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1. 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 the 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. 

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2. A smartphone-integrated dielectrophoretic platform for rapid and in-situ monitoring of environmental water quality through LAMP assays

   Thio, Si Kuan; Bae, Sungwoo; Park, Sung-Yong (January 2021, The 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS 2021))

   A smartphone-integrated dielectrophoretic (SiDEP) platform is presented for on-site and real-time monitoring of fecal indicator bacteria (FIB) to examine the presence and concentration levels of fecal contamination in environmental water via loop-mediated isothermal amplification (LAMP) assays on a smartphone. Experimental demonstrations have verified the SiDEP’s capabilities for (1) on-chip water sample processing, (2) portable LAMP assays, and (3) colorimetric analysis of fecal water quality. The SiDEP truly offers a low-cost, portable, and fully-integrated system enabling rapid on-site detection of the presence of FIB and their associated pathogens in environmental water without the need for sophisticated laboratory equipment or skilled personnel. 

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3. Data report: X-ray fluorescence scanning of Site U1574, Vøring Plateau, IODP Expedition 396

   Alvarez_Zarikian, CA; Yager, SL; Harper, DT; Christopoulou, M; Clementi, VJ; Varela, N (October 2024, Proceedings of the International Ocean Discovery Program Expedition reports)

   Semiquantitative elemental results from X-ray fluorescence (XRF) scanning of sediment cores from International Ocean Discovery Program (IODP) Site U1574 in the Vøring Plateau, Norwegian Margin, are presented in this report. XRF elemental data were collected every 1 cm from a stratigraphically complete and continuous cored section with 102% recovery from the sea bottom to ~170 meters below seafloor in Hole U1574C. We report raw element intensities (counts) for Al, Si, K, Ca, Ti, Fe, Br, Sr, and Zr and identify covariation patterns consistent with lithofacies variations. Our high-resolution XRF scanning was conducted to better characterize the sediment depositional history at Site U1574 and to aid interpretation of past environmental and oceanographic conditions in the Norwegian Margin, targeting the earliest incursion of deep water into the young North Atlantic Ocean during the Early to Middle Eocene. The high-resolution XRF data also may help improve the age-depth model for the sediment succession at Site U1574. 

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4. Nanoscale Patterning of Surface Nanobubbles by Focused Ion Beam

   https://doi.org/10.1021/acs.langmuir.4c01534  

   Siddique, Anayet Ullah; Xie, Rui; Horlacher, Danielle; Warren, Roseanne (July 2024, Langmuir)

   Surface nanobubbles forming on hydrophobic surfaces in water present an exciting opportunity as potential agents of top-down and bottom-up nanopatterning. The formation and characteristics of surface nanobubbles are strongly influenced by the physical and chemical properties of the substrate. In this study, focused ion beam (FIB) milling is used for the first time to spatially control the nucleation of surface nanobubbles with 75 nm precision. The spontaneous formation of nanobubbles on alternating lines of a self-assembled monolayer (octadecyltrichlorosilane) patterned by FIB is detected by atomic force microscopy. The effect of chemical vs topographical surface heterogeneity on the formation of nanobubbles is investigated by comparing samples with OTS coating applied pre- vs post-FIB patterning. The results confirm that nanoscale FIB-based patterning can effectively control surface nanobubble position by means of chemical heterogeneity. The effect of FIB milling on nanobubble morphology and properties, including contact angle and gas oversaturation, is also reported. Molecular dynamics simulations provide further insight into the effects of FIB amorphization on surface nanobubble formation. Combined experimental and simulation investigations offer insights to guide future nanobubble-based patterning using FIB milling. 

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5. 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)

   null (Ed.)

   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, 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. 

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