Environmental health of water bodies from a Brazilian Amazon Metropolis based on a conventional and metagenomic approach.

AIMS: The present study aimed to use a conventional and metagenomic approach to investigate the microbiological diversity of water bodies in a network of drainage channels and rivers located in the central area of the city of Belém, northern Brazil, which is considered one of the largest cities in the Brazilian Amazon. METHODS AND RESULTS: In eight of the analyzed points, both bacterial and viral microbiological indicators of environmental contamination-physical-chemical and metals-were assessed. The bacterial resistance genes, drug resistance mechanisms, and viral viability in the environment were also assessed. A total of 473 families of bacteria and 83 families of viruses were identified. Based on the analysis of metals, the levels of three metals (Cd, Fe, and Mn) were found to be above the recommended acceptable level by local legislation. The levels of the following three physicochemical parameters were also higher than recommended: biochemical oxygen demand, dissolved oxygen, and turbidity. Sixty-three bacterial resistance genes that conferred resistance to 13 different classes of antimicrobials were identified. Further, five mechanisms of antimicrobial resistance were identified and viral viability in the environment was confirmed. CONCLUSIONS: Intense human actions combined with a lack of public policies and poor environmental education of the population cause environmental degradation, especially in water bodies. Thus, urgent interventions are warranted to restore the quality of this precious and scarce asset worldwide.

Relative abundance and the fate of human rotavirus in wastewater during treatment processes: identification of potential infectious rotavirus in the final effluents and receiving aquatic milieu in Durban area, South Africa.

The occurrence and persistence of rotaviruses in raw and treated wastewater and their discharge into rivers represent a significant health risk for humans and animals, worldwide. In this study, samples were collected monthly from each of the four Durban wastewater treatment plants (DWWTPs) and receiving rivers for a period of 3 months. Rotavirus was quantified by real-time quantitative PCR (RT-qPCR), and viability was assessed using integrated cell culture (ICC)-qPCR. Rotavirus was detected consistently in 100% of influent wastewaters (mean concentration range, 4.36-4.46 log10 genome equivalent (GE) copies/L) and final effluent samples of three DWWTPs (range, 3.35-3.61 log10 GE copies/L). Overall, 94% (45/48) of the wastewater analyzed and 95% (20/21) of the associated river water samples were positive for rotavirus (range, 2.04-6.77 log10 GE copies/L). The activated sludge process with 0.10-0.43 log10 reduction values (LRV) only moderately reduced the viral loads. Similarly, one of the DWWTPs that operated the biofilter modality produced 0.20 LRV. Though the additional treatment with chlorine produced higher LRV (range, 0.31-0.53) than the corresponding activated sludge or biofilter process, the difference in viral removals was not significant (p > 0.05). The equivalent treatment efficiencies of the four DWWTPs varied from 19 to 43% decay in the population of rotavirus. Further, infectious rotavirus ranging from 66.67 to 100%, 50 to 100%, and 66.67 to 100% were detected in the post-activated sludge, final effluents, and river water samples, respectively. In conclusion, the findings of infectious rotavirus in both the final effluents and associated rivers represent an infection risk for humans or animals during contact. Thus, close monitoring for rotavirus and risk assessment studies under distinct exposure scenarios may further shed light on the health-related risks associated with water recovery and reuse in urban settings.

Thallium spill shifts the structural and functional characteristics of viral communities with different lifestyles in river sediments.

Thallium (Tl), a highly toxic heavy metal, can affect microbial community, while little is known about its effect on viral community. The present study investigated the variation of viral communities, as well as their interactions with microbial hosts under Tl stress. Tl in sediments significantly altered the composition and diversity of the viral communities, but showed no significant links with the prokaryotic communities, which may reveal a potential discrepancy in the sensitivity of the viral and prokaryotic communities to heavy metal stress. Auxiliary metabolic genes (AMGs) involved in denitrification, methane oxidation and organic sulfur transformation were enriched at T1-contaminated sites, while the abundance of AMGs related to methanogenesis and sulfate reduction were higher at pristine sites. Specially, the enrichment of AMGs involved in assimilatory sulfate reduction in Tl-contaminated sites could possibly reduce Tl bioavailability by enhancing the microbially-driven sulfur cycling to generate sulfides that could be complexed with Tl. Moreover, there was a significantly positive correlation between virus-carrying metal resistant genes and the sedimentary Tl concentration, implying that Tl contamination might enhance the metal resistant potential of the viruses. Serving as the functional gene reservoir, the response of viral AMGs to Tl stress could represent a potential pathway for microorganisms to be adapted to the metal-polluted environments. Our study provided novel insights into the impact of Tl spill on viral communities, shedding light on functional characteristics and the links of virus-host interaction with Tl level.

Large-scale single-virus genomics uncovers hidden diversity of river water viruses and diversified gene profiles.

Environmental viruses (primarily bacteriophages) are widely recognized as playing an important role in ecosystem homeostasis through the infection of host cells. However, the majority of environmental viruses are still unknown as their mosaic structure and frequent mutations in their sequences hinder genome construction in current metagenomics. To enable the large-scale acquisition of environmental viral genomes, we developed a new single-viral genome sequencing platform with microfluidic-generated gel beads. Amplification of individual DNA viral genomes in mass-produced gel beads allows high-throughput genome sequencing compared to conventional single-virus genomics. The sequencing analysis of river water samples yielded 1431 diverse viral single-amplified genomes, whereas viral metagenomics recovered 100 viral metagenome-assembled genomes at the comparable sequence depth. The 99.5% of viral single-amplified genomes were determined novel at the species level, most of which could not be recovered by a metagenomic assembly. The large-scale acquisition of diverse viral genomes identified protein clusters commonly detected in different viral strains, allowing the gene transfer to be tracked. Moreover, comparative genomics within the same viral species revealed that the profiles of various methyltransferase subtypes were diverse, suggesting an enhanced escape from host bacterial internal defense mechanisms. Our use of gel bead-based single-virus genomics will contribute to exploring the nature of viruses by accelerating the accumulation of draft genomes of environmental DNA viruses.

Delving into the Aftermath of a Disease-Associated Near-Extinction Event: A Five-Year Study of a Serpentovirus (Nidovirus) in a Critically Endangered Turtle Population.

Bellinger River virus (BRV) is a serpentovirus (nidovirus) that was likely responsible for the catastrophic mortality of the Australian freshwater turtle Myuchelys georgesi in February 2015. From November 2015 to November 2020, swabs were collected from turtles during repeated river surveys to estimate the prevalence of BRV RNA, identify risk factors associated with BRV infection, and refine sample collection. BRV RNA prevalence at first capture was significantly higher in M. georgesi (10.8%) than in a coexisting turtle, Emydura macquarii (1.0%). For M. georgesi, various risk factors were identified depending on the analysis method, but a positive BRV result was consistently associated with a larger body size. All turtles were asymptomatic when sampled and conjunctival swabs were inferred to be optimal for ongoing monitoring. Although the absence of disease and recent BRV detections suggests a reduced ongoing threat, the potential for the virus to persist in an endemic focus or resurge in cyclical epidemics cannot be excluded. Therefore, BRV is an ongoing potential threat to the conservation of M. georgesi, and strict adherence to biosecurity principles is essential to minimise the risk of reintroduction or spread of BRV or other pathogens.

A multi-marker assessment of sewage contamination in streams using human-associated indicator bacteria, human-specific viruses, and pharmaceuticals.

Human sewage contaminates waterways, delivering excess nutrients, pathogens, chemicals, and other toxic contaminants. Contaminants and various sewage indicators are measured to monitor and assess water quality, but these analytes vary in their representation of sewage contamination and the inferences about water quality they support. We measured the occurrence and concentration of multiple microbiological (n = 21) and chemical (n = 106) markers at two urban stream locations in Milwaukee, Wisconsin, USA over two years. Five-day composite water samples (n = 98) were collected biweekly, and sewage influent samples (n = 25) were collected monthly at a Milwaukee, WI water reclamation facility. We found the vast majority of markers were not sensitive enough to detect sewage contamination. To compare analytes for monitoring applications, five consistently detected human sewage indicators were used to evaluate temporal patterns of sewage contamination, including microbiological (pepper mild mottle virus, human Bacteroides, human Lachnospiraceae) and chemical (acetaminophen, metformin) markers. The proportion of human sewage in each stream was estimated using the mean influent concentration from the water reclamation facility and the mean concentration of all stream samples for each sewage indicator marker. Estimates of instream sewage pollution varied by marker, differing by up to two orders of magnitude, but four of the five sewage markers characterized Underwood Creek (mean proportions of human sewage ranged 0.0025 % - 0.075 %) as less polluted than Menomonee River (proportions ranged 0.013 % - 0.14 %) by an order of magnitude more. Chemical markers correlated with each other and yielded higher estimates of sewage pollution than microbial markers, which exhibited greater temporal variability. Transport, attenuation, and degradation processes can influence chemical and microbial markers differently and cause variation in human sewage estimates. Given the range of potential human and ecological health effects of human sewage contamination, robust characterization of sewage contamination that uses multiple lines of evidence supports monitoring and research applications.

Moving beyond classical markers of water quality: detection of enteric viruses and genotoxicity in water of the Sinos River / Indo além dos marcadores clássicos de qualidade da água: detecção de vírus entéricos e genotoxicidade na água do Rio dos Sinos

It is well recognized that the classical biological and chemical markers of environmental pollution do not necessarily indicate the presence or absence of emerging threats to public health, such as waterborne viruses and genotoxicants. The purpose of this preliminary study was to evaluate the presence of material of enteroviruses (EV), rotavirus (RV) and adenovirus (AdV) and genotoxicity in water samples from points of routine monitoring of water quality in the main course of the Sinos River. The points are classified into different levels of pollution in accordance to the Brazilian federal regulations. Viral genomes from EV, AdV were detected in two of the 4 collection points regardless of the level of urbanisation of the surrounding areas. In contrast, genotoxicity was not observed in piava (Leporinus obtusidens) fingerlings cultivated on these same water samples. Results were compared with classical physical, chemical and microbiological parameters. There was no clear evidence of association between any of the classical markers and the presence of viral genomes in the water samples tested.

É amplamente reconhecido que os marcadores biológicos e químicos clássicos para a poluição ambiental não necessariamente indicam a presença ou ausência de ameaças emergentes à saúde pública, tais como vírus transmitidos pela água e genotoxicantes. Este estudo preliminar teve por objetivo detectar material genético de enterovírus (EV), rotavírus (RV) e adenovírus (AdV) e genotoxicidade em amostras de água de pontos de monitoramento de rotina da qualidade da água no curso principal do rio dos Sinos. Os pontos são classificados em níveis diferentes de poluição, de acordo com as normativas federais brasileiras. Genomas virais de EV, RV e RV foram detectados em dois dos quatro pontos de coleta, independente do nível de urbanização das áreas adjacentes. Por outro lado, não foi observada genotoxicidade em alevinos de piava (Leporinus obtusidens) cultivados nestas mesmas amostras de água. Os resultados são comparados com marcadores físicos, químicos e microbiológicos clássicos, não há nenhuma evidência clara da associação entre qualquer um dos marcadores clássicos e da presença de genomas virais nas amostras de água testadas.