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1. Lab-on-a-Smartphone (LOS): A smartphone-integrated, optoelectrowetting-driven environmental sensor for on-site detection of water quality

   https://doi.org/10.1109/SENSORS52175.2022.9967199  

   Thio, Si Kuan; Park, Sung-Yong (January 2022, IEEE Sensors)

   A lab-on-a-smartphone (LOS) presents a portable environmental sensing tool that enables the monitoring of water quality by performing various detection techniques such as smartphone-integrated fluorescence microscopy and portable loop-mediated amplification (LAMP) assays. The LOS can conduct multiple laboratory functions and has experimentally demonstrated (1) automated on-chip water sample processing, (2) on-site fluorescent detection of harmful algae cells, and (3) fecal contamination of water through LAMP assays. The LOS can overcome conventional labor-intensive and time-consuming techniques for the monitoring of microbiological contaminants in environment waters. 

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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 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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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)

   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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4. Rapid detection of viral, bacterial, fungal, and oomycete pathogens on tomato with microneedles, LAMP on a microfluidic chip, and smartphone device

   https://doi.org/10.1094/PHYTO-12-23-0481-R  

   Shymanovich, Tatsiana; Saville, Amanda C; Paul, Rajesh; Wei, Qingshan; Ristaino, Jean Beagle (June 2024, Phytopathology®)

   NA (Ed.)

   Rapid detection of plant diseases before they escalate can improve disease control. Our team has developed rapid nucleic acid extraction methods with microneedles (MN) and combined these with LAMP assays for pathogen detection in the field. In this work, we developed LAMP assays for early blight (Alternaria linariae, A. alternata, and A. solani) and bacterial spot of tomato (Xanthomonas perforans) and validated these LAMP assays and two previously developed LAMP assays for tomato spotted wilt virus and late blight. Tomato plants were inoculated and disease severity was measured. Extractions were performed using MN and LAMP assays were run in tubes (with hydroxynaphthol blue) on a heat block or on a newly designed microfluidic slide chip on a heat block or a slide heater. Fluorescence on the microfluidic chip slides was visualized using EvaGreen and photographed on a smartphone. Plants inoculated with X. perforans or tomato spotted wilt virus tested positive prior to visible disease symptoms, while P. infestans and A. linariae were detected at the time of visual disease symptoms. LAMP assays were more sensitive than PCR and the limit of detection was 1 pg of DNA for both A. linariae and X. perforans. The LAMP assay designed for early blight detected all three species of Alternaria that infect tomato and is thus an Alternaria spp. assay. This study demonstrates the utility of rapid MN extraction followed by LAMP on a microfluidic chip for rapid diagnosis of four important tomato pathogens. 

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5. Amplicons, Metagenomes, and Metatranscriptomes from Sediment and Water

   https://doi.org/10.1128/mra.01230-22  

   Newman, Madison R.; Sanchez, Darlenys; Acosta, Anna M.; Connors, Bernadette J. (March 2023, Microbiology Resource Announcements)

   Thrash, J. Cameron (Ed.)

   ABSTRACT High fecal indicator bacterium (FIB) counts in water have been found to correlate with high sediment FIB counts. To determine the other bacterial populations in common between the two substrates, sediment and water samples from suburban waters known to be impacted by stormwater runoff were examined using next-generation sequencing. 

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