Design of a degenerate primer pair to target a bacterial functional community: The hppd bacterial gene coding for the enzyme targeted by herbicides, a study case

Agroecological transition: towards a better understanding of the impact of ecology-based farming practices on soil microbial ecotoxicology

Alternative farming systems have developed since the beginning of industrial agriculture. Organic, biodynamic, conservation farming, agroecology and permaculture, all share a grounding in ecological concepts and a belief that farmers should work with nature rather than damage it. As ecology-based agricultures rely greatly on soil organisms to perform the functions necessary for agricultural production, it is thus important to evaluate the performance of these systems through the lens of soil organisms, especially soil microbes. They provide numerous services to plants, including growth promotion, nutrient supply, tolerance to environmental stresses and protection against pathogens. An overwhelming majority of studies confirm that ecology-based agricultures are beneficial for soil microorganisms. However, three practices were identified as posing potential ecotoxicological risks: the recycling of organic waste products, plastic mulching, and pest and disease management with biopesticides. The first two because they can be a source of contaminants; the third because of potential impacts on non-target microorganisms. Consequently, developing strategies to allow a safe recycling of the increasingly growing organic matter stocks produced in cities and factories, and the assessment of the ecotoxicological impact of biopesticides on non-target soil microorganisms, represent two challenges that ecology-based agricultural systems will have to face in the future.

Assessing the effects of β-triketone herbicides on HPPD from environmental bacteria using a combination of in silico and microbiological approaches

4-hydroxyphenylpyruvate dioxygenase (HPPD) is the molecular target of β-triketone herbicides in plants. This enzyme, involved in the tyrosine pathway, is also present in a wide range of living organisms, including microorganisms. Previous studies, focusing on a few strains and using high herbicide concentrations, showed that β-triketones are able to inhibit microbial HPPD. Here, we measured the effect of agronomical doses of β-triketone herbicides on soil bacterial strains. The HPPD activity of six bacterial strains was tested with 1× or 10× the recommended field dose of the herbicide sulcotrione. The selected strains were tested with 0.01× to 15× the recommended field dose of sulcotrione, mesotrione, and tembotrione. Molecular docking was also used to measure and model the binding mode of the three herbicides with the different bacterial HPPD. Our results show that responses to herbicides are strain-dependent with Pseudomonas fluorescens F113 HPPD activity not inhibited by any of the herbicide tested, when all three β-triketone herbicides inhibited HPPD in Bacillus cereus ATCC14579 and Shewanella oneidensis MR-1. These responses are also molecule-dependent with tembotrione harboring the strongest inhibitory effect. Molecular docking also reveals different binding potentials. This is the first time that the inhibitory effect of β-triketone herbicides is tested on environmental strains at agronomical doses, showing a potential effect of these molecules on the HPPD enzymatic activity of non-target microorganisms. The whole-cell assay developed in this study, coupled with molecular docking analysis, appears as an interesting way to have a first idea of the effect of herbicides on microbial communities, prior to setting up microcosm or even field experiments. This methodology could then largely be applied to other family of pesticides also targeting an enzyme present in microorganisms.

Virtual screening based on pharmacophore model for developing novel HPPD inhibitors

4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an important target for herbicide design. A multilayered virtual screening workflow was constructed by combining two pharmacophore models based on ligand and crystal complexes, molecular docking, molecular dynamics (MD), and biological activity determination to identify novel small-molecule inhibitors of HPPD. About 110, 000 compounds of Bailingwei and traditional Chinese medicine databases were screened. Of these, 333 were analyzed through docking experiments. Five compounds were selected by analyzing the binding pattern of inhibitors with amino acid residues in the active pocket. All five compounds could produce stable coordination with cobalt ion, and form favorable π-π interactions. MD simulation demonstrated that Phe381 and Phe424 made large contributions to the strength of binding. The enzyme activity experiment verified that compound-139 displayed excellent potency against AtHPPD (IC₅₀ = 0.742 μM), however, compound-5222 had inhibitory effect on human HPPD (IC₅₀ = 6 nM). Compound-139 exhibited herbicidal activity to some extent on different gramineous weeds. This work provided a strong insight into the design and development of novel HPPD inhibitor using in silico techniques.

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

Maize cultivators often use β-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 β-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 β-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 β-triketones have no visible impact toward both total and hppd soil bacteria communities.