http://hdl.handle.net/10993/142 Search this channel search https://orbilu.uni.lu/simple-search http://hdl.handle.net/10993/55302 Title: Motile bacteria leverage bioconvection for eco-physiological benefits in a natural aquatic environment <br/> <br/>Author, co-author: Di Nezio, Francesco; Roman, Samuele; Buetti-Dinh, Antoine; Sepulveda Steiner, Oscar; Bouffard, Damien; Sengupta, Anupam; Storelli, Nicola <br/> <br/>Abstract: Bioconvection, the active self-sustaining transport phenomenon triggered by the accumulation of motile microbes under competing physico-chemical cues, has been long studied, with recent reports suggesting its role in driving ecologically-relevant fluid flows. Yet, how this collective behaviour impacts the ecophysiology of swimming microbes remains unexplored. Here, through physicochemical profiles and physiological characterizations analysis of the permanently stratified meromictic Lake Cadagno, we characterize the community structure of a dense layer of anaerobic phototrophic sulfur bacteria, and report that the associated physico-chemical conditions engender bioconvection when bulk of the motile purple sulfur bacterium Chromatium okenii synchronize their movement against the gravity direction. The combination of flow cytometry and fluorescent in situ hybridization (FISH) techniques uncover the eco-physiological effects resulting from bioconvection, and simultaneous measurements using dialysis bags and 14C radioisotope, allowed us to quantify in situ the diurnal and nocturnal CO2 fixation activity of the three co-existing species in the bacterial layer. The results provide a direct measure of the cellular fitness, with comparative transcriptomics data - of C. okenii populations present in regions of bioconvection vis-a-vis populations in bioconvection-free regions - indicating the transcripts potentially involved in the bioconvection process. This work provides direct evidence of the impact of bioconvection on C. okenii metabolism, and highlights the functional role of bioconvection in enhancing the metabolic advantage of C. okenii relative to other microbial species inhabiting the microbial layer. Wed, 07 Jun 2023 19:33:21 GMT http://hdl.handle.net/10993/55285 Title: Controlled motility in the cyanobacterium Trichodesmium regulates aggregate architecture <br/> <br/>Author, co-author: Pfreundt, Ulrike; Słomka, Jonasz; Schneider, Giulia; Sengupta, Anupam; Carrara, Francesco; Fernandez, Vicente; Ackermann, Martin; Stocker, Roman <br/> <br/>Abstract: The ocean’s nitrogen is largely fixed by cyanobacteria, including Trichodesmium, which forms aggregates comprising hundreds of filaments arranged in organized architectures. Aggregates often form upon exposure to stress and have ecological and biophysical characteristics that differ from those of single filaments. Here, we report that Trichodesmium aggregates can rapidly modulate their shape, responding within minutes to changes in environmental conditions. Combining video microscopy and mathematical modeling, we discovered that this reorganization is mediated by “smart reversals” wherein gliding filaments reverse when their overlap with other filaments diminishes. By regulating smart reversals, filaments control aggregate architecture without central coordination. We propose that the modulation of gliding motility at the single-filament level is a determinant of Trichodesmium’s aggregation behavior and ultimately of its biogeochemical role in the ocean. Mon, 05 Jun 2023 22:23:51 GMT http://hdl.handle.net/10993/55281 Title: Hybrid LCA–ABM of dairy farming systems including nonlinear optimization under environmental, technical and economic constraints <br/> <br/>Author, co-author: Bayram, Alper Mon, 05 Jun 2023 11:53:41 GMT http://hdl.handle.net/10993/54844 Title: Altered infective competence of the human gut microbiome in COVID-19 <br/> <br/>Author, co-author: de Nies, Laura; Galata, Valentina; Martin-Gallausiaux, Camille; Despotovic, Milena; Busi, Susheel Bhanu; Snoeck, Chantal J.; Delacour, Lea; Budagavi, Deepthi Poornima; Laczny, Cedric Christian; Habier, Janine; Lupu, Paula-Cristina; Halder, Rashi; Fritz, Joëlle V.; Marques, Tainá; Sandt, Estelle; O'Sullivan, Marc Paul; Ghosh, Soumyabrata; Satagopam, Venkata; Consortium, CON-Vince; Krüger, Rejko; Fagherazzi, Guy; Ollert, Markus; He, Feng; May, Patrick; Wilmes, Paul <br/> <br/>Abstract: BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls. CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract. Wed, 12 Apr 2023 03:30:21 GMT http://hdl.handle.net/10993/54557 Title: Soil viral particles as tracers of surface water sources and flow paths <br/> <br/>Author, co-author: Florent, Perrine Julie <br/> <br/>Abstract: Albeit recent technological developments (e.g. field deployable instruments operating at high temporal frequencies), experimental hydrology is a discipline that remains measurement limited. From this perspective, trans-disciplinary approaches may create valuable opportunities to enlarge the number of tools available for investigating hydrological processes. Tracing experiments are usually performed in order to investigate the water flow pathways and water sources in underground areas. Since the 19th century, researchers have worked with hydrological tracers to do this. Among them, the fluorescent dyes and the isotopes are the most commonly used to follow the water flow while others like salts or bacteriophages are employed as additional tracers to those mentioned above. Bacteriophages are the least known of all, but it has been studied since the 1960s as hydrological tracers, especially in karstic environments. The purpose is to evaluate the potential for bacteriophages naturally occurring in soils to serve as a new environmental tracer of hydrological processes. We hypothesize that such viral particles can be a promising tool in water tracing experiments since they are safe for ecosystems. In both fields of hydrology and virology, the knowledge regarding the fate of bacteriophages within the pedosphere is still limited. Their study would not only allow proposing potential new candidates to enlarge the hydrological tracers available, but also improving the current knowledge about the bacteriophage communities in soil and their interactions with certain environmental factors. For this purpose, we aim at describing the bacteriophage communities occurring in the soil through shotgun metagenomics analysis. Those viruses are widely spread in the pedosphere, and we assume that they have specific signatures according to the type of soil. Then, bacteriophage populations will be investigated in the soil water to analyse the dis/similarities between the two communities as well as their dynamics in the function of the precipitation events. This way, with a relatively high abundance of soil and soil water and a capacity of being mobilised, good bacteriophage candidates could be selected as hydrological tracers. Thu, 09 Mar 2023 18:12:36 GMT http://hdl.handle.net/10993/54255 Title: The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry <br/> <br/>Author, co-author: Mohammed Taha, Hiba; Aalizadeh, Reza; Alygizakis, Nikiforos; Antignac, Jean-Philippe; Arp, Hans Peter H.; Bade, Richard; Baker, Nancy; Belova, Lidia; Bijlsma, Lubertus; Bolton, Evan E.; Brack, Werner; Celma, Alberto; Chen, Wen-Ling; Cheng, Tiejun; Chirsir, Parviel; Čirka, Ľuboš; D’Agostino, Lisa A.; Djoumbou Feunang, Yannick; Dulio, Valeria; Fischer, Stellan; Gago-Ferrero, Pablo; Galani, Aikaterini; Geueke, Birgit; Głowacka, Natalia; Glüge, Juliane; Groh, Ksenia; Grosse, Sylvia; Haglund, Peter; Hakkinen, Pertti J.; Hale, Sarah E.; Hernandez, Felix; Janssen, Elisabeth M.-L.; Jonkers, Tim; Kiefer, Karin; Kirchner, Michal; Koschorreck, Jan; Krauss, Martin; Krier, Jessy; Lamoree, Marja H.; Letzel, Marion; Letzel, Thomas; Li, Qingliang; Little, James; Liu, Yanna; Lunderberg, David M.; Martin, Jonathan W.; McEachran, Andrew D.; McLean, John A.; Meier, Christiane; Meijer, Jeroen; Menger, Frank; Merino, Carla; Muncke, Jane; Muschket, Matthias; Neumann, Michael; Neveu, Vanessa; Ng, Kelsey; Oberacher, Herbert; O’Brien, Jake; Oswald, Peter; Oswaldova, Martina; Picache, Jaqueline A.; Postigo, Cristina; Ramirez, Noelia; Reemtsma, Thorsten; Renaud, Justin; Rostkowski, Pawel; Rüdel, Heinz; Salek, Reza M.; Samanipour, Saer; Scheringer, Martin; Schliebner, Ivo; Schulz, Wolfgang; Schulze, Tobias; Sengl, Manfred; Shoemaker, Benjamin A.; Sims, Kerry; Singer, Heinz; Singh, Randolph R.; Sumarah, Mark; Thiessen, Paul A.; Thomas, Kevin V.; Torres, Sonia; Trier, Xenia; van Wezel, Annemarie P.; Vermeulen, Roel C. H.; Vlaanderen, Jelle J.; von der Ohe, Peter C.; Wang, Zhanyun; Williams, Antony J.; Willighagen, Egon L.; Wishart, David S.; Zhang, Jian; Thomaidis, Nikolaos S.; Hollender, Juliane; Slobodnik, Jaroslav; Schymanski, Emma <br/> <br/>Abstract: Abstract Background The NORMAN Association ( https://www.norman-network.com/ ) initiated the NORMAN Suspect List Exchange (NORMAN-SLE https://www.norman-network.com/nds/SLE/ ) in 2015, following the NORMAN collaborative trial on non-target screening of environmental water samples by mass spectrometry. Since then, this exchange of information on chemicals that are expected to occur in the environment, along with the accompanying expert knowledge and references, has become a valuable knowledge base for “suspect screening” lists. The NORMAN-SLE now serves as a FAIR (Findable, Accessible, Interoperable, Reusable) chemical information resource worldwide. Results The NORMAN-SLE contains 99 separate suspect list collections (as of May 2022) from over 70 contributors around the world, totalling over 100,000 unique substances. The substance classes include per- and polyfluoroalkyl substances (PFAS), pharmaceuticals, pesticides, natural toxins, high production volume substances covered under the European REACH regulation (EC: 1272/2008), priority contaminants of emerging concern (CECs) and regulatory lists from NORMAN partners. Several lists focus on transformation products (TPs) and complex features detected in the environment with various levels of provenance and structural information. Each list is available for separate download. The merged, curated collection is also available as the NORMAN Substance Database (NORMAN SusDat). Both the NORMAN-SLE and NORMAN SusDat are integrated within the NORMAN Database System (NDS). The individual NORMAN-SLE lists receive digital object identifiers (DOIs) and traceable versioning via a Zenodo community ( https://zenodo.org/communities/norman-sle ), with a total of \textgreater 40,000 unique views, \textgreater 50,000 unique downloads and 40 citations (May 2022). NORMAN-SLE content is progressively integrated into large open chemical databases such as PubChem ( https://pubchem.ncbi.nlm.nih.gov/ ) and the US EPA’s CompTox Chemicals Dashboard ( https://comptox.epa.gov/dashboard/ ), enabling further access to these lists, along with the additional functionality and calculated properties these resources offer. PubChem has also integrated significant annotation content from the NORMAN-SLE, including a classification browser ( 101 ). Conclusions The NORMAN-SLE offers a specialized service for hosting suspect screening lists of relevance for the environmental community in an open, FAIR manner that allows integration with other major chemical resources. These efforts foster the exchange of information between scientists and regulators, supporting the paradigm shift to the “one substance, one assessment” approach. New submissions are welcome via the contacts provided on the NORMAN-SLE website ( https://www.norman-network.com/nds/SLE/ ). Mon, 30 Jan 2023 06:53:27 GMT http://hdl.handle.net/10993/54240 Title: Towards a harmonized identification scoring system in LC-HRMS/MS based non-target screening (NTS) of emerging contaminants <br/> <br/>Author, co-author: Alygizakis, Nikiforos; Lestremau, Francois; Gago-Ferrero, Pablo; Gil-Solsona, Rubén; Arturi, Katarzyna; Hollender, Juliane; Schymanski, Emma; Dulio, Valeria; Slobodnik, Jaroslav; Thomaidis, Nikolaos S. <br/> <br/>Abstract: Non-target screening (NTS) methods are rapidly gaining in popularity, empowering researchers to search for an ever-increasing number of chemicals. Given this possibility, communicating the confidence of identification in an automated, concise and unambiguous manner is becoming increasingly important. In this study, we compiled several pieces of evidence necessary for communicating NTS identification confidence and developed a machine learning approach for classification of the identifications as reliable and unreliable. The machine learning approach was trained using data generated by four laboratories equipped with different instrumentation. The model discarded substances with insufficient identification evidence efficiently, while revealing the relevance of different parameters for identification. Based on these results, a harmonized IP-based system is proposed. This new NTS-oriented system is compatible with the currently widely used five level system. It increases the precision in reporting and the reproducibility of current approaches via the inclusion of evidence scores, while being suitable for automation. Fri, 27 Jan 2023 21:31:46 GMT http://hdl.handle.net/10993/54239 Title: Global Challenges: Opening up Chemistry, Pandemics, and Air Pollution <br/> <br/>Author, co-author: Schymanski, Emma <br/> <br/>Abstract: As the first half of 2022 comes to a close, it is an interesting time to reflect on some recent trends. In many ways, the world is “opening” up again, with many colleagues going to their first “in person” conferences since the start of the pandemic in early 2020. A significant leap forward for open chemistry was made in 2021, with the Chemical Abstracts Service (CAS) Registry embracing a hybrid model and releasing half a million chemicals as the CAS Common Chemistry set under an open license. (1)ACS Environmental Au continues to develop as one of the key gold open access journals for publishing work on environmental topics. (2) The European Union has just launched the €400 million European Partnership for the Assessment of Risks from Chemicals (PARC), with ∼200 partners (3) and a whole work package on FAIR (Findable, Accessible, Interoperable, Reusable) (4,5) and Open (6) data. While these trends are cause for optimism, the CAS Registry continues to climb toward the 200 million chemical mark (7) and many of us were blown away by the sheer immensity of the chemical pollution problem at recent meetings. Other colleagues, e.g., those affected by war, by lockdowns, or with insufficient funds, are unable to share in the “post-pandemic” reopening, conferences, and travel. Others cannot afford the costs associated with open access or still do not see the benefits of open science. Why the focus on these disjoint subjects? Both chemical pollution and the COVID-19 pandemic are global challenges requiring global solutions, where failure to act comes with a high price. Landrigan et al. estimated that 9 million premature deaths (16% of the global total) were caused by pollution in 2015. (8) Worldwide deaths directly due to the COVID-19 pandemic are already over 6 million (9) (January 2020 to May 2022). While public awareness is high, individuals often feel powerless to tackle global challenges─yet the pandemic has proven that individual actions can make an incredible collective difference. The same applies to open data and the exchange of research results─the collective benefit from many individual contributions can be extraordinary. Fri, 27 Jan 2023 20:12:34 GMT http://hdl.handle.net/10993/54238 Title: Enhancing spectral quality in complex environmental matrices: Supporting suspect and non-target screening in zebra mussels with ion mobility <br/> <br/>Author, co-author: Menger, Frank; Celma, Alberto; Schymanski, Emma; Lai, Foon Yin; Bijlsma, Lubertus; Wiberg, Karin; Hernández, Félix; Sancho, Juan V.; Ahrens, Lutz <br/> <br/>Abstract: Identification of bioaccumulating contaminants of emerging concern (CECs) via suspect and non-target screening remains a challenging task. In this study, ion mobility separation with high-resolution mass spectrometry (IM-HRMS) was used to investigate the effects of drift time (DT) alignment on spectrum quality and peak annotation for screening of CECs in complex sample matrices using data independent acquisition (DIA). Data treatment approaches (Binary Sample Comparison) and prioritisation strategies (Halogen Match, co-occurrence of features in biota and the water phase) were explored in a case study on zebra mussel (Dreissena polymorpha) in Lake Mälaren, Sweden’s largest drinking water reservoir. DT alignment evidently improved the fragment spectrum quality by increasing the similarity score to reference spectra from on average (±standard deviation) 0.33 ± 0.31 to 0.64 ± 0.30 points, thus positively influencing structure elucidation efforts. Thirty-two features were tentatively identified at confidence level 3 or higher using MetFrag coupled with the new PubChemLite database, which included predicted collision cross-section values from CCSbase. The implementation of predicted mobility data was found to support compound annotation. This study illustrates a quantitative assessment of the benefits of IM-HRMS on spectral quality, which will enhance the performance of future screening studies of CECs in complex environmental matrices. Fri, 27 Jan 2023 20:08:56 GMT http://hdl.handle.net/10993/53815 Title: Prenatal and childhood exposure to per-/polyfluoroalkyl substances (PFASs) and its associations with childhood overweight and/or obesity: a systematic review with meta- analyses <br/> <br/>Author, co-author: Frigerio, Gianfranco; Ferrari, Chiara Matilde; Fustinoni, Silvia <br/> <br/>Abstract: Background Per-/polyfluoroalkyl substances (PFASs) are persistent organic pollutants and suspected endocrine disruptors. Objective The aim of this work was to conduct a systematic review with meta-analysis to summarise the associations between prenatal or childhood exposure to PFASs and childhood overweight/obesity. Methods The search was performed on the bibliographic databases PubMed and Embase with text strings containing terms related to prenatal, breastfeeding, childhood, overweight, obesity, and PFASs. Only papers describing a biomonitoring study in pregnant women or in children up to 18 years that assessed body mass index (BMI), waist circumference (WC), or fat mass in children were included. When the estimates of the association between a PFAS and an outcome were reported from at least 3 studies, a meta-analysis was conducted; moreover, to correctly compare the studies, we developed a method to convert the different effect estimates and made them comparable each other. Meta-analyses were performed also stratifying by sex and age, and sensitivity analyses were also performed. Results In total, 484 and 779 articles were retrieved from PubMed and Embase, respectively, resulting in a total of 826 articles after merging duplicates. The papers included in this systematic review were 49: 26 evaluating prenatal exposure to PFASs, 17 childhood exposure, and 6 both. Considering a qualitative evaluation, results were conflicting, with positive, negative, and null associations. 30 papers were included in meta-analyses (19 prenatal, 7 children, and 4 both). Positive associations were evidenced between prenatal PFNA and BMI, between PFOA and BMI in children who were more than 3 years, and between prenatal PFNA and WC. Negative associations were found between prenatal PFOS and BMI in children who were 3 or less years, and between PFHxS and risk of overweight. Relatively more consistent negative associations were evidenced between childhood exposure to three PFASs (PFOA, PFOS, and PFNA) and BMI, in particular PFOS in boys. However, heterogeneity among studies was high. Conclusion Even though heterogeneous across studies, the pooled evidence suggests possible associations, mostly positive, between prenatal exposure to some PFASs and childhood BMI/WC; and relatively stronger evidence for negative associations between childhood exposure to PFASs and childhood BMI. Objective. The aim of this work was to conduct a systematic review with meta-analysis to summarise the associations between prenatal or childhood exposure to PFASs and childhood overweight/obesity. Methods. The search was performed on the bibliographic databases PubMed and Embase with text strings containing terms related to prenatal, childhood, overweight, obesity, and PFASs. Only papers describing a biomonitoring study in pregnant women or in children up to 18 years that assessed body mass index (BMI), waist circumference (WC), or fat mass in children were included. When the estimates of the association between a PFAS and an outcome were reported from at least 3 studies, a meta-analysis was conducted; moreover, to correctly compare the studies, we developed a method to convert the different effect estimates and made them comparable each other. Results. In total, 354 and 565 articles were retrieved from PubMed and Embase, respectively, resulting in a total of 613 articles after merging duplicates. The papers included in this systematic review were 31: 18 evaluating prenatal exposure to PFASs, 11 childhood exposure, and 2 both. Overall, results were conflicting, with positive, negative, and null associations. 17 papers were included in meta-analyses (12 prenatal, 3 children, and 2 both). The method implemented for data conversion allowed a suitable comparison of different effect estimates. Meta-analyses evaluating the associations between prenatal exposure to PFOA, PFOS, PFNA, PFHxS, and the outcomes BMI, WC, and Dual-Energy X-ray Absorptiometry (DXA) showed no significant results. Meta-analyses for the associations between childhood exposure to PFASs and the outcomes BMI showed no significant results except for a negative association between PFNA and BMI (pooled estimate from a random effect model: -0.045; 95%CI: -0.087, -0.002), however, more studies are required to confirm the strength of this association. Conclusion. To increase the reliability of meta-analyses in environmental epidemiology we suggest the conversion of effect estimates to compare different studies. The pooled evidence of the meta-analyses of the present study suggests that there is no overall association between exposure to PFASs and childhood overweight/obesity. Fri, 13 Jan 2023 16:34:31 GMT http://hdl.handle.net/10993/52976 Title: Active reconfiguration of cytoplasmic lipid droplets governs migration of nutrient-limited phytoplankton <br/> <br/>Author, co-author: Sengupta, Anupam; Dhar, Jayabrata; Danza, Francesco; Ghoshal, Arkajyoti; Müller, Elisabeth; Kakavand, Narges <br/> <br/>Abstract: Nutrient availability, along with light and temperature, drives marine primary production. The ability to migrate vertically, a critical trait of motile phytoplankton, allows species to optimize nutrient uptake, storage, and growth. However, this traditional view discounts the possibility that migration in nutrient-limited waters may be actively modulated by the emergence of energy-storing organelles. Here, we report that bloom-forming raphidophytes harness energy-storing cytoplasmic lipid droplets (LDs) to biomechanically regulate vertical migration in nutrient-limited settings. LDs grow and translocate directionally within the cytoplasm, steering strain-specific shifts in the speed, trajectory, and stability of swimming cells. Nutrient reincorporation restores their swimming traits, mediated by an active reconfiguration of LD size and coordinates. A mathematical model of cell mechanics establishes the mechanistic coupling between intracellular changes and emergent migratory behavior. Amenable to the associated photophysiology, LD-governed behavioral shift highlights an exquisite microbial strategy toward niche expansion and resource optimization in nutrient-limited oceans. Wed, 07 Dec 2022 04:30:23 GMT http://hdl.handle.net/10993/52862 Title: Forecasting of a complex microbial community using meta-omics <br/> <br/>Author, co-author: Delogu, Francesco; Kunath, Benoît; Queirós, P. M.; Halder, Rashi; Lebrun, Laura; Pope, P. B.; May, Patrick; Widder, S.; Muller, E. E. L.; Wilmes, Paul <br/> <br/>Abstract: Microbial communities are complex assemblages whose dynamics are shaped by abiotic and biotic factors. A major challenge concerns correctly forecasting the community behaviour in the future. In this context, communities in biological wastewater treatment plants (BWWTPs) represent excellent model systems, because forecasting them is required to ultimately control and operate the plants in a sustainable manner. Here, we forecast the microbial community from the water-air interface of the anaerobic tank of a BWWTP via longitudinal meta-omics (metagenomics, metatranscriptomics and metaproteomics) data covering 14 months at weekly intervals. We extracted all the available time-dependent information, summarised it in 17 temporal signals (explaining 91.1 of the temporal variance) and linked them over time to rebuild the sequence of ecological phenomena behind the community dynamics. We forecasted the signals over the following five years and tested the predictions with 21 extra samples. We were able to correctly forecast five signals accounting for 22.5 of the time-dependent information in the system and generate mechanistic predictions on the ecological events in the community (e.g. a predation cycle involving bacteria, viruses and amoebas). Through the forecasting of the 17 signals and the environmental variables readings we reconstructed the gene abundance and expression for the following 5 years, showing a nearly perfect trend prediction (coefficient of determination >= 0.97) for the first 2 years. The study demonstrates the maturity of microbial ecology to forecast composition and gene expression of open microbial ecosystems using year-spanning interactions between community cycles and environmental parameters. Thu, 24 Nov 2022 04:30:22 GMT http://hdl.handle.net/10993/52773 Title: Mechanisms of Micropollutant Elimination in Vertical Flow Constructed Wetlands <br/> <br/>Author, co-author: Brunhoferova, Hana <br/> <br/>Abstract: One of the biggest global challenges is the enormous growth of the population. With the growing population rises consequentially production and release of anthropogenic compounds, which then, due to insufficient wastewater treatment system, become pollutants, more precisely micropollutants (MPs). Advanced wastewater technologies presented in this dissertation are solutions applied for targeted elimination of MPs. Ozonation and adsorption on Activated Carbon or their combination belong to the most used advanced wastewater treatment technologies in Europe, however, they are suited for effluents of larger wastewater treatment plants. Therefore, an attempt has been made to test Constructed Wetlands (CWs) as an advanced wastewater treatment technology for small-to-medium sized WWTPs, which are typical for rural areas at the catchment of the river Sûre, the geographical border between Luxembourg and Germany. The efficiency of the CWs for the removal of 27 selected compounds has been tested at different scales (laboratory to pilot) in the Interreg Greater Region project EmiSûre 2017-2021 (Développement de stratégies visant à réduire l'introduction de micropolluants dans les cours d'eau de la zone transfrontalière germanoluxembourgeoise). The results of the project confirmed high ability of CWs to remove MPs from municipal effluents. The quantification of the main mechanisms contributing to the elimination of MPs within the CWs was thus established as the main target of the present PhD research, given the evidence of their high ability in the EmiSûre project. The main mechanisms have been identified as adsorption on the soil of the wetland, phytoremediation by the wetland macrophytes and bioremediation by the wetland microorganisms. The nature of the doctoral thesis is cumulative, the core of the thesis are the following four publications: • Publication [I] describes the usage of CWs as a post-treatment step for municipal effluents. • Publication [II] assesses the role of adsorption of the targeted MPs on the used substrates within the studied CWs and presents characterization of the wetland substrates. • Publication [III] describes the role of the wetland macrophytes in the phytoremediation of the targeted MPs within the studied CWs. Furthermore, it reveals a comparison of the different macrophyte types in varying vegetation stadia. • Publication [IV] outlines the role of the wetland microbes in the bioremediation of the targeted MPs within the studied CWs. Moreover, the wetland microbes known to be able to digest MPs or contribute to the elimination of MPs are identified and quantified. Results suggest adsorption as leading removal mechanism (achieved average removal 18 out of 27 compounds >80%), followed by bioremediation (achieved average removal 18 out of 27 compounds >40%) and phytoremediation (achieved average removal 17 out of 27 compounds <20%). The research described contributes to the extension of knowledge about CWs applied for the elimination of MPs from water. Some of the outcomes (deepened knowledge about soil influencing adsorption, recommendations for adjustment of operational parameters, etc.) could be used as a tool for enhancement of the wetland’s treatment efficiency. The research is concluded by recommendations for further investigations of the individual mechanisms (e.g. application of artificial aeration or circulation of the reaction matrix could result in enhancement of bioremediation). Tue, 15 Nov 2022 15:07:05 GMT http://hdl.handle.net/10993/52764 Title: Mobilome-driven segregation of the resistome in biological wastewater treatment <br/> <br/>Author, co-author: de Nies, Laura; Busi, Susheel Bhanu; Kunath, Benoît; May, Patrick; Wilmes, Paul <br/> <br/>Abstract: Biological wastewater treatment plants (BWWTP) are considered to be hotspots of evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of fifteen AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS and sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both MGEs. Combined and timepoint-specific analyses of gene, transcript and protein abundances further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, for which MGEs also contributed differentially to the dissemination of ARGs. Collectively our findings pave the way towards understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health. Tue, 15 Nov 2022 04:30:18 GMT http://hdl.handle.net/10993/52111 Title: Docteur <br/> <br/>Author, co-author: Iglesias González, Alba <br/> <br/>Abstract: The last century has been characterized by the increasing presence of synthetic chemicals in human surroundings, with as consequence, the increasing exposure of individuals to a wide variety of chemical substances on a regular basis. The Lancet Commission on Pollution and Health estimated that since synthetic chemicals started to be available for common use at the end of the 1940s, more than 140,000 new chemicals have been produced, including five thousand used globally in massive volume. In parallel, awareness of the adverse effects of pollutant mixtures, possibly more severe than single-chemical exposures, has drawn attention towards the need of multi-residue analytical methods to obtain the most comprehensive information on human chemical exposome. Human biomonitoring, consisting in the measurement of pollutants in biological matrices, provides information that integrates all the possible sources of exposure, and is specific to the subject the sample is collected from. For this purpose, hair appears as a particularly promising matrix to assess chemical exposure thanks to its multiple benefits. Hair enables to detect both parent chemicals and metabolites, it is suitable to investigate exposure to chemicals from different families, and allows the detection of persistent and non-persistent chemicals. Moreover, contrary to fluids such as urine and blood, which only give information on the short-term exposure and present great variability in chemical concentration, hair is representative of wider time windows that can easily cover several months. Children represent the most vulnerable part of the population, and exposure to pollutants at young ages has been associated with severe health effects during childhood, but also during the adult life. Nevertheless, most epidemiological studies investigating exposure to pollutants are still conducted on adults, and data on children remain much more limited. The present study named “Biomonitoring of children exposure to pollutants based on hair analysis” investigated the relevance of hair analysis for assessing children exposure to pollutants. In this study, 823 hair samples were collected from children and adolescents living in 9 different countries (Luxembourg, France, Spain, Uganda, Indonesia, Ecuador, Suriname, Paraguay and Uruguay), and 117 hair samples were also collected from French adults. All samples were analysed for the detection of 153 organic compounds (140 were pesticides, 4 PCBs, 7 BDEs and 2 bisphenols). Moreover, the hair samples of French adults and children were also analysed for the detection of polycyclic aromatic hydrocarbons (PAH) and their metabolites (n = 62), nicotine, cotinine and metals (n = 36). The results obtained here clearly demonstrated that children living in different geographical areas are simultaneously exposed to multiple chemicals from different chemical classes. Furthermore, the presence of persistent organic pollutants in all children, and not only in adults, suggests that exposure to these chemicals is still ongoing, although these chemicals were banned decades ago. In the sub-group of Luxembourgish children, information collected within questionnaires in parallel to hair sample collection allowed to identify some possible determinant of exposure, such as diet (organic vs conventional), residence area (urban vs countryside), and presence of pets at home. Moreover, results showed higher levels of concentration in younger children, and higher exposure of boys to non-persistent pesticides than girls, which could possibly be attributed to differences in metabolism, behaviour and gender-specific activities. Finally, the study also highlighted high level of similarity in the chemical exposome between children from the same family compared to the rest of the population. The present study strongly supports the use of hair analysis for assessing exposure to chemical pollutants, and demonstrates the relevance of multi-residue methods to investigate exposome. Sat, 17 Sep 2022 16:11:02 GMT http://hdl.handle.net/10993/52047 Title: Did lemurs have sweepstake tickets? An exploration of Simpson's model for the colonization of Madagascar by mammals <br/> <br/>Author, co-author: Stankiewicz, Jacek; Thiart, C.; Masters, J. C.; De Wit, M. J. Thu, 08 Sep 2022 15:05:45 GMT http://hdl.handle.net/10993/51987 Title: An archaeal compound as a driver of Parkinson’s disease pathogenesis <br/> <br/>Author, co-author: Trezzi, Jean-Pierre; Aho, Velma; Jäger, Christian; Schade, Sebastian; Janzen, Annette; Hickl, Oskar; Kunath, Benoit; Thomas, Melanie; Schmit, Kristopher; Garcia, Pierre; Sciortino, Alessia; Martin-Gallausiaux, Camille; Halder, Rashi; Huarte, Oihane Uriarte; Heurtaux, Tony; Heins-Marroquin, Ursula; Gomez-Giro, Gemma; Weidenbach, Katrin; Delacour, Lea; Laczny, Cedric Christian; Novikova, Polina; Ramiro-Garcia, Javier; Singh, Randolph; Andújar, Begoña Talavera; Lebrun, Laura; Daujeumont, Annegrait; Habier, Janine; Dong, Xiangyi; Gavotto, Floriane; Heintz-Buschart, Anna; Schneider, Jochen; Jehmlich, Nico; Bergen, Martin Von; Schymanski, Emma; Schmitz, Ruth; Schwamborn, Jens Christian; Glaab, Enrico; Linster, Carole; Kitami, Toshimori; Buttini, Manuel; May, Patrick; Trenkwalder, Claudia; Oertel, Wolfgang; Mollenhauer, Brit; Wilmes, Paul <br/> <br/>Abstract: Patients with Parkinson’s disease (PD) exhibit differences in their gut microbiomes compared to healthy individuals. Although differences have most commonly been described in the abundances of bacterial taxa, changes to viral and archaeal populations have also been observed. Mechanistic links between gut microbes and PD pathogenesis remain elusive but could involve molecules that promote α-synuclein aggregation. Here, we show that 2-hydroxypyridine (2-HP) represents a key molecule for the pathogenesis of PD. We observe significantly elevated 2-HP levels in faecal samples from patients with PD or its prodrome, idiopathic REM sleep behaviour disorder (iRBD), compared to healthy controls. 2-HP is correlated with the archaeal species Methanobrevibacter smithii and with genes involved in methane metabolism, and it is detectable in isolate cultures of M. smithii. We demonstrate that 2-HP is selectively toxic to transgenic α-synuclein overexpressing yeast and increases α-synuclein aggregation in a yeast model as well as in human induced pluripotent stem cell derived enteric neurons. It also exacerbates PD-related motor symptoms, α-synuclein aggregation, and striatal degeneration when injected intrastriatally in transgenic mice overexpressing human α-synuclein. Our results highlight the effect of an archaeal molecule in relation to the gut-brain axis, which is critical for the diagnosis, prognosis, and treatment of PD. Thu, 01 Sep 2022 03:30:35 GMT http://hdl.handle.net/10993/51816 Title: Roles of bacteriophages, plasmids and CRISPR immunity in microbial community dynamics revealed using time-series integrated meta-omics <br/> <br/>Author, co-author: Martinez Arbas, Susana; Narayanasamy, Shaman; Herold, Malte; Lebrun, Laura; Hoopmann, Michael R.; Li, Sujun; Lam, Tony J.; Kunath, Benoît J.; Hicks, Nathan D.; Liu, Cindy M.; Price, Lance B.; Laczny, Cedric Christian; Gillece, John D.; Schupp, James M.; Keim, Paul S.; Moritz, Robert L.; Faust, Karoline; Tang, Haixu; Ye, Yuzhen; Skupin, Alexander; May, Patrick; Muller, Emilie E. L.; Wilmes, Paul <br/> <br/>Abstract: Viruses and plasmids (invasive mobile genetic elements (iMGEs)) have important roles in shaping microbial communities, but their dynamic interactions with CRISPR-based immunity remain unresolved. We analysed generation-resolved iMGE–host dynamics spanning one and a half years in a microbial consortium from a biological wastewater treatment plant using integrated meta-omics. We identified 31 bacterial metagenome-assembled genomes encoding complete CRISPR–Cas systems and their corresponding iMGEs. CRISPR-targeted plasmids outnumbered their bacteriophage counterparts by at least fivefold, highlighting the importance of CRISPR-mediated defence against plasmids. Linear modelling of our time-series data revealed that the variation in plasmid abundance over time explained more of the observed community dynamics than phages. Community-scale CRISPR-based plasmid–host and phage–host interaction networks revealed an increase in CRISPR-mediated interactions coinciding with a decrease in the dominant ‘Candidatus Microthrix parvicella’ population. Protospacers were enriched in sequences targeting genes involved in the transmission of iMGEs. Understanding the factors shaping the fitness of specific populations is necessary to devise control strategies for undesirable species and to predict or explain community-wide phenotypes. <br/> <br/>Commentary: Number: 1 Publisher: Nature Publishing Group Mon, 01 Aug 2022 08:48:09 GMT http://hdl.handle.net/10993/51807 Title: Assessing the impact of micropollutants mitigation measures using vertical flow constructed wetlands for municipal wastewater catchments in the greater region: a reference case for rural areas <br/> <br/>Author, co-author: Venditti, Silvia; Kiesch, Anne; Brunhoferova, Hana; Schlienz, Markus; Knerr, Henning; Dittmer, Ulrich; Hansen, Joachim <br/> <br/>Abstract: The present research aims at giving an approach to the issue of surface water contamination due to micropollutants in rural areas. The catchment of the Sûre river was selected as a reference case for the Greater Region, characterized mainly by settlements with low population density, small water bodies and small- to medium-sized wastewater treatment plants (WWTPs). For these WWTPs, conventional technical solutions for micropollutants elimination are not suitable; therefore, an adapted mitigation strategy is needed to prevent the impact of micropollutants, especially during the dry season. As a suitable alternative to more intensive technologies, Constructed Wetlands (CW) in Vertical Flow (VF) configuration have been successfully tested over one-year period and the elimination rate of 27 micropollutants was quantified. Emission reduction by VF was then considered in a static mass balance model that calculates the longitudinal concentrations profile for the entire river catchment. The EmiSûre approach which focuses on river quality (concentrations of pollutants) instead of emitted loads, effectively allowed to simulate adopted measures a priori and resulted efficient to support decision-makers with WWTPs upgrade scenarios. Fri, 29 Jul 2022 03:30:22 GMT http://hdl.handle.net/10993/51573 Title: Using Bayes factors to compare dynamical models of hydrological systems <br/> <br/>Author, co-author: Mingo Ndiwago, Damian; Nijzink, Remko; Ley, Christophe; Schymanski, Stanislaus; Hale, Jack Thu, 07 Jul 2022 03:30:20 GMT