TY - JOUR A1 - Piro, Vitor C. A1 - Renard, Bernhard Y. T1 - Contamination detection and microbiome exploration with GRIMER JF - GigaScience N2 - Background: Contamination detection is a important step that should be carefully considered in early stages when designing and performing microbiome studies to avoid biased outcomes. Detecting and removing true contaminants is challenging, especially in low-biomass samples or in studies lacking proper controls. Interactive visualizations and analysis platforms are crucial to better guide this step, to help to identify and detect noisy patterns that could potentially be contamination. Additionally, external evidence, like aggregation of several contamination detection methods and the use of common contaminants reported in the literature, could help to discover and mitigate contamination. Results: We propose GRIMER, a tool that performs automated analyses and generates a portable and interactive dashboard integrating annotation, taxonomy, and metadata. It unifies several sources of evidence to help detect contamination. GRIMER is independent of quantification methods and directly analyzes contingency tables to create an interactive and offline report. Reports can be created in seconds and are accessible for nonspecialists, providing an intuitive set of charts to explore data distribution among observations and samples and its connections with external sources. Further, we compiled and used an extensive list of possible external contaminant taxa and common contaminants with 210 genera and 627 species reported in 22 published articles. Conclusion: GRIMER enables visual data exploration and analysis, supporting contamination detection in microbiome studies. The tool and data presented are open source and available at https://gitlab.com/dacs-hpi/grimer. KW - Contamination KW - Microbiome KW - Visualization KW - Taxonomy Y1 - 2023 U6 - https://doi.org/10.1093/gigascience/giad017 SN - 2047-217X VL - 12 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Steding, Svenja A1 - Schneider, Wilfried T1 - Prognose des Schadstoffaustrags aus mehrphasigen DNAPL-Pools mittels semi-analytischem Berechnungsmodell JF - Grundwasser : Zeitschrift der Fachsektion Hydrogeologie in der Deutschen Gesellschaft für Geowissenschaften (FH-DGG) N2 - Multicomponent DNAPL pools are among the most common reasons for groundwater contamination and represent highly persistent source areas. Although several studies have already shown that their constituents influence each other's solubility, existing models neglect these interactions. For this reason, a semi-analytical model has been developed, considering the pool composition as temporally variable. Based on Raoult's law, the molar fraction, the effective solubility and finally the mass discharge due to advection, dispersion and diffusion of each component are determined. The results significantly differ from studies on single-phase pools. It is shown that mass discharges can both increase and decrease over time and that the longevity of DNAPL pools as well as the time until threshold values are fullfilled will be significantly underestimated if Raoult's law is neglected. Additionally, a sensitivity analysis reveals that poorly soluble minor components must not be neglected, whereas highly soluble ones can. N2 - Mehrphasige DNAPL-Pools zählen zu den häufigsten Ursachen für Grundwasserkontaminationen und sind bekannt für ihre Langlebigkeit. Obwohl Untersuchungen bereits gezeigt haben, dass die Phasen sich in ihrer Wasserlöslichkeit gegenseitig beeinflussen, werden diese Interaktionen von bisherigen Modellen vernachlässigt. Aus diesem Grund wurde ein semi-analytisches Berechnungsmodell entwickelt, welches die Poolzusammensetzung als zeitlich variabel behandelt. Basierend auf dem Raoult’schen Gesetz werden für jede Komponente Molanteil, effektive Wasserlöslichkeit und schließlich der Schadstoffaustrag infolge Advektion, Dispersion und Diffusion bestimmt. Die Ergebnisse unterscheiden sich deutlich von Studien an einphasigen Pools. So wird gezeigt, dass Schadstofffrachten über die Zeit sowohl zu- als auch abnehmen können und dass ohne Berücksichtigung des Raoult’schen Gesetzes sowohl die Langlebigkeit von DNAPL-Pools als auch die Dauer bis zur Unterschreitung von Grenzwerten teils deutlich unterschätzt wird. Eine Sensitivitätsanalyse zeigt zudem, dass schwer lösliche Nebenbestandteile nicht vernachlässigt werden dürfen, leicht lösliche hingegen schon. T2 - Prediction of mass discharge from multicomponent DNAPL pools using a semi-analytical model KW - Contamination KW - Source longevity KW - Raoult's law KW - Matrix diffusion KW - Minor KW - components Y1 - 2021 U6 - https://doi.org/10.1007/s00767-021-00490-2 SN - 1430-483X SN - 1432-1165 VL - 26 IS - 3 SP - 241 EP - 253 PB - Springer CY - Berlin ; Heidelberg ER - TY - JOUR A1 - Kuhn, Eugênia Carla A1 - Tavares Jacques, Maurício A1 - Teixeira, Daniela A1 - Meyer, Sören A1 - Gralha, Thiago A1 - Roehrs, Rafael A1 - Camargo, Sandro A1 - Schwerdtle, Tanja A1 - Bornhorst, Julia A1 - Ávila, Daiana Silva T1 - Ecotoxicological assessment of Uruguay River and affluents pre- and biomonitoring JF - Environmental science and pollution research : ESPR N2 - Uruguay River is the most important river in western Rio Grande do Sul, separating Brazil from Argentina and Uruguay. However, its pollution is of great concern due to agricultural activities in the region and the extensive use of pesticides. In a long term, this practice leads to environmental pollution, especially to the aquatic system. The objective of this study was to analyze the physicochemical characteristics, metals and pesticides levels in water samples obtained before and after the planting and pesticides' application season from three sites: Uruguay River and two minor affluents, Mezomo Dam and Salso Stream. For biomonitoring, the free-living nematode Caenorhabditis elegans was used, which were exposed for 24 h. We did not find any significant alteration in physicochemical parameters. In the pre- and post-pesticides' samples we observed a residual presence of three pesticides (tebuconazole, imazethapyr, and clomazone) and metals which levels were above the recommended (As, Hg, Fe, and Mn). Exposure to both pre- and post-pesticides' samples impaired C. elegans reproduction and post-pesticides samples reduced worms' survival rate and lifespan. PCA analysis indicated that the presence of metals and pesticides are important variables that impacted C. elegans biological endpoints. Our data demonstrates that Uruguay River and two affluents are contaminated independent whether before or after pesticides' application season. In addition, it reinforces the usefulness of biological indicators, since simple physicochemical analyses are not sufficient to attest water quality and ecological safety. KW - Heavy metals KW - Pesticides KW - Contamination KW - Arsenic KW - Environmental KW - pollution KW - Uruguay River Y1 - 2021 U6 - https://doi.org/10.1007/s11356-020-11986-4 SN - 0944-1344 SN - 1614-7499 VL - 28 IS - 17 SP - 21730 EP - 21741 PB - Springer CY - Berlin ; Heidelberg ER -