Corrigendum: Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters.

[This corrects the article on p. 2200 in vol. 8, PMID: 29201017.].

Characterization of Metagenomes in Urban Aquatic Compartments Reveals High Prevalence of Clinically Relevant Antibiotic Resistance Genes in Wastewaters.

The dissemination of antimicrobial resistance (AMR) is an escalating problem and a threat to public health. Comparative metagenomics was used to investigate the occurrence of antibiotic resistant genes (ARGs) in wastewater and urban surface water environments in Singapore. Hospital and municipal wastewater (n = 6) were found to have higher diversity and average abundance of ARGs (303 ARG subtypes, 197,816 x/Gb) compared to treated wastewater effluent (n = 2, 58 ARG subtypes, 2,692 x/Gb) and surface water (n = 5, 35 subtypes, 7,985 x/Gb). A cluster analysis showed that the taxonomic composition of wastewaters was highly similar and had a bacterial community composition enriched in gut bacteria (Bacteroides, Faecalibacterium, Bifidobacterium, Blautia, Roseburia, Ruminococcus), the Enterobacteriaceae group (Klebsiella, Aeromonas, Enterobacter) and opportunistic pathogens (Prevotella, Comamonas, Neisseria). Wastewater, treated effluents and surface waters had a shared resistome of 21 ARGs encoding multidrug resistant efflux pumps or resistance to aminoglycoside, macrolide-lincosamide-streptogramins (MLS), quinolones, sulfonamide, and tetracycline resistance which suggests that these genes are wide spread across different environments. Wastewater had a distinctively higher average abundance of clinically relevant, class A beta-lactamase resistant genes (i.e., blaKPC, blaCTX-M, blaSHV, blaTEM). The wastewaters from clinical isolation wards, in particular, had a exceedingly high levels of blaKPC-2 genes (142,200 x/Gb), encoding for carbapenem resistance. Assembled scaffolds (16 and 30 kbp) from isolation ward wastewater samples indicated this gene was located on a Tn3-based transposon (Tn4401), a mobilization element found in Klebsiella pneumonia plasmids. In the longer scaffold, transposable elements were flanked by a toxin-antitoxin (TA) system and other metal resistant genes that likely increase the persistence, fitness and propagation of the plasmid in the bacterial host under conditions of stress. A few bacterial species (Enterobacter cloacae, Klebsiella pneumoniae, Citrobacter freundii, Pseudomonas aeruginosa) that were cultured from the isolation ward wastewaters on CHROMagar media harbored the blaKPC-2 gene. This suggests that hospital wastewaters derived from clinical specialty wards are hotspots for the spread of AMR. Assembled scaffolds of other mobile genetic elements such as IncQ and IncF plasmids bearing quinolone resistance genes (qnrS1, qnrS2) and the class A beta-lactamase gene (blaTEM-1) were recovered in wastewater samples which may aid the transfer of AMR.

Fate and transport of perfluoro- and polyfluoroalkyl substances including perfluorooctane sulfonamides in a managed urban water body.

Transport and fate of perfluoro- and polyfluoroalkyl substances (PFASs) in an urban water body that receives mainly urban runoff was investigated. Water, suspended solids, and sediment samples were collected during the monsoon (wet) and inter-monsoon (dry) season at different sites and depths. Samples were analyzed for C7 to C12 perfluoroalkyl carboxylate homologues (PFCAs) (PFHpA, PFOA, PFNA, PFDA, PFUnA, PFDoA), perfluorohexane, perfluorooctane, and 6:2-fluorotelomer sulfonate (PFHxS, PFOS, and 6:2FtS, respectively), perfluorooctane sulfonamide (FOSA), N-ethyl FOSA (sulfluramid), N-ethyl sulfonamidoethanol (N-EtFOSE), and N-methyl and N-ethyl sulfonamidoacetic acid (N-EtFOSAA and N-MeFOSAA, respectively). Concentrations in wet samples were only slightly higher. The sum total PFAS (ΣPFAS) concentrations dissolved in the aqueous phase and sorbed to suspended solids (SS) ranged from 107 to 253 ng/L and 11 to 158 ng/L, respectively. PFOA, PFOS, PFNA, PFHxS, and PFDA contributed most (approximately 90 %) to the dissolved ΣPFASs. N-EtFOSA dominated the particulate PFAS burden in wet samples. K D values of PFOA and PFOS calculated from paired SS and water concentrations varied widely (1.4 to 13.7 and 1.9 to 98.9 for PFOA and PFOS, respectively). Field derived K D was significantly higher than laboratory K D suggesting hydrophobic PFASs sorbed to SS resist desorption. The ΣPFAS concentrations in the top sedimentary layer ranged from 8 to 42 µg/kg and indicated preferential accumulation of the strongly sorbing long-chain PFASs. The occurrence of the metabolites N-MeFOSAA, N-EtFOSAA and FOSA in the water column and sediments may have resulted from biological or photochemical transformations of perfluorooctane sulfonamide precursors while the absence of FOSA, N-EtFOSA and 6:2FtS in sediments was consistent with biotransformation.

Effects of sulfate on microcystin production, photosynthesis, and oxidative stress in Microcystis aeruginosa.

Increasing sulfate in freshwater systems, caused by human activities and climate change, may have negative effects on aquatic organisms. Microcystis aeruginosa (M. aeruginosa) is both a major primary producer and a common toxic cyanobacterium, playing an important role in the aquatic environment. This study first investigated the effects of sulfate on M. aeruginosa. The experiment presented here aims at analyzing the effects of sulfate on physiological indices, molecular levels, and its influencing mechanism. The results of our experiment showed that sulfate (at 40, 80, and 300 mg L(-1)) inhibited M. aeruginosa growth, increased both intracellular and extracellular toxin contents, and enhanced the mcyD transcript level. Sulfate inhibited the photosynthesis of M. aeruginosa, based on the decrease in pigment content and the down-regulation of photosynthesis-related genes after sulfate exposure. Furthermore, sulfate decreased the maximum electron transport rate, causing the cell to accumulate surplus electrons and form reactive oxygen species (ROS). Sulfate also increased the malondialdehyde (MDA) content, which showed that sulfate damaged the cytomembrane. This damage contributed to the release of intracellular toxin to the culture medium. Although sulfate increased superoxide dismutase (SOD) activities, expression of sod, and total antioxidant capacity in M. aeruginosa, it still overwhelmed the antioxidant system since the ROS level simultaneously increased, and finally caused oxidative stress. Our results indicate that sulfate has direct effects on M. aeruginosa, inhibits photosynthesis, causes oxidative stress, increases toxin production, and affects the related genes expression in M. aeruginosa.

Next-generation sequencing (NGS) for assessment of microbial water quality: current progress, challenges, and future opportunities.

Water quality is an emergent property of a complex system comprised of interacting microbial populations and introduced microbial and chemical contaminants. Studies leveraging next-generation sequencing (NGS) technologies are providing new insights into the ecology of microbially mediated processes that influence fresh water quality such as algal blooms, contaminant biodegradation, and pathogen dissemination. In addition, sequencing methods targeting small subunit (SSU) rRNA hypervariable regions have allowed identification of signature microbial species that serve as bioindicators for sewage contamination in these environments. Beyond amplicon sequencing, metagenomic and metatranscriptomic analyses of microbial communities in fresh water environments reveal the genetic capabilities and interplay of waterborne microorganisms, shedding light on the mechanisms for production and biodegradation of toxins and other contaminants. This review discusses the challenges and benefits of applying NGS-based methods to water quality research and assessment. We will consider the suitability and biases inherent in the application of NGS as a screening tool for assessment of biological risks and discuss the potential and limitations for direct quantitative interpretation of NGS data. Secondly, we will examine case studies from recent literature where NGS based methods have been applied to topics in water quality assessment, including development of bioindicators for sewage pollution and microbial source tracking, characterizing the distribution of toxin and antibiotic resistance genes in water samples, and investigating mechanisms of biodegradation of harmful pollutants that threaten water quality. Finally, we provide a short review of emerging NGS platforms and their potential applications to the next generation of water quality assessment tools.

Oxidative toxicity of perfluorinated chemicals in green mussel and bioaccumulation factor dependent quantitative structure-activity relationship.

Concerns regarding perfluorinated chemicals (PFCs) have risen in recent years because of their ubiquitous presence and high persistency. However, data on the environmental impacts of PFCs on marine organisms are very limited. Oxidative toxicity has been suggested to be one of the major toxic pathways for PFCs to induce adverse effects on organisms. To investigate PFC-induced oxidative stress and oxidative toxicity, a series of antioxidant enzyme activities and oxidative damage biomarkers were examined to assess the adverse effects of the following 4 commonly detected compounds: perfluoro-octanesulfonate, perfluoro-ocanoic acid, perfluorononanoic acid, and perfluorodecanoic acid, on green mussel (Perna viridis). Quantitative structure-activity relationship (QSAR) models were also established. The results showed that all the tested PFCs are able to induce antioxidant response and oxidative damage on green mussels in a dose-dependent manner. At low exposure levels (0 µg/L-100 µg/L), activation of antioxidant enzymes (catalase [CAT] and superoxide dismutase [SOD]) was observed, which is an adaptive response to the excessive reactive oxygen species induced by PFCs, while at high exposure levels (100 µg/L-10 000 µg/L), PFCs were found to inhibit some enzyme activity (glutathione S-transferase and SOD) where the organism's ability to respond in an adaptive manner was compromised. The oxidative stress under high PFC exposure concentration also led to lipid and DNA damage. PFC-induced oxidative toxicity was found to be correlated with the bioaccumulation potential of PFCs. Based on this relationship, QSAR models were established using the bioaccumulation factor (BAF) as the molecular descriptor for the first time. Compared with previous octanol-water partition coefficient-dependent QSAR models, the BAF-dependent QSAR model is more suitable for the impact assessment of PFCs and thus provides a more accurate description of the toxic behavior of these compounds.

Genotoxicity of perfluorinated chemicals (PFCs) to the green mussel (Perna viridis).

Concerns regarding perfluorinated chemicals (PFCs) have grown significantly in recent years. However, regulations and guidelines regarding the emission and treatment of PFCs are still missing in most parts of the world, mostly due to the lack of PFC toxicity data. In the current study, the genotoxic effects of four common PFCs, named perfluorooctanesulfonate (PFOS), perfluoroocanoic acid (PFOA), perfluorononanoic acid (PFNA) and perfluorodecanoic acid (PFDA) were investigated on marine mussels. The effects of exposure time and concentration on the toxic behavior of the compounds were also examined. Genotoxicity of PFCs was assessed in biomarker assays, showing that exposure to the target compounds could damage the organism's genetic material to varying extents, including DNA strand breaks and fragmentation, chromosomal breaks and apoptosis. The adverse effects increased with both exposure concentration and time and were related with the organism burden of PFCs. The integrated biomarker response analysis demonstrated that PFOS exhibited a higher genotoxicity than the other tested compounds. The EC50 values and confidence intervals based on integrative genotoxicity were 33 (29-37), 594 (341-1036), 195 (144-265) and 78 (73-84) µg/L for PFOS, PFOA, PFNA and PFDA respectively, classifying PFOS as a highly genotoxic compound. Although primary DNA damage was shown to be recoverable after exposure ceased, permanent genetic damage caused by elevated PFC concentrations was not restored. This is the first ecotoxicity study of PFCs that focuses on the genotoxic effects of the compounds, clearly indicating the genotoxicity of the tested PFCs and demonstrating that functional groups have a major impact on the compounds' genotoxic behavior.

Multi-biomarker responses in green mussels exposed to PFCs: effects at molecular, cellular, and physiological levels.

Perfluorinated chemicals (PFCs) are extremely persistent and have been found extensively in the environment and wildlife. Oceans are the final sink for many persistent organic pollutants (POPs) including PFCs. However, to date, there has been a lack of studies that investigated the environmental consequences of PFCs on marine organisms. To fill in this gap, environmental toxicity of two dominant PFCs, perfluorooctane sulfonate (PFOS) and perfluorooctanoate (PFOA), was examined in a sentinel species, green mussel Perna viridis, using a series of biomarkers corresponding to different biological levels (molecular, cellular, and physiological). Correlations among these biomarkers were also investigated. The results showed that the tested compounds can induce a series adverse effect at different biological levels, including oxidative stress, DNA damage, membrane instability, suppressed filtration rate, and reduced body weight. Correlation analysis revealed that excess production of reactive oxygen species could be the major toxic pathway. An indirect mode of toxic action was also explored where adverse impacts could be secondary effects of PFC exposure. The joint analysis of biomarkers from multiple biological levels resulted in a comprehensive understanding of how PFC exposure can influence the health of organisms. The correlations of these biomarkers also provided a new perspective of the ecological consequences of PFCs.

Roles of singlet oxygen and triplet excited state of dissolved organic matter formed by different organic matters in bacteriophage MS2 inactivation.

Inactivation of bacteriophage MS2 by reactive oxygen species (ROS) and triplet excited state of dissolved organic matter ((3)DOM*) produced by irradiation of natural and synthetic sensitizers with simulated sunlight of wavelengths greater than 320 nm was investigated. Natural sensitizers included purified DOM isolates obtained from wastewater and river waters, and water samples collected from Singapore River, Stamford Canal, and Marina Bay Reservoir in Singapore. Linear correlations were found between MS2 inactivation rate constants (kobs) and the photo-induced reaction rate constants of 2,4,6-trimethylphenol (TMP), a probe compound shown to react mainly with (3)DOM*. Linear correlations between MS2 kobs and singlet oxygen ((1)O2) concentrations were also found for both purified DOM isolates and natural water samples. These correlations, along with data from quenching experiments and experiments with synthetic sensitizers, Rose Bengal (RB), 3'-methoxyacetophenone (3'-MAP), and nitrite [Formula: see text] , suggest that (1)O2, (3)DOM*, and hydroxyl radicals ((•)OH) could inactivate bacteriophage MS2. Linear correlations between MS2 kobs and Specific Ultraviolet Absorption determined at 254 nm (SUVA254) were also found for both purified DOM isolates and natural samples. These results suggest the potential use of TMP as a chemical probe and SUVA254 as an indicator for virus inactivation in natural and purified DOM water samples.

Environmental toxicity of PFCs: an enhanced integrated biomarker assessment and structure-activity analysis.

Perfluorinated chemicals (PFCs) are a group of compounds with varying carbon chains and functional groups. Currently, available toxicity studies of PFCs are limited mainly to dominant species. While many other PFCs are detected in the environment and biota, it is important to extend toxicity studies to different types of PFCs to better assess their environmental and ecological impacts. In the present study, the environmental toxicity of perfluorooctanesulfonate, perfluoroocanoic acid, perfluorononanoic acid, and perfluorodecanoic acid were evaluated in green mussel, Perna viridis, using a new and improved integrated biomarker approach, the enhanced integrated biomarker response (EIBR) system, with biomarkers from multiple biological levels. Structure-activity relationships were also examined based on the biomarker results. The results show that the 4 PFCs have distinct toxicity patterns and the integrative toxicity, in terms of the EIBR value, is governed by the fluorinated chain length. In addition to commonly recognized chain length and functional group effects, several structural factors are also involved in the toxic actions of PFCs, including hydrophobicity and molecular size, and so on. By integrating biomarkers from multiple biological levels with weight-of-evidence, the proposed EIBR provides a new perspective and an ecologically relevant assessment of the environmental toxicity of the pollutants. The results of EIBR and structure-activity analysis are also useful to predict toxic behaviors of other PFCs in the group and facilitate the decision-making process.

Novel perspectives on the bioaccumulation of PFCs--the concentration dependency.

The effects of exposure concentration on the bioaccumulation of four perfluorinated chemicals (PFCs): perfluorooctanesulfonate (PFOS), perfluoroocanoic acid (PFOA), perfluorononanoic acid (PFNA), and perfluorodecanoic acid (PFDA), was investigated using green mussels, Perna viridis. Mussels were exposed to concentrations of 1 µgL(-1) and 10 µgL(-1) of each PFC for 56 days, and the bioaccumulation factors (BAF) were found to range from 15 to 859 L/kg and from 12 to 473 L/kg at 1 µgL(-1) and 10 µgL(-1), respectively. For all compounds, the BAF was larger at the lower dosage. Results suggest that the bioaccumulation of PFCs is concentration dependent. This concentration dependency can be explained by a nonlinear adsorption mechanism, which was further supported by the experimental results. The sensitivity of BAF to exposure concentration was found to be positively related to perfluorinated chain length and the binding affinity of the compounds. Bioaccumulation of long chain carboxylates and sulfonates are more easily affected by concentration changes. The validity of the conventional kinetic method was examined by comparing the results with the fundamental steady-state method: in addition to the above-mentioned batch test, mussels were also subject to 24-day exposure (1 µgL(-1) and 10 µgL(-1)) followed by 24-day depuration. Contradictions were found in the resulting kinetic BAF and model curving fittings. A new kinetic model based on adsorption mechanism was proposed, which potentially provide more accurate description of the bioaccumulation process of PFCs.

In situ hybridization of a marine fish virus, Singapore grouper iridovirus with a nucleic acid probe of major capsid protein.

A DNA probe of 531 base pairs for Singapore grouper iridovirus (SGIV) was generated by polymerase chain reaction and labeled with nonradioactive digoxigenin. An in situ hybridization based method was developed to detect SGIV in formalin-fixed tissues from maricultured Malabar grouper, Epinephelus malabaricus Bloch and Schneider. The in situ hybridization detected SGIV in the kidney, spleen, liver, intestine, stomach and gills from naturally infected fish. Strong hybridization signals were obtained from the kidney and spleen tissues, while intermediate intensity signals were observed in the intestine and liver tissues. The weakest signals were obtained from the stomach and gills. The signals were located specifically within epithelial, endothelial and sub-endothelial hypertrophic cells in all tested tissues. The in situ hybridization procedure will provide an important diagnostic tool to complement histopathological methods, and contribute to epidemiological studies on the origin and distribution of iridovirus in mariculture.

Antigenic characterization of a marine fish iridovirus from grouper, Epinephelus spp.

Iridoviruses, recognized as causative agents of serious systemic diseases, have been identified from more than 20 fish species. Antigenic properties of a pathogenic iridovirus isolated from grouper, Epinephelus spp., in Singapore (SGIV) were investigated using rabbit IgG against the virus. Antisera were prepared by immunization of rabbit with purified virions. The rabbit IgG was purified from antiserum using a protein A-agarose column and adsorbed onto acetone-dried grouper (GP) cells. The viral surface-exposed antigens were visualized by a combination of immunogold transmission electron-microscopy and by indirect immunofluorescence, and the viral antigenic related proteins were discriminated by Western blot. The cross immunofluorescence assay showed that the grouper virus isolate was serologically close to viruses of the genus Ranavirus of family Iridoviridae. The viral antigens were detected from virus infected-cell cultures as early as 4 h of post infection using IFAT, and could be detectable in virus-infected fish blood as early as 3 days post infection. Immuno-dot assays revealed that the rabbit anti-SGIV IgG allowed sensitive detection of SGIV viral antigens. This study will facilitate the development of diagnostic techniques and vaccines for grouper iridovirus.