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1. 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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2. In Situ Growth of Halophilic Bacteria in Saline Fracture Fluids from 2.4 km below Surface in the Deep Canadian Shield

   https://doi.org/10.3390/life10120307  

   Wilpiszeski, Regina L.; Sherwood Lollar, Barbara; Warr, Oliver; House, Christopher H. (December 2020, Life)

   null (Ed.)

   Energy derived from water-rock interactions such as serpentinization and radiolysis, among others, can sustain microbial ecosystems deep within the continental crust, expanding the habitable biosphere kilometers below the earth’s surface. Here, we describe a viable microbial community including sulfate-reducing microorganisms from one such subsurface lithoautotrophic ecosystem hosted in fracture waters in the Canadian Shield, 2.4 km below the surface in the Kidd Creek Observatory in Timmins, Ontario. The ancient groundwater housed in fractures in this system was previously shown to be rich in abiotically produced hydrogen, sulfate, methane, and short-chain hydrocarbons. We have further investigated this system by collecting filtered water samples and deploying sterile in situ biosampler units into boreholes to provide an attachment surface for the actively growing fraction of the microbial community. Scanning electron microscopy, energy-dispersive X-ray spectroscopy, and DNA sequencing analyses were undertaken to classify the recovered microorganisms. Moderately halophilic taxa (e.g., Marinobacter, Idiomarina, Chromohalobacter, Thiobacillus, Hyphomonas, Seohaeicola) were recovered from all sampled boreholes, and those boreholes that had previously been sealed to equilibrate with the fracture water contained taxa consistent with sulfate reduction (e.g., Desulfotomaculum) and hydrogen-driven homoacetogenesis (e.g., Fuchsiella). In contrast to this “corked” borehole that has been isolated from the mine environment for approximately 7 years at the time of sampling, we sampled additional open boreholes. The waters flowing freely from these open boreholes differ from those of the long-sealed borehole. This work complements ongoing efforts to describe the microbial diversity in fracture waters at Kidd Creek in order to better understand the processes shaping life in the deep terrestrial subsurface. In particular, this work demonstrates that anaerobic bacteria and known halophilic taxa are present and viable in the fracture waters presently outflowing from existing boreholes. Major cations and anions found in the fracture waters at the 2.4 km level of the mine are also reported. 

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3. Draft Genome Sequence of the Free-Living, Iridescent Bacterium Tenacibaculum mesophilum Strain ECR

   https://doi.org/10.1128/MRA.01302-20  

   Mickol, Rebecca L.; Louyakis, Artemis S.; Kee, H. Lynn; Johnson, Lisa K.; Dawson, Scott C.; Hargreaves, Katherine R.; Chadwick, Grayson L.; Newman, Dianne K.; Leadbetter, Jared R.; Brown, C. Titus (January 2021, Microbiology Resource Announcements)

   Maresca, Julia A. (Ed.)

   ABSTRACT Here, we report the genome sequence of Tenacibaculum mesophilum strain ECR, which was isolated from the river/ocean interface at Trunk River in Falmouth, Massachusetts. The isolation and sequencing were performed as part of the 2016 and 2018 Microbial Diversity courses at the Marine Biological Laboratory in Woods Hole, Massachusetts. 

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4. Urban runoff drives titanium dioxide engineered particle concentrations in urban watersheds: field measurements

   https://doi.org/10.1039/d2en00826b  

   Nabi, Md Mahmudun; Wang, Jingjing; Erfani, Mahdi; Goharian, Erfan; Baalousha, Mohammed (March 2023, Environmental Science: Nano)

   Urban runoff is a significant source of pollutants, including incidental and engineered nanoparticles, to receiving surface waters. The aim of this study is to investigate the impact of urbanization on the concentrations of TiO 2 engineered particles in urban surface waters. The study area boundaries are limited to the Lower Saluda and Nicholas Creek-Broad River from upstream, and outlet of upper Congaree River in Columbia, South Carolina, United States from downstream. This sampling area captures a significant footprint of the urban area of the city of Columbia. Water samples were collected daily from four sites during two rain events. All samples were analyzed for total metal concentrations following acid digestion and for particle number concentration and elemental composition using single particle-inductively coupled plasma-time of flight-mass spectrometry (SP-ICP-TOF-MS). The Ti/Nb ratios in the Broad and Congaree River samples are generally higher than those of natural background ratios, indicating contamination of these two rivers with anthropogenic Ti-bearing particles. Clustering of multi-metal nanoparticles (mmNPs) demonstrated that Ti-bearing particles are distributed mainly among three clusters, FeTiMn, AlSiFe, and TiMnFe, which are typical of naturally occurring iron oxide, clay, and titanium oxide particles, indicating the absence of significant number of anthropogenic multi-element Ti-bearing particles. Thus, anthropogenic Ti-bearing particles are attributed to single-metal particles; that is pure TiO 2 particles. The total concentration of anthropogenic TiO 2 in the rivers was determined by mass balance calculation using bulk titanium concentration and increases in Ti/Nb above the natural background ratio. The concentration of anthropogenic TiO 2 increases following the order 0 to 24 μg L −1 in the Lower Saluda River <0 to 663 μg L −1 in the Broad River <43 to 1051 μg L −1 in Congaree River at Cayce <58 to 5050 μg L −1 in the Congaree River at Columbia. The concentration of anthropogenic TiO 2 increases with increases in urban runoff. The source of anthropogenic TiO 2 is attributed to diffuse urban runoff. This study demonstrates that diffuse urban runoff results in high concentrations of TiO 2 particles in urban surface waters during and following rainfall events which may pose increased risks to aquatic organisms during these episodic events. 

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5. Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

   https://doi.org/10.3389/frmbi.2023.1199766  

   Rodríguez-Ramos, Josué; Oliverio, Angela; Borton, Mikayla A.; Danczak, Robert; Mueller, Birgit M.; Schulz, Hanna; Ellenbogen, Jared; Flynn, Rory M.; Daly, Rebecca A.; Schopflin, LeAundra; et al (August 2023, Frontiers in Microbiomes)

   Although river ecosystems constitute a small fraction of Earth’s total area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. To address this gap, we assessed how viral and microbial communities change over a 48-hour period by sampling surface water and pore water compartments of the wastewater-impacted River Erpe in Germany. We sampled every 3 hours resulting in 32 samples for which we obtained metagenomes along with geochemical and metabolite measurements. From our metagenomes, we identified 6,500 viral and 1,033 microbial metagenome assembled genomes (MAGs) and found distinct community membership and abundance associated with each river compartment (e.g.,Competibacteraceaein surfacewater andSulfurimonadaceaein pore water). We show that 17% of our viral MAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of theCompetibacteraceae, which we suggest are potential contributors to river carbon and nitrogen cycling via denitrification and nitrogen fixation. Together, these findings demonstrate that members of the surface water microbiome from this urban river are stable over multiple diurnal cycles. These temporal insights raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles. 

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