Development and implementation of eco-genomic tools for aquatic ecosystem biomonitoring: the SYNAQUA French-Swiss program

The effectiveness of environmental protection measures is based on the early identification and diagnosis of anthropogenic pressures. Similarly, restoration actions require precise monitoring of changes in the ecological quality of ecosystems, in order to highlight their effectiveness. Monitoring the ecological quality relies on bioindicators, which are organisms revealing the pressures exerted on the environment through the composition of their communities. Their implementation, based on the morphological identification of species, is expensive because it requires time and experts in taxonomy. Recent genomic tools should provide access to reliable and high-throughput environmental monitoring by directly inferring the composition of bioindicators’ communities from their DNA (metabarcoding). The French-Swiss program SYNAQUA (INTERREG France-Switzerland 2017–2019) proposes to use and validate the tools of environmental genomic for biomonitoring and aims ultimately at their implementation in the regulatory bio-surveillance. SYNAQUA will test the metabarcoding approach focusing on two bioindicators, diatoms, and aquatic oligochaetes, which are used in freshwater biomonitoring in France and Switzerland. To go towards the renewal of current biomonitoring practices, SYNAQUA will (1) bring together different actors: scientists, environmental managers, consulting firms, and biotechnological companies, (2) apply this approach on a large scale to demonstrate its relevance, (3) propose robust and reliable tools, and (4) raise public awareness and train the various actors likely to use these new tools. Biomonitoring approaches based on such environmental genomic tools should address the European need for reliable, higher-throughput monitoring to improve the protection of aquatic environments under multiple pressures, guide their restoration, and follow their evolution.     

Polynomial Surrogates for Open-Channel Flows in Random Steady State

Assessing epistemic uncertainties is considered as a milestone for improving numerical predictions of a dynamical system. In hydrodynamics, uncertainties in input parameters translate into uncertainties in simulated water levels through the shallow water equations. We investigate the ability of generalized polynomial chaos (gPC) surrogate to evaluate the probabilistic features of water level simulated by a 1-D hydraulic model (MASCARET) with the same accuracy as a classical Monte Carlo method but at a reduced computational cost. This study highlights that the water level probability density function and covariance matrix are better estimated with the polynomial surrogate model than with a Monte Carlo approach on the forward model given a limited budget of MASCARET evaluations. The gPC-surrogate performance is first assessed on an idealized channel with uniform geometry and then applied on the more realistic case of the Garonne River (France) for which a global sensitivity analysis using sparse least-angle regression was performed to reduce the size of the stochastic problem. For both cases, Galerkin projection approximation coupled to Gaussian quadrature that involves a limited number of forward model evaluations is compared with least-square regression for computing the coefficients when the surrogate is parameterized with respect to the local friction coefficient and the upstream discharge. The results showed that a gPC-surrogate with total polynomial degree equal to 6 requiring 49 forward model evaluations is sufficient to represent the water level distribution (in the sense of the \(\ell _2\) norm), the probability density function and the water level covariance matrix for further use in the framework of data assimilation. In locations where the flow dynamics is more complex due to bathymetry, a higher polynomial degree is needed to retrieve the water level distribution. The use of a surrogate is thus a promising strategy for uncertainty quantification studies in open-channel flows and should be extended to unsteady flows. It also paves the way toward cost-effective ensemble-based data assimilation for flood forecasting and water resource management.     

Interaction webs in arctic ecosystems: Determinants of arctic change?

How species interact modulate their dynamics, their response to environmental change, and ultimately the functioning and stability of entire communities. Work conducted at Zackenberg, Northeast Greenland, has changed our view on how networks of arctic biotic interactions are structured, how they vary in time, and how they are changing with current environmental change: firstly, the high arctic interaction webs are much more complex than previously envisaged, and with a structure mainly dictated by its arthropod component. Secondly, the dynamics of species within these webs reflect changes in environmental conditions. Thirdly, biotic interactions within a trophic level may affect other trophic levels, in some cases ultimately affecting land–atmosphere feedbacks. Finally, differential responses to environmental change may decouple interacting species. These insights form Zackenberg emphasize that the combination of long-term, ecosystem-based monitoring, and targeted research projects offers the most fruitful basis for understanding and predicting the future of arctic ecosystems.     

Polycyclic aromatic hydrocarbons: bees, honey and pollen as sentinels for environmental chemical contaminants

Three beehive matrices, sampled in six different apiaries from West France, were analyzed for the presence of four polycyclic aromatic hydrocarbons (PAH4: benzo[a]pyrene, benzo[a]anthracene, benzo[b]fluoranthene and chrysene). Samples were collected during four different periods in both 2008 and 2009. Honey samples showed the lowest levels of PAH4 contamination (min = 0.03 μg kg⁻¹; max = 5.80 μg kg⁻¹; mean = 0.82 μg kg⁻¹; Sd = 1.17). Bee samples exhibited higher levels of PAH4 contamination (min = 0.32 μg kg⁻¹; max = 73.83 μg kg⁻¹; mean = 7.03 μg kg⁻¹; Sd = 17.83) with a great dispersion of the concentrations due to four main events of high concentrations. Pollen samples showed only one major episode with the highest PAH4 concentration found (min = 0.33 μg kg⁻¹; max = 129.41 μg kg⁻¹; mean = 7.10 μg kg⁻¹; Sd = 22.28). The PAH4 concentrations found were significantly influenced by the landscape context for all beehive samples.     

Carbamazepine, carbamazepine epoxide and dihydroxycarbamazepine sorption to soil and occurrence in a wastewater reuse site in Tunisia

Although a number of manufactured nanoparticles are applied for the medical and clinical purposes, the understanding of interaction between nanomaterials and biological systems are still insufficient. Using nematode Caenorhabditis elegans model organism, we here investigated the in vivo toxicity or safety of hydroxylated fullerene nanoparticles known to detoxify anti-cancer drug-induced oxidative damages in mammals. The survival ratio of C. elegans rapidly decreased by the uptake of nanoparticles from their L4 larval stage with resulting in shortened lifespan (20 d). Both reproduction rate and body size of C. elegans were also reduced after exposure to 100 μg mL⁻¹ of fullerol. We found ectopic cell corpses caused by apoptotic cell death in the adult worms grown with fullerol nanoparticles. By the mutation of core pro-apoptotic regulator genes, ced-3 and ced-4, these nanoparticle-induced cell death were significantly suppressed, and the viability of animals consequently increased despite of nanoparticle uptake. The apoptosis-mediated toxicity of nanoparticles particularly led to the disorder of digestion system in the animals containing a large number of undigested foods in their intestine. These results demonstrated that the water-soluble fullerol nanoparticles widely used in medicinal applications have a potential for inducing apoptotic cell death in multicellular organisms despite of their antioxidative detoxifying property.     

Genotoxicity of sediment extracts of the Berre lagoon (France)

To evaluate the genotoxic risk that contaminated sediment could constitute for benthic organisms, three contaminated (VA, VC and VN) and one uncontaminated (RN) sediment samples were collected in the Berre lagoon (France). Potentially bioavailable contaminants in sediments were obtained using sediment extraction with synthetic seawater adjusted to pH 4 or pH 6, simulating the range of pH prevailing in the digestive tract of benthic organisms. The genotoxic activities of these extracts were evaluated by three short-term bioassays: the Salmonella mutagenicity test using the Salmonella typhimurium strain TA102, the alkaline comet assay and the micronucleus assay on the Chinese Hamster Ovary cells CHO-K1. Results of the Salmonella mutagenicity assay detected a mutagenic response for RN extract at pH 6, and for VA extract at pH 4. Results of the comet and micronucleus assays detected low genotoxic/clastogenic activities for VA and VC extracts at pH 6 and higher activities for RN, VA and VC extracts at pH 4. To identify if metals (Al, Fe, Mn, As, Cd, Co, Cr, Cu, Hg, Ni, Pb and Zn) were involved in these genotoxic activities, their concentrations were determined in the extracts, and their speciation was assessed by thermodynamic calculations. Results showed that extracts from sites VA, VC and VN generally presented the highest trace metal contents for both extractants, while the site RN presented lower trace metal contents but the highest Fe and Mn contents. Thermodynamic calculations indicated that Fe, Mn, As and in a lower extend Co, Ni and Zn were mainly present under free forms in extracts, and were consequently, more likely able to induce a genotoxic effect. Results globally showed no correspondence between free metal contents and genotoxic activities. They suggested that these positive results could be due to uncharacterized compounds, acting as direct genotoxic agents or enhancing the genotoxic properties of analyzed metals.     

Visualization and localization of bromotoluene distribution in Hedera helix using NanoSIMS

Some plants are known as indoor air purifiers. A large number of studies report kinetic purification results for an extensive panel of plants, i.e. the pollutant concentration (volatile organic compounds, as known as VOC, most of the time) is continuously monitored by gas chromatography. However, only a few papers describe the mechanisms involved in such processes. This study deals with the use of secondary ion mass spectrometry imaging as an efficient tool to locate atmospheric pollutant as bromotoluene within the Hedera helix plant (leaf, roots) and the substrate on which it was previously grown. Hedera helix plants have been placed in a pollution chamber with control of the exposure parameters. Plant and soil samples excised were transferred into a fixative solution of glutaraldehyde and paraformaldehyde for a few days, were dehydrated using ethanol and were embedded with resin. Cross sections were made from the pale brown solids obtained. Then, a device using a cathodic pulverization device capable of depositing a few nanometers of gold atoms over the sample was used to make the surface electronically conductive for the NanoSIMS. Hence, polluted and unpolluted samples of Hedera helix and substrates were obtained following a careful procedure that allowed for the discrimination between polluted and nonpolluted ones. Nanoscale spatial resolution was an invaluable tool (NanoSIMS) to achieve this, and proved that VOCs, such as bromotoluene, were actually trapped by plants such as Hedera helix.     

Cross-Media Environmental Impacts of Air Pollution Regulations for a Coal-Fired Power Plant

The types and rates of pollutant emissions from a coal-fired power plant depend upon plant design, coal characteristics, and environmental control policy. In the past, air pollution regulations were often promulgated without rigorous analysis of the resulting energy penalties and secondary environmental impacts that occur in other environmental media (air, land, or water), which are counterproductive to overall environmental quality. This paper describes a Comparative Assessment Model that has been developed to consider systematically such tradeoffs for conventional and advanced coal-to-electric technologies. The model is applied to quantify the secondary (“cross-media”) environmental and resource impacts resulting from alternative air pollution control policies that reduce sulfur dioxide emissions from a 1000 MW power plant. Multimedia pollutant burdens are presented, together with the increased requirements for coal, limestone, and water that are incurred in generating a fixed net quantity of electricity. The development of sound public policy requires that environmental regulations be sensitive to adverse effects in all environmental media, and that tradeoffs involved in the regulation of specific pollutants to one medium be rigorously and systematically characterized.     

DNA damage in caged Gammarus fossarum amphipods: a tool for freshwater genotoxicity assessment

The aim of this study was to propose a tool for freshwater environmental genotoxicity assessment using Gammarus fossarum, a high ecologically relevant species. In a first part, gammarids were caged upstream and downstream wastewater treatment plant effluent output. The sensitivity of genotoxic responses of haemocytes, oocytes and spermatozoa was compared using the Comet assay. Spermatozoa appeared to be the most sensitive, suitable and relevant cell type for genotoxicity risk assessment. In a second part, a watershed-scale study was conducted over 2 years to evaluate the applicability of our caging procedure. The genotoxic impact of a contamination was followed, taking into account seasonal variability. DNA damage in spermatozoa exhibited low basal level and low variability in control upstream sites, providing a reliable discrimination of polluted sites. Finally, DNA damage in caged G. fossarum has been proved to be a sensitive and reproducible tool for freshwater genotoxicity assessment.     

Atmospheric fate of non-volatile and ionizable compounds

A modified version of the Multimedia Activity Model for Ionics MAMI, including two-layered atmosphere, air-water interface partitioning, intermittent rainfall and variable cloud coverage was developed to simulate the atmospheric fate of ten low volatility or ionizable organic chemicals. Probabilistic simulations describing the uncertainty of substance and environmental input properties were run to evaluate the impact of atmospheric parameters, ionization and air-water (or air-ice) interface enrichment.The rate of degradation and the concentration of OH radicals, the duration of dry and wet periods, and the parameters describing air-water partitioning (K_AW and temperature) and ionization (pK_a and pH) are the key parameters determining the potential for long range transport. Wet deposition is an important removal process, but its efficiency is limited, primarily by the duration of the dry period between precipitation events.Given the underlying model assumptions, the presence of clouds contributes to the higher persistence in the troposphere because of the capacity of cloud water to accumulate and transport non-volatile (e.g. 2,4-D) and surface-active chemicals (e.g. PFOA). This limits the efficiency of wet deposition from the troposphere enhancing long-range transport.