Location: Global Change and Photosynthesis Research
2022 Annual Report
Objectives
Objective 1: Determine the structure and functions of microbial communities in cropping systems that include chemical and non-chemical weed control tactics, and elucidate their interactions with herbicide resistant weeds, and response to various weed management tactics under climate change.
1.1 Characterize the microbial community structure associated with the rhizosphere of problematic weed species in Midwest cropping systems.
1.2 Characterize the microbial community structure associated with herbicide resistant weeds.
Objective 2: Develop alternative cropping systems that include the integration of new chemical and non-chemical tactics for managing weeds for Midwest specialty crops production and improve the knowledge or understanding of influences of the climate variability on crop and weed management outcomes.
2.1 Determine the scope of the problem of weeds and their management in processing vegetable legumes, specifically snap bean.
2.2 Quantify snap bean cultivar variability in herbicide tolerance and traits important to weed competitiveness.
2.3 Model effectiveness of preemergence herbicides across variation in rainfall and soil temperature.
2.4 Determine the relationships among weed control and weather variability on corn yield loss due to weeds.
2.5 Investigate the role of sweet corn postharvest weed seed control in reducing weed seedbank inputs.
Approach
Many of the pressing weed issues in the nation's cropping systems have resulted from the simplification of weed management systems through over-reliance on specific herbicides, causing economic losses of tens of billions of dollars annually. Weeds have adapted to this selection pressure through evolution of herbicide resistances. Moreover, emerging chemical 'solutions' to manage herbicide resistant weeds in agronomic crops offers no benefit to specialty crop production systems because herbicide tolerant cultivars are either not available or largely unaccepted, yet these crops face greater sensitivity to weed competition, off-target herbicide injury, and adverse weather. Our research aims to develop strategies that may help to reduce the risk that weeds pose to food production in the face of climate change. We will utilize an array of experimental approaches at various spatial and temporal scales, all aimed at building resilience in weed management systems to reduce weed fitness and enhance crop performance. Study systems will range in spatial scale from plant-microbe rhizosphere dynamics to weed community assemblages of specialty crop fields in multiple states. The temporal scale of our study systems will range from days, for microbial research, to decades, for long-term weed management trials. Our experimental approaches are diverse, including microbial ecology, weed ecology, genetics, modeling, and agronomic research using both empirical hypothesis testing and observational analyses. The knowledge gained through this research addresses specific agricultural problems of national importance including those associated with pest management, food security, and grower profitability.
Progress Report
In support of Objective 1, greenhouse experiments were completed to address for the first time the characterization of the microbial taxonomic community structure of rhizosphere fractions from three pigweed species Amaranthus palmeri (Palmer amaranth), A. retroflexus (redroot pigweed), and A. tuberculatum (waterhemp). Sequence data to date identified distinct patterns of communities in rhizosphere bulk soils, plant rhizospheres, and rhizoplanes specific to these closely related plant species. Due to the expectation of high background molecular signals typically associated with agricultural soils, high replication (n=8) was required for initial validation of methods and data analyses, along with conducting two independent greenhouse studies with each species. Where standard methods did not previously exist for collection of DNA/RNA samples from rhizospheres and rhizoplanes specific to the three weed species, new methods were established, including handling of large datasets. Analyses based on comparative community profiles not only demonstrated bacterial and archaeal communities are distinct between the three amaranth species, but the rhizosphere compartments for a given plant species are also distinct (one manuscript in preparation). High throughput sequencing technology was successfully applied for detailed taxonomic characterization (over 40,000 annotated taxa per sample) and will form the basis for identification of taxa associated with microbial functional genes that will be considered for assessing key weed-microbe mechanisms of relationships. Related to the latter, efforts continue to identify microbial constituents and metabolic genes responding to climate change conditions such as increased precipitation (i.e. El Nino effect), sunlight intensities (i.e. photosynthesis effects), and longer durations of higher temperature aimed at adding significant new information to the microbial gene database built from our unit’s work continuing research in this area.
For Objective 2, significant progress has been made on developing alternative cropping systems that include the integration of new chemical and non-chemical tactics for managing weeds for Midwest specialty crops production and improve the knowledge or understanding of influences of the climate variability on crop and weed management outcomes. A team of weed scientists throughout the U.S. has surveyed growers’ fields of lima bean and snap bean. Fields have been surveyed near the time of harvest, capturing several variables of the weed community and crop condition. For most fields, field records including crop management practices have been obtained. To date, 267 snap bean fields and 64 lima bean fields have been surveyed. Data are being compiled. Additional fields will be surveyed during the 2022 field season to enrich the database and provide valuable experience to students working on the project. The SNap Bean Association Panel (SNAP), a genotyped diversity panel with nearly 400 entries, was used to determine tolerance to several herbicides including sulfentrazone, pyroxasulfone, metribuzin, and flumioxazin under field conditions. Two years of data from sulfentrazone trials has been analyzed, including the use of Genome- Wide Association modeling, which identified genomic regions associated with sulfentrazone tolerance. A manuscript has been prepared and published in Frontiers in Agronomy. Two years of data from pyroxasulfone trials also has been analyzed and a manuscript is in preparation. The single year of field trials with metribuzin and flumioxazin are being repeated in the 2022 field season to confirm results. Additional field trials with a subset of the SNAP were conducted with lines tolerant or sensitive to protoporphyrinogen (PPO)-inhibiting herbicides. Herbicides evaluated included PPO-inhibitors sulfentrazone, flumioxazin, fomesafen, lactofen, and saflufenacil; very long chain fatty acid inhibitor dimethenamid-P; and photosystem II-inhibitor metribuzin. This field trial is being repeated in 2022 to obtain a second year of data and confirm results. The SNAP is also being used to understand crop competitiveness with weeds; specifically, the role of biological nitrogen fixation in crop-weed interactions. Field trials in Urbana prove difficult to elucidate these interactions because of excessively high nitrogen levels even in fields deprived of added nitrogen for five years.
However, controlled environment studies underway show promise and are ongoing. Research determining the extent to which sweet corn injury from dicamba can be managed with herbicide tolerance alleles and an herbicide safener has been completed and published. Analyses of historic herbicide evaluation datasets from University of Illinois continues to yield new information on the extent to which variable weather influences herbicide performance and crop losses due to weeds. Several machine-learning techniques were employed to identify linkages among weather, weed control, and yield of corn and soybean. Two manuscripts were prepared and are now published in high-impact journals. This research is being expanded by developing collaborations with extension weed scientists across the United States with the intent to compile their states’ herbicide evaluation trials into a single database. Moreover, ongoing cover crop research includes: 1) developing a grower-oriented web application to predict cereal rye phenology that will be useful in determining cover crop termination dates, and 2) examining interactions between S-metolachlor and cereal rye residues on shattercane, velvetleaf, and waterhemp emergence and seedling growth. The cereal rye phenology model also has been utilized in a processed-based crop model to predict soil carbon sequestration for the state of Illinois. A manuscript is currently under review. Finally, an experiment from the previous project (5012-12220-009-00D) is being completed. Specifically, we have estimated local eradication costs for invasive Miscanthus populations throughout the Eastern and Midwestern United States. A manuscript is currently under review.
Accomplishments
1. Determined climate change demands near perfect weed control in corn and soybean. Estimates of future grain yields in the face of climate change assume weed-free conditions. Given the adaptability of weeds (e.g. current herbicide resistance epidemic), is that assumption realistic? ARS researchers in Urbana, Illinois, with university colleagues used a novel approach with existing herbicide evaluation trials conducted over three decades to identify the main drivers of yield loss in corn and soybean. Abnormally hot or dry conditions were found during flowering – conditions expected to occur more frequently in much of the U.S. cornbelt – exacerbated crop losses when weed control was less than perfect. As agriculture adapts to climate change, the research underscores the critical importance of also developing integrated weed management systems that are more effective in the to aid producers with maximizing yield to help feed a growing population.
2. Identified manageable risk of sweet corn injury from dicamba. Use of dicamba herbicide has increased exponentially in recent years with the adoption of dicamba-tolerant (DT) soybean. Volatility of the product driven by later-season applications to DT soybean results in off-target dicamba movement which can injure sensitive crops. This research determined the extent to which sweet corn injury from dicamba can be managed. ARS researchers at Urbana, Illinois, with university partners showed how crop cultivar, herbicide formulation, and timing of dicamba exposure reduces risk of sweet corn injury from dicamba. This new knowledge offers tangible approaches that growers, sweet corn seed companies, and herbicide manufacturers are adopting to protect domestic production of one of the United States' most favorite vegetables.
Review Publications
Landau, C.A., Hager, A.G., Williams II, M.M. 2021. Diminishing weed control exacerbates maize yield loss to adverse weather. Global Change Biology. 27(23):6156-6165. https://doi.org/10.1111/gcb.15857.
Dong, Y., Sanford, R.A., Connor, L.M., Chee-Sanford, J.C., Wimmer, B.T., Iranmanesh, A., Shi, L., Krapac, I.G., Locke, R.A., Shao, H. 2021. Differential structure and functional gene response to geochemistry associated with the suspended and attached shallow aquifer microbiomes from the Illinois Basin, IL. Water Research. 202. Article 117431. https://doi.org/10.1016/j.watres.2021.117431.
Dhaliwal, D.S., Ainsworth, E.A., Williams II, M.M. 2021. Historical trends in sweet corn plant density tolerance using era hybrids (1930–2010s). Frontiers in Plant Science. 12. Article 707852. https://doi.org/10.3389/fpls.2021.707852.
Landau, C.A., Bernards, M.L., Hager, A.G., Williams II, M.M. 2022. Significance of application timing, formulation, and cytochrome P450 genotypic class on sweet corn response to dicamba. Weed Science. 70(2):167-173. https://doi.org/10.1017/wsc.2022.5.
Landau, C.A., Hager, A.G., Williams II, M.M. 2022. Deteriorating weed control and variable weather portends greater soybean yield losses in the future. Science of the Total Environment. 830. Article 154764. https://doi.org/10.1016/j.scitotenv.2022.154764.
Saballos, A., Soler-Garzon, A., Brooks, M.D., Hart, J., Lipka, A., Miklas, P.N., Peachey, R.E., Tranel, P., Williams, M. 2022. Multiple genomic regions govern tolerance to sulfentrazone in snap bean (Phaseolus vulgaris L.). Frontiers in Agronomy. 4. Article 869770. https://doi.org/10.3389/fagro.2022.869770.
