Determination of specific types and relative levels of QPCR inhibitors in environmental water samples using excitation-emission matrix spectroscopy and PARAFAC

A preliminary study on detecting human DNA in aquatic environments: Potential of eDNA in forensics

Human environmental DNA (eDNA) application have not been fully applied or adequately considered in the fields of eDNA and forensics. Nonetheless, this technique holds great potential as a complementary tool for detecting human DNA in aquatic environments, particularly in cases involving crimes connect to such environments. However, the detectability or stability of eDNA can vary depending on several factors. Therefore, this preliminary study investigates the detection and degradation rates of human eDNA, as well as the recovery of nuclear short tandem repeat (STR) profiles and mitochondrial DNA (mtDNA) sequencing, using water samples from both saltwater and freshwater sources. To conduct the experiment, whole human blood was spiked into the water samples. Water samples were then filtered using a 5 µm pore size filter, and samples were collected at various time intervals up to 23 days. A human specific qPCR assay targeting HV1 region of human mtDNA was used to detect human eDNA. Results demonstrated that human eDNA remains detectable for up to 36 hours in freshwater samples and up 84 hours in saltwater samples. The limit of detection (LOD) of human eDNA, (205 copies/µl), was achieved after 60 hours in freshwater and 180 hours in saltwater samples. Partial STR profiles could be recovered up to 24 hours for freshwater and saltwater. Results from mtDNA sequencing indicate that full mtDNA profiles could be recovered from freshwater samples up to 48 hours and remained detectable up to 72 hours in saltwater. Overall, the findings of this study underscore the importance of considering and incorporating human eDNA analysis as a valuable tool in forensic practice. By harnessing the power of eDNA, law enforcement agencies can enhance their investigation capabilities, improve the accuracy of forensic reconstructions, and ultimately contribute to the resolution of cases involving aquatic environments. Further research and validation are needed to optimize and expand the utilization of eDNA techniques in forensic investigations.

Fucoidan-based antibody-free magnetic nanoparticle for on-site detection of waterborne SARS-CoV-2

The portable and sensitive point-of-care-test (POCT) method is in urgent need to detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) for ensuring public health and safety. However, detection of trace number of pathogens in real water sample from the environment still faces challenges, because complex environment disruptors can rapidly degrade targets. Herein, magnetic beads coated with fucoidan and polydopamine (Fuc-PDA-MBs) were introduced as the capture carrier for pretreatment of samples. Fucoidan, a sulfated polysaccharide, can recognize the SARS-CoV-2 spike (S1) protein receptor-binding domain (S1 RBD) and was chosen for replacement of antibody in enrichment. Environmental water seeded with SARS-CoV-2 spike pseudovirus was applied to test performance of Fuc-PDA-MBs method. Under optimal conditions, the use of Fuc-PDA-MBs showed average 76 % capture efficiency at SARS-CoV-2 spike pseudovirus concentration ranging from 107.62 to 104.34 gene copies (gc)/L. Compared with Electronegative filtration (ENF), Fuc-PDA-MBs showed better virion sorption effectiveness. Fuc-PDA-MBs also validated by raw contaminated urban wastewater and showed high recovery results for SARS-CoV-2 variants. To rapidly detect virus in POCT, nucleic acid extraction-free Loop-Mediated Isothermal Amplification (LAMP) was used for simplifying experimental process. The Fuc-PDA-MBs-LAMP assay showed the quantitation limit of sample (LOQ) was 105.49 gc/L. The whole procedure could be completed within 90 min, including 30 min for virus pre-enrichment, 10 min nucleic acid release and 45 min LAMP analysis. Compared with regular antibody-based immunodetection, this integrated system provides broad-spectrum, economic way to detect SARS-CoV-2 mutants in complex environments and also adaptable for high throughput test, which might be used for on-site early warning of SARS-CoV-2 outbreaks in developing area.

Fluorescein diacetate hydrolytic activity as a sensitive tool to quantify nitrogen/sulfur gene content in urban river sediments in China

The relative abundance of functional genes used to quantify the abundance of functional genes in communities is controversial. Quantitative PCR (qPCR) technology offers a powerful tool for quantifying functional gene abundance. However, humic substances can inhibit qPCR in sediment/soil samples. Therefore, finding a convenient and effective quantitative analysis method for sediment/soil samples is necessary. The functional genes and physicochemical properties in sediments with different-level pollutions were analyzed in this study. Correlations between physicochemical properties and the relative abundance of functional genes were used to test whether relative abundance in gene prediction quantifies the abundance of functional genes. The abundance of functional genes could be corrected by multiplying the fluorescein diacetate (FDA) hydrolytic rates by the relative abundance of functional genes since the FDA assay has been widely used as a rapid and sensitive method for quantifying microbial activity in sediments. Redundancy analysis showed significant interrelations between the functional genes and the physicochemical properties of sediments. The relative abundance of functional genes is unreliable for quantifying the abundance of functional genes because of the weak correlation (R < 0.5, P < 0.05) between different pollutants and the relative abundance of functional genes. However, a significant positive correlation between concentrations of different pollutants and the activities of associated enzymes was obtained (R > 0.933, P < 0.05), which revealed that the abundance of functional genes could be reliably quantified by the relative abundance and FDA hydrolytic rate. This study proposed an alternative method besides qPCR to quantify the absolute abundance of functional genes, which overcomes the problem of humic interference in the quantitative analysis of sediment/soil samples.

Centralized and decentralized wastewater-based epidemiology to infer COVID-19 transmission - A brief review

Wastewater-based epidemiology has shown to be a promising and innovative approach to measure a wide variety of illicit drugs that are consumed in the communities. In the same way as for illicit drugs, wastewater-based epidemiology is a promising approach to understand the prevalence of viruses in a community-level. The ongoing coronavirus disease 2019 (COVID-19) pandemic created an unprecedented burden on public health and diagnostic laboratories all over the world because of the need for massive laboratory testing. Many studies have shown the applicability of a centralized wastewater-based epidemiology (WBE) approach, where samples are collected at WWTPs. A more recent concept is a decentralized approach for WBE where samples are collected at different points of the sewer system and at polluted water bodies. The second being particularly important in countries where there are insufficient connections from houses to municipal sewage pipelines and thus untreated wastewater is discharged directly in environmental waters. A decentralized approach can be used to focus the value of diagnostic tests in what we call targeted-WBE, by monitoring wastewater in parts of the population where an outbreak is likely to happen, such as student dorms, retirement homes and hospitals. A combination of centralized and decentralized WBE should be considered for an affordable, sustainable, and successful WBE implementation in high-, middle- and low-income countries.

Vaccinomics to Design a Multiepitope Vaccine against Legionella pneumophila

Legionella pneumophila is found in the natural aquatic environment and can resist a wide range of environmental conditions. There are around fifty species of Legionella, at least twenty-four of which are directly linked to infections in humans. L. pneumophila is the cause of Legionnaires' disease, a potentially lethal form of pneumonia. By blocking phagosome-lysosome fusion, L. pneumophila lives and proliferates inside macrophages. For this disease, there is presently no authorized multiepitope vaccine available. For the multi-epitope-based vaccine (MEBV), the best antigenic candidates were identified using immunoinformatics and subtractive proteomic techniques. Several immunoinformatics methods were utilized to predict B and T cell epitopes from vaccine candidate proteins. To construct an in silico vaccine, epitopes (07 CTL, 03 HTL, and 07 LBL) were carefully selected and docked with MHC molecules (MHC-I and MHC-II) and human TLR4 molecules. To increase the immunological response, the vaccine was combined with a 50S ribosomal adjuvant. To maximize vaccine protein expression, MEBV was cloned and reverse-translated in Escherichia coli. To prove the MEBV's efficacy, more experimental validation is required. After its development, the resulting vaccine is greatly hoped to aid in the prevention of L. pneumophila infections.

Aptamers and Aptamer-Coupled Biosensors to Detect Water-Borne Pathogens

Aptamers can serve as efficient bioreceptors for the development of biosensing detection platforms. Aptamers are short DNA or RNA oligonucleotides that fold into specific structures, which enable them to selectively bind to target analytes. The method used to identify aptamers is Systematic Evolution of Ligands through Exponential Enrichment (SELEX). Target properties can have an impact on aptamer efficiencies. Therefore, characteristics of water-borne microbial targets must be carefully considered during SELEX for optimal aptamer development. Several aptamers have been described for key water-borne pathogens. Here, we provide an exhaustive overview of these aptamers and discuss important microbial aspects to consider when developing such aptamers.

Design and Validation of Passive Environmental DNA Samplers Using Granular Activated Carbon and Montmorillonite Clay

Environmental DNA (eDNA) analysis is gaining prominence as a tool for species and biodiversity monitoring in aquatic environments. eDNA shed by organisms is captured in grab samples, concentrated by filtration, extracted, and analyzed using molecular methods. Conventional capture and filtration methods are limited because (1) filtration does not capture all extracellular DNA, (2) eDNA can degrade during sample transport and storage, (3) filters often clog in turbid waters, reducing the eDNA captured, and (4) grab samples are time sensitive due to pulse eDNA inputs. To address these limitations, this work designs and validates Passive Environmental DNA Samplers (PEDS). PEDS consist of an adsorbent-filled sachet that is suspended in water to collect eDNA over time. Both extracellular and cellular DNA are captured, and the extracellular DNA is protected from degradation. The eDNA captured over time may be more representative than a grab sample. Two adsorbents, Montmorillonite Clay (MC) and Granular Activated Carbon (GAC), are tested. In laboratory experiments, MC-PEDS adsorbed five times more extracellular DNA and desorbed up to four times more than GAC-PEDS (despite high levels of eDNA loss during desorption). In microcosm and field experiments, GAC-PEDS captured over an order of magnitude more eDNA than MC-PEDS. Field results further validated PEDS as an effective eDNA capture method compared to conventional methods.

Potential indicators of virus transport and removal during soil aquifer treatment of treated wastewater effluent

Increased water demands have led to a notable interest in the use of treated wastewater for reuse. Typically, this results from the implementation of advanced treatment of final effluent from wastewater treatment plants prior to reuse for potable or non-potable purposes. Soil aquifer treatment (SAT) is a natural treatment process in which water from sources of varying quality is infiltrated into the soil to further improve its quality. The goal of this study was to determine the log₁₀ reduction values (LRVs) of viruses naturally present in treated effluent and evaluate two potential indicators of virus removal and transport, pepper mild mottle virus (PMMoV) and crAssphage, during SAT of treated effluent. Groundwater was sampled at three wells with different attributes within the Sweetwater Recharge Facility (SWRF) in Tucson, AZ. These sites vary greatly in operational parameters such as effluent infiltration rates and wetting/drying cycles, which may influence virus removal efficiency. Detection of adenovirus, enterovirus, PMMoV, and crAssphage were determined by qPCR/RT-qPCR and log₁₀ reduction values (LRVs) were determined. PMMoV and crAssphage were detected in groundwater associated with a set of recharge basins that exhibited shorter wetting/drying cycles and faster infiltration rates. LRVs for crAssphage and PMMoV at this site ranged from 3.9 to 5.8, respectively. Moreover, PMMoV was detected downflow of the SAT sites, indicating the potential degradation of microbial groundwater quality in the region surrounding managed aquifer recharge facilities. Overall, PMMoV and crAssphage showed potential as conservative process indicators of virus removal during SAT, particularly for attribution of LRV credits. Moreover, the detection of these viruses indicated the potential influence of wetting/drying cycles on virus removal by SAT, a parameter that has not yet been studied with respect to biological contaminants.

Microbial aerobic denitrification dominates nitrogen losses from reservoir ecosystem in the spring of Zhoucun reservoir

The mechanism and factors influencing nitrogen loss in the Zhoucun reservoir were explored during the spring. The results showed that the nitrate and total nitrogen concentration decreased from 1.84 ± 0.01 mg/L and 2.34 ± 0.06 mg/L to 0.06 ± 0.01 mg/L and 0.48 ± 0.09 mg/L, respectively. Meanwhile, the nitrate and total nitrogen removal rate reached 97.02% ± 0.25 and 79.38% ± 3.32, respectively. Moreover, the abundance of nirS gene and aerobic denitrification bacteria increased from 1.04-3.38 × 10³ copies/mL and 0.71 ± 0.22 × 10² cfu/mL to 5.36-5.81 × 10³ copies/mL and 8.64 ± 2.08 × 10³ cfu/mL, respectively. The low MW fractions of DOM (<5 kDa) increased from 0.94 ± 0.02 mg/L in February to 1.51 ± 0.09 mg/L in April. E3/E4 and absorption spectral slope ratio (S_R) showed that fulvic acid accounted for the main proportion with autochthonous characteristics. These findings were consistent with the fluorescence components and fluorescence characteristic indices based on EEM-PARAFAC. Meanwhile, the microbial metabolism activity increased significantly from February to April, which contributed to the cycle of nutrients within the reservoir water system. Moreover, the abundance of the bacterial species involved in denitrification (Exiguobacterium, Brevundimonas, Deinococcus, Paracoccus, and Pseudomonas) increased significantly. The relative abundance of KOs related to nitrogen metabolism, were initially increased and then decreased. Specifically, K02567 (napA) represented the main proportion of KOs related to denitrification. The abundance of napA-type denitrifying bacteria (Dechloromonas, Pseudomonas, Azospira, Rhodopseudomonas, Aeromonas, Zobellella, Sulfuritalea, Bradyrhizobium, Achromobacter, Enterobacter, Thauera, and Magnetospirillum) increased significantly during the period of nitrogen loss. Furthermore, the levels of nitrate, T, DO, and AWCD were the most important factors affecting the N-functional bacteria composition. The systematic investigation of the nitrogen loss would provide a theoretical foundation for the remediation of the water reservoir via aerobic denitrification in the future.

Efficiency of sequential UV/H2O2 and biofilm process for the treatment of secondary effluent

In response to the shortage of water resources, multiple processes have been applied to turn wastewater secondary effluent (SE) into potable water. However, trace organic contaminants (TOrCs) and high concentrations of organic matter contained in SE pose a significant challenge to the reclamation. In this manuscript, combined UV-based and biofilm processes were used to treat the SE spiked with ibuprofen (IBU) and clofibric acid (CA). The efficiency of these sequential treatments was characterized in terms of changes in dissolved organic carbon (DOC), absorbance at 254 nm (A₂₅₄), fluorescence excitation-emission matrix (FEEM), the concentration of IBU and CA, and molecular weight of SE. Parallel factor (PARAFAC) was applied as the analysis method for FEEM of the samples and two fluorescent components were successfully identified: humic-like substances (C1) and protein-like matter (C2). Large reductions in A₂₅₄, C1, C2, IBU, and CA were observed during the UV-based processes, especially with the addition of H₂O₂. Nearly 50% of A₂₅₄, 80% of the component C1 were decreased and almost complete removal of the component C2 and TOrCs was achieved by UV/2.0 mM H₂O₂ after 90-min treatment. During the oxidation processes, the formation of lower molecular weight (LMW) compounds was detected, and the biodegradability of the organic matters was greatly increased. Although no significant DOC reduction was obtained in UV-based processes, an obvious further DOC reduction (30~60%) was achieved by biofilm treatment following UV-based processes, especially after UV/H₂O₂ treatments. In the meantime, large amounts of LMW were removed in the biofilm treatment process. This manuscript provides an effective advanced treatment of SE for the removal of DOC and TOrCs, facilitating the wastewater reclamation.

Real-Time Water Quality Monitoring at a Great Lakes National Park

Quantitative polymerase chain reaction (qPCR) was used by the USEPA to establish new recreational water quality criteria in 2012 using the indicator bacteria enterococci. The application of this method has been limited, but resource managers are interested in more timely monitoring results. In this study, we evaluated the efficacy of qPCR as a rapid, alternative method to the time-consuming membrane filtration (MF) method for monitoring water at select beaches and rivers of Sleeping Bear Dunes National Lakeshore in Empire, MI. Water samples were collected from four locations (Esch Road Beach, Otter Creek, Platte Point Bay, and Platte River outlet) in 2014 and analyzed for culture-based (MF) and non-culture-based (i.e., qPCR) endpoints using and enterococci bacteria. The MF and qPCR enterococci results were significantly, positively correlated overall ( = 0.686, < 0.0001, = 98) and at individual locations as well, except at the Platte River outlet location: Esch Road Beach ( = 0.441, = 0.031, = 24), Otter Creek ( = 0.592, = 0.002, = 24), and Platte Point Bay ( = 0.571, = 0.004, = 24). Similarly, MF and qPCR results were significantly, positively correlated ( = 0.469, < 0.0001, = 95), overall but not at individual locations. Water quality standard exceedances based on enterococci levels by qPCR were lower than by MF method: 3 and 16, respectively. Based on our findings, we conclude that qPCR may be a viable alternative to the culture-based method for monitoring water quality on public lands. Rapid, same-day results are achievable by the qPCR method, which greatly improves protection of the public from water-related illnesses.

Reducing uncertainty in estimating virus reduction by advanced water treatment processes

Treatment of wastewater for potable reuse requires the reduction of enteric viruses to levels that pose no significant risk to human health. Advanced water treatment trains (e.g., chemical clarification, reverse osmosis, ultrafiltration, advanced oxidation) have been developed to provide reductions of viruses to differing levels of regulatory control depending upon the levels of human exposure and associated health risks. Importance in any assessment is information on the concentration and types of viruses in the untreated wastewater, as well as the degree of removal by each treatment process. However, it is critical that the uncertainty associated with virus concentration and removal or inactivation by wastewater treatment be understood to improve these estimates and identifying research needs. We reviewed the critically literature to assess to identify uncertainty in these estimates. Biological diversity within families and genera of viruses (e.g. enteroviruses, rotaviruses, adenoviruses, reoviruses, noroviruses) and specific virus types (e.g. serotypes or genotypes) creates the greatest uncertainty. These aspects affect the methods for detection and quantification of viruses and anticipated removal efficiency by treatment processes. Approaches to reduce uncertainty may include; 1) inclusion of a virus indicator for assessing efficiency of virus concentration and detection by molecular methods for each sample, 2) use of viruses most resistant to individual treatment processes (e.g. adenoviruses for UV light disinfection and reoviruses for chlorination), 3) data on ratio of virion or genome copies to infectivity in untreated wastewater, and 4) assessment of virus removal at field scale treatment systems to verify laboratory and pilot plant data for virus removal.

Surveillance of human enteric viruses in coastal waters using concentration with methacrylate monolithic supports prior to detection by RT-qPCR

This is the first surveillance study using methacrylate monolithic supports to concentrate environmental coastal water samples, prior to molecular target detection by RT-qPCR. Rotaviruses (RoV) and Noroviruses (NoV) were monitored in a polluted area at the Bay of Koper (Gulf of Trieste, Northern Adriatic Sea) and at a nearby bathing area and mussel farm areas. RoV and NoV are released into the Bay of Koper, with higher rates close to the discharge of the wastewater treatment plant, however, they can be detected at recreational and mussel farming areas. Our results showed that water bodies considered safe based on FC concentrations, can still have low, yet potentially infective, concentrations of human viruses.

Enhanced detection of pathogenic enteric viruses in coastal marine environment by concentration using methacrylate monolithic chromatographic supports paired with quantitative PCR

Currently, around 50% of the world's population lives in towns and cities within 100 km of the coast. Monitoring of viruses that are frequently present in contaminated coastal environments, such as rotavirus (RoV) and norovirus (NoV), which are also the major cause of human viral gastroenteritis, is essential to ensure the safe use of these water bodies. Since exposure to as few as 10-100 particles of RoV or NoV may induce gastrointestinal disease, there is a need to develop a rapid and sensitive diagnostic method for their detection in coastal water samples. In this study, we evaluate the application of methacrylate monolithic chromatographic columns, commercially available as convective interaction media (CIM^®), to concentrate pathogenic enteric viruses from saline water samples prior to virus quantification by one-step reverse transcription quantitative PCR (RT-qPCR). Using RoV and NoV as model enteric viruses, we present our results on the most effective viral concentration conditions from saline water matrices using butyl (C4) hydrophobic interaction monolithic support (CIM^® C4). C4 monolithic columns exhibit a good capacity to bind both RoV and NoV and both viruses can be eluted in a single step. Our protocol using a 1 ml C4 column enables processing of 400 ml saline water samples in less than 60 min and increases the sensitivity of RoV and NoV detection by approximately 50-fold and 10-fold respectively. The protocol was also scaled up using larger capacity 8 ml C4 columns to process 4000 ml of seawater samples with concentration factors of 300-fold for RoV and 40-fold for NoV, without any significant increase in processing time. Furthermore, C4 monolithic columns were adapted for field use in an on-site application of RoV concentration from seawater samples with performance equivalent to that of the reference laboratory setup. Overall, the results from successful deployment of CIM C4 columns for concentration of rotavirus and norovirus in seawater samples reiterate the utility of monolithic supports as efficient, scalable and modular preparative tools for processing environmental water samples to enhance viral detection using molecular methods.

Modified low-salt CTAB extraction of high-quality DNA from contaminant-rich tissues

The increasing use of high-throughput sequencing platforms has made the isolation of pure, high molecular weight DNA a primary concern for studies of a diverse range of organisms. Purification of DNA remains a significant challenge in many tissue and sample types due to various organic and inorganic molecules that coprecipitate with nucleic acids. Molluscs, for example, contain high concentrations of polysaccharides which often coprecipitate with DNA and can inhibit downstream enzymatic reactions. We modified a low-salt CTAB (MoLSC) extraction protocol to accommodate contaminant-rich animal tissues and compared this method to a standard CTAB extraction protocol and two commercially available animal tissue DNA extraction kits using oyster adductor muscle. Comparisons of purity and molecular integrity showed that our in-house protocol yielded genomic DNA generally free of contaminants and shearing, whereas the traditional CTAB method and some of the commercial kits yielded DNA unsuitable for some applications of massively parallel sequencing. Our open-source MoLSC protocol provides a cost-effective, scalable, alternative DNA extraction method that can be easily optimized and adapted for sequencing applications in other contaminant-rich samples.

Fluorescence quenching effects of antibiotics on the main components of dissolved organic matter

Dissolved organic matter (DOM) in wastewater can be characterized using fluorescence excitation-emission matrix and parallel factor (EEM-PARAFAC) analysis. Wastewater from animal farms or pharmaceutical plants usually contains high concentration of antibiotics. In this study, the quenching effect of antibiotics on the typical components of DOM was explored using fluorescence EEM-PARAFAC analysis. Four antibiotics (roxarsone, sulfaquinoxaline sodium, oxytetracycline, and erythromycin) at the concentration of 0.5∼4.0 mg/L and three typical components of DOM (tyrosine, tryptophan, and humic acid) were selected. Fluorescence quenching effects were observed with the addition of antibiotics. Among these four antibiotics, roxarsone (2.9∼20.2 %), sulfaquinoxaline sodium (0∼32.0 %), and oxytetracycline (0∼41.8 %) led to a stronger quenching effect than erythromycin (0∼8.0 %). From the side of DOM, tyrosine and tryptophan (0.5∼41.8 %) exhibited a similar quenching effect, but they were higher than humic acids (0∼20.2 %) at the same concentration of antibiotics. For humic acid, a significant quenching effect was observed only with the addition of roxarsone. This might be the first report about the fluorescence quenching effect caused by antibiotics. The results from this study confirmed the interference of antibiotics on the fluorescence intensity of the main components of DOM and highlighted the importance of correcting fluorescence data in the wastewater containing antibiotics.

Characterization of dissolved organic matter in municipal wastewater using fluorescence PARAFAC analysis and chromatography multi-excitation/emission scan: a comparative study

Dissolved organic matter (DOM) in municipal wastewater was mainly characterized using high-performance liquid chromatography (HPLC) and size exclusion chromatography (HPSEC) with multi-excitation/emission fluorescence scan. Meanwhile, fluorescence excitation-emission-matrix combined with parallel factor analysis (EEM-PARAFAC) was also applied. Compared with chromatography fluorescence fingerprints, the EEM-PARAFAC model could not reflect the variety of DOM species with similar fluorescence but different physicochemical properties. The chromatography results showed that the protein-like species were variable among different municipal wastewater treatment plants, some of which are in combination with humic-like species; while there were two major humic-like species fractionated by hydrophilicity and molecular weight (MW), which are also the major contributors to UV absorbance at 254 nm. It was also identified that the relatively hydrophilic humic fractions were slightly larger than the relatively hydrophobic humic fractions. In all the investigated wastewater treatment plants, the relatively hydrophilic and larger MW humic fraction mainly contributed to the fluorescence intensity of humic-like EEM-PARAFAC components. As well as facilitating interpretations of EEM-PARAFAC components, the HPLC/HPSEC fluorescence fingerprints also contributed to a better understanding of fluorescent DOM species in municipal wastewater.