Salinity Tolerance and Osmoadaptation Strategies in Four Genera of Anammox Bacteria: Brocadia, Jettenia, Kuenenia, and Scalindua

The salinity tolerance and osmoadaptation strategies in four phylogenetically distant anammox species, Brocadia, Jettenia, Kuenenia, and Scalindua, were investigated by using highly enriched cell cultures. The first-emerged "Ca. Scalindua sp." showed optimum growth at 1.5-3% salinity and was tolerant to ∼10% salinity (a slight halophile). The second-emerged "Ca. Kuenenia stuttgartiensis" was tolerant to ∼6% salinity with optimum growth at 0.25-1.5% (a halotolerant). These early-emerged "Ca. Scalindua sp." and ″Ca. K. stuttgartiensis" rapidly accumulated K+ ions and simultaneously synthesized glutamate as a counterion. Subsequently, part of the glutamate was replaced by trehalose. In contrast, the late-emerged "Ca. B. sinica" and "Ca. J. caeni" were unable to accumulate sufficient amounts of K+─glutamate and trehalose, resulting in a significant decrease in activity even at 1-2% salinity (nonhalophiles). In addition, the external addition of glutamate may increase anammox activity at high salinity. The species-dependent salinity tolerance and osmoadaptation strategies were consistent with the genetic potential required for the biosynthesis and transport of these osmolytes and the evolutionary history of anammox bacteria: Scalindua first emerged in marine environments and then Kuenenia and other two species gradually expanded their habitat to estuaries, freshwater, and terrestrial environments, while Brocadia and Jettenia likely lost their ability to accumulate K+─glutamate.

Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture

Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4+ is scarce as compared with NO2-. Remineralization of organic nitrogen compounds including urea and cyanate (OCN-) into NH4+ has been believed as an NH4+ source of the anammox process in oxygen minimum zones. However, urea- or OCN-- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN- degradation in a marine anammox bacterial consortium were investigated based on 15N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN- degradation, urea was anoxically decomposed to NH4+ by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN- was abiotically degraded to NH4+. The produced NH4+ was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32-42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).

Quantitative analysis of SARS-CoV-2 RNA in wastewater and evaluation of sampling frequency during the downward period of a COVID-19 wave in Japan

Wastewater-based epidemiology (WBE) is a practical approach for detecting the presence of SARS-CoV-2 infections and assessing the epidemic trend of the coronavirus disease 2019 (COVID-19). The purpose of this study was to evaluate the minimum sampling frequency required to properly identify the COVID-19 trend during the downward epidemic period when using a highly sensitive RNA detection method. WBE was conducted using the Efficient and Practical virus Identification System with ENhanced Sensitivity for Solids (EPISENS-S), a highly sensitive SARS-CoV-2 RNA detection method, at nine neighboring wastewater treatment plants (WWTPs). These WWTPs were in the same prefecture in Japan, and they had different sewer types, sampling methods, and sampling frequencies. The overall detection rate of SARS-CoV-2 RNA was 97.8 % during the entire study period when the geometric means of new COVID-19 cases per 100,000 inhabitants were between 3.3 and 7.7 in each WWTP. The maximum SARS-CoV-2 RNA concentration in wastewater was 2.14 × 104 copies/L, which corresponded to pepper mild mottle virus (PMMoV)-normalized concentrations of 6.54 × 10-3. We evaluated the effect of sampling frequencies on the probability of a significant correlation with the number of newly reported COVID-19 cases by hypothetically reducing the sampling frequency in the same dataset. When the wastewater sampling frequency occurred 5, 3, 2, and 1 times per week, these results exhibited significant correlations of 100 % (5/5), 89 % (8/9), 85 % (23/27), and 48 % (13/27), respectively. To achieve significant correlation with a high probability of over 85 %, a minimum sampling frequency of twice per week is required, even if sampling methods and sewer types are different. WBE using the EPISENS-S method and a sampling frequency of more than twice a week can be used to properly monitor COVID-19 wave epidemic trends, even during downward periods.

Tracking the effects of the COVID-19 pandemic on viral gastroenteritis through wastewater-based retrospective analyses

The COVID-19 pandemic possibly disrupted the circulation and seasonality of gastroenteritis viruses (e.g., Norovirus (NoV), Sapovirus (SaV), group A rotavirus (ARoV), and Aichivirus (AiV)). Despite the growing application of wastewater-based epidemiology (WBE), there remains a lack of sufficient investigations into the actual impact of the COVID-19 pandemic on the prevalence of gastroenteritis viruses. In this study, we measured NoV GI and GII, SaV, ARoV, and AiV RNA concentrations in 296 influent wastewater samples collected from three wastewater treatment plants (WWTPs) in Sapporo, Japan between October 28, 2018 and January 12, 2023 using the highly sensitive EPISENS™ method. The detection ratios of SaV and ARoV after May 2020 (SaV: 49.8 % (134/269), ARoV: 57.4 % (151/263)) were significantly lower than those before April 2020 (SaV: 93.9 % (31/33), ARoV: 97.0 % (32/33); SaV: p < 3.5×10-7, ARoV: p < 1.5×10-6). Furthermore, despite comparable detection ratios before (88.5 %, 23/26) and during (66.7 %, 80/120) the COVID-19 pandemic (p = 0.032), the concentrations of NoV GII revealed a significant decrease after the onset of the pandemic (p < 1.5×10-7, Cliff's delta = 0.72). NoV GI RNA were sporadically detected (24.7 %, 8/33) before April 2020 and after May 2020 (6.5 %, 17/263), whereas AiV was consistently (100 %, 33/33) detected from wastewater throughout the study period (95.8 %, 252/263). The WBE results demonstrated the significant influence of COVID-19 countermeasures on the circulation of gastroenteritis viruses, with variations observed in the magnitude of their impact across different types of viruses. These epidemiological findings highlight that the hygiene practices implemented to prevent COVID-19 infections may also be effective for controlling the prevalence of gastroenteritis viruses, providing invaluable insights for public health units and the development of effective disease management guidelines.

Growth of the Nitrosomonas europaea cells in the biofilm and planktonic growth mode: Responses of extracellular polymeric substances production and transcriptome

Nitrosomonas europaea, an aerobic ammonia oxidizing bacterium, is responsible for the first and rate-limiting step of the nitrification process, and their ammonia oxidation activities are critical for the biogeochemical cycling and the biological nitrogen removal of wastewater treatment. In the present study, N. europaea cells were cultivated in the inorganic or organic media (the NBRC829 and the nutrient-rich, NR, media, respectively), and the cells proliferated in the form of planktonic and biofilm in those media, respectively. The N. europaea cells in the biofilm growth mode produced larger amounts of the extracellular polymeric substances (EPS), and the composition of the EPS was characterized by the chemical analyses including Fourier transform infrared spectroscopy (FT-IR) and 1H-nuclear magnetic resonance (NMR) measurements. The RNA-Seq analysis of N. europaea in the biofilm or planktonic growth mode revealed that the following gene transcripts involved in central nitrogen metabolisms were abundant in the biofilm growth mode; amo encoding ammonia monooxygenase, hao encoding hydroxylamine dehydrogenase, the gene encoding nitrosocyanine, nirK encoding copper-containing nitrite reductase. Additionally, the transcripts of the pepA and wza involved in the bacterial floc formation and the translocation of EPS, respectively, were also abundant in the biofilm-growth mode. Our study was first to characterize the EPS production and transcriptome of N. europaea in the biofilm and planktonic growth mode.

Oxygen tolerance and detoxification mechanisms of highly enriched planktonic anaerobic ammonium-oxidizing (anammox) bacteria

Oxygen is a key regulatory factor of anaerobic ammonium oxidation (anammox). Although the inhibitory effect of oxygen is evident, a wide range of oxygen sensitivities of anammox bacteria have been reported so far, which makes it difficult to model the marine nitrogen loss and design anammox-based technologies. Here, oxygen tolerance and detoxification mechanisms of four genera of anammox bacteria; one marine species ("Ca. Scalindua sp.") and four freshwater anammox species ("Ca. Brocadia sinica", "Ca. Brocadia sapporoensis", "Ca. Jettenia caeni", and "Ca. Kuenenia stuttgartiensis") were determined and then related to the activities of anti-oxidative enzymes. Highly enriched planktonic anammox cells were exposed to various levels of oxygen, and oxygen inhibition kinetics (50% inhibitory concentration (IC50) and upper O2 limits (DOmax) of anammox activity) were quantitatively determined. A marine anammox species, "Ca. Scalindua sp.", exhibited much higher oxygen tolerance capability (IC50 = 18.0 µM and DOmax = 51.6 µM) than freshwater species (IC50 = 2.7-4.2 µM and DOmax = 10.9-26.6 µM). The upper DO limit of "Ca. Scalindua sp." was much higher than the values reported so far (~20 µM). Furthermore, the oxygen inhibition was reversible even after exposed to ambient air for 12-24 h. The comparative genome analysis confirmed that all anammox species commonly possess the genes considered to function for reduction of O2, superoxide anion (O2•-), and H2O2. However, the superoxide reductase (Sor)-peroxidase dependent detoxification system alone may not be sufficient for cell survival under microaerobic conditions. Despite the fact that anaerobes normally possess no or little superoxide dismutase (Sod) or catalase (Cat), only Scalindua exhibited high Sod activity of 22.6 ± 1.9 U/mg-protein with moderate Cat activity of 1.6 ± 0.7 U/mg-protein, which was consistent with the genome sequence analysis. This Sod-Cat dependent detoxification system could be responsible for the higher O2 tolerance of Scalindua than other freshwater anammox species lacking the Sod activity.

Identification of SARS-CoV-2 variants in wastewater using targeted amplicon sequencing during a low COVID-19 prevalence period in Japan

Wastewater-based epidemiology is expected to be able to identify SARS-CoV-2 variants at an early stage via next-generation sequencing. In the present study, we developed a highly sensitive amplicon sequencing method targeting the spike gene of SARS-CoV-2, which allows for sequencing viral genomes from wastewater containing a low amount of virus. Primers were designed to amplify a relatively long region (599 bp) around the receptor-binding domain in the SARS-CoV-2 spike gene, which could distinguish initial major variants of concern. To validate the methodology, we retrospectively analyzed wastewater samples collected from a septic tank installed in a COVID-19 quarantine facility between October and December 2020. The relative abundance of D614G mutant in SARS-CoV-2 genomes in the facility wastewater increased from 47.5 % to 83.1 % during the study period. The N501Y mutant, which is the characteristic mutation of the Alpha-like strain, was detected from wastewater collected on December 24, 2020, which agreed with the fact that a patient infected with the Alpha-like strain was quarantined in the facility on this date. We then analyzed archived municipal wastewater samples collected between November 2020 and January 2021 that contained low SARS-CoV-2 concentrations ranging from 0.23 to 0.43 copies/qPCR reaction (corresponding to 3.30 to 4.15 log₁₀ copies/L). The targeted amplicon sequencing revealed that the Alpha-like variant with D614G and N501Y mutations was present in municipal wastewater collected on December 4, 2020 and later, suggesting that the variant had already spread in the community before its first clinical confirmation in Japan on December 25, 2020. These results demonstrate that targeted amplicon sequencing of wastewater samples is a powerful surveillance tool applicable to low COVID-19 prevalence periods and may contribute to the early detection of emerging variants.

Impact of the COVID-19 pandemic on the prevalence of influenza A and respiratory syncytial viruses elucidated by wastewater-based epidemiology

Since the COVID-19 pandemic, a decrease in the prevalence of Influenza A virus (IAV) and respiratory syncytial virus (RSV) has been suggested by clinical surveillance. However, there may be potential biases in obtaining an accurate overview of infectious diseases in a community. To elucidate the impact of the COVID-19 on the prevalence of IAV and RSV, we quantified IAV and RSV RNA in wastewater collected from three wastewater treatment plants (WWTPs) in Sapporo, Japan, between October 2018 and January 2023, using highly sensitive EPISENS™ method. From October 2018 to April 2020, the IAV M gene concentrations were positively correlated with the confirmed cases in the corresponding area (Spearman's r = 0.61). Subtype-specific HA genes of IAV were also detected, and their concentrations showed trends that were consistent with clinically reported cases. RSV A and B serotypes were also detected in wastewater, and their concentrations were positively correlated with the confirmed clinical cases (Spearman's r = 0.36-0.52). The detection ratios of IAV and RSV in wastewater decreased from 66.7 % (22/33) and 42.4 % (14/33) to 4.56 % (12/263) and 32.7 % (86/263), respectively in the city after the COVID-19 prevalence. The present study demonstrates the potential usefulness of wastewater-based epidemiology combined with the preservation of wastewater (wastewater banking) as a tool for better management of respiratory viral diseases.

Wastewater-based prediction of COVID-19 cases using a highly sensitive SARS-CoV-2 RNA detection method combined with mathematical modeling

Wastewater-based epidemiology (WBE) has the potential to predict COVID-19 cases; however, reliable methods for tracking SARS-CoV-2 RNA concentrations (C_RNA) in wastewater are lacking. In the present study, we developed a highly sensitive method (EPISENS-M) employing adsorption-extraction, followed by one-step RT-Preamp and qPCR. The EPISENS-M allowed SARS-CoV-2 RNA detection from wastewater at 50 % detection rate when newly reported COVID-19 cases exceed 0.69/100,000 inhabitants in a sewer catchment. Using the EPISENS-M, a longitudinal WBE study was conducted between 28 May 2020 and 16 June 2022 in Sapporo City, Japan, revealing a strong correlation (Pearson's r = 0.94) between C_RNA and the newly COVID-19 cases reported by intensive clinical surveillance. Based on this dataset, a mathematical model was developed based on viral shedding dynamics to estimate the newly reported cases using C_RNA data and recent clinical data prior to sampling day. This developed model succeeded in predicting the cumulative number of newly reported cases after 5 days of sampling day within a factor of √2 and 2 with a precision of 36 % (16/44) and 64 % (28/44), respectively. By applying this model framework, another estimation mode was developed without the recent clinical data, which successfully predicted the number of COVID-19 cases for the succeeding 5 days within a factor of √2 and 2 with a precision of 39 % (17/44) and 66 % (29/44), respectively. These results demonstrated that the EPISENS-M method combined with the mathematical model can be a powerful tool for predicting COVID-19 cases, especially in the absence of intensive clinical surveillance.

The detectability and removal efficiency of SARS-CoV-2 in a large-scale septic tank of a COVID-19 quarantine facility in Japan

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to be present in sewage, and wastewater-based epidemiology has attracted much attention. However, the physical partitioning of SARS-CoV-2 in wastewater and the removal efficiency of treatment systems require further investigation. This study aimed to investigate the detectability and physical partitioning of SARS-CoV-2 in wastewater and assess its removal in a large-scale septic tank employing anaerobic, anoxic, and oxic processes in a sequential batch reactor, which was installed in a coronavirus disease 2019 (COVID-19) quarantine facility. The amount of SARS-CoV-2 RNA in wastewater was determined with polyethylene glycol (PEG) precipitation followed by quantitative polymerase chain reaction (qPCR), and the association of SARS-CoV-2 with wastewater solids was evaluated by the effect of filtration prior to PEG precipitation (pre-filtration). The amount of SARS-CoV-2 RNA detected from pre-filtered samples was substantially lower than that of samples without pre-filtration. These results suggest that most SARS-CoV-2 particles in wastewater are associated with the suspended solids excluded by pre-filtration. The removal efficiency of SARS-CoV-2 in the septic tank was evaluated based on the SARS-CoV-2 RNA concentrations in untreated and treated wastewater, which was determined by the detection method optimized in this study. Escherichia coli and pepper mild mottle virus (PMMoV) were also quantified to validate the wastewater treatment system's performance. The mean log₁₀ reduction values of SARS-CoV-2, E. coli, and PMMoV were 2.47 (range, 2.25-2.68), 2.81 (range, 2.45-3.18), and 0.66 (range, 0.61-0.70), respectively, demonstrating that SARS-CoV-2 removal by the wastewater treatment system was comparable to or better than the removal of fecal indicators. These results suggest that SARS-CoV-2 can be readily removed by the septic tank. This is the first study to determine the removal efficiency of SARS-CoV-2 in a facility-level sequencing batch activated sludge system.

The Efficient and Practical virus Identification System with ENhanced Sensitivity for Solids (EPISENS-S): A rapid and cost-effective SARS-CoV-2 RNA detection method for routine wastewater surveillance

Wastewater-based epidemiology has attracted attention as a COVID-19 surveillance tool. Here, we developed a practical method for detecting SARS-CoV-2 RNA in wastewater (the EPISENS-S method), which employs direct RNA extraction from wastewater pellets formed via low-speed centrifugation. The subsequent multiplex one-step RT-preamplification reaction with forward and reverse primers for SARS-CoV-2 and a reverse primer only for pepper mild mottle virus (PMMoV) allowed for qPCR quantification of the targets with different abundances in wastewater from the RT-preamplification product. The detection sensitivity of the method was evaluated using wastewater samples seeded with heat-inactivated SARS-CoV-2 in concentrations of 2.11 × 10³ to 2.11 × 10⁶ copies/L. The results demonstrated that the sensitivity of the EPISENS-S method was two orders of magnitude higher than that of the conventional method (PEG precipitation, followed by regular RT-qPCR; PEG-QVR-qPCR). A total of 37 untreated wastewater samples collected from two wastewater treatment plants in Sapporo, Japan when 1.6 to 18 new daily reported cases per 100,000 people were reported in the city (March 4 to July 8, 2021), were examined using the EPISENS-S method to confirm its applicability to municipal wastewater. SARS-CoV-2 RNA was quantified in 92 % (34/37) of the samples via the EPISENS-S method, whereas none of the samples (0/37) was quantifiable via the PEG-QVR-qPCR method. The PMMoV concentrations measured by the EPISENS-S method ranged from 2.60 × 10⁶ to 1.90 × 10⁸ copies/L, and the SARS-CoV-2 RNA concentrations normalized by PMMoV ranged from 5.71 × 10^-6 to 9.51 × 10^-4 . The long-term trend of normalized SARS-CoV-2 RNA concentration in wastewater was consistent with that of confirmed COVID-19 cases in the city. These results demonstrate that the EPISENS-S method is highly sensitive and suitable for routine COVID-19 wastewater surveillance.

High electrical energy harvesting performance of an integrated microbial fuel cell and low voltage booster-rectifier system treating domestic wastewater

To harvest directly usable electrical energy from real domestic wastewater, a new power management system (PMS), transistor-based low voltage boosters followed by a voltage rectifier (LVBR), was developed and tested for its energy harvesting performance. Three air-cathode MFCs were individually linked with LVBs, which were electrically stacked in parallel and then connected with a single voltage rectifier (MFC-LVBR). The MFC-LVBR system could increase V_MFCto 11.9 ± 0.6 V without voltage reversal, which was capable of charging a lithium-ion batteryand supercapacitor-based power banks. When the integrated MFC-LVBR system was linked with a lithium-ion battery, the highest normalized energy recovery (NER_COD) of 0.76 kWh/kg-COD (NER_volumeof 0.22 kWh/m³) was achieved with a minimal energy loss of 14.4%, whichwas much higher than those previously reported values.Furthermore, the electrical energy charged in the lithium-ion battery successfully powered a DC peristaltic pump requiring a minimum operating power of 0.46 W.

Metagenomic Analysis of Five Phylogenetically Distant Anammox Bacterial Enrichment Cultures

Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic ana­lysis of our 5 established anammox bacterial enrichment cultures was performed in the present study. Fourteen high-quality metagenome-assembled genomes (MAGs) were obtained, including those of 5 anammox Planctomycetota (Candidatus Brocadia, Ca. Kuenenia, Ca. Jettenia, and Ca. Scalindua), 4 Bacteroidota, and 3 Chloroflexota. Based on the gene sets of metabolic pathways involved in the degradation of polymeric substances found in Chloroflexota and Bacteroidota MAGs, they are expected to be scavengers of extracellular polymeric substances and cell debris.

Temporal dynamics of Campylobacter and Arcobacter in a freshwater lake that receives fecal inputs from migratory geese

Migratory geese could influence the microbiological water quality; however, their impacts on pathogen dynamics remain largely unknown. In this study, we analyzed the population dynamics of Campylobacter and Arcobacter group bacteria (AGB) in a freshwater lake in Japan over two years. The bacteria were quantified by using both culture-dependent and -independent methods. The potential sources of these bacteria were examined by a high-throughput flaA sequencing approach. Campylobacter was abundantly detected both by culture-dependent and -independent methods in the lake, especially when migratory geese were present in the lake. High-throughput flaA sequencing suggests that geese were the likely source of Campylobacter in the lake. The viable population of Campylobacter exceeds the concentrations that can potentially cause 10^-4 infections per person per year when water is used to grow fresh vegetables. The occurrence of AGB, on the other hand, was not directly related to the population of migratory geese. AGB were not detected in geese fecal samples. Diverse AGB flaA genotypes occurred in the lake over multiple seasons. Our results suggest that AGB likely comprise a part of the indigenous microbial population of the lake and grow in response to high nutrient, warm temperature, and low dissolved oxygen concentrations in the lake. Geese therefore can indirectly impact the AGB population by providing nutrients to cause eutrophication and lower the dissolved oxygen concentration. Since geese travel long-distance and disperse their fecal microbiota and nutrients to wide areas, they may have significant impacts on water quality and public health.

Growth of nitrite-oxidizing Nitrospira and ammonia-oxidizing Nitrosomonas in marine recirculating trickling biofilter reactors

Aerobic ammonia and nitrite oxidation reactions are fundamental biogeochemical reactions contributing to the global nitrogen cycle. Although aerobic nitrite oxidation yields 4.8-folds less Gibbs free energy (∆G_r ) than aerobic ammonia oxidation in the NH₄ ⁺ -feeding marine recirculating trickling biofilter reactors operated in the present study, nitrite-oxidizing and not ammonia-oxidizing Nitrospira (sublineage IV) outnumbered ammonia-oxidizing Nitrosomonas (relative abundance; 53.8% and 7.59% respectively). CO₂ assimilation efficiencies during ammonia or nitrite oxidation were 0.077 μmol-¹⁴ CO₂ /μmol-NH₃ and 0.053-0.054 μmol-¹⁴ CO₂ /μmol-NO₂ ^- respectively, and the difference between ammonia and nitrite oxidation was much smaller than the difference of ∆G_r . Free-energy efficiency of nitrite oxidation was higher than ammonia oxidation (31%-32% and 13% respectively), and high CO₂ assimilation and free-energy efficiencies were a determinant for the dominance of Nitrospira over Nitrosomonas. Washout of Nitrospira and Nitrosomonas from the trickling biofilter reactors was also examined by quantitative PCR assay. Normalized copy numbers of Nitrosomonas amoA were 1.5- to 1.7-folds greater than Nitrospira nxrB and 16S rRNA gene in the reactor effluents. Nitrosomonas was more susceptible for washout than Nitrospira in the trickling biofilter reactors, which was another determinant for the dominance of Nitrospira in the trickling biofilter reactors.

The Intrapopulation Genetic Diversity of RNA Virus May Influence the Sensitivity of Chlorine Disinfection

RNA virus populations are not clonal; rather, they comprise a mutant swarm in which sequences are slightly different from the master sequence. Genetic diversity within a population (intrapopulation genetic diversity) is critical for RNA viruses to survive under environmental stresses. Disinfection has become an important practice in the control of pathogenic viruses; however, the impact of intrapopulation genetic diversity on the sensitivity of disinfection, defined as -log10 (postdisinfected infectious titer/predisinfected titer), has not been elucidated. In this study, we serially passaged populations of rhesus rotavirus. We demonstrated that populations with reduced chlorine sensitivity emerged at random and independently of chlorine exposure. Sequencing analysis revealed that compared with sensitive populations, less-sensitive ones had higher non-synonymous genetic diversity of the outer capsid protein gene, suggesting that changes in the amino acid sequences of the outer capsid protein were the main factors influencing chlorine sensitivity. No common mutations were found among less-sensitive populations, indicating that rather than specific mutations, the diversity of the outer capsid protein itself was associated with the disinfection sensitivity and that the disinfection sensitivity changed stochastically. Simulation results suggest that the disinfection sensitivity of a genetically diverse population is destabilized if cooperative viral clusters including multiple sequences are formed. These results advocate that any prevention measures leading to low intrapopulation genetic diversity are important to prevent the spread and evolution of pathogenic RNA viruses in society.

NH2OH Disproportionation Mediated by Anaerobic Ammonium-oxidizing (Anammox) Bacteria

Anammox bacteria produce N₂ gas by oxidizing NH₄⁺ with NO₂^–, and hydroxylamine (NH₂OH) is a potential intermediate of the anammox process. N₂ gas production occurs when anammox bacteria are incubated with NH₂OH only, indicating their capacity for NH₂OH disproportionation with NH₂OH serving as both the electron donor and acceptor. Limited information is currently available on NH₂OH disproportionation by anammox bacteria; therefore, the stoichiometry of anammox bacterial NH₂OH disproportionation was examined in the present study using ¹⁵N-tracing techniques. The anammox bacteria, Brocadia sinica, Jettenia caeni, and Scalindua sp. were incubated with the addition of ¹⁵NH₂OH, and the production of ¹⁵N-labeled nitrogenous compounds was assessed. The anammox bacteria tested performed NH₂OH disproportionation and produced ^15-15N₂ gas and NH₄⁺ as reaction products. The addition of acetylene, an inhibitor of the anammox process, reduced the activity of NH₂OH disproportionation, but not completely. The growth of B. sinica by NH₂OH disproportionation (–240.3‍ ‍kJ mol NH₂OH^–1 under standard conditions) was also tested in 3 up-flow column anammox reactors fed with 1) 0.7‍ ‍mM NH₂OH only, 2) 0.7‍ ‍mM NH₂OH and 0.5‍ ‍mM NH₄⁺, and 3) 0.7‍ ‍mM NH₂OH and 0.5‍ ‍mM NO₂^–. NH₂OH consumption activities were markedly reduced after 7‍ ‍d of operation, indicating that B. sinica was unable to maintain its activity or biomass by NH₂OH disproportionation.

Effect of poised cathodic potential on anodic ammonium nitrogen removal from domestic wastewater by air-cathode microbial fuel cells

Performances of anodic ammonia oxidation have been investigated for various bioelectrochemical systems at a wide range of poised anodic potentials in the literature. The effect of poised cathodic potential on ammonium nitrogen (NH₄⁺-N) and total nitrogen (TN, sum of NH₄⁺-N, NO₂^--N, and NO₃^--N) removal from domestic wastewater by single chamber air-cathode microbial fuel cells (MFCs) was investigated. Poising the air-cathode potential at +0.7 V vs. SHE significantly increased current generation (from 11 ± 1 mA to 22.8 ± 5 mA) and oxygen permeation into the MFC through the air-cathode (from 75.4 ± 1.2 g-O₂/m³/d to 151 ± 3.7 g-O₂/m³/d), which consequently resulted in a high NH₄⁺-N removal rate of 150 ± 13 g-NH₄⁺-N/m³/d and TN removal rate of 63 ± 16 g-TN/m³/d. These high NH₄⁺-N and TN removal rates could be attributed to the enhancement of dual respiratory pathways: the electrode-assisted anodic and aerobic NH₄⁺ oxidation.

Transcriptomic response of HepG2 cells exposed to three common anti-inflammatory drugs: Ketoprofen, mefenamic acid, and diclofenac in domestic wastewater effluents

The biological impacts of residual pharmaceuticals in the complex wastewater effluents have not been fully understood. Here, we investigated changes in the transcriptomic responses of hepatobrastoma (HepG2) cells exposed to a single or partially combined three common non-steroidal anti-inflammatory drugs (NSAIDs); ketoprofen (KPF), mefenamic acid (MFA) and diclofenac (DCF), in domestic wastewater effluents. After 48 h sub-lethal exposure to single compounds, the DNA microarray analysis identified 57-184 differently expressed genes (DEGs). The hierarchical clustering analysis and GO enrichment of the DEGs showed that gene expression profiles of the NSAIDs were distinct from each other although they are classified into the same therapeutic category. Four maker genes (i.e., EGR1, AQP3, SQSTM1, and NAG1) were further selected from the common DEGs, and their expressions were quantified by qPCR assay in a dose-dependent manner (ranging from μg/L to mg/L). The results revealed the insignificant induction of the marker genes at 1 μg/L of KPF, MFA, and DCF, suggesting negligible biological impacts of the NSAIDs on gene expression (early cellular responses) of HepG2 at typical concentration levels found in the actual wastewater effluents. Based on the quantitative expression analysis of the selected marker genes, the present study indicated that the presence of wastewater effluent matrix may mitigate the potentially adverse cellular impacts of the NSAIDs.

Maintenance power requirements of anammox bacteria "Candidatus Brocadia sinica" and "Candidatus Scalindua sp."

Little is known about the cell physiology of anammox bacteria growing at extremely low growth rates. Here, "Candidatus Brocadia sinica" and "Candidatus Scalindua sp." were grown in continuous anaerobic membrane bioreactors (MBRs) with complete biomass retention to determine maintenance energy (i.e., power) requirements at near-zero growth rates. After prolonged retentostat cultivations, the specific growth rates (μ) of "Ca. B. sinica" and "Ca. Scalindua sp." decreased to 0.000023 h^-1 (doubling time of 1255 days) and 0.000157 h^-1 (184 days), respectively. Under these near-zero growth conditions, substrate was continuously utilized to meet maintenance energy demands (m_e) of 6.7 ± 0.7 and 4.3 ± 0.7 kJ mole of biomass-C^-1 h^-1 for "Ca. B. sinica" and "Ca. Scalindua sp.", which accorded with the theoretically predicted values of all anaerobic microorganisms (9.7 and 4.4 kJ mole of biomass-C^-1 h^-1at 37 °C and 28 °C, respectively). These m_e values correspond to 13.4 × 10^-15 and 8.6 × 10^-15 watts cell^-1 for "Ca. B. sinica" and "Ca. Scalindua sp.", which were five orders of magnitude higher than the basal power limit for natural settings (1.9 × 10^-19 watts cells^-1). Furthermore, the minimum substrate concentrations required for growth (S_min) were calculated to be 3.69 ± 0.21 and 0.09 ± 0.05 μM NO₂^- for "Ca. B. sinica" and "Ca. Scalindua sp.", respectively. These results match the evidence that "Ca. Scalindua sp." with lower maintenance power requirement and S_min are better adapted to energy-limited natural environments than "Ca. B. sinica", suggesting the importance of these parameters on ecological niche differentiation in natural environments.

Bioelectrochemical anoxic ammonium nitrogen removal by an MFC driven single chamber microbial electrolysis cell

Nitrogen removal from wastewater is an indispensable but highly energy-demanding process, and thus more energy-saving treatment processes are required. Here, we investigated the performance of bioelectrochemical ammonium nitrogen (NH₄⁺-N) removal from real domestic wastewater without energy-intensive aeration by a single chamber microbial electrolysis cell (MEC) that was electrically powered by a double chamber microbial fuel cell (MFC). Anoxic NH₄⁺-N oxidation and total nitrogen (TN) removal rates were determined at various applied voltages (0-1.2 V), provided by the MFC. The MEC achieved a NH₄⁺-N oxidation rate of 151 ± 42 g NH₄⁺-N m^-3 d^-1 and TN removal rate of 95 ± 42 g-TN m^-3 d^-1 without aeration at the applied voltage of 0.8 V (the anode potential E_anode = +0.633 ± 0.218 V vs. SHE). These removal rates were much higher than the previously reported values and conventional biological nitrogen removal processes. Open and closed-circuit MEC batch experiments confirmed that anoxic NH₄⁺-N oxidation was an electrochemically mediated biological process (that is, an anode acted as an electron acceptor) and denitrification occurred simultaneously without NO₂^- and NO₃^- accumulation. Moreover, ex-situ¹⁵N tracer experiment and microbial community analysis revealed that anammox and heterotrophic denitrification mainly contributed to the TN removal. Thus, the bioelectrochemical anodic NH₄⁺-N oxidation was coupled with anammox and denitrification in this MFC-assisted MEC system. Taken together, our MFC-driven single chamber MEC could be a high rate energy-saving nitrogen removal process without external carbon and energy input and high energy-demanding aeration.

Inhibitory effect of polysulfide, an endogenous sulfur compound, on oxidative stress-induced TRPA1 activation

Polysulfide (PS), an endogenous sulfur compound, generated by oxidation of hydrogen sulfide, has a stimulatory action on the nociceptive TRPA1 channel. TRPA1 is also activated by reactive oxygen species such as hydrogen peroxide (H₂O₂) produced during inflammation. Here, we examined the effect of PS on H₂O₂-induced responses in native and heterologously expressed TRPA1 using a cell-based calcium assay. We also carried out behavioral experiments in vivo. In mouse sensory neurons, H₂O₂ elicited early TRPA1-dependent and late TRPA1-independent increases of [Ca²⁺]_i. The former was suppressed by the pretreatment with PS. In cells heterologously expressed TRPA1, PS suppressed [Ca²⁺]_i responses to H₂O₂. Simultaneous measurement of [Ca²⁺]_i and the intracellular PS level revealed that scavenging effect of PS was not related to the inhibitory effect. Removal of extracellular Ca²⁺, a calmodulin inhibitor and dithiothreitol attenuated the inhibitory effect of PS. Pretreatment with PS diminished nociceptive behaviors induced by H₂O₂. The present data suggest that PS suppresses oxidative stress-induced TRPA1 activation due to cysteine modification and Ca²⁺/calmodulin signaling. Thus, endogenous sulfurs may have regulatory roles in nociception via functional changes in TRPA1 under inflammatory conditions.

Glycogen metabolism of the anammox bacterium "Candidatus Brocadia sinica"

Presence of glycogen granules in anaerobic ammonium-oxidizing (anammox) bacteria has been reported so far. However, very little is known about their glycogen metabolism and the exact roles. Here, we studied the glycogen metabolism in "Ca. Brocadia sinica" growing in continuous retentostat cultures with bicarbonate as a carbon source. The effect of the culture growth phase was investigated. During the growing phase, intracellular glycogen content increased up to 32.6 mg-glucose (g-biomass dry wt)-1 while the specific growth rate and ATP/ADP ratio decreased. The accumulated glycogen begun to decrease at the onset of entering the near-zero growth phase and was consumed rapidly when substrates were depleted. This clearly indicates that glycogen was synthesized and utilized as an energy storage. The proteomic analysis revealed that "Ca. B. sinica" synthesized glycogen via three known glycogen biosynthesis pathways and simultaneously degraded during the progress of active anammox, implying that glycogen is being continuously recycled. When cells were starved, a part of stored glycogen was converted to trehalose, a potential stress protectant. This suggests that glycogen serves at least as a primary carbon source of trehalose synthesis for survival. This study provides the first physiological evidence of glycogen metabolism in anammox bacteria and its significance in survival under natural substrate-limited habitat.

Viral Interference as a Factor of False-Negative in the Infectious Adenovirus Detection Using Integrated Cell Culture-PCR with a BGM Cell Line

This study investigated the influence of viral interference on the detection of enteric viruses using the integrated cell culture (ICC)-PCR with a BGM cell line. It was possible to detect 10² plaque-forming units (PFU)/flask of enterovirus 71 (EV71) in spite of the presence of 10⁴ PFU/flask of adenovirus 40 (AdV40). Meanwhile, 10⁴ PFU/flask of AdV40 was not detected in the presence of 10² PFU/flask of EV71. This inhibition of AdV40 detection using ICC-PCR was attributable to the growth of EV71, because the addition of a growth inhibitor of EV71 (rupintrivir) neutralized the detection inhibition of AdV40. The growth inhibition of AdV40 under co-infection with EV71 is probably caused by the immune responses of EV71-infected cells. AdV is frequently used as a fecal contamination indicator of environmental water, but this study demonstrated that false-negative detection of infectious AdV using ICC-PCR could be caused by the co-existence of infectious EV in a water sample. The addition of rupintrivir could prevent false-negative detection of AdV using ICC-PCR. This study, therefore, emphasizes the importance of confirming the presence of multiple enteric viruses in a sample derived from environmental water prior to the application of ICC-PCR because the viral interference phenomenon may lead to the false-negative detection of target viruses.

Influence of δ18 O of water on measurements of δ18 O of nitrite and nitrate

RATIONALE

Oxygen isotope ratio measurements of NO₂ ^- and NO₃ ^- by the azide method and denitrifier method are sensitive to the δ¹⁸ O value of the sample water. However, the influence of δ¹⁸ O_H2O on those measurements has not been quantitatively evaluated and documented so far. Therefore, we investigated the influence of δ¹⁸ O_H2O of a sample on the δ¹⁸ O analysis of NO₂ ^- and NO₃ ^- .

METHODS

We prepared NO₂ ^- and NO₃ ^- standards (with known δ¹⁸ O_NO2- and δ¹⁸ O_NO3- values) dissolved in waters having different δ¹⁸ O_H2O values (δ¹⁸ O_H2O  = -12.6, 25.9, 56.7, and 110.1‰). Nitrite and nitrate were converted into N₂ O using the azide method and the denitrifier method, respectively. The isotope ratios of the generated N₂ O were measured with a Sercon purge-and-trap gas chromatography/isotope ratio mass spectrometry (PT-GC/IRMS) system. The measured δ¹⁸ O values of the produced N₂ O were plotted against known δ¹⁸ O_NO2- and δ¹⁸ O_NO3- values to evaluate the influence of exchange of an oxygen atom with H₂ O during the conversion of NO₂ ^- into N₂ O and NO₃ ^- into N₂ O, respectively.

RESULTS

The degree of oxygen isotope exchange was 10.8 ± 0.3% in the azide method and 5.5 ± 1.0% in the denitrifier method, indicating that the azide method is more susceptible to artifacts arising from differences in the δ¹⁸ O_H2O value of water than the denitrifier method. Thus, the intercept of the standard calibration curve must be corrected to account for differences in δ¹⁸ O_H2O . Abiotic NO₂ -H₂ O equilibrium isotope effect experiments yielded a rate constant of (1.13 ± 007) × 10^-2 (h^-1 ) and an equilibrium isotope effect of 11.9 ± 0.1‰ under the condition of pH = 7.5, 30°C, and 2.5% salinity.

CONCLUSIONS

Oxygen isotope ratio measurements of NO₂ ^- by the azide method are highly sensitive to δ¹⁸ O_H2O as a result of significant oxygen isotope exchange between NO₂ ^- and H₂ O. Therefore, to obtain the most accurate measurements water with the same δ¹⁸ O_H2O value as that of the sample must be used to make the NO₂ ^- and NO₃ ^- standards.

Simple assay for colorimetric quantification of unamplified bacterial 16S rRNA in activated sludge using gold nanoprobes

Domestic and industrial wastewater treatment systems are vital in the protection of natural ecosystems and human health. Identification of microbial communities in the systems is essential to stable treatment performance. However, the current tools of microbial community analysis are labor intensive and time consuming, and require expensive equipment. Therefore, we developed a simple assay for colorimetric quantification of bacterial 16S rRNA extracted from environmental samples. The assay is based on RNA extraction with commercial kits, mixing the unamplified RNA sample with Au-nanoprobes and NaCl, and analyzing the absorbance spectra. Our experimental results confirmed that the assay format was valid. By analyzing the synthesized DNA, we optimized the operational parameters affecting the assay. We achieved adequate capture DNA density by setting the capture DNA probe concentration at 10 μM during the functionalization step. The required incubation time after NaCl addition was 30 min. The binding site of the target had negligible effect on DNA detection. Under the optimized condition, a calibration curve was created using 16S rRNA extracted from activated sludge. The curve was linear above 5.0 × 10⁷ copies/μL of bacterial 16S rRNA concentration, and the limit of detection was 1.17 × 10⁸ copies/μL. Using the calibration curve, the bacterial 16S rRNA concentration in activated sludge samples could be quantified with deviations between 48% and 208% against those determined by RT-qPCR. The findings of our study introduce an innovative tool for the quantification of 16S rRNA concentration as the activity of key bacteria in wastewater treatment processes, achieving stable treatment performance.

Simultaneous removal of nitrate and heavy metals in a continuous flow nitrate-dependent ferrous iron oxidation (NDFO) bioreactor

Nitrogen and heavy metals can co-occur in various industrial wastewaters such as coke-oven wastewater. Removal of these contaminants is important, but cost-efficient removal technology is limited. In this study, we examined the usefulness of nitrate-dependent ferrous iron oxidation (NDFO) for the simultaneous removal of nitrate and heavy metals (iron and zinc), by using an NDFO strain Pseudogulbenkiania sp. NH8B. Based on the batch culture assays, nitrate, Fe, and Zn were successfully removed from a basal medium as well as coke-oven wastewater containing 5 mM nitrate, 10 mM Fe(II), and 10 mg/L Zn. Zinc in the water was most likely co-precipitated with Fe(III) oxides produced during the NDFO reaction. Simultaneous removal of nitrate, Fe, and Zn was also achieved in a continuous-flow reactor fed with a basal medium containing 10 mM nitrate, 5 mM Fe(II), 4 mM acetate, and 10 mg/L Zn. However, when the reactor is fed with coke-oven wastewater supplemented with 10 mM nitrate, 5 mM Fe(II), 4 mM acetate, and 10 mg/L ZnCl₂, the reactor performance significantly decreased, most likely due to the inhibition of bacterial growth by thiocyanate or organic contaminants present in the coke-oven wastewater. Use of mixed culture of NDFO bacteria and thiocyanate/organic-degrading denitrifiers should help improve the reactor performance.

Cell Density-dependent Anammox Activity of Candidatus Brocadia sinica Regulated by N-acyl Homoserine Lactone-mediated Quorum Sensing

The activity of anaerobic ammonia-oxidizing (anammox) bacteria is considered to depend on cell density; however, this has not yet been confirmed due to the fastidious nature of anammox bacteria (e.g., slow growth, oxygen sensitivity, and rigid aggregate formation). In the present study, the cell density-dependent occurrence of anammox activity (^14-15N₂ gas production rate) was investigated using planktonic enrichment cultures of Candidatus Brocadia sinica. This activity was detectable when the density of cells was higher than 10⁷‍ ‍cells‍ ‍mL^–1 and became stronger with increases in cell density. At the cell densities, the transcription of the BROSI_A1042 and BROSI_A3652 genes, which are potentially involved in the biosynthesis and reception of N-acyl homoserine lactone (AHL), was detectable in Brocadia sinica cells. The presence of AHL molecules in the MBR culture of B. sinica was confirmed by an AHL reporter assay and gas chromatography mass spectrometry analysis. The exogenous addition of the MBR culture extract and AHL molecules (a cocktail of C₆, C₈, C₁₀, and C₁₂-homoserine lactones) increased the specific ^14-15N₂ production rate of B. sinica. These results suggest that the specific anammox activity of B. sinica is regulated by AHL-mediated quorum sensing.

The Effect of GD1a Ganglioside-Expressing Bacterial Strains on Murine Norovirus Infectivity

In this study, we investigated the impact of GD1a-expressing bacterial strains on the infectivity of murine norovirus (MNV). Eligible bacterial strains were screened from a sewage sample using flow cytometry, and their genetic sequences of 16S rRNA were determined. The enzyme-linked immunosorbent assay (ELISA) was employed to analyze the binding between bacteria and MNV particles, and the plaque assay was used to assess the effects of GD1a-positive and negative strains on MNV infectivity. The result from ELISA shows that MNV particles are able to bind to both GD1a-positive and negative bacterial strains, but the binding to the GD1a-positive strain is more significant. The infectivity assay result further shows that the MNV infectious titer declined with an increasing concentration of GD1a-positive bacteria. The addition of anti-GD1a antibody in the infectivity assay led to the recovery of the MNV infectious titer, further confirming that the binding between MNV particles and bacterial GD1a ganglioside compromises MNV infectivity. Our findings highlight the role indigenous bacteria may play in the lifecycle of waterborne enteric viruses as well as the potential of exploiting them for virus transmission intervention and water safety improvement.

Bottleneck Size-Dependent Changes in the Genetic Diversity and Specific Growth Rate of a Rotavirus A Strain

RNA viruses form a dynamic distribution of mutant swarms (termed "quasispecies") due to the accumulation of mutations in the viral genome. The genetic diversity of a viral population is affected by several factors, including a bottleneck effect. Human-to-human transmission exemplifies a bottleneck effect, in that only part of a viral population can reach the next susceptible hosts. In the present study, two lineages of the rhesus rotavirus (RRV) strain of rotavirus A were serially passaged five times at a multiplicity of infection (MOI) of 0.1 or 0.001, and three phenotypes (infectious titer, cell binding ability, and specific growth rate) were used to evaluate the impact of a bottleneck effect on the RRV population. The specific growth rate values of lineages passaged under the stronger bottleneck (MOI of 0.001) were higher after five passages. The nucleotide diversity also increased, which indicated that the mutant swarms of the lineages under the stronger bottleneck effect were expanded through the serial passages. The random distribution of synonymous and nonsynonymous substitutions on rotavirus genome segments indicated that almost all mutations were selectively neutral. Simple simulations revealed that the presence of minor mutants could influence the specific growth rate of a population in a mutant frequency-dependent manner. These results indicate a stronger bottleneck effect can create more sequence spaces for minor sequences.IMPORTANCE In this study, we investigated a bottleneck effect on an RRV population that may drastically affect the viral population structure. RRV populations were serially passaged under two levels of a bottleneck effect, which exemplified human-to-human transmission. As a result, the genetic diversity and specific growth rate of RRV populations increased under the stronger bottleneck effect, which implied that a bottleneck created a new space in a population for minor mutants originally existing in a hidden layer, which includes minor mutations that cannot be distinguished from a sequencing error. The results of this study suggest that the genetic drift caused by a bottleneck in human-to-human transmission explains the random appearance of new genetic lineages causing viral outbreaks, which can be expected according to molecular epidemiology using next-generation sequencing in which the viral genetic diversity within a viral population is investigated.

Simple and reliable enumeration of Escherichia coli concentrations in wastewater samples by measuring β-d-glucuronidase (GUS) activities via a microplate reader

Monitoring of Escherichia coli concentrations at wastewater treatment plants (WWTPs) is important to ensure process performance and protect public health. However, conventional E. coli enumeration methods are complicated and time- and labor-consuming. Here, we report a novel simple and reliable method based on β-d-glucuronidase (GUS) activity assay to enumerate E. coli concentrations in wastewater (WW) samples. An aliquot (20 μL) of the medium with fluorogenic enzyme substrate for E. coli and 180 μL of a WW sample were added to one well of a 96-well microplate. The microplate was placed in a microplate reader at 37 °C. To this end, the fluorescence intensity of a fluorogenic enzyme substrate for E. coli was measured every 10 min over 3 h to determine GUS activity. The linear increase in the fluorescence intensity representing the GUS activities showed a positive correlation with E. coli concentrations in wastewater samples. However, the correlation equations were specific to WWTPs, which could be due to the difference in the E. coli population structures among WWTPs. We observed that the wastewater matrix is not a limitation to measure the GUS activity, and a WWTP-specific correlation equation can be used as a calibration curve to estimate the E. coli concentrations in the samples collected from that site. A comparison of the results with those of culture-dependent Colilert method proved that the current method is simple and useful for the enumeration of E. coli concentrations in wastewater samples reliably.

Ecological niche differentiation among anammox bacteria

Anaerobic ammonium oxidizing (anammox) bacteria can directly convert ammonium and nitrite to nitrogen gas anaerobically and were responsible for a substantial part of the fixed nitrogen loss and re-oxidation of nitrite to nitrate in freshwater and marine ecosystems. Although a wide variety of studies have been undertaken to investigate the abundance and biodiversity of anammox bacteria so far, ecological niche differentiation of anammox bacteria is still not fully understood. To assess their growth behavior and consequent population dynamics at a given environment, the Monod model is often used. Here, we summarize the Monod kinetic parameters such as the maximum specific growth rate (μ_max) and the half-saturation constant for nitrite (K_NO2-) and ammonium (K_NH4+) of five known candidatus genera of anammox bacteria. We also discuss potential pivotal environmental factors and metabolic flexibility that influence the community compositions of anammox bacteria. Particularly biodiversity of the genus "Scalindua" might have been largely underestimated. Several anammox bacteria have been successfully enriched from various source of biomass. We reevaluate their enrichment methods and culture medium compositions to gain a clue of niche differentiation of anammox bacteria. Furthermore, we formulate the current issues that must be addressed. Overall this review re-emphasizes the importance of enrichment cultures (preferably pure cultures), physiological characterization and direct microbial competition studies using enrichment cultures in laboratories.

Required Chlorination Doses to Fulfill the Credit Value for Disinfection of Enteric Viruses in Water: A Critical Review

A credit value of virus inactivation has been assigned to the disinfection step in international and domestic guidelines for wastewater reclamation and reuse. To fulfill the credit value for water disinfection, water engineers need to apply an appropriate disinfection strength, expressed as a CT value (mg × min/L), which is a product of disinfectant concentration and contact time, against enteric viruses in wastewater. In the present study, we extracted published experimental data on enteric virus inactivation using free chlorine and monochloramine and applied the Tobit analysis and simple linear regression analysis to calculate the range of CT values (mg × min/L) needed for 4-log₁₀ inactivation. Data were selected from peer-reviewed papers containing kinetics data of virus infectivity and chlorine residual in water. Coxsackie B virus and echovirus require higher CT values (lower susceptibility) for 4-log₁₀ inactivation than adenovirus and a human norovirus surrogate (murine norovirus) with free chlorine. On the other hand, adenovirus has lower susceptibility to monochloramine compared to murine norovirus, coxsackievirus, and echovirus. The factors that influence the required CT value are virus type, pH, water temperature, and water matrix. This systematic review demonstrates that enteroviruses and adenovirus are appropriate representative enteric viruses to evaluate water disinfection using free chlorine and monochloramine, respectively.

Mixture toxicity of the combinations of silver nanoparticles and environmental pollutants

Although toxicity of silver nanoparticles (AgNPs) has been well studied, the mixture toxicity of the combination of AgNPs and other environmental pollutants is still largely unknown. Here, we investigated the mixture toxicity of the combinations of AgNPs and common environmental pollutants such as arsenic (As), cadmium (Cd), and chromium (Cr) on human hepatoma cell line (HepG2) at noncytotoxic concentrations based on analyses of cytotoxicity, genotoxicity, reactive oxygen species (ROS) generation, and modes of cell death. In addition, DNA microarray analysis was performed to understand the cellular responses at a molecular level. AgNPs-As and AgNPs-Cd combinations exhibited synergistic effect on cytotoxicity while AgNPs-Cr showed additive effect. The AgNPs-Cd combination caused much stronger synergism than AgNPs-As combination. Based on cellular and molecular level analyses, the synergistic effect could be explained by overproduction of reactive oxygen species (ROS), which induced DNA damage and consequently apoptotic cell death. On the other hand, the additive effect caused by AgNPs-Cr could be attributed to reduction of the mixture toxicity by precipitation of Cr ions. Taken together, our results clearly demonstrated that the mixture toxicity of AgNPs with As, Cd, or Cr at noncytotoxic concentrations had different toxicity effects. Particularly, toxicogenomic approach using DNA microarray was useful to assess the mechanisms of the mixture toxicity.

Transcriptomic analysis of HepG2 cells exposed to fractionated wastewater effluents suggested humic substances as potential inducer of whole effluent toxicity

We performed a transcriptome-based bioassay (TSB assay) using human hepatoma HepG2 cells to evaluate the potential toxicity of whole wastewater effluents from two membrane bioreactors (MBRs) and a conventional activated sludge process (AS). The biologically active agent(s) in the wastewater effluents were characterized based on expression of the marker genes (i.e., CYP1A1, AKR1B10, GCLM and GPX2) selected by DNA microarray analysis, after the wastewater effluent samples were concentrated by a reverse osmosis (RO) membrane and further fractionated by various manipulations. The qPCR assay of marker genes demonstrated that the induction of CYP1A1 and GPX2 was mitigated after passing through C18 and chelate columns. In addition, clear induction of CYP1A1 was observed in the smallest size fraction with 1 k Da or smaller organic molecules in all the tested effluents. These results together with the water quality data of the fractionated samples suggested that responsible constituents for potentially adverse and abnormal transcriptomic responses in HepG2 could have hydrophobic nature and act with metal-dissolved organic matter (DOM) complexes in 1 k Da or smaller size fraction. Although DOM is known to play two contradictory roles as a protector and an inducer of toxicants, our present study indicated the DOM in wastewater effluent, particularly humic substances with acidic nature, functioned as a toxicity inducer of residual chemicals in the effluents. This study provided a new insight into the nature of "toxic unknowns" in the wastewater effluents, which should be monitored whole through the reclamation process and prioritized for removal.

Complete Genome Sequence of a Novel Myoviridae Phage, SfΦ01, Infecting Shigella spp

The Shigella bacterium is one of the most significant causes of waterborne and foodborne bacterial dysentery. A lytic bacteriophage infecting Shigella flexneri was isolated from wastewater in Japan. We report here the complete genome sequence of this bacteriophage, revealing that it belongs to the Myoviridae family and possesses linear genomic DNA.

Development of a simple analytical method to determine arsenite using a DNA aptamer and gold nanoparticles

A simple analytical method was developed to determine the arsenite (As(III)) concentration using a DNA aptamer and gold nanoparticles (AuNPs). Prior to sample measurements, the method sensing mechanism was confirmed by analyzing the particle size of the AuNPs at each step of the analysis procedure, and the key operational parameters that affect the method performance were optimized. The optimal final NaCl concentration, incubation time with NaCl and pH of a 3-(N-morpholino) propanesulfonic acid buffer were 60 mM, 10 min and 7.3, respectively. A calibration curve was created under optimized operational conditions. The calibration curve was linear from a 1.0- to 10-μM As(III) concentration. The detection limit was 2.1 μM (161 μg/L). Using the calibration curve, we evaluated groundwater samples spiked with As(III). As(III) concentrations in groundwater pretreated with a 0.2-μm-pore-size membrane filter and cation-exchange resin were determined by using the method, which suggests that the proposed method can be used to determine the As(III) concentration in groundwater.

Sign-constrained linear regression for prediction of microbe concentration based on water quality datasets

This study presents a novel methodology for estimating the concentration of environmental pollutants in water, such as pathogens, based on environmental parameters. The scientific uniqueness of this study is the prevention of excess conformity in the model fitting by applying domain knowledge, which is the accumulated scientific knowledge regarding the correlations between response and explanatory variables. Sign constraints were used to express domain knowledge, and the effect of the sign constraints on the prediction performance using censored datasets was investigated. As a result, we confirmed that sign constraints made prediction more accurate compared to conventional sign-free approaches. The most remarkable technical contribution of this study is the finding that the sign constraints can be incorporated in the estimation of the correlation coefficient in Tobit analysis. We developed effective and numerically stable algorithms for fitting a model to datasets under the sign constraints. This novel algorithm is applicable to a wide variety of the prediction of pollutant contamination level, including the pathogen concentrations in water.

Dual nitrogen and oxygen isotope fractionation during anaerobic ammonium oxidation by anammox bacteria

Natural abundance of stable nitrogen (N) and oxygen (O) isotopes are invaluable biogeochemical tracers for assessing the N transformations in the environment. To fully exploit these tracers, the N and O isotope effects (¹⁵ε and ¹⁸ε) associated with the respective nitrogen transformation processes must be known. However, the N and O isotope effects of anaerobic ammonium oxidation (anammox), one of the major fixed N sinks and NO₃^- producers, are not well known. Here, we report the dual N and O isotope effects associated with anammox by three different anammox bacteria including "Ca. Scalindua japonica", a putative marine species, which were measured in continuous enrichment culture experiments. All three anammox species yielded similar N isotope effects of NH₄⁺ oxidation to N₂ (¹⁵ε_NH4→N2) ranging from 30.9‰ to 32.7‰ and inverse kinetic isotope effects of NO₂^- oxidation to NO₃^- (¹⁵ε_NO2→NO3 = -45.3‰ to -30.1‰). In contrast, ¹⁵ε_NO2→N2 (NO₂^- reduction to N₂) were significantly different among three species, which is probably because individual anammox bacteria species might possess different types of nitrite reductase. We also report the combined O isotope effects for NO₂^- oxidation (¹⁸E_NO2→NO3) by anammox bacteria. These obtained dual N and O isotopic effects could provide significant insights into the contribution of anammox bacteria to the fixed N loss and NO₂^- reoxidation (N recycling) in various natural environments.

Membrane Fouling Potentials of an Exoelectrogenic Fouling-Causing Bacterium Cultured With Different External Electron Acceptors

Integrated microbial fuel cell (MFC) and membrane bioreactor (MBR) systems are a promising cost-effective and energy-saving technology for wastewater treatment. Membrane fouling is still an important issue of such integrated systems in which aeration (oxygen) is replaced with anode electrodes (anodic respiration). Here, we investigated the effect of culture conditions on the membrane fouling potential of fouling-causing bacteria (FCB). In the present study, Klebsiella quasipneumoniae strain S05, which is an exoelectrogenic FCB isolated from a MBR treating municipal wastewater, was cultured with different external electron acceptors (oxygen, nitrate, and solid-state anode electrode). As results, the fouling potential of S05 was lowest when cultured with anode electrode and highest without any external electron acceptor (p < 0.05, respectively). The composition of soluble microbial products (SMP) and extracellular polymeric substances (EPS) was also dependent on the type of electron acceptor. Protein and biopolymer contents in SMP were highly correlated with the fouling potential (R² = 0.73 and 0.81, respectively). Both the fouling potential and yield of protein and biopolymer production were significantly mitigated by supplying electron acceptors sufficiently regardless of its types. Taken together, the aeration of MBR could be replaced with solid-state anode electrodes without enhancement of membrane fouling, and the anode electrodes must be placed sufficiently to prevent the dead spaces in the integrated reactor.

Specific interactions of rotavirus HAL1166 with Enterobacter cloacae SENG-6 and their contribution on rotavirus HAL1166 removal

Contribution of specific interactions between human enteric viruses and wastewater suspended solids on human enteric virus removal by microfiltration was studied. A cross-flow microfiltration system was used with rotavirus HAL1166 and Enterobacter cloacae SENG-6 as the model virus and wastewater suspended solid. Cleavage of rotavirus HAL1166 protein VP4 by trypsin produces the VP8* subunit, which specifically interacts with histo-blood group antigen (HBGA). In the presence of Enterobacter cloacae SENG-6, the trypsin-treated rotavirus concentration reduced with time (R² > 0.6) compared to the reduction of non-trypsin treated rotavirus. Calculation of the gel/cake layer deposited on the membrane, consisting of Enterobacter cloacae SENG-6 and either trypsin-treated or non-trypsin treated rotavirus HAL1166, revealed that the microflocs consisting of trypsin-treated rotavirus and Enterobacter cloacae SENG-6 have lower porosity and permeability, displaying higher resistance to virus passage through the membrane. The results provide evidence that specific wastewater suspended solids-human enteric virus interaction can contribute to increasing the removal of human enteric viruses by microfiltration.

Aggregation ability of three phylogenetically distant anammox bacterial species

Anaerobic ammonium-oxidizing (anammox) bacteria are well known for their aggregation ability. However, very little is known about cell surface physicochemical properties of anammox bacteria and thus their aggregation abilities have not been quantitatively evaluated yet. Here, we investigated the aggregation abilities of three different anammox bacterial species: "Candidatus Brocadia sinica", "Ca. Jettenia caeni" and "Ca. Brocadia sapporoensis". Planktonic free-living enrichment cultures of these three anammox species were harvested from the membrane bioreactors (MBRs). The physicochemical properties (e.g., contact angle, zeta potential, and surface thermodynamics) were analyzed for these anammox bacterial species and used in the extended DLVO theory to understand the force-distance relationship. In addition, their extracellular polymeric substances (EPSs) were characterized by X-ray photoelectron spectroscopy and nuclear magnetic resonance. The results revealed that the "Ca. B. sinica" cells have the most hydrophobic surface and less hydrophilic functional groups in EPS than other anammox strains, suggesting better aggregation capability. Furthermore, aggregate formation and anammox bacterial populations were monitored when planktonic free-living cells were cultured in up-flow column reactors under the same conditions. Rapid development of microbial aggregates was observed with the anammox bacterial population shifts to a dominance of "Ca. B. sinica" in all three reactors. The dominance of "Ca. B. sinica" could be explained by its better aggregation ability and the superior growth kinetic properties (higher growth rate and affinity to nitrite). The superior aggregation ability of "Ca. B. sinica" indicates significant advantages (efficient and rapid start-up of anammox reactors due to better biomass retention as granules and consequently stable performance) in wastewater treatment application.

Anammox biomass carrying efficiency of polyethylene non-woven sheets as a carrier material

To access the effects of the surface modification and fabric structure of polyethylene (PE) non-woven fabric sheets on retaining the attachment efficiency of anammox biomass, three different non-woven sheets were prepared and inserted in an anammox reactor. The hydrophobic surface modification with 10% KMnO₄ and gelatin did not improve the attachment efficiency of the anammox biomass on the surface of the PE non-woven fibers. Densely packed PE-755 having the highest specific surface area to volume ratio (SA/V) (755) retained 221.4 mg biomass per unit sheet, whereas PE-181 having the lowest SA/V (181) retained only 66.4 mg biomass per unit. Accordingly, the volumetric anammox activity of non-woven sheet PE-755 was the highest among the three PE non-woven sheets because of the strong positive relationship between the specific anammox activity and biomass amount (R = 0.835, P < .01). The specific surface area to volume ratio (cm² cm^-3) as well as the bulk density should be considered as important parameters for the selection of non-woven biocarriers for anammox biomass.

High-Throughput flaA Short Variable Region Sequencing to Assess Campylobacter Diversity in Fecal Samples From Birds

Current approach to identify sources of human pathogens is largely dependent on the cultivation and isolation of target bacteria. For rapid pathogen source identification, culture-independent strain typing method is necessary. In this study, we designed new primer set that broadly covers flaA short variable region (SVR) of various Campylobacter species, and applied the flaA SVR sequencing method to examine the diversity of Campylobacter spp. in geese fecal samples (n = 16) with and without bacteria cultivation. Twenty-three Campylobacter strains isolated from the 16 geese fecal samples were grouped similarly by conventional flaA restriction fragment length polymorphism (RFLP) method and by the flaA SVR sequencing method, but higher discriminant power was observed in the flaA SVR sequencing approach. For culture-independent flaA SVR sequencing analysis, we developed and optimized the sequence data analysis pipeline to identify as many genotypes as possible, while minimizing the detection of genotypes generated by sequencing errors. By using this pipeline, 51,629 high-quality flaA sequence reads were clustered into 16 operational taxonomic units (=genotypes) by using 98% sequence similarity and >50 sequence duplicates. Almost all flaA genotypes obtained by culture-dependent method were also identified by culture-independent flaA SVR MiSeq sequencing method. In addition, more flaA genotypes were identified probably due to high throughput nature of the MiSeq sequencing. These results suggest that the flaA SVR sequencing could be used to analyze the diversity of Campylobacter spp. without bacteria isolation. This method is promising to rapidly identify potential sources of Campylobacter pathogens.

Experimental Evidence for in Situ Nitric Oxide Production in Anaerobic Ammonia-Oxidizing Bacterial Granules

Although nitric oxide (NO) emissions from anaerobic ammonium oxidation (anammox)-based processes were reported previously, the NO production pathways are poorly understood. Here, we investigated the NO production pathways in anammox granules in detail by combining ¹⁵N-stable isotope tracer experiments with various inhibitors, microsensor measurements, and transcriptome analysis for key genes of NO₂^- reduction. NO was emitted from the anammox granules, which account for 0.07% of the N₂ emission. ¹⁵N-stable isotope-tracer experiments indicated that most of the N₂ was produced by anammox bacteria, whereas NO was produced from NO₂^- reduction by anammox and denitrifying bacteria. The NO emission rate was highest at pH 8.0 and accelerated by increasing NH₄⁺ and NO₂^- concentrations in the culture media. The microsensor analyses showed the in situ NO production rate was highest in the outer layer of the anammox granule where anammox activity was also highest. The detected in situ NO concentrations of up to 2.7 μM were significantly above physiological thresholds known to affect a wide range of microorganisms present in wastewater. Hence, NO likely plays pivotal roles in the microbial interactions in anammox granules, which needs to be further investigated.

Rapid cultivation of free-living planktonic anammox cells

Despite that anaerobic ammonium oxidizing (anammox) bacteria are key players in the global nitrogen cycle, no pure cultures are still available. Planktonic cell culture with high purity is, therefore, essential for physiological and biochemical studies of anammox bacteria. However, development of such planktonic cell cultures requires an enormous amount of time and effort. Here we developed a novel rapid method for cultivating free-living planktonic anammox cells. First, anammox granules were physically dispersed, immobilized in 6% polyvinyl alcohol-4% sodium alginate (PVA-SA) gel beads, and then pre-cultured in an up-flow column reactor. Anammox bacteria grew rapidly as loosely flocculated micro-clusters in the gel beads. After 18 days of pre-cultivation, mature gel beads were harvested, physically dispersed by vortex and inoculated into a membrane bioreactor (MBR). The MBR was then continuously operated at a low nitrogen loading rate (<0.9 kg-TN m^-3 d^-1). After 17 days of operation, active free-living planktonic anammox cells with purity >95% were successfully developed in the MBR. Total culture time (gel beads and MBR) to accomplish free-living planktonic anammox cells was only 35 days, which was significantly shorter than the previous reports. This new cultivation technique could greatly facilitate various microbial, physiological and biochemical studies of anammox bacteria.

Multiple-endpoints gene alteration-based (MEGA) assay: A toxicogenomics approach for water quality assessment of wastewater effluents

Wastewater effluents contain a significant number of toxic contaminants, which, even at low concentrations, display a wide variety of toxic actions. In this study, we developed a multiple-endpoints gene alteration-based (MEGA) assay, a real-time PCR-based transcriptomic analysis, to assess the water quality of wastewater effluents for human health risk assessment and management. Twenty-one genes from the human hepatoblastoma cell line (HepG2), covering the basic health-relevant stress responses such as response to xenobiotics, genotoxicity, and cytotoxicity, were selected and incorporated into the MEGA assay. The genes related to the p53-mediated DNA damage response and cytochrome P450 were selected as markers for genotoxicity and response to xenobiotics, respectively. Additionally, the genes that were dose-dependently regulated by exposure to the wastewater effluents were chosen as markers for cytotoxicity. The alterations in the expression of an individual gene, induced by exposure to the wastewater effluents, were evaluated by real-time PCR and the results were validated by genotoxicity (e.g., comet assay) and cell-based cytotoxicity tests. In summary, the MEGA assay is a real-time PCR-based assay that targets cellular responses to contaminants present in wastewater effluents at the transcriptional level; it is rapid, cost-effective, and high-throughput and can thus complement any chemical analysis for water quality assessment and management.