Research Project: Understanding and Responding to Multiple-Herbicide Resistance in Weeds

Location: Global Change and Photosynthesis Research

2020 Annual Report

Objectives
Objective 1: Determine how crop management practices (such as cultivar selection) and abiotic factors affect weed ecology in the upper Midwest, especially in vegetable and bioenergy crops. Sub-objective 1a: Identify cover crop residues that favor edamame over the weed. Sub-objective 1b: Quantify the impact of Miscanthus invasion and removal on plant community composition. Sub-objective 1c: Quantify the role of soil environmental parameters (e.g., C, C:N and NO3-:NO2- ratios, pH, diurnal temperature variations, soil moisture) in controlling nitrification along with N-loss (denitrification) vs. N-retention (DNRA), and evaluate the link between measured N-cycle processes to weed seed germination and seedling development. Objective 2: Improve the feasibility of using multi-tactic integrated weed management approaches for regaining control of weeds with resistances to multiple herbicides, and for preventing or slowing the evolution of herbicide resistance in susceptible weed populations. Sub-objective 2a: Evaluate the impact of harvest weed seed control (HWSC) on population dynamics and management of multiple-herbicide-resistant weed genotypes in field crops. Sub-objective 2b: Develop and compare weed management systems in edamame, utilizing cover crops, herbicides, and physical weeding.

Approach
Multi-tactic integrated weed management (IWM) offers one potential approach to address the problem of multiple herbicide resistant (MHR) weeds. In IWM systems, suites of multiple complementary tactics are deployed throughout weed life cycles to increase efficacy of weed suppression, prevent survival of weeds that escape earlier management, and reduce weed populations over the long-term. In this project, we evaluate the utility of chemical, cultural, biological, and physical tactics in IWM systems for weed suppression and crop yield protection in fields with MHR weed populations. Edamame (vegetable soybean) cultivars tolerant to cover crop residues will be combined with cover crops, recently registered herbicides, and physical weeding to examine the potential of IWM in legume vegetable production systems. The contribution of improved knowledge of soil N cycling to aid better prediction of weed seedling emergence and community composition also will be evaluated in this production system. In field crops, interactions among weed seed destruction at crop harvest, cover crops, and tank mixtures of herbicides will be quantified for their impact on MHR weeds in corn and soybean. Finally, in a continuation of previous research, the impact of escaped invasive bioenergy crops on weeds of arable areas will be measured.

Progress Report
The cost of monitoring and eradicating a controlled Miscanthus invasion study was quantified over the 5-year period of this project (subobjective 1b). Each spring and summer, replicated field trials in floodplain forests and old fields were closely monitored and all plants were removed. Each year progressively fewer re-sprouts were observed. Demographic and economic data have been analyzed. A manuscript is in preparation. Harvest weed seed control (HWSC) has been explored as a way to manage multiple herbicide resistant weed genotypes (subobjective 2a). Initially, a device for mechanical destruction of weed seeds was tested as a stationary device. A journal article describing this experiment was recently published. In 2016, a 5-year field study was established to test HSWC on the population dynamics and management of multiple herbicide resistant weeds. The field trial currently is in the final year. A series of experiments have been conducted to improve the development of multi-tactic integrated weed management approaches for regaining weed control in vegetable crops (subobjectives 1a & 2b). In edamame, several field experiments were conducted to determine the role of seed size, planting depth, and use of cover crop mulches on crop emergence and seedling competitiveness. Aspects of this research were expanded to include lima bean and snap bean. Several additional field experiments focused on the underlying genetic, environmental, and management drivers to crowding stress tolerance in sweet corn. Knowledge about biological processes affecting nitrogen (N) cycling in soil has been significantly advanced by developing and continuously expanding a large database of important functional genes (nrfA, nosZ) and new molecular probes to allow a comprehensive account of under-recognized key microbial populations in agricultural soils (subobjective 1c). Current sequencing technologies were applied to genetic pools from soils taken in multi-year field experiments and controlled microcosms. Using high-throughput sample arrays, diverse genes involved in N2O reduction, ammonification (DNRA), and other N-cycle processes were characterized and linked to legacy effects of edaphic factors like moisture drainage, diurnal temperature soil profiles, and N-fertilizers in agricultural field sites. Datasets from multi-year field studies are in analyses, including improvements made to bioinformatics computational tools, in part now made publicly available. Weed success correlated to microbial N-cycling processes (subobjective 1c) was investigated following the establishment of a growing dataset characterizing the microbial functional community present in two field sites established since 2012. Data from sampling of soil across depths at fixed locations with either annual herbicide application or limited weed control occurred in 2016-2019 for analysis of microbial community structures using molecular probes developed during the life of the project. Sequence data analysis is nearing completion and dataset preparation is in progress for multivariate analyses to measure correlations between microbial functional genes to legacies of weed control at the site. This final dataset will be critical in establishing baselines for weed species testing in upcoming controlled-environment and field environment tests. Controlled environment soil microcosms were used to monitor velvetleaf seed germination in soil with a history of corn/soybean production with weed presence or receiving annual routine herbicide treatments (subobjective 1c). The first trial was completed in fall 2019. New seed lots of velvetleaf are in development to establish homogeneity in age, viability status, and microbial exposure prior to use in the next germination trial. The maximized telework requirement due to the pandemic hampered the necessary seed production efforts and consequent setup and conduct of experimental trial 2. A total of 68 peer-reviewed publications have been reported in annual reports for the life of this project.

Accomplishments
1. Glyphosate does not affect soil microorganisms. 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 agriculture. Despite this widespread use, there remains considerable debate on the consequences of glyphosate exposure. In collaboration with university partners, ARS researchers at Beltsville, Maryland, Stoneville, Mississippi, and Urbana, Illinois, compared the microbial communities associated with crop roots in a variety of organic and conventional corn and soybean farming systems. No effects of glyphosate were found on soil microbial communities associated with glyphosate-resistant crop varieties across these diverse farming systems. This accomplishment is important because it is well-replicated in both time and space in realistic farming systems with well-documented glyphosate use histories. The impact of this work is providing research-based knowledge that glyphosate use, and no-till agriculture the herbicide enables, is not at risk of altering soil microbial communities in a negative manner.

2. Genetic mutations responsible for sweet corn herbicide sensitivity identified. Herbicide sensitivity among certain sweet corn lines plagued the sweet corn industry until the last decade. Although scientists identified the gene (nsf1) likely responsible for herbicide sensitivity to a variety of herbicides, questions remained about the functional connection of specific mutations of this gene to herbicide sensitivity. The product of the gene, a protein from a family of enzymes known for detoxifying compounds, was expressed from sweet corn lines differing in herbicide responses. Activity of the proteins were then measured. ARS scientists at Urbana, Illinois, identified specific mutations of nsf1 and how those mutations related to herbicide response. Corn breeders are using this knowledge to eliminate herbicide-sensitive sweet corn lines. This work provides a deeper understanding of herbicide action and has broad application to all types of corn and perhaps other plants.

3. Molecular probes were designed and validated for detection of microbial genes encoding reduction of the greenhouse gas nitrous oxide (N2O) in soil. Contrary to decades-long wisdom that only known denitrifying bacteria were responsible for the biological reduction of N2O to dinitrogen gas (N2), ARS scientists in collaboration with University of Illinois Urbana-Champaign partners discovered this microbial activity can be mediated by highly diverse bacteria previously unaccounted for in natural soil, sediment, and water. The lack of molecular tools to accurately detect this diversity was identified and probes were developed for the responsible functional gene nosZ. These probes can not only be used to accurately detect the breadth of known nosZ in natural environments, they were designed to be compatible with new high-throughput sequencing technologies microfluidic arrays enabling large number of samples to be analyzed with multiple different gene targets. The significance of this finding now allows researchers to conduct comprehensive studies that will fill current gaps in knowledge about the biological fate of N fertilizers in agricultural systems and soil N2O emissions.

Review Publications
Dhaliwal, D., Williams II, M.M. 2020. Economically optimal plant density for machine-harvested edamame. HortScience. 55(3):368-373. https://doi.org/10.21273/HORTSCI14642-19.
Dhaliwal, D., Williams II, M.M. 2020. Understanding variability in optimum plant density and recommendation domains for crowding stress tolerant processing sweet corn. PLoS One. 15(2):e0228809. https://doi.org/10.1371/journal.pone.0228809.
Shan, J., Corvini, P., Shaeffer, A., Chee Sanford, J.C., Yan, X., Ji, R. 2019. Influence of the geophagous earthworm Aporrectodea sp. on the fate of bisphenol A and a branched 4-nonylphenol isomer in soil. Science of the Total Environment. 693:133574. https://doi.org/10.1016/j.scitotenv.2019.07.380.
Dhaliwal, D.S., Williams II, M.M. 2019. Optimum plant density for crowding stress tolerant processing sweet corn. PLoS One. 14(9):e0223107. https://doi.org/10.1371/journal.pone.0223107.
Leguizamon, E.S., Ferrari, G., Williams II, M.M., Burgos, N.R., Travlos, I., Korres, N.E. 2019. Response of annual weeds to glyphosate: evaluation and optimization of application rate based on fecundity-avoidance biomass threshold criterion. Agronomy. 9:851. https://doi.org/10.3390/agronomy9120851.
Kepler, R., Epp Schmidt, D.J., Yarwood, S.A., Cavigelli, M.A., Buyer, J.S., Duke, S.O., Reddy, K.N., Williams, M., Bradley, C.A., Maul, J.E. 2020. Soil microbial communities in diverse agroecosystems exposed to glyphosate. Applied and Environmental Microbiology. https://doi.org/10.1128/AEM.01744-19.
Choe, E., Williams II, M.M. 2020. Expression and comparison of sweet corn CYP81A9s in relation to nicosulfuron sensitivity. Pest Management Science. https://doi.org/10.1002/ps.5848.
Chee-Sanford, J.C., Connor, L.M., Krichels, A., Yang, W.H., Sanford, R.A. 2020. Hierarchical detection of diverse Clade II (atypical) nosZ genes using new primer sets for classical- and multiplex PCR array applications. Journal of Microbiological Methods. 172:105908. https://doi.org/10.1016/j.mimet.2020.105908.
Chen, S., Chee-Sanford, J.C., Yang, W.H., Sanford, R.A., Chen, J., Yan, X., Shan, J. 2019. Effects of triclosan and triclocarban on denitrification and N2O emissions in paddy soil. Science of the Total Environment. 695:133782. https://doi.org/10.1016/j.scitotenv.2019.133782.
Lowry, C.J., Bosworth, S.C., Goslee, S.C., Kersbergen, R.J., Pollnac, F.W., Skinner, R., Warren, N.D., Smith, R.G. 2019. Effects of expanding functional trait diversity on productivity and stability in cultivar mixtures of perennial ryegrass. Agriculture, Ecosystems and Environment. 287:106691. https://doi.org/10.1016/j.agee.2019.106691.
Haramoto, E., Lowry, C.J., Pearce, B. 2019. Cover crops are not affected by tobacco soil residual herbicides but also do not provide consistent weed management benefits. Weed Technology. 34:383–393. https://doi.org/10.1017/wet.2019.123.