Stephen Duke

• Ph.D.
• Research Leader at USDA, ARS

Substantial losses in agriculture due to plant diseases, pests, and weeds have made the use of pesticides indispensable. Chemical interventions raise environmental concerns, and the increasing evolution and spread of resistance of these agricultural pests to commercially available products highlight the urgency of finding new alternatives. Endophyt...

Metabolites isolated from Penicillium palitans , obtained from deep sea sediments in the maritime Antarctica, were investigated for phytotoxic and antifungal activities. The fungus was submitted to solid state fermentation, and its crude extract was produced. Chromatographic separations of the P. palitans methylene chloride crude extract led to the...

The evolution and spread of antibiotic resistance are problems with important consequences for bacterial disease treatment. Antibiotic use in animal production and the subsequent export of antibiotic resistance elements in animal manure to soil is a concern. Recent reports suggest that exposure of pathogenic bacteria to glyphosate increases antibio...

During the past 30 yr an impasse has developed in the discovery and commercialization of synthetic herbicides with new molecular targets and novel chemistries. Similarly, there has been little success with bioherbicides, both microbial and chemical. These bioherbicides are needed to combat fast-growing herbicide resistance and to fulfill the need f...

Low doses of glyphosate from application drift can be phytotoxic or stimulate growth of glyphosate-susceptible crops. The application of Si can prevent herbicide-caused plant stress. The effects of Si application (3 mM Si) on low doses (0, 36, 72, and 180 g a.e. ha⁻¹) of glyphosate were determined on Sorghum bicolor in a greenhouse study. Growth pa...

The potential adverse effects of glyphosate on glyphosate‐resistant (GR) crops are still a matter of controversy. The effects of glyphosate at recommended application rates (either a single application of 580 g ae ha⁻¹ of glyphosate at stage V5 or a sequential application of 580 + 980 g ae ha⁻¹ at stage V3 and V7, respectively) on growth, mineral c...

A bacterium growing on infected leaves of Hydrocotyle umbellata, commonly known as dollarweed, was isolated and identified as Pantoea ananatis. An ethyl acetate extract of tryptic soy broth (TSB) liquid culture filtrate of the bacterium was subjected to silica gel chromatography to isolate bioactive molecules. Indole was isolated as the major compo...

Low glyphosate doses that produce hormesis may alter the susceptibility to herbicides of weeds or enhance their propagation and dispersal. The objective of this work was to evaluate the hormetic effects of glyphosate on the vegetative, phenological and reproductive development in resistant (R) and susceptible (S) Conyza sumatrensis biotypes. The gl...

Hostile and harsh environments to most organisms represent more than 80% of the earth’s surface. These extreme environments shelter interesting microbial communities that can live in habitats that combine polyextremophile conditions, including cold, hot, dry, oligotrophic conditions, and high solar radiation over the year. Microorganisms inhabiting...

New fungicide modes of action are needed for fungicide resistance management strategies. Several commercial herbicide targets found in fungi that are not utilized by commercial fungicides are discussed as possible fungicide molecular targets. These are acetyl CoA carboxylase, acetolactate synthase, 5-enolpyruvylshikimate-3-phosphate synthase, gluta...

The identification of natural and environmentally friendly pesticides is a key area of interest for the agrochemical industry, with many potentially active compounds being sourced from numerous plant species. In this study, we report the bioassay-guided isolation and identification of phytotoxic and antifungal compounds from the ethyl acetate extra...

Natural products are a main source of new chemical entities for use in drug and pesticide discovery. In order to discover lead compounds with high herbicidal activity, a series of new pyrido[2,3-d] pyrimidine derivatives were designed and synthesized using 2-chloronicotinic acid as the starting material. Their structures were characterized with ¹H...

Weeds are a significant threat to the production of agronomic, horticultural, and ornamental crops, as direct competition for resources can result in substantial yield shortfalls (WSSA 2023). A review of research data generated across the United States and Canada indicated that unmanaged weeds have the potential to reduce corn and soybean productio...

The U.S. Department of Agriculture–Agricultural Research Service (USDA-ARS) has been a leader in weed science research covering topics ranging from the development and use of integrated weed management (IWM) tactics to basic mechanistic studies, including biotic resistance of desirable plant communities and herbicide resistance. ARS weed scientists...

Inhibitors targeting the 4-hydroxyphenyl pyruvate dioxygenase (HPPD) enzyme are well established herbicides and HPPD is also a primary enzyme within the tyrosine metabolism pathway in hematophagous arthropods, which is an essential metaboilic pathway post-blood feeding to prevent tyrosine-mediated toxicity. The objective of this study was to charac...

Microbial biopesticides to control plant pathogens and insects in crops have had significant success. However, there have been relatively few successes for microbial bioherbicides in crops, despite considerable numbers of publications and commercial product introductions in this area. Marketed microbial bioherbicide products for use in agriculture...

Glyphosate-resistant (GR) maize is dominant in countries where it is grown. Significant, adverse effects of glyphosate application to GR maize have been reported, but few data from robust studies exist to determine if such effects are common. In this study, the effects of recommended application rates (single and sequential applications) were used...

New insecticide modes of action are needed for insecticide resistance management strategies. The number of molecular targets of commercial herbicides and insecticides are fewer than 35 for both. Few commercial insecticide targets are found in plants, but ten targets of commercial herbicides are found in insects. For several of these commonly held t...

Protoporphyrinogen oxidase (PPO) inhibiting herbicides remain an important and useful chemistry 60 years after their first introduction. In this review, based on topics introduced at the WSSA 2021 symposium titled “A History, Overview, and Plan of Action on PPO Inhibiting Herbicides”, we discuss the current state of PPO inhibiting herbicides. Renew...

Since the discovery of penicillin in 1928, one of the most famous bioactive molecules that changed the world, studies pertaining to secondary metabolites produced by fungi increased to be explored as prototype drugs for use as pharmaceuticals and agrochemicals. Although thousands of natural products are discovered every year, the recurrent discover...

The continuing need to protect food and fiber production to address the demands of an expanding global population requires new pest management tools for crop protection. Natural products (NPs) have been and continue to be a key source of inspiration for new active ingredients (AIs) for crop protection, accounting for 17% of all crop protection AIs....

Spliceostatin C (SPC) is a component of a bioherbicide isolated from the soil bacterium Burkholderia rinojensis. The chemical structure of SPC closely resembles spliceostatin A (SPA) which was characterized as an anticancer agent and splicing inhibitor. SPC inhibited the growth of Arabidopsis thaliana seedlings with an IC50 value of 2.2 µM. The see...

Natural products are a source for pesticide or drug discovery. In order to discover lead compounds with high fungicidal or herbicidal activity, new niacinamide derivatives derived from the natural product niacinamide, containing chiral flexible chains, were designed and synthesized. Their structures were confirmed by ¹H NMR, ¹³C NMR and HRMS analys...

In order to find new lead compounds with high pesticidal activity, a series of 1,3,4-oxadiazole thioether compounds (5 series) were designed by using penthiopyrad as a synthon. They were synthesized easily via five steps by using ethyl 4,4,4-trifluoro-3-oxobutanoate and triethyl orthoformate as starting materials. The synthesized compounds were cha...

A new series of cyclopropane-1,1-dicarboxylic (CPD) acid analogues were designed and synthesized. CPD is an inhibitor of ketol-acid reductoisomerase (KARI), an enzyme of the branched chain amino acid pathway in plants. The structures of CPD analogues were characterized by ¹H NMR and HRMS. The structure of N,N′-bis(4-(tert-butyl)phenyl)cyclopropane-...

Worldwide regulatory agencies should (re)examine the consideration of: (i) sub-threshold responses, (ii) non-linear dose-response models able to detect sub-threshold responses of both a beneficial and detrimental nature, and (iii) abandoning the use of default dose-response models for their risk assessment. Mounting evidence for significant sub-thr...

The hormesis phenomenon is now well recognized, detectable and quantifiable through modeling. The modeling of a single curve and its sub-NOAEL (No-Observable-Adverse-Effect-Level) quantities is fundamental, but stepping beyond this by multiple curve fittings and sub-NOAEL predictions under different biasing objectives (e.g. plant growth factors, ph...

Over the past 40 years, two very similar molecules, the herbicide mesotrione and the pharmaceutical nitisinone, have been found to kill weeds, treat the hereditary disease type I tyrosinemia, and kill blood-feeding insects, chronologically in that order. These two compounds effectively accomplish these seemingly diverse tasks by inhibiting the same...

Thirty novel dioxolane ring compounds were designed and synthesized. Their chemical structures were confirmed by 1H NMR, HRMS, and single crystal X-ray diffraction analysis. Bioassays indicated that these dioxolane ring derivatives exhibited excellent fungicidal activity against Rhizoctonia solani, Pyricularia oryae, Botrytis cinerea, Colletotrichu...

Resveratrol and its dimethoxylated derivative, pterostilbene, are produced by several plant species, including a few edible crops such as peanut (Arachis hypogaea L.), grapes (Vitis spp.), and blueberries (Vaccinium spp.), as well some plants used in traditional medicine. Both compounds are inducible, antimicrobial compounds with activity against b...

Hormesis is a common response of both herbicide-susceptible and -resistant plants to herbicides. Herbicide resistance in weeds is rapidly evolving, and, although little studied, there is growing evidence that hormesis plays a role in the changes in sensitivity of weed populations to herbicides. This can occur in susceptible weed populations in whic...

Perception of hormesis as a significant dose-response phenomenon is found in many sciences without predicting and/or quantifying this low-dose effect with statistical models. Only a minority of papers published on hormesis in plant biology or other sciences apply available statistical modelling of the dose-response relationships, along with signifi...

BACKGROUND Herbicide hormesis is characterized by stimulation of various growth and developmental parameters, such as biomass and height, at low herbicide doses. Other possible hormetic effects are earlier flowering, higher seed weight, more seeds, and a shorter plant life cycle, which could favor the propagation of the species. This study tested t...

New herbicide modes of action (MOAs) are in great demand because of the burgeoning evolution of resistance of weeds to existing commercial herbicides. This need has been exacerbated by the almost complete lack of introduction of herbicides with new MOAs for almost 40 years. There are many highly phytotoxic compounds with MOAs not represented by com...

Weeding has been the bane of humanity since the dawn of agriculture. For about 70 years, synthetic herbicides have removed much of the drudgery of this onerous task. Glyphosate was introduced as a non-selective herbicide in 1974. Its ideal properties made it a very popular herbicide, and the introduction of glyphosate-resistant (GR) crops allowed i...

Natural products (NPs) have a long history as sources of compounds for crop protection. Perhaps a more important role for NPs has been as models and inspiration for the discovery and development of synthetic crop protection compounds. NPs and their synthetic mimics account for 18% of all crop protection compounds, whereas another 38% of all crop pr...

The chemical and biological properties of glyphosate are key to understanding its fate in the environment and potential risks to non-target organisms. Glyphosate is polar and water soluble and therefore does not bioaccumulate, biomagnify, or accumulate to high levels in the environment. It sorbs strongly to particles in soil and sediments and this...

Many scientific articles describe the potential of natural or new synthetic molecules for crop protection. However, we hardly see them entering to the market. Why is that so? The hurdles are high and activity alone is not enough. This work intends to illustrate the early research and development processes for the crop protection industry, taking as...

Nicotinic acid, also known as niacin, is a natural product, which is widely found in plants and animals. To discover novel natural-product-based herbicides, a series of N-(arylmethoxy)-2-chloronicotinamides were designed and synthesized. Some of the new N-(arylmethoxy)-2-chloronicotinamides exhibited excellent herbicidal activity against Agrostis s...

Food production to adequately supply the world population represents a great challenge for the agricultural sector. Phytopathogenic microbes and weeds are two of the biggest problems in causing high losses in agriculture. The use of pesticides is indispensable in managing these problems. However, the extensive use of these agrochemicals can cause d...

Glyphosate is the most used herbicide globally. It is a unique non-selective herbicide with a mode of action that is ideal for vegetation management in both agricultural and non-agricultural settings. Its use was more than doubled by the introduction of transgenic, glyphosate-resistant (GR) crops. All of its phytotoxic effects are the result of inh...

Sorgoleone, a hydrophobic compound exuded from root hair cells of Sorghum spp., accounts for much of the allelopathic activity of the genus. The enzymes involved in the biosynthesis of this compound have been identified and functionally characterized. Here, we report the successful assembly of the biosynthetic pathway and the significant impact of...

Bioassay-guided fractionation of the ethyl acetate extract of Amyris elemifera leaves was carried out to identify phytotoxic and antifungal constituents. A novel phytotoxic furanocoumarin 8-(3-methylbut-2-enyloxy)-marmesin acetate (1) and its deacyl analog 8-(3-methylbut-2-enyloxy)-marmesin (2) were isolated. The X-ray crystal structure determinati...

The metabolic pathways in the apicoplast organelle of Plasmodium parasites are similar to those in plastids in plant cells and are suitable targets for malaria drug discovery. Some phytotoxins released by plant pathogenic fungi have been known to target metabolic pathways of the plastid; thus, they may also serve as potential antimalarial drug lead...

Knowledge of the mode of action of an allelochemical can be valuable for several reasons, such as proving and elucidating the role of the compound in nature and evaluating its potential utility as a pesticide. However, discovery of the molecular target site of a natural phytotoxin can be challenging. Because of this, we know little about the molecu...

Five sesquiterpene-α-amino acid quaternary ammonium hybrids and the sesquiterpene core with no amino acid moiety linked were isolated from the n-butanol partition of the Stereum complicatum fungal culture grown on potato dextrose broth. Chemical structures were unambiguously elucidated by high resolution electrospray ionization mass spectrometry (H...

Stereoselective syntheses of new pyranopyrans that are related to the natural product diplopyrone, which is a phytotoxin implicated in cork oak decline, have been achieved from carbohydrate starting materials in two approaches that are based on C-glycosides as key intermediates. A C-alkynyl glycoside prepared by Ferrier rearrangement was used as th...

We hypothesized that eucalyptus has clone-dependent responses to glyphosate, and such differential responses might be associated with morphological, metabolic and/or photosynthetic changes. Experiments were carried out under controlled conditions of temperature, photoperiod and nutrition, focusing on evaluating the response of Eucalyptus × urogrand...

Natural products are a source of many novel compounds with biological activity for discovery of new pesticides and pharmaceuticals. Quinoxaline is a fused N-heterocycle in many natural products and synthetic compounds, seven novel quinoxaline derivatives were designed and synthesized via three steps. Pesticidal activities of title quinoxaline deriv...

The widely successful use of synthetic herbicides over the past 70 years has imposed strong and widespread selection pressure, leading to the evolution of herbicide resistance in hundreds of weed species. Both target-site resistance (TSR) and non-target-site resistance (NTSR) mechanisms have evolved to most herbicide classes. TSR often involves mut...

Glyphosate is the most used herbicide worldwide, which has contributed to concerns about its environmental impact. Compared with most other herbicides, glyphosate has a half-life in soil and water that is relatively short (averaging about 30 d in temperate climates), mostly due to microbial degradation. Its primary microbial product, aminomethylpho...

Glyphosate is the most used herbicide on the planet because of its excellent efficacy on almost all weeds species and due to the large-scale adoption of transgenic, glyphosate-resistant (GR) crops. Agnes Rimando became an expert in glyphosate analysis almost 20 years ago to support research on GR crop safety and on mechanisms of evolved glyphosate...

Herein, we describe the isolation and identification of four new and three known sesquiterpenes from the culture broth of the fungus Stereum complicatum. Chemical structures were elucidated based on HR-DART-MS, 1D and 2D NMR experiments. Compounds were identified as sterostrein X (1), sterostrein Y (2), hirsutenol G (3), sterpurol C (4), sterostrei...

An investigation of the secondary metabolites was carried out on Thymelaea hirsuta collected from Lampedusa, the largest island of the Pelagie archipelago, located about 100 km from the North African coast and 200 km from the coast of Sicily. Ten compounds were isolated and found to belong to different classes of natural products as chromenes, cycl...

No herbicide with a new molecular site of action (SOA) has been introduced since the 1980s. Since then, the widespread evolution of resistance of weeds to most commercial herbicides has greatly increased the need for herbicides with new SOAs. Two untried strategies for the discovery on new herbicide SOAs are discussed. Some primary metabolism inter...

The culture broth of Burkholderia rinojensis strain A396 is herbicidal to a number of weed species with greater observed efficacy against broadleaf than grass weeds. A portion of this activity is attributed to romidepsin, a 16-membered cyclic depsipeptide bridged by a 15-membered macrocyclic disulfide. Romidepsin, which is present in small amounts...

Increasing the efficiency of food production systems while reducing negative environmental effects remains a key societal challenge to successfully meet the needs of a growing global population. The herbicide glyphosate has become a nearly ubiquitous component of agricultural production across the globe, enabling an increasing adoption of no-till a...

Expression of genes involved in diterpene biosynthesis, especially momilactone and gibberellins (GAs), in rice plants (Oryza sativa L.) in response to barnyard grass (Echinochloa crus-galli) stress was examined. The three analyzed class II diterpene synthases had the highest fold change expression. Transcription patterns of genes for two homologs o...

Several new 1,3,4-oxadiazole derivatives containing a pyrazole ring were designed and synthesized from ethyl acetoacetate and triethyl orthoformate as starting materials via multi-step reactions. The compound structures were confirmed by melting point, ¹H NMR and HRMS. They were evaluated for fungicidal and herbicidal activities. Four of the compou...

The mechanism of phytotoxicity of citral was probed in Arabidopsis thaliana using RNA‐Seq and in silico binding analyses. Inhibition of growth by 50% by citral downregulated transcription of 9156 and 5541 genes in roots and shoots, respectively, after 1 h. Only 56 and 62 genes in roots and shoots, respectively, were upregulated. In the shoots, the...

Fungi occur in virtually all types of living and non-living substrates of Antarctica in different environments. However, knowledge of the diversity, ecological roles, and biotechnological applications of Antarctic fungi remain limited. The major resident Antarctic fungal phylum is Ascomycota and its anamorphs, followed by Basidiomycota and a few tr...

Weed science, as an integral part of agricultural production needs to evolve by moving away from its mono-disciplinary perspective at targeting weeds, sometimes a single species, through the overreliance on few single herbicide mechanisms of action. Herbicides remain a simple and cost-effective way to control weeds but they are rapidly losing their...

BACKGROUND New modes of action are needed for herbicides. The flavonoid synthesis intermediate t‐chalcone causes apoptosis‐like symptoms in roots and bleaching of shoots of Arabidospsis, suggesting a unique mode of action as a phytotoxin. RESULTS Using RNA‐Seq, transcriptome changes were monitored in Arabidopsis seedlings during the first 24 h of...

The literature of biological activity of herbicides is vast. Thus, this short review contains only what we consider to the most important aspects of the topic. We divide the herbicides into three main groups: 1) herbicides that target biochemical pathways and physiological processes involved with photosynthesis, 2) herbicides that inhibit the forma...

The discovery of potent natural and ecofriendly pesticides is one of the focuses of the agrochemical industry, and plant species are a source of many potentially active compounds. We describe the bioassay-guided isolation of antifungal and phytotoxic compounds from the ethyl acetate extract of Ambrosia salsola twigs and leaves. With this methodolog...

Bioassay-guided fractionation of an EtOAc extract of the broth of the endophytic fungus Nemania sp. UM10M (Xylariaceae) isolated from a diseased Torreya taxifolia leaf afforded three known cytochalasins, 19,20-epoxycytochalasins C (1) and D (2), and 18-deoxy-19,20-epoxy-cytochalasin C (3). All three compounds showed potent in vitro antiplasmodial a...

Eragrostis plana (Nees) is an allelopathic plant with invasive potential in South American pastures. To isolate and identify phytotoxic compounds from leaves and roots of E. plana, a bioassay-directed isolation of the bioactive constituents was performed. This is the first report on a new diterpene carbon skeleton, the neocassanes, and of three new...

A series of triazole derivatives containing a pyrazole moiety were synthesized and characterized by 1H NMR, 13C NMR, and HRMS. The herbicidal activities of these compounds were tested against lettuce and bentgrass. Most of the tested compounds were moderately herbicidal activity against lettuce and bentgrass. Among them, compounds 6f and 6g had the...

In light of public concerns about sustainable food production, the necessity of human and environmental protection, along with the evolution of herbicide-resistant weeds, a review of current weed control strategies is needed. Sustainable weed control requires an integrated approach based on knowledge of each crop and the weeds that threaten it. Im...