Environmental Metabolic Footprinting: A novel application to study the impact of a natural and a synthetic β-triketone herbicide in soil

Natural products for biocontrol: review of their fate in the environment and impacts on biodiversity

Biocontrol solutions (macroorganisms, microorganisms, natural substances, semiochemicals) are presented as potential alternatives to conventional plant protection products (PPPs) because they are supposed to have lower impacts on ecosystems and human health. However, to ensure the sustainability of biocontrol solutions, it is necessary to document the unintended effects of their use. Thus, the objectives of this work were to review (1) the available biocontrol solutions and their regulation, (2) the contamination of the environment (soil, water, air) by biocontrol solutions, (3) the fate of biocontrol solutions in the environment, (4) their ecotoxicological impacts on biodiversity, and (5) the impacts of biocontrol solutions compared to those of conventional PPPs. Very few studies concern the presence of biocontrol solutions in the environment, their fate, and their impacts on biodiversity. The most important number of results were found for the organisms that have been used the longest, and most often from the angle of their interactions with other biocontrol agents. However, the use of living organisms (microorganisms and macroorganisms) in biocontrol brings a specific dimension compared to conventional PPPs because they can survive, multiply, move, and colonize other environments. The questioning of regulation stems from this specific dimension of the use of living organisms. Concerning natural substances, the few existing results indicate that while most of them have low ecotoxicity, others have a toxicity equivalent to or greater than that of the conventional PPPs. There are almost no result regarding semiochemicals. Knowledge of the unintended effects of biocontrol solutions has proved to be very incomplete. Research remains necessary to ensure their sustainability.

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.

Long-term effects of oil contamination on soil quality and metabolic function

Widespread soil contamination with oil and the toxicity of petroleum hydrocarbons to soil biota make it extremely important to study microbial responses to oil stress. Soil metabolites reflect the main metabolic pathways in the soil microbial community. The examination of changes in the soil metabolic profile and metabolic function is essential for a better understanding of the nature of the pollution and restoration of the disturbed soils. The present study aimed to assess the long-term effect of oil on the ecological state of the soil, evaluate quantitative and qualitative differences in metabolite composition between soil contaminated with oil and non-contaminated soil, and reveal biologically active metabolites that are related to oil contamination and can be used for contamination assessment. A long-term field experiment was conducted to examine the effects of various oil concentrations on the biochemical properties and metabolic profile of the soil. Podzolic soil contaminated with oil demonstrated the long-term inhibition of soil biological activity and vegetation. Oil affected the metabolic activity of soil fungi increasing the production of toxic metabolites. A metabolomic approach was employed to determine soil metabolites. The metabolite profile was found to vary greatly between oil-contaminated and non-contaminated soils. Carbohydrates had the largest number of metabolites negatively affected by oil, while the content of organic acids, phenolic compounds, and terpenoids was mainly increased in oil-contaminated soil. The evaluation of the long-term impact of oil on microbial metabolism can make a valuable contribution to the assessment of soil quality and the activity of soil microorganisms being under stress from oil pollution. The results contribute to a further understanding of the role of microorganisms in the ecological functions of contaminated soil, which can be useful in the development of rehabilitation strategies for disturbed sites.

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.

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.

Local Phenomena Shape Backyard Soil Metabolite Composition

Soil covers most of Earth's continental surface and is fundamental to life-sustaining processes such as agriculture. Given its rich biodiversity, soil is also a major source for natural product drug discovery from soil microorganisms. However, the study of the soil small molecule profile has been challenging due to the complexity and heterogeneity of this matrix. In this study, we implemented high-resolution liquid chromatography-tandem mass spectrometry and large-scale data analysis tools such as molecular networking to characterize the relative contributions of city, state and regional processes on backyard soil metabolite composition, in 188 soil samples collected from 14 USA States, representing five USA climate regions. We observed that region, state and city of collection all influence the overall soil metabolite profile. However, many metabolites were only detected in unique sites, indicating that uniquely local phenomena also influence the backyard soil environment, with both human-derived and naturally-produced (plant-derived, microbially-derived) metabolites identified. Overall, these findings are helping to define the processes that shape the backyard soil metabolite composition, while also highlighting the need for expanded metabolomic studies of this complex environment.

Metabolomic characterization of sunflower leaf allows discriminating genotype groups or stress levels with a minimal set of metabolic markers

INTRODUCTION

Plant and crop metabolomic analyses may be used to study metabolism across genetic and environmental diversity. Complementary analytical strategies are useful for investigating metabolic changes and searching for biomarkers of response or performance.

METHODS AND OBJECTIVES

The experimental material consisted in eight sunflower lines with two line status, four restorers (R, used as males) and four maintainers (B, corresponding to females) routinely used for sunflower hybrid varietal production, respectively to complement or maintain the cytoplasmic male sterility PET1. These lines were either irrigated at full soil capacity (WW) or submitted to drought stress (DS). Our aim was to combine targeted and non-targeted metabolomics to characterize sunflower leaf composition in order to investigate the effect of line status genotypes and environmental conditions and to find the best and smallest set of biomarkers for line status and stress response using a custom-made process of variables selection.

RESULTS

Five hundred and eighty-eight metabolic variables were measured by using complementary analytical methods such as 1H-NMR, MS-based profiles and targeted analyses of major metabolites. Based on statistical analyses, a limited number of markers were able to separate WW and DS samples in a more discriminant manner than previously published physiological data. Another metabolic marker set was able to discriminate line status.

CONCLUSION

This study underlines the potential of metabolic markers for discriminating genotype groups and environmental conditions. Their potential use for prediction is discussed.

Assessment of the ecotoxicological impact of natural and synthetic β-triketone herbicides on the diversity and activity of the soil bacterial community using omic approaches

The emergence of pesticides of natural origin appears as an environmental-friendly alternative to synthetic pesticides for managing weeds. To verify this assumption, leptospermone, a natural β-triketone herbicide, and sulcotrione, a synthetic one, were applied to soil microcosms at 0× (control), 1× or 10× recommended field dose. The fate of these two herbicides (i.e. dissipation and formation of transformation products) was monitored to assess the scenario of exposure of soil microorganisms to natural and synthetic herbicides. Ecotoxicological impact of both herbicides was explored by monitoring soil bacterial diversity and activity using next-generation sequencing of 16S rRNA gene amplicons and soil metabolomics. Both leptospermone and sulcotrione fully dissipated over the incubation period. During their dissipation, transformation products of natural and synthetic β-triketone were detected. Hydroxy-leptospermone was almost completely dissipated by the end of the experiment, while CMBA, the major metabolite of sulcotrione, remained in soil microcosms. After 8 days of exposure, the diversity and structure of the soil bacterial community treated with leptospermone was significantly modified, while less significant changes were observed for sulcotrione. For both herbicides, the diversity of the soil bacterial community was still not completely recovered by the end of the experiment (45 days). The combined use of next-generation sequencing and metabolomic approaches allowed us to assess the ecotoxicological impact of natural and synthetic pesticides on non-target soil microorganisms and to detect potential biomarkers of soil exposure to β-triketones.

Metabolomics approaches for the discrimination of disease suppressive soils for Rhizoctonia solani AG8 in cereal crops using 1H NMR and LC-MS

The suppression of soilborne crop pathogens such as Rhizoctonia solani AG8 may offer a sustainable and enduring method for disease control, though soils with these properties are difficult to identify. In this study, we analysed the soil metabolic profiles of suppressive and non-suppressive soils over 2 years of cereal production. We collected bulk and rhizosphere soil at different cropping stages and subjected soil extracts to liquid chromatography-mass spectrometry (LC-MS) and proton nuclear magnetic resonance spectroscopy (¹H NMR) analyses. Community analyses of suppressive and non-suppressive soils using principal component analyses and predictive modelling of LC-MS and NMR datasets respectively, revealed distinct biochemical profiles for the two soil types with clustering based on suppressiveness and cropping stage. NMR spectra revealed the suppressive soils to be more abundant in sugar molecules than non-suppressive soils, which were more abundant in lipids and terpenes. LC-MS features that were significantly more abundant in the suppressive soil were identified and assessed as potential biomarkers for disease suppression. The structures of a potential class of LC-MS biomarkers were elucidated using accurate mass data and MS fragmentation spectrum information. The most abundant compound found in association with suppressive soils was confirmed to be a macrocarpal, which is an antimicrobial secondary metabolite. Our study has demonstrated the utility of environmental metabolomics for the study of disease suppressive soils, resulting in the discovery of a macrocarpal biomarker for R. solani AG8 suppressive soil which can be further studied functionally in association with suppression pot trials and microbial isolation studies.

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

Pesticides are regularly used for a variety of applications and are disseminated throughout the environment. These substances may have significant negative impacts. To date, the half-life, t_1/2, was often used to study the fate of pesticides in environmental matrices (water, soil, sediment). However, this value gives limited information. First, it does not evaluate the formation of by-products, resulting in the need for additional experiments to be performed to evaluate biodegradation and biotransformation products. T_1/2 also fails to consider the chemical's impact on biodiversity. Resilience time, a new and integrative proxy, was recently proposed as an alternative to t_1/2, with the potential to evaluate all the post-application effects of the chemical on the environment. The 'Environmental Metabolic Footprinting' (EMF) approach, giving an idea of the resilience time, was used to evaluate the impact of botanicals on soil. The goal is to optimise the EMF to study the impact of a microbial insecticide, the Bacillus thuringiensis israelensis (Bti), on sediment. The difficulty of this work lies in the commercial solution of Bti that is really complex, and this complexity yields chromatograms that are extremely difficult to interpret; t_1/2 cannot be used. No methodologies currently exist to monitor the impact of these compounds on the environment. We will test the EMF to determine if it is sensitive enough to tolerate such complex mixtures. A pure chemical insecticide, the α-cypermethrin, will be also studied. The article shows that the EMF is able to distinguish meta-metabolome differences between control and exposed (with Bti) sediments.

Evidence for photolytic and microbial degradation processes in the dissipation of leptospermone, a natural β-triketone herbicide

Bioherbicides appear as an ecofriendly alternative to synthetic herbicides, generally used for weed management, because they are supposed to have low side on human health and ecosystems. In this context, our work aims to study abiotic (i.e., photolysis) and biotic (i.e,. biodegradation) processes involved in the fate of leptospermone, a natural β-triketone herbicide, by combining chemical and microbiological approaches. Under controlled conditions, the photolysis of leptospermone was sensitive to pH. Leptospermone has a half-life of 72 h under simulated solar light irradiations. Several transformation products, including hydroxy-leptospermone, were identified. For the first time, a bacterial strain able to degrade leptospermone was isolated from an arable soil. Based on its 16S ribosomal RNA (rRNA) gene sequence, it was affiliated to the Methylophilus group and was accordingly named as Methylophilus sp. LS1. Interestingly, we report that the abundance of OTUs, similar to the 16S rRNA gene sequence of Methylophilus sp. LS1, was strongly increased in soil treated with leptospermone. The leptospermone was completely dissipated by this bacteria, with a half-life time of 6 days, allowing concomitantly its growth. Hydroxy-leptospermone was identified in the bacterial culture as a major transformation product, allowing us to propose a pathway of transformation of leptospermone including both abiotic and biotic processes.

Structural and functional measures of marine microbial communities: An experiment to assess implications for oil spill management

Microbial communities are ecologically important in aquatic environments and impacts on microbes have the potential to affect a number of functional processes. We have amended seawater with a crude oil and assessed changes in species composition as well as a measure of functional diversity (the ability of the community to utilise different carbon sources) and the community level metabolic signature. We found that there was a degree of functional redundancy in the community we tested. Oiled assemblages became less diverse and more dominated by specialist hydrocarbon degraders, carbon source utilisation increased initially but there was no change in metabolic signature in this small scale laboratory experiment. This study supports the decision framework around management of oil spills. This package of methods has the potential to be used in the testing and selection of new dispersants for use in oil spill response.

Presence of the β-triketone herbicide tefuryltrione in drinking water sources and its degradation product in drinking waters

Triketone herbicides are becoming popular because of their herbicidal activity against sulfonylurea-resistant weeds. Among these herbicides, tefuryltrione (TFT) is the first registered herbicide for rice farming, and recently its distribution has grown dramatically. In this study, we developed analytical methods for TFT and its degradation product 2-chloro-4-methylsulfonyl-3-[(tetrahydrofuran-2-yl-methoxy) methyl] benzoic acid (CMTBA). TFT was found frequently in surface waters in rice production areas at concentrations as high as 1.9 μg/L. The maximum observed concentration was lower than but close to 2 μg/L, which is the Japanese reference concentration of ambient water quality for pesticides. However, TFT was not found in any drinking waters even though the source waters were purified by conventional coagulation and filtration processes; this was due to chlorination, which transforms TFT to CMTBA. The conversion rate of TFT to CMBA on chlorination was almost 100%, and CMTBA was stable in the presence of chlorine. Moreover, CMTBA was found in drinking waters sampled from household water taps at a similar concentration to that of TFT in the source water of the water purification plant. Although the acceptable daily intake and the reference concentration of CMTBA are unknown, the highest concentration in drinking water exceeded 0.1 μg/L, which is the maximum allowable concentration for any individual pesticide and its relevant metabolites in the European Union Drinking Directive.