Biodegradation of a complex hydrocarbon mixture and biosurfactant production by Burkholderia thailandensis E264 and an adapted microbial consortium.

Bioremediation is considered to be an effective treatment for hydrocarbon removal from polluted soils. However, the effectiveness of this treatment is often limited by the low availability of targeted contaminants. Biosurfactants produced by some microorganisms can increase organic compound solubility and might then overcome this limitation. Two different inocula producers of biosurfactants (Burkholderia thailandensis E264 and SHEMS1 microbial consortium isolated from a hydrocarbon-contaminated soil) were incubated in Bushnell-Haas medium supplemented with hydrocarbons to investigate their biodegradation potential. Experimental results showed their ability to degrade 9.1 and 6.1% of hydrocarbons respectively after 65 days of incubation with an initial total hydrocarbon concentration of 16 g L-1. The biodegradation was more effective for the light and medium fractions (C10 to C36). B. thailandensis and SHEMS1 consortium produced surfactants after 14 days of culture during the stationary phase with hydrocarbons as the sole carbon and energy source. However, biosurfactant production did not appear to directly increase hydrocarbon degradation efficiency. The complexity and recalcitrance of hydrocarbon mixture used in this study appeared to continue to limit its biodegradation even in the presence of biosurfactants. In conclusion, B. thailandensis and SHEMS1 consortium can degrade recalcitrant hydrocarbon compounds and are therefore good candidates for the bioremediation of environments polluted by total hydrocarbons.

Experimental Evidence for Manure-Borne Bacteria Invasion in Soil During a Coalescent Event: Influence of the Antibiotic Sulfamethazine.

The fertilization of agricultural soil by organic amendment that may contain antibiotics, like manure, can transfer bacterial pathogens and antibiotic-resistant bacteria to soil communities. However, the invasion by manure-borne bacteria in amended soil remains poorly understood. We hypothesized that this kind of process is both influenced by the soil properties (and those of its microbial communities) and by the presence of contaminants such as antibiotics used in veterinary care. To test that, we performed a microcosm experiment in which four different soils were amended or not with manure at an agronomical dose and exposed or not to the antibiotic sulfamethazine (SMZ). After 1 month of incubation, the diversity, structure, and composition of bacterial communities of the soils were assessed by 16S rDNA sequencing. The invasion of manure-borne bacteria was still perceptible 1 month after the soil amendment. The results obtained with the soil already amended in situ with manure 6 months prior to the experiment suggest that some of the bacterial invaders were established in the community over the long term. Even if differences were observed between soils, the invasion was mainly attributable to some of the most abundant OTUs of manure (mainly Firmicutes). SMZ exposure had a limited influence on soil microorganisms but our results suggest that this kind of contaminant can enhance the invasion ability of some manure-borne invaders.

Insights into the Function and Horizontal Transfer of Isoproturon Degradation Genes (pdmAB) in a Biobed System.

Biobeds, designed to minimize pesticide point source contamination, rely mainly on biodegradation processes. We studied the interactions of a biobed microbial community with the herbicide isoproturon (IPU) to explore the role of the pdmA gene, encoding the large subunit of an N-demethylase responsible for the initial demethylation of IPU, via quantitative PCR (qPCR) and reverse transcription-PCR (RT-qPCR) and the effect of IPU on the diversity of the total bacterial community and its active fraction through amplicon sequencing of DNA and RNA, respectively. We further investigated the localization and dispersal mechanisms of pdmAB in the biobed packing material by measuring the abundance of the plasmid pSH (harboring pdmAB) of the IPU-degrading Sphingomonas sp. strain SH (previously isolated from the soil used in the biobed) compared with the abundance of the pdmA gene and metagenomic fosmid library screening. pdmA abundance and expression increased concomitantly with IPU mineralization, verifying its major role in IPU transformation in the biobed system. DNA- and RNA-based 16S rRNA gene sequencing analysis showed no effects on bacterial diversity. The pdmAB-harboring plasmid pSH showed a consistently lower abundance than pdmA, suggesting the localization of pdmAB in replicons other than pSH. Metagenomic analysis identified four pdmAB-carrying fosmids. In three of these fosmids, the pdmAB genes were organized in a well-conserved operon carried by sphingomonad plasmids with low synteny with pSH, while the fourth fosmid contained an incomplete pdmAB cassette localized in a genomic fragment of a Rhodanobacter strain. Further analysis suggested a potentially crucial role of IS6 and IS256 in the transposition and activation of the pdmAB operon.IMPORTANCE Our study provides novel insights into the interactions of IPU with the bacterial community of biobed systems, reinforces the assumption of a transposable nature of IPU-degrading genes, and verifies that on-farm biobed systems are hot spots for the evolution of pesticide catabolic traits.

s-triazine degrading bacterial isolate Arthrobacter sp. AK-YN10, a candidate for bioaugmentation of atrazine contaminated soil.

The Arthrobacter sp. strain AK-YN10 is an s-triazine pesticide degrading bacterium isolated from a sugarcane field in Central India with history of repeated atrazine use. AK-YN10 was shown to degrade 99 % of atrazine in 30 h from media supplemented with 1000 mg L(-1) of the herbicide. Draft genome sequencing revealed similarity to pAO1, TC1, and TC2 catabolic plasmids of the Arthrobacter taxon. Plasmid profiling analyses revealed the presence of four catabolic plasmids. The trzN, atzB, and atzC atrazine-degrading genes were located on a plasmid of approximately 113 kb.The flagellar operon found in the AK-YN10 draft genome suggests motility, an interesting trait for a bioremediation agent, and was homologous to that of Arthrobacter chlorophenolicus. The multiple s-triazines degradation property of this isolate makes it a good candidate for bioremediation of soils contaminated by s-triazine pesticides.

Tracking atrazine degradation in soil combining 14C-mineralisation assays and compound-specific isotope analysis.

The quantification of pesticide dissipation in agricultural soil is challenging. In this study, we investigated atrazine biodegradation in both liquid and soil experiments bioaugmented with distinct atrazine-degrading bacterial isolates. This was achieved by combining 14C-mineralisation assays and compound-specific isotope analysis of atrazine. In liquid experiments, the three bacterial isolates mineralised over 40% of atrazine, demonstrating their potential for extensive degradation. However, the kinetics of mineralisation and degradation varied among the isolates. Carbon stable isotope fractionation was similar for Pseudomonas isolates ADPT34 and ADP2T0, but slightly higher for Chelatobacter SR27. In soil experiments, atrazine primarily degraded into atrazine-desethyl, while atrazine-hydroxy was mainly observed in experiments with SR27. Atrazine mineralisation in soil by ADPT34 and SR27 exceeded 40%, whereas ADP2T0 exhibited a mineralisation rate of 10%. In experiments with ADPT34 and SR27, atrazine 14C-residues were predominantly found in the non-extractable fraction, whereas they accumulated in the extractable fraction in the experiment with ADP2T0. Compound-specific isotope analysis (CSIA) relies on changes of stable isotope ratios and holds potential to evaluate herbicide transformation in soil. CSIA of atrazine indicated atrazine biodegradation in water and solvent extractable soil fractions and varied between 29% and 52%, depending on the bacterial isolate. Despite atrazine degradation in both soil fractions, a significant portion of atrazine residues persisted, depending on the bacterial degrader, initial cell concentration, and mineralisation and degradation rates. Overall, our approach can aid in quantifying atrazine persistence and degradation in soil, and in optimizing bioaugmentation strategies for remediating soils contaminated with persistent herbicides.

Engineering multi-degrading bacterial communities to bioremediate soils contaminated with pesticides residues.

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.

Response of a diuron-degrading community to diuron exposure assessed by real-time quantitative PCR monitoring of phenylurea hydrolase A and B encoding genes.

A real-time quantitative PCR method was developed to detect and quantify phenlylurea hydrolase genes' (puhA and puhB) sequences from environmental DNA samples to assess diuron-degrading genetic potential in some soil and sediment microbial communities. In the soil communities, mineralization rates (determined with [ring-¹4C]-labeled diuron) were linked to diuron-degrading genetic potentials estimated from puhB number copies, which increased following repeated diuron treatments. In the sediment communities, mineralization potential did not depend solely on the quantity of puhB copies, underlining the need to assess gene expression. In the sediment samples, both puhB copy numbers and mineralization capacities were highly conditioned by whether or not diuron-treated soil was added. This points to transfers of degradative potential from soils to sediments. No puhA gene was detected in soil and sediment DNA extracts. Moreover, some sediments exhibited high diuron mineralization potential even though puhB genes were not detected, suggesting the existence of alternative diuron degradation pathways.

Estimating the biodegradation of pesticide in soils by monitoring pesticide-degrading gene expression.

Assessing in situ microbial abilities of soils to degrade pesticides is of great interest giving insight in soil filtering capability, which is a key ecosystem function limiting pollution of groundwater. Quantification of pesticide-degrading gene expression by reverse transcription quantitative PCR (RT-qPCR) was tested as a suitable indicator to monitor pesticide biodegradation performances in soil. RNA extraction protocol was optimized to enhance the yield and quality of RNA recovered from soil samples to perform RT-qPCR assays. As a model, the activity of atrazine-degrading communities was monitored using RT-qPCRs to estimate the level of expression of atzD in five agricultural soils showing different atrazine mineralization abilities. Interestingly, the relative abundance of atzD mRNA copy numbers was positively correlated to the maximum rate and to the maximal amount of atrazine mineralized. Our findings indicate that the quantification of pesticide-degrading gene expression may be suitable to assess biodegradation performance in soil and monitor natural attenuation of pesticide.

Accelerated Biodegradation of Veterinary Antibiotics in Agricultural Soil following Long-Term Exposure, and Isolation of a Sulfamethazine-degrading sp.

The World Health Organization has identified antibiotic resistance as one of the top three threats to global health. There is concern that the use of antibiotics as growth promoting agents in livestock production contributes to the increasingly problematic development of antibiotic resistance. Many antibiotics are excreted at high rates, and the land application of animal manures represents a significant source of environmental exposure to these agents. To evaluate the long-term effects of antibiotic exposure on soil microbial populations, a series of field plots were established in 1999 that have since received annual applications of a mixture of sulfamethazine (SMZ), tylosin (TYL), and chlortetracycline (CTC). During the first 6 yr (1999-2004) soils were treated at concentrations of 0, 0.01 0.1, and 1.0 mg kg soil, in subsequent years at concentrations of 0, 0.1, 1.0, and 10 mg kg soil. The lower end of this concentration range is within that which would result from an annual application of manure from medicated swine. Following ten annual applications, the fate of the drugs in the soil was evaluated. Residues of SMZ and TYL, but not CTC were removed much more rapidly in soil with a history of exposure to 10 mg/kg drugs than in untreated control soil. Residues of C-SMZ were rapidly and thoroughly mineralized to CO in the historically treated soils, but not in the untreated soil. A SMZ-degrading sp. was isolated from the treated soil. Overall, these results indicate that soil bacteria adapt to long-term exposure to some veterinary antibiotics resulting in sharply reduced persistence. Accelerated biodegradation of antibiotics in matrices exposed to agricultural, wastewater, or pharmaceutical manufacturing effluents would attenuate environmental exposure to antibiotics, and merits investigation in the context of assessing potential risks of antibiotic resistance development in environmental matrices.

Effect of subtherapeutic and therapeutic sulfamethazine concentrations on transcribed genes and translated proteins involved in Microbacterium sp. C448 resistance and degradation.

Microbacterium sp. C448, isolated from a soil regularly exposed to sulfamethazine (SMZ), can use various sulphonamide antibiotics as the sole carbon source for growth. The basis for the regulation of genes encoding the sulphonamide metabolism pathway, the dihydropteroate synthase sulphonamide target (folP), and the sulphonamide resistance (sul1) genes is unknown in this organism. In the present study, the response of the transcriptome and proteome of Microbacterium sp. C448 following exposure to subtherapeutic (33 µM) or therapeutic (832 µM) SMZ concentrations was evaluated. Therapeutic concentration induced the highest sad expression and Sad production, consistent with the activity of SMZ degradation observed in cellulo. Following complete SMZ degradation, Sad production tended to return to the basal level observed prior to SMZ exposure. Transcriptomic and proteomic kinetics were concomitant for the resistance genes and proteins. The abundance of Sul1 protein, 100-fold more abundant than FolP protein, did not change in response to SMZ exposure. Moreover, non-targeted analyses highlighted the increase of a deaminase RidA and a putative sulphate exporter expression and production. These two novel factors involved in the 4-aminophenol metabolite degradation and the export of sulphate residues formed during SMZ degradation, respectively, provided new insights into the Microbacterium sp. C448 SMZ detoxification process.

Community diversity determines the evolution of synthetic bacterial communities under artificial selection.

Artificial selection can be conducted at the community level in the laboratory through a differential propagation of the communities according to their level of expression of a targeted function. Working with communities instead of individuals as selection units brings in additional sources of variation in the considered function that can influence the outcome of the artificial selection. In this study, we wanted to assess the effect of manipulating the initial community richness on artificial selection efficiency, defined as the change in the targeted function over time. We applied artificial selection for a high productivity on synthetic bacterial communities varying for their richness (from one to 16 strains). Overall, the selected communities were 16% more productive than the control communities, but a convergence of community composition might have limited the effect of diversity on artificial selection efficiency. Community richness positively influenced community productivity and metabolic capacities and was a strong determinant of the dynamics of community evolution. We propose that applying artificial selection on communities varying for their diversity could be a way to find communities differing for their level of expression of a function but also for their responsiveness to artificial selection, provided that their initial composition is different enough.

Assessing the importance of interspecific interactions in the evolution of microbial communities.

Interspecific interactions play an important role in the establishment of a community phenotype. Furthermore, the evolution of a community can both occur through an independent evolution of the species composing the community and the interactions among them. In this study, we investigated how important the evolution of interspecific interactions was in the evolutionary response of eight two-bacterial species communities regarding productivity. We found evidence for an evolution of the interactions in half of the studied communities, which gave rise to a mean change of 15% in community productivity as compared to what was expected from the individual responses. Even when the interactions did not evolve themselves, they influenced the evolutionary responses of the bacterial strains within the communities, which further affected community response. We found that evolution within a community often promoted the adaptation of the bacterial strains to the abiotic environment, especially for the dominant strain in a community. Overall, this study suggested that the evolution of the interspecific interactions was frequent and that it could increase community response to evolution.

Evidence for taxonomic and functional drift of an atrazine-degrading culture in response to high atrazine input.

We evaluated the effects of variations in atrazine input on the evolution of a bacterial culture adapted to a low atrazine concentration. This initial culture (M3-K) was subjected to weekly subculturing in the presence of a high concentration of atrazine as the only N source (100 mg l(-1)). After four subculturing, M3-K evolved to a new bacterial culture (M3) which exhibited a significant increase in the extent of atrazine mineralization in comparison with the initial culture. Molecular analyses of M3-K and M3 cultures by cloning, restriction analysis, and sequencing of the 16S rRNA genes revealed significant differences in culture structure and composition. M3-K culture comprised mainly Actinobacteria (40%), ß-Proteobacteria (26%), and Bacteroidetes (16%). After exposure to a high atrazine concentration, the dominance of Actinobacteria decreased (14%), Bacteroidetes increased (27%), and ß-Proteobacteria were replaced by γ-Proteobacteria (32%). Quantitative PCR revealed that the abundance of atzB and atzC genes relative to total bacteria decreased by a factor of 3-4 following the increase in atrazine concentration, while the relative abundance of trzD increased significantly (≈400 times). Presented study shows that variations in atrazine input drive both functional and compositional shifts in the atrazine-degrading bacterial culture.

Isolation and characterization of an isoproturon mineralizing Sphingomonas sp. strain SH from a French agricultural soil.

The phenylurea herbicide isoproturon, 3-(4-isopropylphenyl)-1,1-dimethylurea (IPU), was found to be rapidly mineralized in an agricultural soil in France that had been periodically exposed to IPU. Enrichment cultures from samples of this soil isolated a bacterial strain able to mineralize IPU. 16S rRNA sequence analysis showed that this strain belonged to the phylogeny of the genus Sphingomonas (96% similarity with Sphingomonas sp. JEM-14, AB219361) and was designated Sphingomonas sp. strain SH. From this strain, a partial sequence of a 1,2-dioxygenase (catA) gene coding for an enzyme degrading catechol putatively formed during IPU mineralization was amplified. Phylogenetic analysis revealed that the catA sequence was related to Sphingomonas spp. and showed a lack of congruence between the catA and 16S rRNA based phylogenies, implying horizontal gene transfer of the catA gene cluster between soil microbiota. The IPU degrading ability of strain SH was strongly influenced by pH with maximum degradation taking place at pH 7.5. SH was only able to mineralize IPU and its known metabolites including 4-isopropylaniline and it could not degrade other structurally related phenylurea herbicides such as diuron, linuron, monolinuron and chlorotoluron or their aniline derivatives. These observations suggest that the catabolic abilities of the strain SH are highly specific to the metabolism of IPU.

Complete Genome Sequences of Four Atrazine-Degrading Bacterial Strains, Pseudomonas sp. Strain ADPe, Arthrobacter sp. Strain TES, Variovorax sp. Strain 38R, and Chelatobacter sp. Strain SR38.

We report here the complete genome sequences of four atrazine-degrading bacteria. Their genomes will serve as references for determining the genetic changes that have occurred during an evolution experiment.

Antibiotrophy: Key Function for Antibiotic-Resistant Bacteria to Colonize Soils-Case of Sulfamethazine-Degrading Microbacterium sp. C448.

Chronic and repeated exposure of environmental bacterial communities to anthropogenic antibiotics have recently driven some antibiotic-resistant bacteria to acquire catabolic functions, enabling them to use antibiotics as nutritive sources (antibiotrophy). Antibiotrophy might confer a selective advantage facilitating the implantation and dispersion of antibiotrophs in contaminated environments. A microcosm experiment was conducted to test this hypothesis in an agroecosystem context. The sulfonamide-degrading and resistant bacterium Microbacterium sp. C448 was inoculated in four different soil types with and without added sulfamethazine and/or swine manure. After 1 month of incubation, Microbacterium sp. (and its antibiotrophic gene sadA) was detected only in the sulfamethazine-treated soils, suggesting a low competitiveness of the strain without antibiotic selection pressure. In the absence of manure and despite the presence of Microbacterium sp. C448, only one of the four sulfamethazine-treated soils exhibited mineralization capacities, which were low (inferior to 5.5 ± 0.3%). By contrast, manure addition significantly enhanced sulfamethazine mineralization in all the soil types (at least double, comprised between 5.6 ± 0.7% and 19.5 ± 1.2%). These results, which confirm that the presence of functional genes does not necessarily ensure functionality, suggest that sulfamethazine does not necessarily confer a selective advantage on the degrading strain as a nutritional source. 16S rDNA sequencing analyses strongly suggest that sulfamethazine released trophic niches by biocidal action. Accordingly, manure-originating bacteria and/or Microbacterium sp. C448 could gain access to low-competition or competition-free ecological niches. However, simultaneous inputs of manure and of the strain could induce competition detrimental for Microbacterium sp. C448, forcing it to use sulfamethazine as a nutritional source. Altogether, these results suggest that the antibiotrophic strain studied can modulate its sulfamethazine-degrading function depending on microbial competition and resource accessibility, to become established in an agricultural soil. Most importantly, this work highlights an increased dispersal potential of antibiotrophs in antibiotic-polluted environments, as antibiotics can not only release existing trophic niches but also form new ones.

Assessing the Effects of ß-Triketone Herbicides on the Soil Bacterial and hppd Communities: A Lab-to-Field Experiment.

Maize cultivators often use ß-triketone herbicides to prevent the growth of weeds in their fields. These herbicides target the 4-HPPD enzyme of dicotyledons. This enzyme, encoded by the hppd gene, is widespread among all living organisms including soil bacteria, which are considered as "non-target organisms" by the legislation. Within the framework of the pesticide registration process, the ecotoxicological impact of herbicides on soil microorganisms is solely based on carbon and nitrogen mineralization tests. In this study, we used more extensive approaches to assess with a lab-to-field experiment the risk of ß-triketone on the abundance and the diversity of both total and hppd soil bacterial communities. Soil microcosms were exposed, under lab conditions, to 1× or 10× the recommended dose of sulcotrione or its commercial product, Decano®. Whatever the treatment applied, sulcotrione was fully dissipated from soil after 42 days post-treatment. The abundance and the diversity of both the total and the hppd bacterial communities were not affected by the herbicide treatments all along the experiment. Same measurements were led in real agronomical conditions, on three different fields located in the same area cropped with maize: one not exposed to any plant protection products, another one exposed to a series of plant protection products (PPPs) comprising mesotrione, and a last one exposed to different PPPs including mesotrione and tembotrione, two ß-triketones. In this latter, the abundance of the hppd community varied over time. The diversity of the total and the hppd communities evolved over time independently from the treatment received. Only slight but significant transient effects on the abundance of the hppd community in one of the tested soil were observed. Our results showed that tested ß-triketones have no visible impact toward both total and hppd soil bacteria communities.

Assessment of the effects of oxamyl on the bacterial community of an agricultural soil exhibiting enhanced biodegradation.

Modern agricultural practices largely rely on pesticides to protect crops against various pests and to ensure high yields. Following their application to crops a large amount of pesticides ends up in soil where they may affect non-target organisms, among which microorganisms. We assessed the effects of the carbamate nematicide oxamyl on the whole bacterial diversity of an agricultural soil exhibiting enhanced biodegradation of oxamyl through 16S rRNA amplicon next generation sequencing (NGS) and on the oxamyl-degrading bacterial community through cehA q-PCR analysis and 14C-oxamyl mineralization assays. Oxamyl was rapidly mineralized by the indigenous microorganisms reaching >70% within a month. Concomitantly, a significant increase in the number of oxamyl-degrading microorganisms was observed. NGS analysis of the total (DNA) and active (RNA) bacterial community showed no changes in α-diversity indices in response to oxamyl exposure. Analysis of the ß-diversity revealed significant changes in the composition of the soil bacterial community after 13 and 30 days of oxamyl exposure only when the active fraction of the bacterial community was considered. These changes were associated with seven OTUs related to Proteobacteria (5), Acidobacteria (1) and Actinobacteria (1). The relative abundance of the dominant bacterial phyla were not affected by oxamyl, except of Bacteroidetes and Gemmatimonadetes which decreased after 13 and 30 days of oxamyl exposure respectively. To conclude, oxamyl induced changes in the abundance of oxamyl-degrading microorganisms and on the diversity of the soil bacterial community. The latter became evident only upon RNA-based NGS analysis emphasizing the utility of such approaches when the effects of pesticides on the soil microbial community are explored.

Environmental risk assessment of antibiotics in agroecosystems: ecotoxicological effects on aquatic microbial communities and dissemination of antimicrobial resistances and antibiotic biodegradation potential along the soil-water continuum.

Antibiotics have a wide application range in human and veterinary medicines. Being designed for pharmacological stability, most antibiotics are recalcitrant to biodegradation after ingestion and can be persistent in the environment. Antibiotic residues have been detected as contaminants in various environmental compartments where they cause human and environmental threats, notably with respect to the potential emergence and proliferation of antibiotic-resistant bacteria. An important component of managing environmental risk caused by antibiotics is to understand exposure of soil and water resources to their residues. One challenge is to gain knowledge on the fate of antibiotics in the ecosystem along the soil-water continuum, and on the collateral impact of antibiotics on environmental microorganisms responsible for crucially important ecosystem functions. In this context, the ANTIBIOTOX project aims at studying the environmental fate and impact of two antibiotics of the sulfonamide class of antibiotics, sulfamethazine (SMZ), and sulfamethoxazole (SMX).

Assessment of the ecotoxicological impact of natural and synthetic ß-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 ß-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 ß-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 ß-triketones.