Showing papers by "Swiss Federal Institute of Aquatic Science and Technology published in 2021"
Uppsala University1, Rensselaer Polytechnic Institute2, University of Minnesota3, Leibniz Association4, University of Regina5, Queen's University Belfast6, University of Missouri7, Miami University8, European Space Agency9, Dundalk Institute of Technology10, University of Helsinki11, University of Nevada, Reno12, University of Warmia and Mazury in Olsztyn13, University of Gdańsk14, Moscow State University15, University of Potsdam16, University of Oklahoma17, Wisconsin Department of Natural Resources18, New York City Department of Environmental Protection19, Institut national de la recherche agronomique20, University of Milan21, National Institute for Environmental Studies22, University of Hamburg23, Ontario Ministry of the Environment24, IRSA25, University of California, Davis26, Laval University27, Swiss Federal Institute of Aquatic Science and Technology28, University of Innsbruck29, ETH Zurich30, Vrije Universiteit Brussel31, National Institute of Water and Atmospheric Research32, Institute of Ecosystem Studies33, State University of New York at Oneonta34
TL;DR: In this paper, the authors analyzed a combined total of 45,148 dissolved oxygen and temperature profiles and calculate trends for 393 temperate lakes that span 1941 to 2017, finding that a decline in dissolved oxygen is widespread in surface and deep water habitats.
Abstract: The concentration of dissolved oxygen in aquatic systems helps to regulate biodiversity1,2, nutrient biogeochemistry3, greenhouse gas emissions4, and the quality of drinking water5. The long-term declines in dissolved oxygen concentrations in coastal and ocean waters have been linked to climate warming and human activity6,7, but little is known about the changes in dissolved oxygen concentrations in lakes. Although the solubility of dissolved oxygen decreases with increasing water temperatures, long-term lake trajectories are difficult to predict. Oxygen losses in warming lakes may be amplified by enhanced decomposition and stronger thermal stratification8,9 or oxygen may increase as a result of enhanced primary production10. Here we analyse a combined total of 45,148 dissolved oxygen and temperature profiles and calculate trends for 393 temperate lakes that span 1941 to 2017. We find that a decline in dissolved oxygen is widespread in surface and deep-water habitats. The decline in surface waters is primarily associated with reduced solubility under warmer water temperatures, although dissolved oxygen in surface waters increased in a subset of highly productive warming lakes, probably owing to increasing production of phytoplankton. By contrast, the decline in deep waters is associated with stronger thermal stratification and loss of water clarity, but not with changes in gas solubility. Our results suggest that climate change and declining water clarity have altered the physical and chemical environment of lakes. Declines in dissolved oxygen in freshwater are 2.75 to 9.3 times greater than observed in the world’s oceans6,7 and could threaten essential lake ecosystem services2,3,5,11. Analysis of temperate lakes finds a widespread decline in dissolved oxygen concentrations in surface and deep waters, which is associated with reduced solubility at warmer surface water temperatures and increased stratification at depth.
171 citations
TL;DR: Environmental surveillance of SARS-CoV-2 RNA on high-touch surfaces may be a useful tool to provide early warning of COVID-19 case trends.
Abstract: Environmental surveillance of surface contamination is an unexplored tool for understanding transmission of SARS-CoV-2 in community settings. We conducted longitudinal swab sampling of high-touch non-porous surfaces in a Massachusetts town during a COVID-19 outbreak from April to June 2020. Twenty-nine of 348 (8.3%) surface samples were positive for SARS-CoV-2 RNA, including crosswalk buttons, trash can handles, and door handles of essential business entrances (grocery store, liquor store, bank, and gas station). The estimated risk of infection from touching a contaminated surface was low (less than 5 in 10,000) by quantitative microbial risk assessment, suggesting fomites play a minimal role in SARS-CoV-2 community transmission. The weekly percentage of positive samples (out of n = 33 unique surfaces per week) best predicted variation in city-level COVID-19 cases with a 7-day lead time. Environmental surveillance of SARS-CoV-2 RNA on high-touch surfaces may be a useful tool to provide early warning of COVID-19 case trends.
139 citations
TL;DR: BiofilmQ as discussed by the authors is a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in 3D space and time.
Abstract: Biofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ-a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.
129 citations
TL;DR: In this paper, the authors report a genomic analysis of SARS-CoV-2 in 48 raw wastewater samples collected from three wastewater treatment plants in Switzerland between July 9 and December 21, 2020.
Abstract: The SARS-CoV-2 lineages B.1.1.7 and 501.V2, which were first detected in the United Kingdom and South Africa, respectively, are spreading rapidly in the human population. Thus, there is an increased need for genomic and epidemiological surveillance in order to detect the strains and estimate their abundances. Here, we report a genomic analysis of SARS-CoV-2 in 48 raw wastewater samples collected from three wastewater treatment plants in Switzerland between July 9 and December 21, 2020. We find evidence for the presence of several mutations that define the B.1.1.7 and 501.V2 lineages in some of the samples, including co-occurrences of up to three B.1.1.7 signature mutations on the same amplicon in four samples from Lausanne and one sample from a Swiss ski resort dated December 9 - 21. These findings suggest that the B.1.1.7 strain could be detected by mid December, two weeks before its first verification in a patient sample from Switzerland. We conclude that sequencing SARS-CoV-2 in community wastewater samples may help detect and monitor the circulation of diverse lineages.
102 citations
TL;DR: In this article, the authors use the Quantitative Microbial Risk Assessment framework to examine the risks of community transmission of SARS-CoV-2 through surfaces and evaluate the effectiveness of hand and surface disinfection as potential interventions.
Abstract: SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is perceived to be primarily transmitted via person-to-person contact through droplets produced while talking, coughing, and sneezing Transmission may also occur through other routes, including contaminated surfaces;nevertheless, the role that surfaces have on the spread of the disease remains contested Here, we use the Quantitative Microbial Risk Assessment framework to examine the risks of community transmission of SARS-CoV-2 through surfaces and to evaluate the effectiveness of hand and surface disinfection as potential interventions Using conservative assumptions on input parameters of the model (e g , dose-response relationship, ratio of genome copies to infective virus), the average of the median risks for single hand-to-surface contact followed by hand-to-face contact range from 1 6 × 10-4 to 5 6 × 10-9 for modeled prevalence rates of 0 2%-5% For observed prevalence rates (0 2%, 1%), this corresponds to a low risk of infection (<10-6) Hand disinfection substantially reduces risks of transmission independently of the disease's prevalence and contact frequency In contrast, the effectiveness of surface disinfection is highly dependent on the prevalence and the frequency of contacts The work supports the current perception that contaminated surfaces are not a primary mode of transmission of SARS-CoV-2 and affirms the benefits of making hand disinfectants widely available © 2020 American Chemical Society All rights reserved
99 citations
TL;DR: CyanoMetDB as mentioned in this paper is a large-scale dataset of cyanobacterial secondary metabolites from 850 peer-reviewed articles published between 1967 and 2020, including microcytsins, cyanopeptolins, other depsipeptides, microginins, aeruginosins, cyclamides, cryptophycins, saxitoxins, spumigins, microviridins, and anatoxins among other metabolites.
96 citations
TL;DR: In this article, the authors investigated how the dynamics of new COVID-19 infections estimated based on wastewater monitoring or confirmed cases compare to true COVID19 incidence dynamics, and they focused on the first pandemic wave in Switzerland (February to April, 2020), when test positivity ranged up to 26%.
84 citations
TL;DR: In this paper, the authors presented a continuous, annually resolved atmospheric 14C concentration (fractionation-corrected ratio of 14CO2 to CO2) record reconstructed from absolutely dated tree rings covering nearly all of the last millennium (ad 969-1933).
Abstract: The Sun provides the principal energy input into the Earth system and solar variability represents a significant external climate forcing. Although observations of solar activity (sunspots) cover only the last about 400 years, radionuclides produced by cosmic rays and stored in tree rings or ice cores serve as proxies for solar activity extending back thousands of years. However, the presence of weather-induced noise or low temporal resolution of long, precisely dated records hampers cosmogenic nuclide-based studies of short-term solar variability such as the 11-yr Schwabe cycle. Here we present a continuous, annually resolved atmospheric 14C concentration (fractionation-corrected ratio of 14CO2 to CO2) record reconstructed from absolutely dated tree rings covering nearly all of the last millennium (ad 969–1933). The high-resolution and precision 14C record reveals the presence of the Schwabe cycle over the entire time range. The record confirms the ad 993 solar energetic particle event and reveals two new candidates (ad 1052 and ad 1279), indicating that strong solar events that might be harmful to modern electronic systems probably occur more frequently than previously thought. In addition to showing decadal-scale solar variability over the last millennium, the high-temporal-resolution record of atmospheric radiocarbon also provides a useful benchmark for making radiocarbon dating more accurate over this interval. 11-year solar cycles consistently occurred throughout the last thousand years, according to a synthesis of annually resolved tree ring radiocarbon records from central Europe.
84 citations
TL;DR: Fastsimcoal2 as mentioned in this paper extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework.
Abstract: Motivation: fastsimcoal2 extends fastsimcoal, a continuous time coalescent-based genetic simulation program, by enabling the estimation of demographic parameters under very complex scenarios from the site frequency spectrum under a maximum-likelihood framework.
Results: Other improvements include multi-threading, handling of population inbreeding, extended input file syntax facilitating the description of complex demographic scenarios, and more efficient simulations of sparsely structured populations and of large chromosomes.
Availability and implementation: fastsimcoal2 is freely available on http://cmpg.unibe.ch/software/fastsimcoal2/. It includes console versions for Linux, Windows and MacOS, additional scripts for the analysis and visualization of simulated and estimated scenarios, as well as a detailed documentation and ready-to-use examples.
82 citations
TL;DR: This work proposes conceptualizing integration as a multidimensional interactive process as an open-ended learning process without pre-determined outcomes that remains subject to continuous revision.
79 citations
TL;DR: In this paper, the spectral, radiometric and spatial performance of the PRISMA Level 1 Top-Of-Atmosphere radiance (LTOA) product were analyzed.
University of Innsbruck1, University of Guelph2, ETH Zurich3, Natural History Museum4, University of Illinois at Urbana–Champaign5, Liverpool John Moores University6, University of Nottingham7, University of Zurich8, Swiss Federal Institute of Aquatic Science and Technology9, Washington State University10
TL;DR: The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays and provides guidance on validation and reporting standards for newly developed assays.
Abstract: The use of environmental DNA (eDNA) analysis for species monitoring requires rigorous validation - from field sampling to the analysis of PCR-based results - for meaningful application and interpretation. Assays targeting eDNA released by individual species are typically validated with no predefined criteria to answer specific research questions in one ecosystem. Hence, the general applicability of assays as well as associated uncertainties and limitations, often remain undetermined. The absence of clear guidelines for assay validation prevents targeted eDNA assays from being incorporated into species monitoring and policy; thus, their establishment is essential for realizing the potential of eDNA-based surveys. We describe the measures and tests necessary for successful validation of targeted eDNA assays and the associated pitfalls to form the basis of guidelines. A list of 122 variables was compiled, consolidated into 14 thematic blocks, (e.g. “ in silico analysis”), and arranged on a 5-level validation scale from “incomplete” to “operational” with defined minimum validation criteria for each level. These variables were evaluated for 546 published single-species assays. The resulting dataset was used to provide an overview of current validation practices and test the applicability of the validation scale for future assay rating. Of the 122 variables, 20% to 76% were reported; the majority (30%) of investigated assays were classified as Level 1 (incomplete), and 15% did not achieve this first level. These assays were characterised by minimal in silico and in vitro testing, but their share in annually published eDNA assays has declined since 2014. The meta-analysis demonstrates the suitability of the 5-level validation scale for assessing targeted eDNA assays. It is a user-friendly tool to evaluate previously published assays for future research and routine monitoring, while also enabling the appropriate interpretation of results. Finally, it provides guidance on validation and reporting standards for newly developed assays.
TL;DR: This pioneer study is the first evidence of the microplastic presence above PBL and their potential long-range transport from their point of release even crossing distant borders.
University of Washington1, Katholieke Universiteit Leuven2, University of California, Berkeley3, University of Toronto4, Rutgers University5, Austral University of Chile6, Leibniz Institute for Neurobiology7, Free University of Berlin8, Case Western Reserve University9, Arizona State University10, University of Michigan11, University of Zurich12, Swiss Federal Institute of Aquatic Science and Technology13, McGill University14, Fordham University15, University of California, Santa Cruz16, University of Warsaw17, University of Connecticut18, Virginia Commonwealth University19
TL;DR: Through this new framework, researchers of urban ecology and evolution are encouraged to fully integrate human social drivers and feedbacks to increase understanding and conservation of ecosystems, their functions and their contributions to people within and outside cities.
Abstract: Cities are uniquely complex systems regulated by interactions and feedbacks between nature and human society. Characteristics of human society-including culture, economics, technology and politics-underlie social patterns and activity, creating a heterogeneous environment that can influence and be influenced by both ecological and evolutionary processes. Increasing research on urban ecology and evolutionary biology has coincided with growing interest in eco-evolutionary dynamics, which encompasses the interactions and reciprocal feedbacks between evolution and ecology. Research on both urban evolutionary biology and eco-evolutionary dynamics frequently focuses on contemporary evolution of species that have potentially substantial ecological-and even social-significance. Still, little work fully integrates urban evolutionary biology and eco-evolutionary dynamics, and rarely do researchers in either of these fields fully consider the role of human social patterns and processes. Because cities are fundamentally regulated by human activities, are inherently interconnected and are frequently undergoing social and economic transformation, they represent an opportunity for ecologists and evolutionary biologists to study urban "socio-eco-evolutionary dynamics." Through this new framework, we encourage researchers of urban ecology and evolution to fully integrate human social drivers and feedbacks to increase understanding and conservation of ecosystems, their functions and their contributions to people within and outside cities.
Leibniz Association1, Academy of Natural Sciences of Drexel University2, Humboldt University of Berlin3, University of Bucharest4, Free University of Berlin5, University of New Brunswick6, Alexander von Humboldt Biological Resources Research Institute7, University of Barcelona8, University of Leeds9, Chinese Academy of Sciences10, Norwegian University of Life Sciences11, American Museum of Natural History12, Universidad Autónoma del Estado de Morelos13, Carleton University14, IMDEA15, Katholieke Universiteit Leuven16, Naturalis17, Vietnam Academy of Science and Technology18, University of Hong Kong19, Ateneo de Manila University20, Museum für Naturkunde21, Technische Universität München22, Ghent University23, Zoological Society of London24, University of Ghana25, University of Potsdam26, University of Costa Rica27, University of Duisburg-Essen28, University of Koblenz and Landau29, Utah State University30, Finnish Environment Institute31, University of Nevada, Reno32, Chongqing University of Posts and Telecommunications33, Swedish University of Agricultural Sciences34, Kabale University35, EARTH University36, Trinity College, Dublin37, Stockholm Resilience Centre38, University of Münster39, Norwegian Institute for Water Research40, University of Otago41, International Union for Conservation of Nature and Natural Resources42, University of the Philippines Diliman43, National Institute for Environmental Studies44, Ilia State University45, University of Douala46, University of Mississippi47, Rhodes University48, World Wide Fund for Nature49, University of Giessen50, Kerala University of Fisheries and Ocean Studies51, North Carolina State University52, University of the South Pacific53, Stellenbosch University54, University of Natural Resources and Life Sciences, Vienna55, Swiss Federal Institute of Aquatic Science and Technology56, University of Bern57, Tribhuvan University58, Kathmandu University59, University of Helsinki60, University of Vermont61, Braunschweig University of Technology62, François Rabelais University63, University of Kansas64, Goethe University Frankfurt65, University of Canterbury66, University of California, Santa Barbara67, Federal University of Paraná68, Helmholtz Centre for Environmental Research - UFZ69
TL;DR: In this article, the authors identified 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity, and proposed a global biodiversity research agenda aiming to advance freshwater biodiversity research globally.
Abstract: Global freshwater biodiversity is declining dramatically, and meeting the challenges of this crisis requires bold goals and the mobilisation of substantial resources. While the reasons are varied, investments in both research and conservation of freshwater biodiversity lag far behind those in the terrestrial and marine realms. Inspired by a global consultation, we identify 15 pressing priority needs, grouped into five research areas, in an effort to support informed stewardship of freshwater biodiversity. The proposed agenda aims to advance freshwater biodiversity research globally as a critical step in improving coordinated actions towards its sustainable management and conservation.
TL;DR: Investigating the spread of clinical Extended Spectrum Beta-Lactamase-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.
Abstract: Horizontal gene transfer, mediated by conjugative plasmids, is a major driver of the global rise of antibiotic resistance. However, the relative contributions of factors that underlie the spread of plasmids and their roles in conjugation in vivo are unclear. To address this, we investigated the spread of clinical Extended Spectrum Beta-Lactamase (ESBL)-producing plasmids in the absence of antibiotics in vitro and in the mouse intestine. We hypothesised that plasmid properties would be the primary determinants of plasmid spread and that bacterial strain identity would also contribute. We found clinical Escherichia coli strains natively associated with ESBL-plasmids conjugated to three distinct E. coli strains and one Salmonella enterica serovar Typhimurium strain. Final transconjugant frequencies varied across plasmid, donor, and recipient combinations, with qualitative consistency when comparing transfer in vitro and in vivo in mice. In both environments, transconjugant frequencies for these natural strains and plasmids covaried with the presence/absence of transfer genes on ESBL-plasmids and were affected by plasmid incompatibility. By moving ESBL-plasmids out of their native hosts, we showed that donor and recipient strains also modulated transconjugant frequencies. This suggests that plasmid spread in the complex gut environment of animals and humans can be predicted based on in vitro testing and genetic data.
Leibniz Association1, Miami University2, Dundalk Institute of Technology3, European Space Agency4, University of Savoy5, University of Shiga Prefecture6, Uppsala University7, University of Montana8, University of Innsbruck9, Florida International University10, University of Oklahoma11, University of Oslo12, International Institute for Sustainable Development13, Laurentian University14, University of Minnesota15, Queen's University Belfast16, University of Regina17, SUPSI18, Lancaster University19, University of Hamburg20, Queen's University21, Ontario Ministry of the Environment22, State University of New York at New Paltz23, IRSA24, University of California, Davis25, Swiss Federal Institute of Aquatic Science and Technology26, Irkutsk State University27, Free University of Berlin28, University of Geneva29, University of Konstanz30, ETH Zurich31, Vrije Universiteit Brussel32, National Institute of Water and Atmospheric Research33
TL;DR: In this paper, the authors used 32 million temperature measurements from 139 lakes to quantify thermal habitat change (percentage of non-overlap) and assess how this change is exacerbated by potential habitat constraints.
Abstract: Lake surfaces are warming worldwide, raising concerns about lake organism responses to thermal habitat changes. Species may cope with temperature increases by shifting their seasonality or their depth to track suitable thermal habitats, but these responses may be constrained by ecological interactions, life histories or limiting resources. Here we use 32 million temperature measurements from 139 lakes to quantify thermal habitat change (percentage of non-overlap) and assess how this change is exacerbated by potential habitat constraints. Long-term temperature change resulted in an average 6.2% non-overlap between thermal habitats in baseline (1978–1995) and recent (1996–2013) time periods, with non-overlap increasing to 19.4% on average when habitats were restricted by season and depth. Tropical lakes exhibited substantially higher thermal non-overlap compared with lakes at other latitudes. Lakes with high thermal habitat change coincided with those having numerous endemic species, suggesting that conservation actions should consider thermal habitat change to preserve lake biodiversity.
TL;DR: The Natural Products Atlas (Npatlas) as discussed by the authors is a database of known microbial natural products structures, which includes a full RESTful application programming interface (API), a new website framework and an expanded database that includes 8128 new compounds.
Abstract: Within the natural products field there is an increasing emphasis on the study of compounds from microbial sources. This has been fuelled by interest in the central role that microorganisms play in mediating both interspecies interactions and host-microbe relationships. To support the study of natural products chemistry produced by microorganisms we released the Natural Products Atlas, a database of known microbial natural products structures, in 2019. This paper reports the release of a new version of the database which includes a full RESTful application programming interface (API), a new website framework, and an expanded database that includes 8128 new compounds, bringing the total to 32 552. In addition to these structural and content changes we have added full taxonomic descriptions for all microbial taxa and have added chemical ontology terms from both NP Classifier and ClassyFire. We have also performed manual curation to review all entries with incomplete configurational assignments and have integrated data from external resources, including CyanoMetDB. Finally, we have improved the user experience by updating the Overview dashboard and creating a dashboard for taxonomic origin. The database can be accessed via the new interactive website at https://www.npatlas.org.
National and Kapodistrian University of Athens1, Swiss Federal Institute of Aquatic Science and Technology2, University of Luxembourg3, Helmholtz Centre for Environmental Research - UFZ4, Research Triangle Park5, Swedish University of Agricultural Sciences6, Spanish National Research Council7, University of Antwerp8, University of California, Davis9, ETH Zurich10
TL;DR: In this article, a rigorously tested, flexible, and less system-dependent unified retention time index (RTI) approach for liquid chromatography (LC) is presented, based on the calibration of the elution pattern.
Abstract: There is an increasing need for comparable and harmonized retention times (tR) in liquid chromatography (LC) among different laboratories, to provide supplementary evidence for the identity of compounds in high-resolution mass spectrometry (HRMS)-based suspect and nontarget screening investigations. In this study, a rigorously tested, flexible, and less system-dependent unified retention time index (RTI) approach for LC is presented, based on the calibration of the elution pattern. Two sets of 18 calibrants were selected for each of ESI+ and ESI-based on the maximum overlap with the retention times and chemical similarity indices from a total set of 2123 compounds. The resulting calibration set, with RTI set to range between 1 and 1000, was proposed as the most appropriate RTI system after rigorous evaluation, coordinated by the NORMAN network. The validation of the proposed RTI system was done externally on different instrumentation and LC conditions. The RTI can also be used to check the reproducibility and quality of LC conditions. Two quantitative structure-retention relationship (QSRR)-based models were built based on the developed RTI systems, which assist in the removal of false-positive annotations. The applicability domains of the QSRR models allowed completing the identification process with higher confidence for substances within the domain, while indicating those substances for which results should be treated with caution. The proposed RTI system was used to improve confidence in suspect and nontarget screening and increase the comparability between laboratories as demonstrated for two examples. All RTI-related calculations can be performed online at http://rti.chem.uoa.gr/.
York University1, State University of New York at New Paltz2, European Space Agency3, Swiss Federal Institute of Aquatic Science and Technology4, University of Maine at Farmington5, Russian Academy of Sciences6, Finnish Environment Institute7, University of Wisconsin-Madison8, Nicolaus Copernicus University in Toruń9, National Institute for Environmental Studies10, Illinois State University11, United States Geological Survey12, Cornell University13, Uppsala University14, Indian Ministry of Environment and Forests15
TL;DR: In this article, the authors provided the first re-assessment of Northern Hemispheric ice trends since 2004 by adding 15 additional years of ice phenology records and 40 lakes to their study.
Abstract: Long-term lake ice phenological records from around the Northern Hemisphere provide unique sensitive indicators of climatic variations, even prior to the existence of physical meteorological measurement stations. Here, we updated ice phenology records for 60 lakes with time-series ranging from 107–204 years to provide the first re-assessment of Northern Hemispheric ice trends since 2004 by adding 15 additional years of ice phenology records and 40 lakes to our study. We found that, on average, ice-on was 11.0 days later, ice-off was 6.8 days earlier, and ice duration was 17.0 days shorter per century over the entire record for each lake. Trends in ice-on and ice duration were six times faster in the last 25-year period (1992–2016) than previous quarter centuries. More extreme events in recent decades, including late ice-on, early ice-off, shorter periods of ice cover, or no ice cover at all, contribute to the increasing rate of lake ice loss. Reductions in greenhouse gas emissions could limit increases in air temperature and abate losses in lake ice cover that would subsequently limit ecological, cultural, and socioeconomic consequences, such as increased evaporation rates, warmer water temperatures, degraded water quality, and the formation of toxic algal blooms.
TL;DR: In this article, the authors highlight approaches ranging from behavioral to structural, functional, and molecular analysis of the larval zebrafish nervous system, providing a holistic view of potential neurotoxic outcomes.
Abstract: The occurrence of neuroactive chemicals in the aquatic environment is on the rise and poses a potential threat to aquatic biota of currently unpredictable outcome. In particular, subtle changes caused by these chemicals to an organism's sensation or behavior are difficult to tackle with current test systems that focus on rodents or with in vitro test systems that omit whole-animal responses. In recent years, the zebrafish (Danio rerio) has become a popular model organism for toxicological studies and testing strategies, such as the standardized use of zebrafish early life stages in the Organisation for Economic Co-operation and Development's guideline 236. In terms of neurotoxicity, the zebrafish provides a powerful model to investigate changes to the nervous system from several different angles, offering the ability to tackle the mechanisms of action of chemicals in detail. The mechanistic understanding gained through the analysis of this model species provides a good basic knowledge of how neuroactive chemicals might interact with a teleost nervous system. Such information can help infer potential effects occurring to other species exposed to neuroactive chemicals in their aquatic environment and predicting potential risks of a chemical for the aquatic ecosystem. In the present article, we highlight approaches ranging from behavioral to structural, functional, and molecular analysis of the larval zebrafish nervous system, providing a holistic view of potential neurotoxic outcomes. Environ Toxicol Chem 2021;40:989-1006. © 2020 SETAC.
TL;DR: In this paper, the authors used noble gases in groundwater to show that the low-altitude, low-to-mid-latitude land surface (45° south to 35° north) cooled by 5.8°±−0.6°C during the last glacial maximum (LGM) period.
Abstract: The magnitude of global cooling during the Last Glacial Maximum (LGM, the coldest multimillennial interval of the last glacial period) is an important constraint for evaluating estimates of Earth's climate sensitivity1,2. Reliable LGM temperatures come from high-latitude ice cores3,4, but substantial disagreement exists between proxy records in the low latitudes1,5-8, where quantitative low-elevation records on land are scarce. Filling this data gap, noble gases in ancient groundwater record past land surface temperatures through a direct physical relationship that is rooted in their temperature-dependent solubility in water9,10. Dissolved noble gases are suitable tracers of LGM temperature because of their complete insensitivity to biological and chemical processes and the ubiquity of LGM-aged groundwater around the globe11,12. However, although several individual noble gas studies have found substantial tropical LGM cooling13-16, they have used different methodologies and provide limited spatial coverage. Here we use noble gases in groundwater to show that the low-altitude, low-to-mid-latitude land surface (45 degrees south to 35 degrees north) cooled by 5.8 ± 0.6 degrees Celsius (mean ± 95% confidence interval) during the LGM. Our analysis includes four decades of groundwater noble gas data from six continents, along with new records from the tropics, all of which were interpreted using the same physical framework. Our land-based result broadly supports a recent reconstruction based on marine proxy data assimilation1 that suggested greater climate sensitivity than previous estimates5-7.
TL;DR: In this article, a patient suffering from a persistent infection with Staphylococcus aureus showed that host-mediated stress, including acidic pH, abscess environment, and antibiotic exposure promoted persister formation in vitro and in vivo.
Abstract: Staphylococcus aureus causes invasive infections and easily acquires antibiotic resistance Even antibiotic-susceptible S aureus can survive antibiotic therapy and persist, requiring prolonged treatment and surgical interventions These so-called persisters display an arrested-growth phenotype, tolerate high antibiotic concentrations, and are associated with chronic and recurrent infections To characterize these persisters, we assessed S aureus recovered directly from a patient suffering from a persistent infection We show that host-mediated stress, including acidic pH, abscess environment, and antibiotic exposure promoted persister formation in vitro and in vivo Multiomics analysis identified molecular changes in S aureus in response to acid stress leading to an overall virulent population However, further analysis of a persister-enriched population revealed major molecular reprogramming in persisters, including down-regulation of virulence and cell division and up-regulation of ribosomal proteins, nucleotide-, and amino acid-metabolic pathways, suggesting their requirement to fuel and maintain the persister phenotype and highlighting that persisters are not completely metabolically inactive Additionally, decreased aconitase activity and ATP levels and accumulation of insoluble proteins involved in transcription, translation, and energy production correlated with persistence in S aureus, underpinning the molecular mechanisms that drive the persister phenotype Upon regrowth, these persisters regained their virulence potential and metabolically active phenotype, including reduction of insoluble proteins, exhibiting a reversible state, crucial for recurrent infections We further show that a targeted antipersister combination therapy using retinoid derivatives and antibiotics significantly reduced lag-phase heterogeneity and persisters in a murine infection model Our results provide molecular insights into persisters and help explain why persistent S aureus infections are so difficult to treat
TL;DR: A systematic review of recently published literature to update and expand the epidemiological evidence on the association between municipal solid waste management practices and resident populations' health risks was conducted by as mentioned in this paper.
Abstract: Municipal solid waste (MSW) can pose a threat to public health if it is not safely managed. Despite prior research, uncertainties remain and refurbished evidence is needed along with new approaches. We conducted a systematic review of recently published literature to update and expand the epidemiological evidence on the association between MSW management practices and resident populations' health risks. Studies published from January 2005 to January 2020 were searched and reviewed following PRISMA guidelines. Eligible MSW treatment or disposal sites were defined as landfills, dumpsites, incinerators, waste open burning, transfer stations, recycling sites, composting plants, and anaerobic digesters. Occupational risks were not assessed. Health effects investigated included mortality, adverse birth and neonatal outcomes, cancer, respiratory conditions, gastroenteritis, vector-borne diseases, mental health conditions, and cardiovascular diseases. Studies reporting on human biomonitoring for exposure were eligible as well. Twenty-nine studies were identified that met the inclusion criteria of our protocol, assessing health effects only associated with proximity to landfills, incinerators, and dumpsites/open burning sites. There was some evidence of an increased risk of adverse birth and neonatal outcomes for residents near each type of MSW site. There was also some evidence of an increased risk of mortality, respiratory diseases, and negative mental health effects associated with residing near landfills. Additionally, there was some evidence of increased risk of mortality associated with residing near incinerators. However, in many cases, the evidence was inadequate to establish a strong relationship between a specific exposure and outcomes, and the studies rarely assessed new generation technologies. Evidence gaps remain, and recommendations for future research are discussed.
TL;DR: In this article, the authors compare the range of communication of different quorum-sensing systems and show that while some systems support long-range communication, others support a form of highly localized communication.
Abstract: In bacterial communities, cells often communicate by the release and detection of small diffusible molecules, a process termed quorum-sensing. Signal molecules are thought to broadly diffuse in space; however, they often regulate traits such as conjugative transfer that strictly depend on the local community composition. This raises the question how nearby cells within the community can be detected. Here, we compare the range of communication of different quorum-sensing systems. While some systems support long-range communication, we show that others support a form of highly localized communication. In these systems, signal molecules propagate no more than a few microns away from signaling cells, due to the irreversible uptake of the signal molecules from the environment. This enables cells to accurately detect micron scale changes in the community composition. Several mobile genetic elements, including conjugative elements and phages, employ short-range communication to assess the fraction of susceptible host cells in their vicinity and adaptively trigger horizontal gene transfer in response. Our results underscore the complex spatial biology of bacteria, which can communicate and interact at widely different spatial scales.
TL;DR: In this paper, a genome-centric quantitative metatranscriptomic approach was exploited to realize high-resolution qualitative and quantitative analyses of bacterial hosts of ARGs (i.e., multiresistance, pathogenicity, activity, and niches) in the 12 urban WWTPs.
Abstract: The global rise and spread of antibiotic resistance greatly challenge the treatment of bacterial infections. Wastewater treatment plants (WWTPs) harbor and discharge antibiotic resistance genes (ARGs) as environmental contaminants. However, the knowledge gap on the host identity, activity, and functionality of ARGs limits transmission and health risk assessment of the WWTP resistome. Hereby, a genome-centric quantitative metatranscriptomic approach was exploited to realize high-resolution qualitative and quantitative analyses of bacterial hosts of ARGs (i.e., multiresistance, pathogenicity, activity, and niches) in the 12 urban WWTPs. We found that ∼45% of 248 recovered genomes expressed ARGs against multiple classes of antibiotics, among which bacitracin and aminoglycoside resistance genes in Proteobacteria were the most prevalent scenario. Both potential pathogens and indigenous denitrifying bacteria were transcriptionally active hosts of ARGs. The almost unchanged relative expression levels of ARGs in the most resistant populations (66.9%) and the surviving ARG hosts including globally emerging pathogens (e.g., Aliarcobacter cryaerophilus) in treated WWTP effluent prioritize future examination on the health risks related to resistance propagation and human exposure in the receiving environment.
Max Planck Society1, University of Konstanz2, Yale University3, McGill University4, Université du Québec à Montréal5, Swiss Federal Institute of Aquatic Science and Technology6, National Institute of Genetics7, Tokyo University of Marine Science and Technology8, University of Freiburg9, University of Aveiro10, Uppsala University11, University of Potsdam12
TL;DR: In this article, a hierarchical trait-based approach is proposed to study the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions.
Abstract: The nutritional diversity of resources can affect the adaptive evolution of consumer metabolism and consumer diversification. The omega-3 long-chain polyunsaturated fatty acids eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) have a high potential to affect consumer fitness, through their widespread effects on reproduction, growth and survival. However, few studies consider the evolution of fatty acid metabolism within an ecological context. In this review, we first document the extensive diversity in both primary producer and consumer fatty acid distributions amongst major ecosystems, between habitats and amongst species within habitats. We highlight some of the key nutritional contrasts that can shape behavioural and/or metabolic adaptation in consumers, discussing how consumers can evolve in response to the spatial, seasonal and community-level variation of resource quality. We propose a hierarchical trait-based approach for studying the evolution of consumers' metabolic networks and review the evolutionary genetic mechanisms underpinning consumer adaptation to EPA and DHA distributions. In doing so, we consider how the metabolic traits of consumers are hierarchically structured, from cell membrane function to maternal investment, and have strongly environment-dependent expression. Finally, we conclude with an outlook on how studying the metabolic adaptation of consumers within the context of nutritional landscapes can open up new opportunities for understanding evolutionary diversification.
TL;DR: In this paper, the main objective of the study was to completely replace soybean in layer diets with defatted meal and fat from black soldier fly larvae without adverse effects for 5 × 10 Lohmann Brown Classic hens.
TL;DR: In this paper, the authors describe an obligate endosymbiont of an anaerobic ciliate, which has a dedicated role in respiration and providing energy for its eukaryotic host.
Abstract: Mitochondria are specialized eukaryotic organelles that have a dedicated function in oxygen respiration and energy production. They evolved about 2 billion years ago from a free-living bacterial ancestor (probably an alphaproteobacterium), in a process known as endosymbiosis1,2. Many unicellular eukaryotes have since adapted to life in anoxic habitats and their mitochondria have undergone further reductive evolution3. As a result, obligate anaerobic eukaryotes with mitochondrial remnants derive their energy mostly from fermentation4. Here we describe ‘Candidatus Azoamicus ciliaticola’, which is an obligate endosymbiont of an anaerobic ciliate and has a dedicated role in respiration and providing energy for its eukaryotic host. ‘Candidatus A. ciliaticola’ contains a highly reduced 0.29-Mb genome that encodes core genes for central information processing, the electron transport chain, a truncated tricarboxylic acid cycle, ATP generation and iron–sulfur cluster biosynthesis. The genome encodes a respiratory denitrification pathway instead of aerobic terminal oxidases, which enables its host to breathe nitrate instead of oxygen. ‘Candidatus A. ciliaticola’ and its ciliate host represent an example of a symbiosis that is based on the transfer of energy in the form of ATP, rather than nutrition. This discovery raises the possibility that eukaryotes with mitochondrial remnants may secondarily acquire energy-providing endosymbionts to complement or replace functions of their mitochondria. ‘Candidatus Azoamicus ciliaticola’ transfers energy to its ciliate host in the form of ATP and enables this host to breathe nitrate, demonstrating that eukaryotes with remnant mitochondria can secondarily acquire energy-providing endosymbionts.
University for Foreigners Perugia1, World Meteorological Organization2, Florida International University3, Swiss Federal Institute of Aquatic Science and Technology4, Imperial College London5, Indian Institute of Technology Bombay6, University of Birmingham7, Uppsala University8, University of Córdoba (Spain)9, University of Agder10, Swedish University of Agricultural Sciences11, Tuscia University12, International Water Management Institute13, Instituto Costarricense de Electricidad14
TL;DR: Widely available digital technologies are empowering citizens who are increasingly well informed and involved in numerous water, climate, and environmental challenges as mentioned in this paper, and citizen science can serve man and serve man.
Abstract: Widely available digital technologies are empowering citizens who are increasingly well informed and involved in numerous water, climate, and environmental challenges. Citizen science can serve man...