To the best of our knowledge, this study constitutes the first attempt to assess the occurrence of enteric viruses in river waters, in areas differentially influenced by anthropogenic pressure. Enteric viruses (enterovirus, norovirus, adenovirus, rotavirus, hepatitis A and E viruses, and bocavirus) were widespread in the industrial and urban areas, and were less frequently detected in the agricultural area. Interestingly, human bocavirus was the most frequently detected virus, outnumbering even adenoviruses, known to be widespread in water environments. The widespread presence of bocavirus in surface waters suggests that a potential role of water in its transmission should not be excluded.

Cyanobacteria blooms are a worldwide concern for water bodies and may be promoted by eutrophication and climate change. The prediction of cyanobacterial blooms and identification of the main triggering factors are of paramount importance for water management. In this study, we analyzed a comprehensive dataset including ten-years measurements collected at Lake Varese, an eutrophic lake in Northern Italy. Microscopic analysis of the water samples was performed to characterize the community distribution and dynamics along the years. We observed that cyanobacteria represented a significant fraction of the phytoplankton community, up to 60% as biovolume, and a shift in the phytoplankton community distribution towards cyanobacteria dominance onwards 2010 was detected. The relationships between cyanobacteria biovolume, nutrients, and environmental parameters were investigated through simple and multiple linear regressions. We found that 14-days average air temperature together with total phosphorus may only partly explain the cyanobacteria biovolume variance at Lake Varese. However, weather forecasts can be used to predict an algal outbreak two weeks in advance and, eventually, to adopt management actions. The prediction of cyanobacteria algal blooms remains challenging and more frequent samplings, combined with the microscopy analysis and the metagenomics technique, would allow a more conclusive analysis.

The spread of antibiotic resistance in the water environment has been widely described. However, still many knowledge gaps exist regarding the selection pressure from antibiotics, heavy metals and other substances present in surface waters as a result of anthropogenic activities, as well as the extent and impact of this phenomenon on aquatic organisms and humans. In particular, the relationship between environmental concentrations of antibiotics and the acquisition of ARGs by antibiotic-sensitive bacteria as well as the impact of heavy metals and other selective agents on antimicrobial resistance (AMR) need to be defined. Currently, established safety values are based on the effects of antibiotic toxicity neglecting the question of AMR spread. In turn, risk assessment of antibiotics in waterbodies remains a complex question implicating multiple variables and unknowns reinforced by the lack of harmonized protocols and official guidelines. In the present review, we discussed current state-of-the-art and the knowledge gaps related to pressure exerted by antibiotics and heavy metals on aquatic environments and their relationship to the spread of AMR. Along with this latter, we reflected on i) the risk assessment in surface waters, ii) selective pressures contributing to its transfer and propagation, and iii) the advantages of metagenomics in investigating AMR. Furthermore, the role of microplastics in co-selection for metal and antibiotic resistance, together with the need for more studies in freshwater are highlighted.

Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments. Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health. In this study, we assessed the microbial composition, with a focus on Cyanobacteria, in Lake Varese, a eutrophic lake located in northern Italy. Water samples were collected and used for obtaining a 16S-based taxonomic profile and performing a shotgun sequencing analysis. The phyla found to exhibit the greatest relative abundance in the lake included Proteobacteria, Cyanobacteria, Actinobacteriota and Bacteroidota. In the epilimnion and at 2.5 × Secchi depth, Cyanobacteria were found to be more abundant compared to the low levels detected at greater depths. The blooms appear to be dominated mainly by the species Lyngbya robusta, and a specific functional profile was identified, suggesting that distinct metabolic processes characterized the bacterial population along the water column. Finally, analysis of the shotgun data also indicated the presence of a large and diverse phage population.

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