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1. Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

   https://doi.org/10.1128/AEM.02525-19  

   Suttner, Brittany ; Johnston, Eric R. ; Orellana, Luis H. ; Rodriguez-R, Luis M. ; Hatt, Janet K. ; Carychao, Diana ; Carter, Michelle Q. ; Cooley, Michael B. ; Konstantinidis, Konstantinos T. ; Ercolini, Danilo ( March 2020 , Applied and Environmental Microbiology)

   ABSTRACT Little is known about the public health risks associated with natural creek sediments that are affected by runoff and fecal pollution from agricultural and livestock practices. For instance, the persistence of foodborne pathogens such as Shiga toxin-producing Escherichia coli (STEC) originating from these practices remains poorly quantified. Towards closing these knowledge gaps, the water-sediment interface of two creeks in the Salinas River Valley of California was sampled over a 9-month period using metagenomics and traditional culture-based tests for STEC. Our results revealed that these sediment communities are extremely diverse and have functional and taxonomic diversity comparable to that observed in soils. With our sequencing effort (∼4 Gbp per library), we were unable to detect any pathogenic E. coli in the metagenomes of 11 samples that had tested positive using culture-based methods, apparently due to relatively low abundance. Furthermore, there were no significant differences in the abundance of human- or cow-specific gut microbiome sequences in the downstream impacted sites compared to that in upstream more pristine (control) sites, indicating natural dilution of anthropogenic inputs. Notably, the high number of metagenomic reads carrying antibiotic resistance genes (ARGs) found in all samples was significantly higher than ARG reads in other available freshwatermore »and soil metagenomes, suggesting that these communities may be natural reservoirs of ARGs. The work presented here should serve as a guide for sampling volumes, amount of sequencing to apply, and what bioinformatics analyses to perform when using metagenomics for public health risk studies of environmental samples such as sediments. IMPORTANCE Current agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food- and waterborne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health are assessed by culture-based tests for the intestinal bacterium Escherichia coli . However, the accuracy of these traditional methods (e.g., low accuracy in quantification, and false-positive signal when PCR based) and their suitability for sediments remain unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the United States in order to assess how agricultural runoff affects the native microbial communities and if the presence of Shiga toxin-producing Escherichia coli (STEC) in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.« less
2. Detection of human fecal pollution in environmental waters using human mitochondrial DNA and correlation with general and human-associated fecal genetic markers

   https://doi.org/10.2166/wh.2019.197  

   Tanvir Pasha, A. B. ; Hinojosa, Jessica ; Phan, Duc ; Lopez, Adrianne ; Kapoor, Vikram ( December 2019 , Journal of Water and Health)

   Abstract Human mitochondrial DNA (mtDNA) genetic markers are abundant in sewage and highly human-specific, suggesting a great potential for the environmental application as human fecal pollution indicators. Limited data are available on the occurrence and co-occurrence of human mtDNA with fecal bacterial markers in surface waters, and how the abundance of these markers is influenced by rain events. A 1-year sampling study was conducted in a suburban watershed impacted by human sewage contamination to evaluate the performance of a human mtDNA-based marker along with the bacterial genetic markers for human-associated Bacteroidales (BacHum and HF183) and Escherichia coli. Additionally, the human mtDNA-based assay was correlated with rain events and other markers. The mtDNA marker was detected in 92% of samples (n = 140) with a mean concentration of 2.96 log10 copies/100 ml throughout the study period. Human mtDNA was detected with greater abundance than human-associated Bacteroidales that could be attributed to differences in the decay of these markers in the environment. The abundance of all markers was positively correlated with rain events, and human mtDNA abundance was significantly correlated with various bacterial markers. In general, these results should support future risk assessment for impacted watersheds, particularly those affected by human fecalmore »pollution, by evaluating the performance of these markers during rain events.« less
3. Demonstration of Tryptophan-Like Fluorescence Sensor Concepts for Fecal Exposure Detection in Drinking Water in Remote and Resource Constrained Settings

   https://doi.org/10.3390/su12093768  

   Bedell, Emily ; Sharpe, Taylor ; Purvis, Timothy ; Brown, Joe ; Thomas, Evan ( May 2020 , Sustainability)

   Low-cost, field-deployable, near-time methods for assessing water quality are not available when and where waterborne infection risks are greatest. We describe the development and testing of a novel device for the measurement of tryptophan-like fluorescence (TLF), making use of recent advances in deep-ultraviolet light emitting diodes (UV-LEDs) and sensitive semiconductor photodiodes and photomultipliers. TLF is an emerging indicator of water quality that is associated with members of the coliform group of bacteria and therefore potential fecal contamination. Following the demonstration of close correlation between TLF and E. coli in model waters and proof of principle with sensitivity of 4 CFU/mL for E. coli, we further developed a two-LED flow-through configuration capable of detecting TLF levels corresponding to “high risk” fecal contamination levels (>10 CFU/100 mL). Findings to date suggest that this device represents a scalable solution for remote monitoring of drinking water supplies to identify high-risk drinking water in near-time. Such information can be immediately actionable to reduce risks.
4. Removal of Fecal Indicator Bacteria by River Networks

   https://doi.org/10.3390/w14040617  

   Huang, Tao ; Wollheim, Wilfred M. ; Jones, Stephen H. ( February 2022 , Water)

   Fecal contamination is a significant source of water quality impairment globally. Aquatic ecosystems can provide an important ecosystem service of fecal contamination removal. Understanding the processes that regulate the removal of fecal contamination among river networks across flow conditions is critical. We applied a river network model, the Framework for Aquatic Modeling in the Earth System (FrAMES-Ecoli), to quantify removal of fecal indicator bacteria by river networks across flow conditions during summers in a series of New England watersheds of different characteristics. FrAMES-Ecoli simulates sources, transport, and riverine removal of Escherichia coli (E. coli). Aquatic E. coli removal was simulated in both the water column and the hyporheic zone, and is a function of hydraulic conditions, flow exchange rates with the hyporheic zone, and die-off in each compartment. We found that, at the river network scale during summers, removal by river networks can be high (19–99%) with variability controlled by hydrologic conditions, watershed size, and distribution of sources in the watershed. Hydrology controls much of the variability, with 68–99% of network scale inputs removed under base flow conditions and 19–85% removed during storm events. Removal by the water column alone could not explain the observed pattern in E. coli, suggestingmore »that processes such as hyporheic removal must be considered. These results suggest that river network removal of fecal indicator bacteria should be taken into consideration in managing fecal contamination at critical downstream receiving waters.« less
5. Impact of Metazooplankton Filter Feeding on Escherichia coli under Variable Environmental Conditions

   https://doi.org/10.1128/AEM.02006-19  

   Ismail, Niveen S. ; Blokker, Brittney M. ; Feeney, Tyler R. ; Kohn, Ruby H. ; Liu, Jingyi ; Nelson, Vivian E. ; Ollive, Mariah C. ; Price, Sarah B. ; Underdah, Emma J. ; Stams, Alfons J. ( December 2019 , Applied and Environmental Microbiology)

   ABSTRACT The fecal indicator bacterial species Escherichia coli is an important measure of water quality and a leading cause of impaired surface waters. We investigated the impact of the filter-feeding metazooplankton Daphnia magna on the inactivation of E. coli . The E. coli clearance rates of these daphnids were calculated from a series of batch experiments conducted under variable environmental conditions. Batch system experiments of 24 to 48 h in duration were completed to test the impacts of bacterial concentration, organism density, temperature, and water type. The maximum clearance rate for adult D. magna organisms was 2 ml h −1 organism −1 . Less than 5% of E. coli removed from water by daphnids was recoverable from excretions. Sorption of E. coli on daphnid carapaces was not observed. As a comparison, the clearance rates of the freshwater rotifer Branchionus calyciflorus were also calculated for select conditions. The maximum clearance rate for B. calyciflorus was 6 × 10 −4  ml h −1 organism −1 . This research furthers our understanding of the impacts of metazooplankton predation on E. coli inactivation and the effects of environmental variables on filter feeding. Based on our results, metazooplankton can play an important role in the reduction of E. colimore »in natural treatment systems under environmentally relevant conditions. IMPORTANCE Escherichia coli is a fecal indicator bacterial species monitored by the U.S. Environmental Protection Agency to assess microbial water quality. Due to the potential human health implications linked to high levels of E. coli , it is important to understand the inactivation or reduction mechanisms in surface waters. Our research examines the capacities of two types of widespread filter-feeding freshwater metazooplankton, Daphnia magna and Brachionus calyciflorus , to reduce E. coli concentrations. We examine the impacts of different environmentally relevant conditions on the clearance rates. Our results contribute to a better understanding of the importance of metazooplankton in controlling E. coli concentrations and what conditions will reduce or increase grazing. These results provide baseline data to support future efforts to develop a quantitative model relating zooplankton uptake rates to relevant environmental variables.« less