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Additional file 1 of Emergence and spread of SARS-CoV-2 variants of concern in Canada: a retrospective analysis from clinical and wastewater data
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Champredon, David; Becker, Devan; Peterson, Shelley W.; Mejia, Edgard; Hizon, Nikho; Schertzer, Andrea; Djebli, Mohamed; Oloye, Femi F.; Xie, Yuwei; Asadi, Mohsen; Cantin, Jenna; Pu, Xia; Osunla, Charles A.; Brinkmann, Markus; McPhedran, Kerry N.; Servos, Mark R.; Giesy, John P.; Mangat, Chand — 2024 Additional file 1. https://creativecommons.org/licenses/by/4.0/legalcode
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DNA and RNA zooplankton metabarcoding to assess the efficacy of different oil spill clean-up techniques in a boreal lake
Federated Research Data Repository / dépôt fédéré de données de recherche
Ankley, Phillip; Xie, Yuwei; Black, Tyler; DeBofsky, Abigail; Perry, McKenzie; Paterson, Michael; Hanson, Mark; Higgins, Scott; Giesy, John; Palace, Vince — 2024-03-27 Emerging tools, namely metabarcoding, has promise for high-throughput and benchmarkable biomonitoring of freshwater zooplankton communities. Additionally, regulators require further information to select best practices for remediating freshwater ecosystems after oil spills. DNA and RNA metabarcoding, or present and active zooplankton, respectively, was applied to compare with traditional morphological identification of freshwater zooplankton in experimental boreal shoreline enclosures. DNA and RNA metabarcoding was also applied in the context of assessing response of the zooplankton community exposed to simulated spills of diluted bitumen (dilbit), with experimental remediation practices of enhanced monitored natural recovery and shoreline cleaner application. Zooplankton samples were collected via pump on day -3 and 11 and 38 days after the simulated dilbit spill. The zooplankton samples were co-extracted for DNA and RNA and were PCR amplified targeting the mitochondrial Cytochrome c Oxidase subunit I gene (CO1) region, with amplicon sequencing following. This dataset includes the demultiplexed sequencing output, the feature table with genus-level taxonomic annotation, and the sample metadata used for hypothesis testing. This dataset contains data from wetland habitat enclosures. Note that a similar study was conducted for rock habitat enclosures, with different analyses and interpretation being conducted on the data (dataset available at https://doi.org/10.20383/102.0332). https://creativecommons.org/licenses/by/4.0/
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Responses of juvenile fathead minnow (Pimephales promelas) gut microbiota to a chronic dietary exposure of benzo[a]pyrene
Federated Research Data Repository / dépôt fédéré de données de recherche
DeBofsky, Abigail; Xie, Yuwei; Challis, Jonathan; Brinkmann, Markus; Hecker, Markus; Giesy, John — 2024-03-27 These data are collected from juvenile fathead minnows (Pimephales promelas) that were exposed to benzo[a]pyrene (BaP) as well as fish exposed to a solvent control for two weeks via the diet. The samples were sterilely collected from whole fathead minnow guts and stored at -80°C until DNA and RNA extraction. The guts were used for 16S rRNA sequencing to analyze the impact of BaP on gut microbial communities. Each fish was analyzed independently (samples were not pooled). The results of this study showed a significant effect of BaP exposure on gut microbial community. https://creativecommons.org/licenses/by/4.0/
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Impacts of the Husky oil spill on gut microbiota of native fish species to the North Saskatchewan River
Federated Research Data Repository / dépôt fédéré de données de recherche
DeBofsky, Abigail; Xie, Yuwei; Jardine, Timothy D.; Jones, Paul; Giesy, John — 2024-03-27 These data are collected from goldeye (Hiodon alosoides), walleye (Sander vitreus), northern pike (Esox lucius), and shorthead redhorse (Moxostoma macrolepidotum) from the North Saskatchewan River in 2017, following the Husky oil spill. The samples (gut contents) were sterilely collected from the guts of each fish and stored at -80C until DNA extraction. The guts were used for 16S rRNA sequencing to analyze differences in the microbiome among species as well as the impact of the Husky oil spill on gut microbial communities. Each fish was analyzed independently (samples were not pooled). The results of this study showed a significant effect of host species on the gut microbiome as well as marginal effects of the Husky oil spill. https://creativecommons.org/licenses/by/4.0/
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Differential sex responses of fathead minnow (Pimephales promelas) gut microbiota to a short-term environmentally-relevant aqueous exposure to benzo[a]pyrene
Federated Research Data Repository / dépôt fédéré de données de recherche
DeBofsky, Abigail; Xie, Yuwei; Grimard, Chelsea; Brinkmann, Markus; Hecker, Markus; Giesy, John — 2024-03-27 Vertebrate gut microbiota are responsible for regulating several beneficial functions, from development of an organism to maintaining energy homeostasis. However, little is known about the impact of chemical exposures on the structure and function of gut microbiota of fishes. To ascertain a link between contaminant exposure and microbial disruption, male and female fathead minnows (Pimephales promelas) were aqueously exposed to low concentrations of benzo[a]pyrene (BaP) (concentrations ranged from 0.0226 g/L to 1.3 g/L) as well as fish exposed to a solvent control for four days. The samples were sterilely collected from whole fathead minnow guts and stored at -80C until DNA extraction. Gut microbiota were assessed using 16S rRNA metagenetics. Low-level aqueous exposure to BaP resulted in community shifts in bacterial composition in female, but not male, fish. Each fish was analyzed independently (samples were not pooled).This research illustrates that in addition to the well-studied molecular endpoints, community composition of fish gut microbiota can also be impacted by chemical stressors, providing an additional pathway for the generation of adverse effects. https://creativecommons.org/licenses/by/4.0/
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RNA metabarcoding to assess zooplankton community response to environmental influence in boreal lake experimental enclosures
Federated Research Data Repository / dépôt fédéré de données de recherche
Ankley, Phillip; Xie, Yuwei; Havens, Sonya; Peters, Lisa; Timlick, Lauren; Rodriguez-Gil, Jose Luis; Giesy, John; Palace, Vince — 2024-03-27 Zooplankton metabarcoding can provide a high-throughput method for characterizing community response to environmental stressors. There are issues, however, with inferring actual response to stressors using DNA metabarcoding as it cannot distinguish alive organisms within bulk samples. Here we used normalized vitality, namely RNA metabarcoding normalized by DNA metabarcoding, to characterize the zooplankton community response to environmental influence. DNA and RNA metabarcoding was also applied in the context of assessing response of the zooplankton community exposed to simulated spills of diluted bitumen (dilbit), with experimental remediation practices of enhanced monitored natural recovery and shoreline cleaner application. Zooplankton samples were collected via pump on days -3 and 11 and 38 days after the simulated dilbit spill. The zooplankton samples were co-extracted for DNA and RNA and were PCR amplified targeting the mitochondrial Cytochrome c Oxidase subunit I gene (CO1) region, with amplicon sequencing following. The dataset includes the demultiplexed sequencing output, the feature table with species-level taxonomic annotation, and the sample metadata. This dataset contains data from enclosures in rock and cobble substrate. Note that a similar study was conducted for wetland habitat enclosures, with different analyses and interpretation being conducted on the data (dataset available at https://doi.org/10.20383/101.0313). https://creativecommons.org/licenses/by/4.0/
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Response of finescale dace (Phoxinus neogaeus) gut microbiome to in situ experimental selenium exposure
Federated Research Data Repository / dépôt fédéré de données de recherche
Ankley, Phillip; Graves, Stephanie; Xie, Yuwei; DeBofsky, Abigail; Weber, Alana; Brinkmann, Markus; Palace, Vince; Hecker, Markus; Janz, David; Giesy, John — 2024-03-27 Selenium is an environmental contaminant of global concern that can cause adverse effects in fish at elevated levels. Fish gut microbiome play essential roles in gastrointestinal function and host health and can be perturbed by environmental contaminants, including metals and metalloids. Here, an in-situ selenium (Se) exposure of female finescale dace (Phoxinus neogaeus) using mesocosms at the International Institute for Sustainable Development - Experimental Lakes Area (IISD-ELA) was conducted to determine the impacts of Se accumulation on the gut microbiome and morphometric endpoints. 16S rDNA metabarcoding was employed to describe the gut microbiome. This dataset includes the demultiplexed sequencing output, the feature table with rarefied counts, the taxonomic annotations of sequences, and the sample metadata. https://creativecommons.org/licenses/by/4.0/
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Wastewater discharges alter microbial community composition in surface waters of the Canadian prairies
Federated Research Data Repository / dépôt fédéré de données de recherche
Esser, Milena; Hoggarth, Cameron; Baulch, Helen M.; Challis, Jonathan K.; Xie, Yuwei; Giesy, John; Hecker, Markus; Brinkmann, Markus — 2024-03-27 Freshwater ecosystems occupy only a small portion of the Earth's surface, but harbor a disproportionate amount of biodiversity that is particularly threatened by wastewater discharges, as one of the most common anthropogenic impact on these systems. As wastewater effluents are also sources of antimicrobial agents and other microorganisms, they reflect a particular threat to natural microbial communities within receiving rivers. Our knowledge about the impact of wastewater effluents on these communities is, however, largely unexplored. In this study, composition of microbial communities upstream and downstream of 5 different wastewater treatment plants within Southern Saskatchewan, Canada were examined. Three matrices, the water column, sediments, and biofilms attached to hard surfaces, were analyzed. The samples were extracted for DNA and were PCR amplified targeting the hypervariable V3-V4 region of the 16S ribosomal RNA subunit I gene of prokaryotes, as well as the hypervariable V3 region of the 18S ribosomal RNA gene of eukaryotic organisms. Amplicons were sequenced performing a 600-cycle paired-end sequencing run on an Illumina® MiSeq sequencer. This dataset includes the demultiplexed sequencing output, the feature table with taxonomic annotation, and the sample metadata. https://creativecommons.org/licenses/by/4.0/
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The impact of fluoxetine on the gut microbiome of Pimephales promelas
Federated Research Data Repository / dépôt fédéré de données de recherche
Weber, Alana; Xie, Yuwei; Challis, Jonathan; DeBofsky, Abigail; Ankley, Phillip; Hecker, Markus; Jones, Paul; Giesy, John — 2024-03-27 This data is supplementary information regarding the effects of fluoxetine on the gut microbiome of Fathead Minnows when aqueously exposed to the compound. After a 28-day exposure to three different concentrations of fluoxetine; 0.01, 10 and 100 µg/L, or control (0 µg/L), fish were euthanized, and gut contents was collected. Using DNA extraction methods, PCR amplification and sequencing, bioinformatics was then performed to interpret the metagenomic data. All tests and data were collected between September 2019 and January 2021 at the University of Saskatchewan, Saskatoon, SK, Canada. This data was generated to better understand how pharmaceuticals found downstream of wastewater treatment plants may impact the gut microbiome of aquatic organisms. https://creativecommons.org/licenses/by/4.0/
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Characterization of high mountain glacier microbiota following inundation with wildfire soot
Federated Research Data Repository / dépôt fédéré de données de recherche
Esser, Milena; Ankley, Phillip; Aubry-Wake, Caroline; Xie, Yuwei; Baulch, Helen; Hoggarth, Cameron; Hecker, Markus; Hollert, Henner; Giesy, John; Pomeroy, John W; Brinkmann, Markus — 2024-03-27 Glacier ecosystems are shrinking at an accelerating rate due to changes in climate, but also due to increased deposition of soot, which has resulted in darkening of glacier surfaces and subsequent changes in absorption of light, associated heat, and altered microbial communities. In this study, compositions of microbial communities on surfaces of the Athabasca Glacier (Alberta, Canada) were measured by use of DNA metabarcoding. Three matrices, glacier ice, cryoconite hole, and glacial surface sediment, were analyzed. The samples were extracted for DNA and were PCR amplified targeting the hypervariable V3-V4 region of the 16S ribosomal RNA subunit I gene of prokaryotes, as well as the hypervariable V3 region of the 18S ribosomal RNA gene of eukaryotic organisms. Amplicons were sequenced performing a 600-cycle paired-end sequencing run on an Illumina® MiSeq sequencer. This dataset includes the demultiplexed sequencing output, the feature table with taxonomic annotation, and the sample metadata. https://creativecommons.org/licenses/by/4.0/

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