Environmental Metabolic Footprinting (EMF) vs. half-life: a new and integrative proxy for the discrimination between control and pesticides exposed sediments in order to further characterise pesticides' environmental impact

Validation of the Chemical and Biological Steps Required Implementing an Advanced Multi-Omics Approach for Assessing the Fate and Impact of Contaminants in Lagoon Sediments

The increasing use of chemicals requires a better understanding of their presence and dynamics in the environment, as well as their impact on ecosystems. The aim of this study was to validate the first steps of an innovative multi-omics approach based on metabolomics and 16S metabarcoding data for analyses of the fate and impact of contaminants in Mediterranean lagoons. Semi-targeted analytical procedures for water and sediment matrices were implemented to assess chemical contamination of the lagoon: forty-six compounds were detected, 28 of which could be quantified in water (between 0.09 and 47.4 ng/L) and sediment (between 0.008 and 26.3 ng/g) samples using the UHPLC-MS/MS instrument. In addition, a non-targeted approach (UHPLC-HRMS) using four different sample preparation protocols based on solid/liquid extractions or an automated pressurized fluid extraction system (EDGE®) was carried out to determine the protocol with the best metabolome coverage, efficiency and reproducibility. Solid/liquid extraction using the solvent mixture acetonitrile/methanol (50/50) was evaluated as the best protocol. Microbial diversity in lagoon sediment was also measured after DNA extraction using five commercial extraction kits. Our study showed that the DNeasy PowerSoil Pro Qiagen kit (Promega, USA) was the most suitable for assessing microbial diversity in fresh sediment.

Soil metabolomics: Deciphering underground metabolic webs in terrestrial ecosystems

Soil metabolomics is an emerging approach for profiling diverse small molecule metabolites, i.e., metabolomes, in the soil. Soil metabolites, including fatty acids, amino acids, lipids, organic acids, sugars, and volatile organic compounds, often contain essential nutrients such as nitrogen, phosphorus, and sulfur and are directly linked to soil biogeochemical cycles driven by soil microorganisms. This paper presents an overview of methods for analyzing soil metabolites and the state-of-the-art of soil metabolomics in relation to soil nutrient cycling. We describe important applications of metabolomics in studying soil carbon cycling and sequestration, and the response of soil organic pools to changing environmental conditions. This includes using metabolomics to provide new insights into the close relationships between soil microbiome and metabolome, as well as responses of soil metabolome to plant and environmental stresses such as soil contamination. We also highlight the advantage of using soil metabolomics to study the biogeochemical cycles of elements and suggest that future research needs to better understand factors driving soil function and health.

LC-HRMS-Driven Computational Toolbox to Assess Extraction Protocols Dedicated to Untargeted Analysis: How to Ease Analyzing Pesticide-Contaminated Soils?

Metabolomics is a powerful approach that allows for high throughput analysis and the acquisition of large biochemical data. Nonetheless, it still faces several challenging requirements, such as the development of optimal extraction and analytical methods able to respond to its high qualitative and quantitative requisites. Hence, the objective of the present article is to suggest a LC-HRMS-based untargeted profiling approach aiming to provide performant tools that help assess the performance and the quality of extraction methods. It is applied in a herbicide-contaminated soil metabolomics context. The trifactorial experimental design consists of 150 samples issued from five different extraction protocols, two types of soils, and three contamination conditions (contaminated soils with two different formulated herbicides against uncontaminated soils). Four performance and quality criteria are investigated using adapted LC-HRMS-driven computational tools. First, 861 metabolic features are annotated, and then the width of metabolome coverage and quantitative performance of the five different extraction protocols are assessed in all samples using various optimized configurations of heatmaps as well as van Krevelen diagrams. Then, the reproducibility of LC-HRMS profiles issued from the five extractions is studied by two different approaches: Euclidean distances and relative standard deviations. The two methods are examined and compared. Their advantages and limitations are thus discussed. After, the capacity of the different extractions to discriminate between contaminated and uncontaminated soils will be evaluated using orthogonal projections to latent structures-discriminant analysis. Different data scaling parameters are tested, and the results are explored and discussed. All of the suggested computational and visualization tools are performed using public-access platforms or open-source software. They can be readapted by metabolomics developers and users according to their study contexts and fields of application.

Untargeted metabolomics as a tool to monitor biocontrol product residues' fate on field-treated Prunus persica

Evidence of chemical plant protection products' (PPPs) long-term impact has been found in all environmental compartments. Therefore, other types of PPPs are developed to complement chemical PPPs like PPPs from natural sources, namely biocontrol products (BPs). Little is known about those new BPs, and it is important to assess their potential long-term environmental impact. Recently, the Environmental Metabolic Footprinting (EMF) approach was developed. It permits studying sample's entire meta-metabolome (endometabolome and xenometabolome) through a kinetics tracking of metabolomes of treated and untreated samples. Those metabolomes are compared time-by-time to estimate the "resilience time" of the samples after treatment. The current study aims to investigate BP residues' dissipation on peach fruits (Prunus persica). For that, an untargeted Liquid Chromatography-Mass Spectrometry metabolomics approach based on the EMF was optimised to separate the xenometabolome of the PPP from the endometabolome of the fruits. This "new version" of the EMF approach is able to target the BP treatment residues' (xenometabolome) dissipation exclusively. Thus, it is able to determine the time needed to have no more residues in the studied matrix: the "dissipation interval". Field experiment was conducted on peach tree orchard against brown rot treated with (i) a plant extract BP (Akivi); (ii) a reference mineral extract BP (Armicarb®); and (iii) a Chemical reference treatment campaign. Formulated Akivi and its by-products' dissipation was monitored, a degradation kinetics appeared but the sampling did not last long enough to allow the determination of the "dissipation interval". Armicarb® and the Chemical reference's residues and by-products showed a persistence pattern along the sampling kinetics. These results indicate that the EMF approach, formerly developed on soil and sediment, is applicable for fruit matrices and can be used to investigate the fate of complex BP treatment on the matrix through the xenometabolome tracking on treated fruits.

Identification of pesticides in water samples by solid-phase extraction and liquid chromatography-electrospray ionization mass spectrometry

The Contaminants of Emerging Concern (CECs), including pesticides, have been a trending topic and Brazil is the country with the highest usage of pesticides worldwide. This study aimed to measure the presence of pesticide residues in the water from different sources in the city of Porto Alegre. We analyzed 55 samples from drinking water treatment plants, public water sites, and sewage treatment plants from winter 2018 to summer 2020 by solid-phase extraction and high-performance liquid chromatography-electrospray ionization mass spectrometry. Among 184 pesticides evaluated, 107 matched validation criteria (linearity, trueness, accuracy, repeatability, reproducibility) and 15 of them were detected in different water samples, including seven insecticides, five antifungals, and three herbicides, with a wide range of toxicity levels and noticeable seasonal differences. For the worst-case scenario evaluation, 20 out of 22 (90.9%) samples exceeded the Risk Quotient of 1. The sum of pesticide concentrations exceeded 100 ng L^-1 in 66.7% of samples in February 19 and in 75% of samples in February 20 and the total pesticide concentration has reached the worrisome mark of 1615 and 954.96 ng L^-1 respectively. Therefore, our results make evident the need to promote public policies to achieve better water quality monitoring. PRACTITIONER POINTS: Among 184 pesticides evaluated, 107 matched validation criteria (linearity, trueness, accuracy, repeatability, reproducibility). A total of 55 different water samples were analyzed, and 15 pesticides were detected and five quantified. For the worst-case scenario evaluation, 20 out of 21 samples exceeded the Risk Quotient of 1 on Feb/20. The pesticide concentrations sum exceeded 100 ng L^-1 in 66.7% of samples on February 19 and in 75% of samples on February 20. It is mandatory to improve water monitoring to guide the development of public policies concerning its quality.

Electrospray ionization and heterogeneous matrix effects in liquid chromatography/mass spectrometry based meta-metabolomics: A biomarker or a suppressed ion?

RATIONALE

Correct biomarker determination in metabolomics is crucial for unbiased conclusions and reliable applications. However, this determination is subject to several drifts, e.g. matrix effects and ion suppression in Liquid Chromatography/Mass Spectrometry (LC/MS)-based approaches. This phenomenon provokes critical issues for biomarker determination, particularly during comparative studies dealing with samples exhibiting heterogeneous complexities.

METHODS

Occurrence of the issue was coincidentally noticed when studying the environmental impact of a complex bioinsecticide: Bacillus thuringiensis israelensis. The studied samples comprised insecticide-spiked sediments and untreated control sediments. QuEChERS extractions followed by LC/ESI-Q/ToF analyses were performed on sediments after 15 days of incubation. Meta-metabolomes containing pesticide xenometabolites and sediment endometabolites were analyzed in depth using XCMS-based computational data preprocessing. Multivariate statistical analyses (PCA, OPLS-DA) and raw data crosschecks were performed to search for environmental biomarkers.

RESULTS

Multivariate analyses and raw data crosschecks led to the selection of nine metabolites as biomarker candidates. However, when exploring the mass spectra, co-elutions were noticed between seven of these metabolites and multi-charged macromolecules originating from the pesticide. Provoked false positives were thus suspected due to a potential ion suppression exclusively occurring in the spiked samples. A dilution-based approach was then applied. It confirmed five metabolites as suppressed ions.

CONCLUSIONS

Ion suppression should be considered as a critical issue for biomarker determination when comparing heterogeneous metabolic profiles. Raw chromatograms and mass spectra crosschecks are mandatory to reveal potential ion suppressions in such cases. Dilution is a suitable approach to filter reliable biomarker candidates before their identification and absolute quantification.

Environmental and socioeconomic effects of mosquito control in Europe using the biocide Bacillus thuringiensis subsp. israelensis (Bti)

Bacillus thuringiensis subsp. israelensis (Bti) has been used in mosquito control programs to reduce nuisance in Europe for decades and is generally considered an environmentally-safe, effective and target-specific biocide. However, the use of Bti is not uncontroversial. Target mosquitoes and affected midges represent an important food source for many aquatic and terrestrial predators and reduction of their populations is likely to result in food-web effects at higher trophic levels. In the context of global biodiversity loss, this appears particularly critical since treated wetlands are often representing conservation areas. In this review, we address the current large-scale use of Bti for mosquito nuisance control in Europe, provide a description of its regulation followed by an overview of the available evidence on the parameters that are essential to evaluate Bti use in mosquito control. Bti accumulation and toxin persistence could result in a chronic expose of mosquito populations ultimately affecting their susceptibility, although observed increase in resistance to Bti in mosquito populations is low due to the four toxins involved. A careful independent monitoring of mosquito susceptibility, using sensitive bioassays, is mandatory to detect resistance development timely. Direct Bti effects were documented for non-target chironomids and other invertebrate groups and are discussed for amphibians. Field studies revealed contrasting results on possible impacts on chironomid abundances. Indirect, food-web effects were rarely studied in the environment. Depending on study design and duration, Bti effects on higher trophic levels were demonstrated or not. Further long-term field studies are needed, especially with observations of bird declines in Bti-treated wetland areas. Socio-economic relevance of mosquito control requires considering nuisance, vector-borne diseases and environmental effects jointly. Existing studies indicate that a majority of the population is concerned regarding potential environmental effects of Bti mosquito control and that they are willing to pay for alternative, more environment-friendly techniques.

Does in vitro selection of biocontrol agents guarantee success in planta? A study case of wheat protection against Fusarium seedling blight by soil bacteria

Biological control is a great hope for reducing the overutilization of pesticides in agricultural soils. It often involves microorganisms or molecules produced by microorganisms that will be able to interact with either a plant or pathogens of this plant to reduce the growth of the pathogen and limit its negative impact on the host plant. When new biocontrol products are developed, strains were mostly selected based on their ability to inhibit a pathogen of interest under in vitro conditions via antagonistic effects. Strains with no in vitro effect are often discarded and not tested in planta. But is the in vitro selection of bacterial agents according to their antagonism activities towards a plant pathogen the best way to get effective biocontrol products? To answer this question, we used wheat and the fungal pathogen Fusarium graminearum as a study pathosystem model. A library of 205 soil bacteria was screened in 2 types of in vitro growth inhibition tests against F. graminearum, and in an in planta experiment. We find strains which do not have inhibition phenotypes in vitro but good efficacy in planta. Interestingly, some strains belong to species (Microbacterium, Arthrobacter, Variovorax) that are not known in the literature for their ability to protect plants against fungal pathogens. Thus, developing a biocontrol product against F. graminearum must be preferentially based on the direct screening of strains for their protective activity on wheat plants against fungal diseases, rather than on their in vitro antagonistic effects on fungal growth.

Removal and extraction efficiency of Quaternary ammonium herbicides paraquat (PQ) from aqueous solution by ketoenol-pyrazole receptor functionalized silica hybrid adsorbent (SiNPz)

Pesticides and herbicides have been used extensively in agricultural practices to control pests and increase crop yields. Paraquat (PQT²⁺, 1,1-dimethyl-4,4-dipyridinium chloride) is one of the herbicide that belois classified as bipyridines and is used over the world. The objective of this study is to use ketoenol–pyrazole receptor functionalized silica hybrid as adsorbent for removal PQT²⁺ from aqueous solution. The adsorbent was synthesized, and characterized using scanning electron microscopy (SEM), nuclear magnetic resonance (NMR), Thermal analysis and other techniques. Different experimental parameters such as the effect of the amount of adsorbent, solution pH and temperatures and contact times were studied. Pseudo-order kinetics models were studied, and our data followed a pseudo second order. Experimental data were analyzed for both Langmuir and Freundlich models and the data fitted well with the Langmuir isotherm model. To understand the mechanism of adsorption, thermodynamic parameters like standard enthalpy, standard Gibbs free energy, and standard entropy were studied. The study indicated that the process is spontaneous, exothermic in nature and follow physisorption mechanisms. The novelty of this study showed surface of pyrazol-enol-imine-substituted silica (SiNPz) has the ability to highlight the surface designed for efficient removal of PQT²⁺, from aqueous solutions more than other studies. The study also showed that ketoenol–pyrazole receptor can be regenerated in five cycles using HNO₃ without affecting its adsorption capacity.