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1. Diversity and health risk potentials of the Enterococcus population in tropical coastal water impacted by Hurricane Lane

   https://doi.org/10.2166/wh.2021.209  

   Saingam, Prakit ; Di, Doris Y. ; Yan, Tao ( October 2021 , Journal of Water and Health)

   Abstract Hurricane-caused stormwater runoffs transport diverse terrestrial pollutants, adversely impact microbiological water quality, and introduce fecal and other pathogens to coastal water environments. This study investigated the genotypic diversity, phylogenetic composition, antibiotic resistance patterns, and virulence gene repertoire of the Enterococcus population in the Hilo Bay coastal water after the immediate impact of Hurricane Lane. DNA fingerprinting of Enterococcus isolates exhibited large genotypic diversity, while 16S rRNA gene sequencing identified four major species, including E. faecalis (34.7%), E. faecium (22.4%), E. hirae (22.4%), and E. durans (18.4%). Four common enterococcal virulence genes (cylA, esp, asa1, and gelE) were detected in the Enterococcus population, with significant portions of E. durans (33.3%), E. faecalis (41.2%), E. faecium (36.4%), and E. hirae (27.3%) isolates possessing two or more virulence genes. Considerable antibiotic resistance to rifampin, erythromycin, tetracycline, and nitrofurantoin was detected in the Enterococcus population, with one E. durans isolate showing vancomycin resistance. The results indicate considerable health implications associated with Enterococcus spp. in the hurricane-impacted tropical coastal water, illustrating the needs for more comprehensive understanding of the microbiological risks associated with storm-impacted coastal water.
2. Patterns of sediment-associated fecal indicator bacteria in an urban estuary: Benthic-pelagic coupling and implications for shoreline water quality.

   O'Mullan, G. ; Juhl, A. ; Reichert, R. ; Schneider, E. ; and Martinez, N. ( January 2019 , Science of the total environment)

   Estuarine and coastal waterways are commonly monitored for fecal and sewage contamination to protect recreator health and ecosystem functions. Such monitoring programs commonly rely on cultivation-based counts of fecal indicator bacteria (FIB) in water column samples. Recent studies demonstrate that sediments and beach sands can be heavily colonized by FIB, and that settling and resuspension of colonized particles may significantly influence the distribution of FIB in the water column. However, measurements of sediment FIB are rarely incorporated into monitoring programs, and geographic surveys of sediment FIB are uncommon. In this study, the distribution of FIB and the extent of benthic-pelagic FIB coupling were examined in the urbanized, lower Hudson River Estuary. Using cultivation-based enumeration, two commonly-measured FIB, enterococci and Escherichia coli, were widely distributed in both sediment and water, and were positively correlated with each other. The taxonomic identity of FIB isolates from water and sediment was confirmed by DNA sequencing. The geometric mean of FIB concentration in sediment was correlated with both the geometric mean of FIB in water samples from the same locations and with sediment organic carbon. These two positive associations likely reflect water as the FIB source for underlying sediments, and longer FIB persistence in themore »sediments compared to the water, respectively. The relative representation of other fecal associated bacterial genera in sediment, determined by 16S rRNA gene sequencing, increased with the sequence representation of the two FIB, supporting the value of these FIB for assessing sediment contamination. Experimental resuspension of sediment increased shoreline water column FIB concentrations, which may explain why shoreline water samples had higher average FIB concentrations than samples collected nearby but further from shore. In combination, these results demonstrate extensive benthic-pelagic coupling of FIB in an urbanized estuary and highlight the importance of sediment FIB distribution and ecology when interpreting water quality monitoring data.« less
3. Metagenomic Sequencing and Quantitative Real-Time PCR for Fecal Pollution Assessment in an Urban Watershed

   https://doi.org/10.3389/frwa.2021.626849  

   Brumfield, Kyle D. ; Cotruvo, Joseph A. ; Shanks, Orin C. ; Sivaganesan, Mano ; Hey, Jessica ; Hasan, Nur A. ; Huq, Anwar ; Colwell, Rita R. ; Leddy, Menu B. ( February 2021 , Frontiers in Water)

   Microbial contamination of recreation waters is a major concern globally, with pollutants originating from many sources, including human and other animal wastes often introduced during storm events. Fecal contamination is traditionally monitored by employing culture methods targeting fecal indicator bacteria (FIB), namely E . coli and enterococci, which provides only limited information of a few microbial taxa and no information on their sources. Host-associated qPCR and metagenomic DNA sequencing are complementary methods for FIB monitoring that can provide enhanced understanding of microbial communities and sources of fecal pollution. Whole metagenome sequencing (WMS), quantitative real-time PCR (qPCR), and culture-based FIB tests were performed in an urban watershed before and after a rainfall event to determine the feasibility and application of employing a multi-assay approach for examining microbial content of ambient source waters. Cultivated E . coli and enterococci enumeration confirmed presence of fecal contamination in all samples exceeding local single sample recreational water quality thresholds ( E . coli , 410 MPN/100 mL; enterococci, 107 MPN/100 mL) following a rainfall. Test results obtained with qPCR showed concentrations of E . coli , enterococci, and human-associated genetic markers increased after rainfall by 1.52-, 1.26-, and 1.11-fold log 10 copies per 100 mL,more »respectively. Taxonomic analysis of the surface water microbiome and detection of antibiotic resistance genes, general FIB, and human-associated microorganisms were also employed. Results showed that fecal contamination from multiple sources (human, avian, dog, and ruminant), as well as FIB, enteric microorganisms, and antibiotic resistance genes increased demonstrably after a storm event. In summary, the addition of qPCR and WMS to traditional surrogate techniques may provide enhanced characterization and improved understanding of microbial pollution sources in ambient waters.« less
4. Metagenomics and the development of viral water quality tools

   https://doi.org/10.1038/s41545-019-0032-3  

   Bibby, Kyle ; Crank, Katherine ; Greaves, Justin ; Li, Xiang ; Wu, Zhenyu ; Hamza, Ibrahim A. ; Stachler, Elyse ( March 2019 , npj Clean Water)

   Human exposure to pathogenic viruses in environmental waters results in a significant global disease burden. Current microbial water quality monitoring approaches, mainly based on fecal indicator bacteria, insufficiently capture human health impacts posed by pathogenic viruses in water. The emergence of the ‘microbiome era’ and high-throughput metagenome sequencing has led to the discovery of novel human-associated viruses, including both pathogenic and commensal viruses in the human microbiome. The discovery of novel human-associated viruses is often followed by their detection in wastewater, highlighting the great diversity of human-associated viruses potentially present in the water environment. Novel human-associated viruses provide a rich reservoir to develop viral water quality management tools with diverse applications, such as regulating wastewater reuse and monitoring agricultural and recreational waters. Here, we review the pathway from viral discovery to water quality monitoring tool, and highlight select human-associated viruses identified by metagenomics and subsequently detected in the water environment (namely Bocavirus, Cosavirus, CrAssphage, Klassevirus, and Pepper Mild Mottle Virus). We also discuss research needs to enable the application of recently discovered human-associated viruses in water quality monitoring, including investigating the geographic distribution, environmental fate, and viability of potential indicator viruses. Examples suggest that recently discovered human pathogens aremore »likely to be less abundant in sewage, while other human-associated viruses (e.g., bacteriophages or viruses from food) are more abundant but less human-specific. The improved resolution of human-associated viral diversity enabled by metagenomic tools provides a significant opportunity for improved viral water quality management tools.

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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