. The outflowing jets of its tidal inlets thus represent a source ofcontamination for the nearby beaches on the barrier island separating the lagoon from the sea.Metagenomic analyses of DNA extracted from sediment samples from six sites in the canals of thecity's historic center were undertaken to characterize the microbial community composition, thepresence of fecal microbes as well as other non-enteric pathogens, and the content of genes relatedto antibiotic (AB) and heavy metal (HM) resistance, and virulence. The six sites hosted similarprokaryotic communities, although variations in community composition likely related to oxygenavailability were observed. All sites displayed relatively high levels of fecal contamination,including the presence of Fecal Indicator Bacteria, sewage- and alternative feces-associated bacteria.Relatively high levels of other potential pathogens were also found. About 1 in 500 genes identifiedat these sites are related to AB and HM resistance; conversely, genes related to virulence were rare.Our data suggest the existence of widespread sediment microbial pollution in the canals of Venice,coupled with the prevalence of ARGs to antibiotics frequently used in humans as well as of HMRGsto toxic metals that still persists in the lagoon. All of this evidence raises concerns about theconsequences on the water quality of the lagoon and adjacent marine areas and the potential risksfor humans, deserving further studies.