Showing papers by "Swiss Federal Institute of Aquatic Science and Technology published in 2019"

Definitions and guidelines for research on antibiotic persistence

Abstract: Increasing concerns about the rising rates of antibiotic therapy failure and advances in single-cell analyses have inspired a surge of research into antibiotic persistence. Bacterial persister cells represent a subpopulation of cells that can survive intensive antibiotic treatment without being resistant. Several approaches have emerged to define and measure persistence, and it is now time to agree on the basic definition of persistence and its relation to the other mechanisms by which bacteria survive exposure to bactericidal antibiotic treatments, such as antibiotic resistance, heteroresistance or tolerance. In this Consensus Statement, we provide definitions of persistence phenomena, distinguish between triggered and spontaneous persistence and provide a guide to measuring persistence. Antibiotic persistence is not only an interesting example of non-genetic single-cell heterogeneity, it may also have a role in the failure of antibiotic treatments. Therefore, it is our hope that the guidelines outlined in this article will pave the way for better characterization of antibiotic persistence and for understanding its relevance to clinical outcomes.

A Combinatorial View on Speciation and Adaptive Radiation

Abstract: Speciation is often thought of as a slow process due to the waiting times for mutations that cause incompatibilities, and permit ecological differentiation or assortative mating. Cases of rapid speciation and particularly cases of rapid adaptive radiation into multiple sympatric species have remained somewhat mysterious. We review recent findings from speciation genomics that reveal an emerging commonality among such cases: reassembly of old genetic variation into new combinations facilitating rapid speciation and adaptive radiation. The polymorphisms in old variants frequently originated from hybridization at some point in the past. We discuss why old variants are particularly good fuel for rapid speciation, and hypothesize that variation in access to such old variants might contribute to the large variation in speciation rates observed in nature.

Wastewater treatment plant resistomes are shaped by bacterial composition, genetic exchange, and upregulated expression in the effluent microbiomes

Abstract: Wastewater treatment plants (WWTPs) are implicated as hotspots for the dissemination of antibacterial resistance into the environment However, the in situ processes governing removal, persistence, and evolution of resistance genes during wastewater treatment remain poorly understood Here, we used quantitative metagenomic and metatranscriptomic approaches to achieve a broad-spectrum view of the flow and expression of genes related to antibacterial resistance to over 20 classes of antibiotics, 65 biocides, and 22 metals All compartments of 12 WWTPs share persistent resistance genes with detectable transcriptional activities that were comparatively higher in the secondary effluent, where mobility genes also show higher relative abundance and expression ratios The richness and abundance of resistance genes vary greatly across metagenomes from different treatment compartments, and their relative and absolute abundances correlate with bacterial community composition and biomass concentration No strong drivers of resistome composition could be identified among the chemical stressors analyzed, although the sub-inhibitory concentration (hundreds of ng/L) of macrolide antibiotics in wastewater correlates with macrolide and vancomycin resistance genes Contig-based analysis shows considerable co-localization between resistance and mobility genes and implies a history of substantial horizontal resistance transfer involving human bacterial pathogens Based on these findings, we propose future inclusion of mobility incidence (M%) and host pathogenicity of antibiotic resistance genes in their quantitative health risk ranking models with an ultimate goal to assess the biological significance of wastewater resistomes with regard to disease control in humans or domestic livestock

The future of extreme climate in Iran.

Abstract: Iran is experiencing unprecedented climate-related problems such as drying of lakes and rivers, dust storms, record-breaking temperatures, droughts, and floods. Here, we use the ensemble of five high-resolution climate models to project maximum and minimum temperatures and rainfall distribution, calculate occurrences of extreme temperatures (temperatures above and below the historical 95th and 5th percentiles, respectively), analyze compound of precipitation and temperature extremes, and determine flooding frequencies across the country. We found that compared to the period of 1980–2004, in the period of 2025–2049, Iran is likely to experience more extended periods of extreme maximum temperatures in the southern part of the country, more extended periods of dry (for ≥120 days: precipitation <2 mm, Tmax ≥30 °C) as well as wet (for ≤3 days: total precipitation ≥110 mm) conditions, and higher frequency of floods. Overall, the combination of these results projects a climate of extended dry periods interrupted by intermittent heavy rainfalls, which is a recipe for increasing the chances of floods. Without thoughtful adaptability measures, some parts of the country may face limited habitability in the future.

Reactivity, Selectivity, and Long-Term Performance of Sulfidized Nanoscale Zerovalent Iron with Different Properties

Abstract: Sulfidized nanoscale zerovalent iron (SNZVI) has desirable properties for in situ groundwater remediation. However, there is limited understanding of how the sulfidation type and particle properties affect the reactivity and selectivity of SNZVI toward groundwater contaminants, or how reactivity changes as the particles age. Here, SNZVI synthesized by either a one-step (SNZVI-1) or two-step (SNZVI-2) process were characterized, and the reactivity of both fresh and aged (1d to 60 d) nanoparticles was assessed. The measured S/Fe ratio was 5.4 ± 0.5 mol % for SNZVI-1 and 0.8 ± 0.1 mol % for SNZVI-2. XPS analysis indicates S2-, S22-, and S n2- species on the surface of both SNZVI-1 and SNZVI-2, while S22- is the dominant species inside of the SNZVI nanoparticles. SNZVI-1 particles were hydrophobic (contact angle = 103 ± 3°), while the other materials were hydrophilic (contact angles were 18 ± 2° and 36 ± 3° for NZVI and SNZVI-2, respectively). SNZVI-1, with greater S content and hydrophobicity, was less reactive with water than either NZVI or SNZVI-2 over a 60 d period, resulting in less H2 evolution. It also had the highest reactivity with TCE and the lowest reactivity with nitrate, consistent with its higher hydrophobicity. In contrast, both NZVI and SNZVI-2 were reactive with both TCE and nitrate. Both types of SNZVI remained more reactive after aging in water over 60 d than NZVI. These data suggest that the properties of the SNZVI made from a one-step synthesis procedure may provide better reactivity, selectivity, and longevity than that made from a two-step process.

Ecosystem tipping points in an evolving world.

Abstract: There is growing concern over tipping points arising in ecosystems because of the crossing of environmental thresholds. Tipping points lead to abrupt and possibly irreversible shifts between alternative ecosystem states, potentially incurring high societal costs. Trait variation in populations is central to the biotic feedbacks that maintain alternative ecosystem states, as they govern the responses of populations to environmental change that could stabilize or destabilize ecosystem states. However, we know little about how evolutionary changes in trait distributions over time affect the occurrence of tipping points and even less about how big-scale ecological shifts reciprocally interact with trait dynamics. We argue that interactions between ecological and evolutionary processes should be taken into account in order to understand the balance of feedbacks governing tipping points in nature.

Future water quality monitoring: improving the balance between exposure and toxicity assessments of real-world pollutant mixtures

Abstract: Environmental water quality monitoring aims to provide the data required for safeguarding the environment against adverse biological effects from multiple chemical contamination arising from anthropogenic diffuse emissions and point sources. Here, we integrate the experience of the international EU-funded project SOLUTIONS to shift the focus of water monitoring from a few legacy chemicals to complex chemical mixtures, and to identify relevant drivers of toxic effects. Monitoring serves a range of purposes, from control of chemical and ecological status compliance to safeguarding specific water uses, such as drinking water abstraction. Various water sampling techniques, chemical target, suspect and non-target analyses as well as an array of in vitro, in vivo and in situ bioanalytical methods were advanced to improve monitoring of water contamination. Major improvements for broader applicability include tailored sampling techniques, screening and identification techniques for a broader and more diverse set of chemicals, higher detection sensitivity, standardized protocols for chemical, toxicological, and ecological assessments combined with systematic evidence evaluation techniques. No single method or combination of methods is able to meet all divergent monitoring purposes. Current monitoring approaches tend to emphasize either targeted exposure or effect detection. Here, we argue that, irrespective of the specific purpose, assessment of monitoring results would benefit substantially from obtaining and linking information on the occurrence of both chemicals and potentially adverse biological effects. In this paper, we specify the information required to: (1) identify relevant contaminants, (2) assess the impact of contamination in aquatic ecosystems, or (3) quantify cause–effect relationships between contaminants and adverse effects. Specific strategies to link chemical and bioanalytical information are outlined for each of these distinct goals. These strategies have been developed and explored using case studies in the Danube and Rhine river basins as well as for rivers of the Iberian Peninsula. Current water quality assessment suffers from biases resulting from differences in approaches and associated uncertainty analyses. While exposure approaches tend to ignore data gaps (i.e., missing contaminants), effect-based approaches penalize data gaps with increased uncertainty factors. This integrated work suggests systematic ways to deal with mixture exposures and combined effects in a more balanced way, and thus provides guidance for future tailored environmental monitoring.

Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds

Abstract: Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development is ongoing, with strong commercial interest, and new uses are continually being discovered. General applications of eDNA and guidelines for best practice in freshwater systems have been established, but habitat-specific assessments are lacking. Ponds are highly diverse, yet understudied systems that could benefit from eDNA monitoring. However, eDNA applications in ponds and methodological constraints specific to these environments remain unaddressed. Following a stakeholder workshop in 2017, researchers combined knowledge and expertise to review these applications and challenges that must be addressed for the future and consistency of eDNA monitoring in ponds. The greatest challenges for pond eDNA surveys are representative sampling, eDNA capture, and potential PCR inhibition. We provide recommendations for sampling, eDNA capture, inhibition testing, and laboratory practice, which should aid new and ongoing eDNA projects in ponds. If implemented, these recommendations will contribute towards an eventual broad standardisation of eDNA research and practice, with room to tailor workflows for optimal analysis and different applications. Such standardisation will provide more robust, comparable, and ecologically meaningful data to enable effective conservation and management of pond biodiversity.

Improving network approaches to the study of complex social-ecological interdependencies

Abstract: Achieving effective, sustainable environmental governance requires a better understanding of the causes and consequences of the complex patterns of interdependencies connecting people and ecosystems within and across scales. Network approaches for conceptualizing and analysing these interdependencies offer one promising solution. Here, we present two advances we argue are needed to further this area of research: (i) a typology of causal assumptions explicating the causal aims of any given network-centric study of social–ecological interdependencies; (ii) unifying research design considerations that facilitate conceptualizing exactly what is interdependent, through what types of relationships and in relation to what kinds of environmental problems. The latter builds on the appreciation that many environmental problems draw from a set of core challenges that re-occur across contexts. We demonstrate how these advances combine into a comparative heuristic that facilitates leveraging case-specific findings of social–ecological interdependencies to generalizable, yet context-sensitive, theories based on explicit assumptions of causal relationships.

Effect-based methods are key. The European Collaborative Project SOLUTIONS recommends integrating effect-based methods for diagnosis and monitoring of water quality

Abstract: The present monitoring and assessment of the chemical status of water bodies fail to characterize the likelihood that complex mixtures of chemicals affect water quality. The European Collaborative Project SOLUTIONS suggests that this likelihood can be estimated with effect-based methods (EBMs) complemented by chemical screening and/or impact modeling. These methods should be used to identify the causes of impacted water quality and to develop programs of measures to improve water quality. Along this line of reasoning, effect-based methods are recommended for Water Framework Directive (WFD) monitoring to cover the major modes of action in the universe of environmentally relevant chemicals so as to evaluate improvements of water quality upon implementing the measures. To this end, a minimum battery of bioassays has been recommended including short-term toxicity to algae, Daphnia and fish embryos complemented with in vitro and short-term in vivo tests on mode-of-action specific effects as proxies for long-term toxicity. The likelihood of adverse impacts can be established with effect-based trigger values, which differentiate good from poor water quality in close alignment with Environmental Quality Standards for individual chemicals, while taking into account mixture toxicity. The use of EBMs is suggested in the WFD as one avenue to establish the likelihood of adverse effects due to chemical pollution in European water systems. The present paper has been written as one component of a series of policy briefs to support decisions on water quality monitoring and management under the WFD.

Recycling nutrients contained in human excreta to agriculture: Pathways, processes, and products

Abstract: The need for better nutrient management has spurred efforts towards more comprehensive recycling of nutrients contained in human excreta to agriculture. Research in this direction has intensified throughout the past years, continuously unfolding new knowledge and technologies. The present review aspires to provide a systematic synthesis of the field by providing an accessible overview of terminology, recovery pathways and treatment options, and products rendered by treatment. Our synthesis suggests that, rather than focusing on a specific recovery pathway or product and on a limited set of nutrients, there is scope for exploring how to maximize nutrient recovery by combining individual pathways and products and including a broader range of nutrients. To this end, finding ways to more effectively share and consolidate knowledge and information on recovery pathways and products would be beneficial. The present review aims to provide a template that aims to facilitate designing human excreta management for maximum nutrient recovery, and that can serve as foundation for organizing and categorizing information for more effective sharing and consolidation.

Vision using multiple distinct rod opsins in deep-sea fishes.

Abstract: Vertebrate vision is accomplished through light-sensitive photopigments consisting of an opsin protein bound to a chromophore. In dim light, vertebrates generally rely on a single rod opsin [rhodopsin 1 (RH1)] for obtaining visual information. By inspecting 101 fish genomes, we found that three deep-sea teleost lineages have independently expanded their RH1 gene repertoires. Among these, the silver spinyfin (Diretmus argenteus) stands out as having the highest number of visual opsins in vertebrates (two cone opsins and 38 rod opsins). Spinyfins express up to 14 RH1s (including the most blueshifted rod photopigments known), which cover the range of the residual daylight as well as the bioluminescence spectrum present in the deep sea. Our findings present molecular and functional evidence for the recurrent evolution of multiple rod opsin-based vision in vertebrates.

Ozone depletion, ultraviolet radiation, climate change and prospects for a sustainable future

Abstract: Changes in stratospheric ozone and climate over the past 40-plus years have altered the solar ultraviolet (UV) radiation conditions at the Earth’s surface. Ozone depletion has also contributed to climate change across the Southern Hemisphere. These changes are interacting in complex ways to affect human health, food and water security, and ecosystem services. Many adverse effects of high UV exposure have been avoided thanks to the Montreal Protocol with its Amendments and Adjustments, which have effectively controlled the production and use of ozone-depleting substances. This international treaty has also played an important role in mitigating climate change. Climate change is modifying UV exposure and affecting how people and ecosystems respond to UV; these effects will become more pronounced in the future. The interactions between stratospheric ozone, climate and UV radiation will therefore shift over time; however, the Montreal Protocol will continue to have far-reaching benefits for human well-being and environmental sustainability.

Synthesis of metal-doped nanoplastics and their utility to investigate fate and behaviour in complex environmental systems.

Abstract: Research on the distribution and effects of particulate plastic has intensified in recent years and yet, due to analytical challenges, our understanding of nanoplastic occurrence and behaviour has remained comparatively elusive. However, process studies could greatly aid in defining key parameters for nanoplastic interactions within and transfers between technical and environmental compartments. Here we provide a method to synthesize nanoplastic particles doped with a chemically entrapped metal used as a tracer, which provides a robust way to detect nanoplastics more easily, accurately and quantitatively in complex media. We show the utility of this approach in batch studies that simulate the activated sludge process of a municipal waste water treatment plant and so better understand the fate of nanoplastics in urban environments. We found that the majority of particles were associated with the sludge (>98%), with an average recovery of over 93% of the spiked material achieved. We believe that this approach can be developed further to study the fate, transport, mechanistic behaviour and biological uptake of nanoplastics in a variety of systems on different scales.

Eco‐evolutionary feedbacks—Theoretical models and perspectives

Abstract: Theoretical models pertaining to feedbacks between ecological and evolutionary processes are prevalent in multiple biological fields. An integrative overview is currently lacking, due to little crosstalk between the fields and the use of different methodological approaches. Here, we review a wide range of models of eco‐evolutionary feedbacks and highlight their underlying assumptions. We discuss models where feedbacks occur both within and between hierarchical levels of ecosystems, including populations, communities and abiotic environments, and consider feedbacks across spatial scales. Identifying the commonalities among feedback models, and the underlying assumptions, helps us better understand the mechanistic basis of eco‐evolutionary feedbacks. Eco‐evolutionary feedbacks can be readily modelled by coupling demographic and evolutionary formalisms. We provide an overview of these approaches and suggest future integrative modelling avenues. Our overview highlights that eco‐evolutionary feedbacks have been incorporated in theoretical work for nearly a century. Yet, this work does not always include the notion of rapid evolution or concurrent ecological and evolutionary time scales. We show the importance of density‐ and frequency‐dependent selection for feedbacks, as well as the importance of dispersal as a central linking trait between ecology and evolution in a spatial context. A plain language summary is available for this article.

State of the Climate in 2018

Abstract: El documento contiene la seccion c. Central America and the Caribbean del capitulo 7. Regional Climates

Is the Hyporheic Zone Relevant beyond the Scientific Community

Abstract: Rivers are important ecosystems under continuous anthropogenic stresses. The hyporheic zone is a ubiquitous, reactive interface between the main channel and its surrounding sediments along the river network. We elaborate on the main physical, biological, and biogeochemical drivers and processes within the hyporheic zone that have been studied by multiple scientific disciplines for almost half a century. These previous efforts have shown that the hyporheic zone is a modulator for most metabolic stream processes and serves as a refuge and habitat for a diverse range of aquatic organisms. It also exerts a major control on river water quality by increasing the contact time with reactive environments, which in turn results in retention and transformation of nutrients, trace organic compounds, fine suspended particles, and microplastics, among others. The paper showcases the critical importance of hyporheic zones, both from a scientific and an applied perspective, and their role in ecosystem services to answer the question of the manuscript title. It identifies major research gaps in our understanding of hyporheic processes. In conclusion, we highlight the potential of hyporheic restoration to efficiently manage and reactivate ecosystem functions and services in river corridors.

A tale of two treatments: the multiple barrier approach to removing chemical contaminants during potable water reuse

Abstract: ConspectusIn response to water scarcity and an increased recognition of the risks associated with the presence of chemical contaminants, environmental engineers have developed advanced water treatment systems that are capable of converting municipal wastewater effluent into drinking water. This practice, which is referred to as potable water reuse, typically relies upon reverse osmosis (RO) treatment followed by exposure to ultraviolet (UV) light and addition of hydrogen peroxide (H2O2). These two treatment processes individually are capable of controlling many of the chemical and microbial contaminants in wastewater; however, a few chemicals may still be present after treatment at concentrations that affect water quality.Low-molecular weight (<200 Da), uncharged compounds represent the greatest challenge for RO treatment. For potable water reuse systems, compounds of greatest concern include oxidation products formed during treatment (e.g., N-nitrosodimethylamine, halogenated disinfection byproducts) and...