Agriculture intensification, massively relying on pesticides, led to the widespread contamination of noncrop terrestrial ecosystems. Soil contamination with pesticide residues widely occurs but its cryptic effects on terrestrial biotic interactions remain unclear, especially at the metabolic scale. We studied the effects of an environmental dose of the herbicide isoproturon on an isoproturon-degrading Sphingomonas soil bacteria - Lolium perenne (Poaceae) and Rhopalosiphum padi (Hemiptera: aphididae) system - in the laboratory. This system is typical of contaminated peri-agricultural ecosystems, such as vegetated buffer strips. We found that isoproturon and its main degradation product transferred from the substrate to aphids, accumulating in plant shoots. No macroscopic effects of the herbicide were observed, but primary metabolites varied in both plants and herbivores. Inoculation of isoproturon-degrading bacteria reduced isoproturon levels in the substrate and suppressed most metabolic variations. Moreover, inoculation of the non-degrading bacterial strain impacted plant metabolism, potentially through mutualistic interaction, underlining the close link between soil microbiota and aboveground organisms. This study shows that isoproturon residues can transfer in a typical grassland trophic system, altering the metabolism of each biological level. It emphasizes the need to consider above- and belowground interactions when assessing seminatural ecosystems' responses to chronic contamination.

Food security in many parts of the world is threatened by reduced water availability, resulting from population growth and climate change. Under these circumstances, irrigating crops with reclaimed water is becoming an increasingly important agricultural practice. A framework is proposed to address these concerns, evaluate how effectively current regulations ensure safe and sustainable water reuse in the context of antimicrobial resistance (AMR), and identify opportunities for more targeted guidance. The paper proposes indicators for water quality assessment that take into account risks specific to AMR and define primary contamination entry points, potential amplification points, and barriers (e.g., contaminant dissipation in soil, delay between irrigation and harvest, postharvest management), along the wastewater-irrigation, water-crop, and production-consumer continuum. In terms of risk management, an overview of the range of water and wastewater treatment options is provided, from secondary sewage treatments to advanced treatments, including weighing the costs and benefits of interventions in the context of local needs and constraints and the availability and quality of alternative irrigation water sources. The recommendations herein were developed through a consensus at an international multidisciplinary expert workshop and literature review.

BACKGROUND:Sclerotinia sclerotiorum is a major crop pathogen commonly managed using fungicides. Efficient biological alternatives are needed but it is essential to determine whether a biocontrol agent persists in soil and affects non-target microbiota. Here, we assessed the environmental fate and the impact of a novel Bacillus sp. strain (SCL1) on soil microbial communities from three contrasted agricultural soils. The fate and effects of SCL1 applied at an agronomical (LD) or elevated (HD) dose were compared with a commercial biocontrol product, tebuconazole, and an untreated control. RESULTS:SCL1 persistence was monitored by selective plate counts and strain-specific quantitative polymerase chain reaction (qPCR) analysis. After inoculation, SCL1 declined rapidly but remained detectable up to day 168; at late time points the SCL1 population stabilized at low levels [~103 colony-forming units (CFU) g-1 in the high-dose treatment], supporting its long-term persistence. Treatment effects on microbial community composition were limited: differentially abundant operational taxonomic units (OTUs) represented up to 9.9% of bacterial and 3.8% of fungal communities. Fungal taxa associated with soil functioning increased under SCL1 treatment in some soils; e.g., Mortierellomycetes in Trugny soil (5.7% in control versus 10.7% under low-dose SCL1 at day 56). CONCLUSION:SCL1 persisted for at least 6 months in soil microcosms and induced small shifts in bacterial and fungal communities, comparable with reference products. These findings support further field studies to evaluate the efficacy of SCL1 against S. sclerotiorum in rapeseed crops, as well as its persistence and potential non-target effects on soil microbiota. © 2026 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

During crop growth cycle, several different plant protection products (PPPs) are often applied in combination or sequentially. Such sequential applications result in unintentional mixtures of residues that may affect ecosystem services supported by non-target organisms such as soil microbes and nematodes. This scenario of sequential PPP application is frequent in agricultural practice but rarely addressed experimentally at field scale with regard to environmental impacts. The objective of this study was to evaluate the effect of individual and sequential application of three PPPs (the herbicide clopyralid, the insecticide zeta-cypermethrin, and the fungicide pyraclostrobin) on soil microbial communities, and on the abundance of free-living nematode. Single applications (at 1× or 10× the agronomical dose) were made to triplicated field plots with each one of the PPPs or all three PPPs in sequence, with untreated plots serving as controls. Plots were sampled before each application and 7 and 28 days thereafter. The composition and abundance of the fungal community were found to be more affected compared to the bacterial community by PPP applications, while the bacterial community structure was influenced mainly by soil properties. Only transient effects of PPP applications were detected on nematode abundance. Higher-tier ecotoxicological tests such as the present field study offer greater ecological relevance compared to laboratory tests but are challenged by environmental variations that should be accounted for when evaluating the ecotoxicity of pesticides on soil microorganisms.

Understanding emerging functions at the scale of a bacterial community is a major challenge in microbial ecology and could lead up to promising tools for engineering microbial communities, for example in bioremediation. Here, through a top-down approach we obtained compositional variants of pesticide and antibiotics-degrading communities and further investigated communities features associated with their degradation abilities. We first tested whether diversity index or functional genes abundance could reliably be used as a proxy for this function, and obtained encouraging, albeit variable results. Further, through the use of statistical tools borrowed from the genomic selection literature, we were able to derive accurate prediction of the mineralisation potential of a bacterial community, based on its composition. However, the parallel between genotype-phenotype and community composition-mineralisation potential suffers a crucial caveat: bacterial abundances vary on a much wider scale than allele dosage at a given locus and are prone to change over time (particularly at the mineralisation scale). Here we observed that using presence/absence data instead of relative abundance can overcome these limitations and provide a clearer functional signal for mineralisation prediction through linear regression models. Random forest can also intrinsically deal with microbial data without transformation and select for significant predictors. We suggest drawing inspiration from the tools and concepts used in genotype-phenotype mapping to elucidate microbial functions at the community level while keeping in mind the significant differences between these two fields. This parallel is here exemplified by the concept of microbial architecture of degrading functions, akin to the genetic architecture of phenotypic traits.

For many years, there has been an unprecedented decline in biodiversity on a global scale, triggered largely by the use of plant protection products. In this context, a collective scientific assessment was conducted to identify current consensus knowledge and further needs regarding the impacts of plant protection products on biodiversity and ecosystem services in France, including its overseas territories. A particular focus was placed on chlordecone, a highly persistent organochlorine insecticide used extensively in the French West Indies (FWI) for more than 20 years (1972-1993) to control the banana root borer, but also in Eastern Europe, the USA, South America and Africa for various uses. The FWI support biodiversity hotspots, with many endemic and endangered species, and include marine and terrestrial protected areas. Such an environmental context is therefore highly relevant for studying the links between chlordecone contamination and potential effects on biodiversity. Thus, the objective of this work was to review the contamination of the FWI environment by chlordecone, its transfer through ecosystems, and its effects on biodiversity and ecosystem services. Literature analysis emphasized valuable knowledge of chlordecone ecodynamics in terrestrial, freshwater, and marine ecosystems. A wide diversity of terrestrial and aquatic organisms is chronically exposed to chlordecone. However, despite 15 years of public policy dedicated to developing knowledge on chlordecone's fate and impacts, the knowledge gap remains critical regarding its effects on biodiversity and on ecosystem services. As the local environment is often contaminated for tens or even hundreds of years, future research is needed to characterize the effects of legacy pollution by chlordecone and its transformation products on organisms and ecosystems.

Soil constitutes a major sink for microplastics (MPs). In agricultural soils, microplastics co-occur with pesticides and veterinary medicines like anthelminthics (AHs). Little is known regarding the influence of microplastics on the dissipation of these organic pollutants. We hypothesized (a) that microplastics due to their hydrophobic surfaces would affect the dissipation of the anthelminthic albendazole (ABZ) and the fungicide pyraclostrobin (PYR), and (b) the outcome of this interaction will vary depending on the type (PBAT-based, Starch-based, and LDPE-based) and the concentration (0.1 and 0.01%) of plastics. (c) Besides microplastics, the co-occurrence of ABZ and PYR will influence each other's dissipation. We tested the dissipation of ABZ and PYR in the presence and absence of microplastics in three soils. The dissipation of ABZ was accelerated in the presence of microplastics in Greek soil (DT50 2.8-8.2 days vs 13.9 days in the control) but not in the other two soils, while microplastics had no effect on the dissipation of PYR in all three soils. No systematic type- or concentration-driven effect of microplastics on ABZ and PYR soil dissipation was observed in the three soils. Regardless of microplastics' presence, ABZ delayed PYR dissipation in Greek soil (DT50 47.5 to 99.4 days), an effect further exacerbated in the presence of microplastics (DT50 47.0-59.9 to 72.1-117.5 days). We suggest that complex tripartite interactions between pesticides-anthelminthics-microplastics are operative in agricultural soils affecting the dissipation of pesticides and anthelminthics. These interactions are not considered in the current framework of chemical risk assessment, and they are expected to have serious implications, undermining environmental quality and soil health.

Preservation of biodiversity and ecosystem services is critical for sustainable development and human well-being. However, an unprecedented erosion of biodiversity is observed and the use of plant protection products (PPP) has been identified as one of its main causes. In this context, at the request of the French Ministries responsible for the Environment, for Agriculture and for Research, a panel of 46 scientific experts ran a nearly 2-year-long (2020–2022) collective scientific assessment (CSA) of international scientific knowledge relating to the impacts of PPP on biodiversity and ecosystem services. The scope of this CSA covered the terrestrial, atmospheric, freshwater, and marine environments (with the exception of groundwater) in their continuity from the site of PPP application to the ocean, in France and French overseas territories, based on international knowledge produced on or transposable to this type of context (climate, PPP used, biodiversity present, etc.). Here, we provide a brief summary of the CSA’s main conclusions, which were drawn from about 4500 international publications. Our analysis finds that PPP contaminate all environmental matrices, including biota, and cause direct and indirect ecotoxicological effects that unequivocally contribute to the decline of certain biological groups and alter certain ecosystem functions and services. Levers for action to limit PPP-driven pollution and effects on environmental compartments include local measures from plot to landscape scales and regulatory improvements. However, there are still significant gaps in knowledge regarding environmental contamination by PPPs and its effect on biodiversity and ecosystem functions and services. Perspectives and research needs are proposed to address these gaps.

Pesticides are widely used in conventional agriculture, either applied separately or incombination during the culture cycle. Due to their occurrence and persistence in soils, pesticideresidues may have an impact on soil microbial communities and on supported ecosystemservices. In this regard, the EFSA (European Food Safety Authority) recently published ascientific opinion inciting to change pesticide risk assessment to better protect soil microbe-mediated processes. Climate change is another major concern for all living organisms includingsoil microbial community stability. Extreme climatic events, such as heat waves or heavyrainfalls, are becoming more and more frequent and their impact on soil microbial diversity andfunctions have already been demonstrated.The objectives of this study were to evaluate the effects of temperature and humiditydisturbances and pesticide active ingredients exposure on soil microbial community structureand functions. To this end, 250 soil microcosms were exposed to either a heat disturbance, ahigh humidity to mimic heavy rain, or no environmental disturbance. After three days ofrecovery, soil microcosms were treated with different active ingredients: clopyralid (herbicide),cypermethrin (insecticide) and pyraclostrobin (fungicide). The treatments were applied aloneor in combination at 1x or 10x of the agronomical dose. We then evaluated the effects of thedisturbances and the active ingredients on various microbial endpoints related to the diversityand the structure of soil microbial communities, and with a specific focus on microbial guildsinvolved in nitrification.Overall, we demonstrated that the impact of environmental disturbances applied to soilmicrocosms, especially heat, on microbial endpoints was stronger than that of the activeingredients applied alone or in combinations. Compounded effects of environmentaldisturbances and active ingredients were detected, but sparsely and were of small scale for thechosen pesticides and applied doses.

This study reports draft genomes of 30 bacteria representative of the plant food system microbiota and isolated from different sources in Italy and France. Individual genomes were reconstructed using PacBIO DNA sequencing: taxonomic classification and distribution of genes involved in microbe-environment interactions are reported to facilitate strains' characterization and utilization.

Microplastics (MPs) frequently co-occur with pesticides and veterinary medicines in agricultural soils. However, their interactive effects on soil microbiota remain largely unknown. Therefore, we investigated the effects of three MP types (LDPE-, PBAT-, and starch-based), applied at two concentrations (0.01% and 0.1%), either alone or in combination with the fungicide pyraclostrobin and/or the anthelminthic albendazole (ABZ), on soil microbial functioning. Nitrate levels, nitrification rates, ammonia-oxidizing microorganisms, and denitrifying bacteria served as indicators of perturbations on soil N cycling in soils from France, the Netherlands, and Greece. Microbial responses were soil-dependent, with the Greek soil being the most affected. In contrast, plastic type- and dose-dependent effects were sporadic and limited in the French and Dutch soil. In the Greek soil, all MP types increased the abundance of ammonia-oxidizing bacteria and nitrification rates, accompanied by a compensatory decline in ammonia-oxidizing archaea and commamox bacteria. These effects were reversed by the co-application of MPs with ABZ. On the other hand, denitrifying bacteria remained unaffected in all soils. Our results are alarming, considering the perturbation of nitrification imposed by MPs and other soil pollutants, which could enhance greenhouse gas emissions or adversely affect soil fertility and agricultural production.

Copper-based plant protection products (PPPs) are widely used in both conventional and organic farming, and to a lesser extent for non-agricultural maintenance of gardens, greenspaces, and infrastructures. The use of copper PPPs adds to environmental contamination by this trace element. This paper aims to review the contribution of these PPPs to the contamination of soils and waters by copper in the context of France (which can be extrapolated to most of the European countries), and the resulting impacts on terrestrial and aquatic biodiversity, as well as on ecosystem functions. It was produced in the framework of a collective scientific assessment on the impacts of PPPs on biodiversity and ecosystem services in France. Current science shows that copper, which persists in soils, can partially transfer to adjacent aquatic environments (surface water and sediment) and ultimately to the marine environment. This widespread contamination impacts biodiversity and ecosystem functions, chiefly through its effects on phototrophic and heterotrophic microbial communities, and terrestrial and aquatic invertebrates. Its effects on other biological groups and biotic interactions remain relatively under-documented.

Insertion sequences (IS) are drivers of bacterial diversification by facilitating recruitment and horizontal transfer of adaptive genes involving composite transposon structures, but their evolutionary role at the community level is rarely addressed. This study explores the dynamics of IS1071 and the cargo of IS1071-associated putative composite transposons in the establishment of a pesticide-degrading microbiome in an on-farm biopurification system (BPS)-which treats pesticide-contaminated wastewater and is considered a hotspot of microbial evolution-during the crucial start-up phase. Pesticide mineralisation assays and quantitative PCR targeting pesticide catabolic genes showed that the microbial community, upon feeding on the pesticide-contaminated wastewater, rapidly evolved into a pesticide-degrading microbiome. Concomitantly, an increase in the relative abundances of several mobile genetic elements, including IS1071, was observed, as well as a striking enrichment of xenobiotic catabolic genes in the cargo of putative IS1071-flanked composite transposons. The IS1071 cargo catabolic genes diversified over time and were mainly of Betaproteobacterial origin. Clear changes in community composition were observed both in the total bacterial community and the Betaproteobacterial community. We conclude that IS1071 supports the rapid establishment of pesticide catabolism in the BPS microbiome, highlighting the contribution of IS elements to microbial community adaptation to environmental changes.

Even decades after being banned in Europe, atrazine and its main metabolites can still be found in soils. While bioaugmentation using pesticide-degrading bacteria is already employed for remediating polluted soils, there is a need to improve its efficiency. Investigating the use of carrier materials to deliver pesticide-degrading microorganisms in situ emerges as a promising approach. Here, we generated atrazine-degrading biocomposites by cultivating either a bacterial strain or a four-species consortium on zeolite as the carrier material. Using a microcosm approach, we evaluated their efficiency to mineralize 14C-atrazine in soil compared to free-living cells, and assessed their side effects on the native soil bacterial community using 16S rRNA metabarcoding. We showed that, right after inoculation, atrazine mineralization potential of the free-living cells was higher than that of the biocomposites. However, microcosms inoculated with the biocomposites displayed significantly higher atrazine mineralization potential after 15 and 45 days of incubation, indicating a higher efficiency but also a better stability in soil. Inoculation of free-living cells and biocomposites differently influenced the diversity and composition of the native microbial community, their impacts being modulated by the atrazine contamination scenario. Altogether, our results provide a thorough evaluation of the efficiency and the ecological impact of atrazine-degrading biocomposites in soil.

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.

By assessing the changes in stable isotope compositions within individual pesticide molecules, Compound Specific Isotope Analysis (CSIA) holds the potential to identify and differentiate sources and quantify pesticide degradation in the environment. However, the environmental application of pesticide CSIA is limited by the general lack of knowledge regarding the initial isotopic composition of active substances in commercially available formulations used by farmers. To address this limitation, we established a database aimed at cataloguing and disseminating isotopic signatures in commercial formulations to expand the use of pesticide CSIA. Our study involved the collection of 25 analytical standards and 120 commercial pesticide formulations from 23 manufacturers. Subsequently, 59 commercial formulations and 25 standards were extracted, and each of their active substance was analyzed for both δ13C (n = 84) and δ15N CSIA (n = 43). The extraction of pesticides did not cause significant isotope fractionation (Δ13C and Δ15N < 1‰). Incorporating existing literature data, stable carbon and nitrogen isotope signatures varied in a relatively narrow range among pesticide formulations for different pesticides (Δ13C and Δ15N < 10‰) and within different formulations for a single substance (Δ13C and Δ15N < 2‰). Overall, this suggests that pesticide CSIA is more suited for identifying pesticide transformation processes rather than differentiating pesticide sources. Moreover, an inter-laboratory comparison showed similar δ13C (Δ13C ≤ 1.2 ‰) for the targeted substances albeit varying GC-IRMS instruments. Insignificant carbon isotopic fractionation (Δ13C < 0.5‰) was observed after 4 years of storing the same pesticide formulations, confirming their viability for long-term storage at 4 °C and future inter-laboratory comparison exercises. Altogether, the ISOTOPEST database, in open access for public use and additional contributions, marks a significant advancement in establishing an environmentally relevant pesticide CSIA approach.

Plastic films efficiently control weed development in agriculture but may have environmental impacts, including alterations of the soil functioning and its microbiota. Canvases made of plant fibres are promising biodegradable alternatives showing uniform soil covering like plastic films, unlike straw mulching which is often laid unevenly on the ground. Hemp is particularly interesting for its resistance and possible effects on the soil microbiota. We tested the effect of several mulches differing in their biodegradability and homogeneity (uniform/uneven soil covering) on soil functioning and crop yield. In greenhouse, we assessed the effects of different mulching on lettuce yields, soil properties (temperature, moisture, enzymatic activities) and the soil microbiota. We cropped lettuces either on bare soil (control), a homogeneous non-biodegradable mulch (plastic film), a biodegradable heterogeneous mulch (hemp straw) and a biodegradable and homogenous mulch (hemp canvas). Plastic film increased soil temperature, decreased most enzymatic activities, and altered the soil microbiota composition. The hemp canvas decreased fungal diversity, while increasing soil moisture, laccase activity, and the abundance of specific Ascomycota, Proteobacteria and Actinobacteria taxa. Plastic and hemp canvas gave similar lettuce yields. Mulching with plastic films and hemp canvases changed soil functioning (C cycle enzymatic activities) and the soil microbiota. Although similar lettuce yields were obtained, effects of the plastic film were likely mediated by the increased soil temperature and accelerated organic matter degradation, while effects of the hemp canvas resulted from increased soil moisture and recalcitrant matter degradation, combined with the stimulation of potentially beneficial soil microorganisms.

Tembotrione (TBT) is a β-triketone herbicide targeting the 4-Hydroxyphenylpyruvate dioxygenase enzyme (4-HPPD) of weeds. This molecule can also affect soil microorganisms, either through both direct and indirect toxic effects for microorganisms expressing 4-HPPD, or by promoting tolerant and/or degrading microbial populations. Our study aimed to characterize the impacts of TBT on the diversity of total- and hppd (coding for 4-HPPD) -soil bacterial communities. Soil microcosms were treated with the active ingredient TBT at the recommended field dose (100 g a.i/ha; D1) or the tenfold dose (D10). Soil samples were collected from 0 to 55 days post-treatment to study: (i) total- and hppd-bacterial diversities using 16SrRNA and hppd amplicons sequencing, respectively; (ii) TBT dissipation in soil. Both total- and hppd-bacterial community composition was not affected by TBT treatments (D1 and D10). However, D10 treatment slightly increased richness and phylogenetic diversity of the total bacterial community while decreasing hppd richness. Overall, the highest dose of TBT seemed to promote TBT-tolerant or TBT-degrading bacterial populations and to deplete TBT-sensitive ones. These effects were transient as TBT was rapidly dissipated with a DT50 of 7 days and 15 days for D1 and D10, respectively. Differential abundance analysis with a Generalized Linear Model allowed the identification of Sphingomonas, Steroidobacter and Lysobacter as genus that were influenced by TBT, and which could be used as a new class of exposure biomarkers.

Background Detecting bacteria at the strain level is crucial in microbiology. Although qPCR is widely used, designing strain-specific primers remains a challenge due to nucleotide sequence similarities among related strains.Methods and Results This paper introduces a simplified, web-based workflow for designing strain-specific primers using publicly available microbial genomes. The method does not require advanced bioinformatics skills and can be applied using a basic computer. Primers designed using this workflow are applied to assess the survival of two close Bacillus strains in soil microcosms.Conclusion The workflow offers an accessible solution for accurate bacterial strain detection, and fills a gap for researchers without specialized training in bioinformatics.### Competing Interest StatementThe authors have declared no competing interest.

Parallel to the important use of pesticides in conventional agriculture there is a growing interest for green technologies to clear contaminated soil from pesticides and their degradation products. Bioaugmentation i. e. the inoculation of degrading micro-organisms in polluted soil, is a promising method still in needs of further developments. Specifically, improvements in the understanding of how degrading microorganisms must overcome abiotic filters and interact with the autochthonous microbial communities are needed in order to efficiently design bioremediation strategies. Here we designed a protocol aiming at studying the degradation of two herbicides, glyphosate (GLY) and isoproturon (IPU), via experimental modifications of two source bacterial communities. We used statistical methods stemming from genomic prediction to link community composition to herbicides degradation potentials. Our approach proved to be efficient with correlation estimates over 0.8 between model predictions and measured pesticide degradation values. Multi-degrading bacterial communities were obtained by coalescing bacterial communities with high GLY or IPU degradation ability based on their community-level properties. Finally, we evaluated the efficiency of constructed multi-degrading communities to remove pesticide contamination in a different soil. While results are less clear in the case of GLY, we showed an efficient transfer of degrading capacities towards the receiving soil even at relatively low inoculation levels in the case of IPU. Altogether, we developed an innovative protocol for building multi-degrading simplified bacterial communities with the help of genomic prediction tools and coalescence, and proved their efficiency in a contaminated soil.