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The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/coronavirus disease 2019 (COVID-19) pandemic has highlighted an important role for efficient surveillance of microbial pathogens. High-throughput sequencing technologies provide valuable surveillance tools, offering opportunities to conduct high-resolution monitoring from diverse sample types, including from environmental sources. However, given their large size and potential to contain mixtures of lineages within samples, such genomic data sets can present challenges for analyzing the data and communicating results with diverse stakeholders. Here, we report MixviR, an R package for exploring, analyzing, and visualizing genomic data from potentially mixed samples of a target microbial group. MixviR characterizes variation at both the nucleotide and amino acid levels and offers the RShiny interactive dashboard for exploring data. We demonstrate MixviR's utility with validation studies using mixtures of known lineages from both SARS-CoV-2 and Mycobacterium tuberculosis and with a case study analyzing lineages of SARS-CoV-2 in wastewater samples over time at a sampling location in Ohio, USA.

W ater resources throughout the north central region of the United States have traditionally been abundant and of high quality. However, increasing demands from agriculture and urban growth, exacerbated by a changing climate, are putting pressures on water quality. Holistic and science-based management strategies can improve water quality, although the definition of “water quality” might depend on its particular use (Koteen et al. 2002). Sound water management decisions must be made based on a foundational knowledge of water resources and their natural and anthropogenic influences, opportunities for addressing changing and emerging threats, and a holistic perspective of how local …

Wastewater-based epidemiology is an effective tool for monitoring infectious disease spread or illicit drug use within communities. At the Ohio State University, we conducted a SARS-CoV-2 wastewater surveillance program in the 2020-2021 academic year and compared results with the university-required weekly COVID-19 saliva testing to monitor COVID-19 infection prevalence in the on-campus residential communities. The objectives of the study were to rapidly track trends in the wastewater SARS-CoV-2 gene concentrations, analyze the relationship between case numbers and wastewater signals when adjusted using human fecal viral indicator concentrations (PMMoV, crAssphage) in wastewater, and investigate the relationship of the SARS-CoV-2 gene concentrations with wastewater parameters. SARS-CoV-2 nucleocapsid and envelope (N1, N2, and E) gene concentrations, determined with reverse transcription droplet digital PCR, were used to track SARS-CoV-2 viral loads in dormitory wastewater once a week at 6 sampling sites across the campus during the fall semester in 2020. During the following spring semester, research was focused on SARS-CoV2 N2 gene concentrations at 5 sites sampled twice a week. Spearman correlations both with and without adjusting using human fecal viral indicators showed a significant correlation (p 0.05) between human COVID-19 positive case counts and wastewater SARS-CoV-2 gene concentrations. Spearman correlations showed significant relationships between N1 gene concentrations and both TSS and turbidity, and between E gene concentrations and both pH and turbidity. These results suggest that wastewater signal increases with the census of infected individuals, in which the majority are asymptomatic, with a statistically significant (p-value0.05) temporal correlation. The study design can be utilized as a platform for rapid trend tracking of SARS-CoV-2 variants and other diseases circulating in various communities.

The global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in more than 129 million confirm cases. Many health authorities around the world have implemented wastewater-based epidemiology as a rapid and complementary tool for the COVID-19 surveillance system and more recently for variants of concern emergence tracking. In this study, three SARS-CoV-2 target genes (N1 and N2 gene regions, and E gene) were quantified from wastewater influent samples (n = 250) obtained from the capital city and 7 other cities in various size in central Ohio from July 2020 to January 2021. To determine human-specific fecal strength in wastewater samples more accurately, two human fecal viruses (PMMoV and crAssphage) were quantified to normalize the SARS-CoV-2 gene concentrations in wastewater. To estimate the trend of new case numbers from SARS-CoV-2 gene levels, different statistical models were built and evaluated. From the longitudinal data, SARS-CoV-2 gene concentrations in wastewater strongly correlated with daily new confirmed COVID-19 cases (average Spearman's r = 0.70, p, Graphical abstract Unlabelled Image

Short-term effects of low head dam removal on water quality of urbanized stream were evaluated, focusing on fecal pollution indicators. Composite river samples were analyzed for Escherichia coli concentrations, nitrates, phosphates, turbidity and human-specific marker (HF183) and antibiotic resistance marker (tetQ) before and after dam removal during dry weather conditions. The sampled Olentangy River water in summer before the dam removal showed poor water quality with mean E. coli concentration of 439 colony forming unit (CFU)/100 mL, mean turbidity of 10 NTU and mean nutrient concentrations of 0.61 and 0.41 mg/L for nitrate and phosphate, respectively. Surprisingly, even one month after the dam removal, E. coli numbers doubled and nitrate concentration tripled compared to pre-removal concentrations. Although the detected HF183 concentrations were below the quantifiable levels, they did not correlate with E. coli concentrations, suggesting E. coli from other than human fecal origin. The correlation between turbidity and E. coli during dry weather further suggests E. coli accumulation in impoundment sediments and release once dam was removed. These short-term effects of dam removal on water quality should be further evaluated, especially if recreation and other beneficial uses of water in the area are expected. Copyright © 2016 John Wiley & Sons, Ltd.

Common problems in a windowfarm system (a vertical and indoor hydroponic system) are phytopathogen infections in plants and excessive buildup of biofilms. The objectives of this study were (i) to promote plant health by making plants more resistant to infection by using beneficial biosurfactant-producing Pseudomonas chlororaphis around the roots and (ii) to minimize biofilm buildup by ultraviolet (UV) irradiation of the water reservoir, thereby extending the lifespan of the whole system with minimal maintenance. Pseudomonas chlororaphis-treated lettuce grew significantly better than nontreated lettuce, as indicated by enhancement of color, mass, length, and number of leaves per head (p < 0.05). The death rate of the lettuce was reduced by ∼50% when the lettuce was treated with P. chlororaphis. UV irradiation reduced the bacteria (4 log reduction) and algae (4 log reduction) in the water reservoirs and water tubing systems. Introduction of P. chlororaphis into the system promoted plant growth and reduced damage caused by the plant pathogen Pythium ultimum. UV irradiation of the water reservoir reduced algal and biofilm growth and extended the lifespan of the system.

Aims: The internalized human pathogens in fresh produce are not effectively removed during conventional washing, and therefore, it may cause foodborne illness when the produce is consumed raw. Thus, effective nonthermal processes are needed to prevent this risk. Methods and Results: Green fluorescence protein-tagged Salmonella Typhimurium was either sprayed on the surface of iceberg lettuce or injected into the bottom part (bulb) of green onions to induce bacterial internalization. The contaminated vegetables were collected after 2 days and subjected to surface disinfection. Different fluencies of UV-C radiation (75–900 mJ cm 2 ) and two fluencies of UV-C (450, 900 mJ cm 2 ) combined with chlorine and peracetic acid (PAA) were applied to the produce to examine the inactivation efficiency of internalized bacteria. A range of 196–252 log reduction in the internalized Salmonella was achieved when the lettuce was treated with higher UV-C fluency (150, 450, 900 mJ cm 2 ) or UV-C combined with chemical disinfectants. Significant reduction (100–149 log CFU g 1 ) in internalized Salmonella was observed in green onion treated with UV-C with the fluency of 150 or 900 mJ cm 2 or UV-C-chlorine/PAA. No significant reduction was observed in either lettuce or green onion treatments when chlorine or PAA was used alone. The food quality measured with firmness was not changed during any treatments. However, a slight colour change was observed in lettuce only when UV-C was used at 900 mJ cm 2 . Conclusion: High fluency UV-C can significantly inactivate the internalized Salmonella in lettuce and green onion while maintaining the food quality. Significance and Impact of the Study: This research provides applicable research outcomes for developing nonthermal methods to inactivate internalized pathogens in fresh produce.

Aims Inactivating microbial contaminants in fresh produce commonly uses chlorine washing. The effectiveness of ozone was explored as an alternative to chlorine in produce washing for ensuring microbial safety while maximizing water reusability. Methods and Results An ozone washing system was designed to permit continuous addition of contaminated produce and the reuse of washing water. The effectiveness of ozonation (

Pollen of forest trees can move on the scales of tens to hundreds of kilometers, but the question of its viability during this long distance dispersal (LDD) has yet to be answered. While empirical studies of pollen viability in forest tree species are rare, controlled and scalable data to outdoor studies of the contribution of UV irradiation on pollen viability are not available. A simple protocol that allows the quantification of the viability response of pollen to UV, temperature, and humidity is developed and described here. Bench-scale conditions that approximate a wide range of atmospheric conditions including different humidity, temperature, and UV irradiation condition are used to determine the independent effects of each abiotic stress factor, and empirical functions are fitted and used to scale these bench-scale experiments to outdoor conditions. As a case study, pollen was sampled from two populations of Pinus taeda during two years and was used to quantify the decrease in viability due to atmospheric conditions during LDD. Contrary to maize pollen, P. taeda pollen viability decreased due to humid and cold conditions. The viability response of pollen to UV-A and UV-B corresponded to a viability reduction of about 10% after a full day of exposure. These laboratory findings were corroborated by an outdoor solar exposure experiment. The Fu-Liou online radiation model and a data set of radiosonde observations were used to estimate the typical conditions that would be encountered by LDD pollen. If initially caught in a strong updraft, dispersing P. taeda pollen could be carried many days and thousands of kilometers in the air. The empirical equations for P. taeda pollen viability reduction due to abiotic stresses predicted that 50% of the pollen would survive 24 hours of LDD under typical external conditions. The viable range of the pollen is, therefore, shorter than the physical dispersal distance. The methods used in our experiments are applicable for determination of dispersing pollen viability, especially when effects of different adverse conditions need to be separated. The empirical viability equations that resulted from our experiments can be used in an atmospheric dispersal model to estimate the viable range of tree pollen.

The disinfection of pathogens in water via ultraviolet light exposure is a growing treatment technology, although the potential repair of UV damage following disinfection is a continued topic of concern in many UV disinfection applications. The conditions for investigating DNA repair of microorganisms are not standardized nor often correctly reported in the literature resulting in contradicting results regarding repair abilities of specific microorganisms. In this work a protocol was developed that enables comparison of photorepair experiments from different laboratories. Four different commonly used lamp types as well as sunlight were investigated to induce photorepair in Escherichia coli. Both time-based and photorepair fluence-based comparisons were performed. It was concluded that both intensity and lamp spectra significantly affect photorepair rate. Based on photorepair fluence calculations, there was no significant difference in photorepair rate between the different lamp types or compared to sunlight, while large differences were indicated using a time-based comparison as typically reported in the literature. Interestingly, the lethal effects of solar light on E. coli overshadowed the photorepair, and after 10 min the number of E. coli cells started to decrease. Because the disinfection efficiency of the sun affected the results, laboratory-based repair experiments may only indicate "potential" photorepair, as sunlight may be more lethal than laboratory photorepair lamps.

Escherichia coli photorepair and dark recovery was investigated in two different water sources. Sterilized drinking water and wastewater effluent treated for reuse were spiked with either wild E. coli isolate or a laboratory-purchased E. coli strain and ultraviolet (UV)-irradiated at fluences from 40 to 120 mJ/cm2. Although no threshold UV fluence was established after which E. coli photo and dark repair did not proceed, the extent of repair was generally low, not exceeding 0.5 log. Contrary to the repair results, the 48-h regrowth of E. coli disinfection survivors reached up to 3 log, likely due to the remaining inactivated E. coli cells that served as a source of biodegradable carbon postdisinfection. Although it is proposed that concerns regarding bacterial repair under drinking and reuse water UV disinfection conditions are overestimated based on experiments at low UV fluences, the long-term postdisinfection safety of water may be underestimated for conditions of low or no disinfection residu...

Biodosimetry is the currently accepted method for validation of fluence delivery in ultraviolet (UV) reactors for water disinfection. This method utilizes the inactivation of a surrogate microorganism to predict the reduction equivalent fluence and subsequent inactivation of a target pathogen. Two common surrogates—Bacillus subtilis spores and MS-2 coliphage—were used to examine the relationship between surrogate type and biodosimetry results. A pilot-scale LP UV reactor was investigated at two flow conditions (7.5 and 15 gpm ) and four different UV 253.7 nm water transmittance (UVT, 1 cm ) values between 82 and 91%. The calculated reduction equivalent fluence differed from a maximum of 30% at 7.5 gal.∕min and 15% at 15 gal.∕min between the surrogates tested, depending on the UVT. These differences were attributed to the sensitivity of organisms used, hydraulic inefficiences, and UV fluence distribution in the reactor, thus the choice of validation microbe may impact the determination of reduction equival...

Aim: Ultraviolet (UV) irradiation for drinking water treatment was examined for inactivation and subsequent dark and photo-repair of Mycobacterium terrae. Methods and Results: UV sources tested were low pressure (monochromatic, 254 nm) and medium pressure (polychromatic UV output) Hg lamps. UV exposure resulted in inactivation, and was followed by dark or photo-repair experiments. Inactivation and repair were quantified utilizing a molecular-based endonuclease sensitive site (ESS) assay and conventional colony forming unit (CFU) viability assay. Mycobacterium terrae was more resistant to UV disinfection compared to many other bacteria, with approximately 2-log reduction at a UV fluence of 10 mJ cm−2 ; similar to UV inactivation of M. tuberculosis. There was no difference in inactivation between monochromatic or polychromatic UV lamps. Mycobacterium terrae did not undergo detectable dark repair. Photo-repair resulted in recovery from inactivation by ∼0·5-log in less than 30 min for both UV lamp systems. Conclusions: Mycobacterium terrae is able to photo-repair DNA damage within a short timeframe. The number of pyrimidine dimers induced by UV light were similar for Escherichia coli and M. terrae, however, this similarity did not hold true for viability results. Significance and Impact of the Study: There is no practical difference between UV sources for disinfection or prevention of DNA repair for M. terrae. The capability of M. terrae to photo-repair UV damage fairly quickly is important for wastewater treatment applications where disinfected effluent is exposed to sunlight. Finally, molecular based assay results should be evaluated with respect to differences in the nucleic acid content of the test micro-organism.

Mycobacteria naturally aggregate in water, a characteristic that may serve to protect them against disinfection in wastewater. Secondary effluent was spiked with Mycobacterium terrae (M. terrae), sequentially filtered through 100-, 41-, and 20-microm nylon filters to partition aggregate sizes, confirmed using particle-size analysis and microscopy. Each sample was exposed to doses of UV light (10 to 60 mJ/cm2 at 254 nm) and free chlorine (27 to 150 mg-min/L at 4 degrees C). Inactivation of M. terrae in wastewater was initially rapid, with 2.5 log reduction at 14 mJ/cm2 and 56 mg-min/L for UV and free chlorine, respectively. However, in effluent and 100-microm filtered wastewater, spiked M. terrae was present to the highest doses evaluated. Interestingly, M. terrae passed through 41- and 20-microm filters were inactivated rapidly, with no survivors after moderate disinfection doses. Inactivation of Mycobacteria in wastewater may be compromised by aggregates larger than 41 microns.

Redox potential (RP) is an easily measured soil characteristic which is affected by many of the chemical, physical and biological processes in the soil, but it has been largely ignored as a useful characteristics in arable soil. The influence of different sequences of crop rotation on RP and nitrification in the topsoil and the subsoil of a Luvic Chernozem were investigated during the vegetation season (April–July) of the years 1994–1999. RP was higher in the topsoil (0–30 cm) than in the subsoil (30–60 cm). In aerobic field conditions we found a significant difference in RP values between cropping sequences. The highest RP and lowest potential nitrification was under the cropping sequence of barley preceded by sugar beet and the lowest RP and highest potential nitrification was found under wheat after alfalfa. RP was negatively correlated with potential nitrification under all copping sequences in the topsoil. We assume that RP could be used as an important indicator of processes in the field, not only in anaerobic soil conditions but also in aerobic conditions.

Pulsed UV (PUV) is a novel UV irradiation system that is a non-mercury lamp-based alternative to currently used continuous-wave systems for water disinfection. PUV polychromatic irradiation disinfection efficiency was compared to that from continuous-wave monochromatic low-pressure (LP) and polychromatic medium-pressure (MP) UV systems, using two types of actinometry (ferrioxalate and iodide-iodate) and an absolute spectral emission method for fluence measurement. All three methods were in good agreement. Once accurate and reliable methods for fluence measurement were established, the inactivation of Escherichia coli and pathogen surrogates phage T4 and T7 were investigated under each technology. Inactivation was significantly faster using PUV irradiation compared to LP or MP UV lamps at equivalent fluence levels. A significant fraction of the enhanced PUV inactivation efficiency was due to wavelengths greater than 295 nm.