Location: Global Change and Photosynthesis Research
2021 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
The complex environment of the plant rhizosphere system requires significant initial effort to establish protocols for routine sampling of specific rhizosphere compartments that are weed species- and soil dependent in support of Objective 1. No established methodological protocols for plant rhizosphere work are available in the literature for the selected weed species identified for this project. To this end, our initial focus on three amaranth weed species (Amaranth palmeri, A. rudis, A. retroflexus) has resulted in establishment of seed/plant lines for exclusive use in greenhouse and field studies, and characterization of the local clay loam soil common in the Midwest U.S. agricultural region, all efforts critical for baseline characterization of the plant rhizosphere microbial recruitment pool and subsequent development of rhizosphere communities. Significant progress has been made to establish methods for routine plant growth and specific collection of rhizosphere-related fractions for downstream molecular (DNA) analyses, with methods requiring particular modifications depending on plant root structure and soil characteristics. We anticipate this to be an iterative process for each additional plant species we intend to target with significantly different growth- and phenotypic characteristics. Molecular community analyses using probes targeting gene or gene regions commonly used for microbial taxonomic identification exist and have various suitability for use but required updates to our in-house probe collections (completed) to include those for the most comprehensive coverage of soil microbial community members. Standard nucleic extraction methods have been established. An in-house database for gene sequences associated with microbial N-cycling is now an ongoing curation effort based on previous years’ work, and in progress now to include additional genes of interest aimed toward identifying potential links between microbial function and weed nutritional benefits.
In support of Objective 2, significant progress has been made on improving the understanding of the influences of climate variability on crop and weed management outcomes. A team of weed scientists from the Northeast U.S. to Pacific Northwest has been assembled and is conducting surveys of growers’ fields of vegetable legumes (specifically lima bean and snap bean). Over the first year of this project, the team has visited dozens of fields and acquired data on weed, crop, soil, and associated field management data. Weed and crop data for the year is compiled, soils samples have been centralized and analyzed, and collection of field management data from collaborating vegetable processors is ongoing. Team meetings have been held and details for year two are nearly finalized. In related snap bean research, a team of public- and private-sector agronomists, economists, and plant breeders have joined an effort to improve snap bean, with a specific interest in building resilience to climate variability. A collaborating vegetable processor has agreed to maintain a snap bean diversity panel being used by the team. In the current project, the panel is being used to quantify snap bean variability in herbicide tolerance and traits important to weed competitiveness. We have evaluated the panel in two environments to date, with more planned in the next growing season. Preliminary analyses of existing data identified several candidate genes conferring tolerance to specific soil-active herbicides. A manuscript is being prepared. Additional follow-up studies (lab and greenhouse) are being developed to identify the extent to which tolerance is conferred to both similar and different herbicidal sites of action. We are also beginning to use the diversity panel to understand crop competitiveness with weeds, including the role of biological nitrogen fixation and any crop competitive advantage in low synthetic-nitrogen-fertilizer environments. Finally, historical datasets are yielding new information on the extent to which variable weather influences performance of widely used soil-active herbicides. The University of Illinois at Urbana-Champaign’s Herbicide Evaluation Program database has been accessed, processed, and linked with associated weather data. Logistic regression modeling has been used to quantify the role of rainfall and temperature on preemergence herbicide efficacy on common lambsquarters, giant foxtail, and waterhemp. One paper has been submitted and published. Additional progress has been made in sweet corn. In previous work, the sweet corn industry recreated important hybrids from the 1930s to the 2010s for an era study on changes in plant density tolerance. Three years of field experiments were completed, data have been analyzed, and a manuscript has been written and submitted. A follow-up meta-analysis of previously published research (both on-farm and research station trials) has been completed and published, showing that increasing plant density of density-tolerant sweet corn (indirect genetic control of weeds) does not increase risk of crop root lodging.
In additional support of Objective 2, progress also is being made in developing alternative cropping systems that integrate new chemical and non-chemical tactics for managing weeds. Previous research showing the suppressive potential of soybean plant density on Palmer amaranth has been analyzed, written up, and published. In other previous work, field experiments were conducted over three years that showed early-terminated cereal rye cover crop has promise in selectively managing weeds in edamame, but not lima bean or snap bean. Data were analyzed, a manuscript was written, and the work is now published. Additional 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. A field experiment was conducted to determine the role of postharvest weed seed control in reducing weed seedbank inputs following sweet corn harvest. Seed production dynamics of velvetleaf, waterhemp, and wild-proso millet are being characterized in multiple planting environments. Currently, weed seed samples are being processed.
Accomplishments
1. Variable weather threatens future efficacy of preemergence herbicides. Preemergence herbicides are the first line of defense against weeds in major agronomic crops such as corn and soybean, and while weather is known to influence their weed control performance, what to expect in a changing climate was poorly known. ARS researchers with university colleagues at Urbana, Illinois, developed the most rigorous approach to date to understand the significance of rainfall and soil temperature variations on activity of the most widely used preemergence herbicides in corn. The idea of data-mining common, yet largely unutilized herbicide efficacy databases, with machine learning techniques has drawn early attention from industry and public-sector scientists alike. Moreover, the findings from this research show that variable weather in the future threatens efficacy of these preemergence herbicides. The work provides a cautionary note on continuing to manage weeds with a ‘business as usual’ approach and underscores the importance of developing more integrated weed management systems with greater resilience to weather variability.
2. Cereal rye cover crop plays important role in edamame weed management. Vegetable legumes grown for processing (i.e. edamame, lima bean, snap bean) contribute to a healthy diet; however, weeds are a major production problem with few tools to manage them economically. ARS researchers at Urbana, Illinois, examined the role of early-terminated cereal rye cover crop on weed suppression and crop yield. While the cover crop system harmed lima bean and snap bean emergence and growth, researchers found the system selectively enhanced weed control in edamame comparable to handweeding. The research offers a new, economically viable solution to weed management in edamame while being the first to reduce reliance on chemical weed control. Grown almost entirely outside the United States a decade ago, the research facilitates the development of a competitive, sustainable domestic edamame industry to feed the growing interest among American consumers.
Review Publications
Korres, N.E., Norsworthy, J., Mauromoustakos, A., Williams II, M.M. 2020. Soybean density and Palmer amaranth (Amaranthus palmeri) establishment time: effects on weed biology, crop yield, and economic returns. Weed Science. 68(5):467-475. https://doi.org/10.1017/wsc.2020.41.
Chen, M., Conroy, J.L., Sanford, R.A., Chee-Sanford, J.C., Connor, L.M. 2020. Interpreting lacustrine bulk sediment d15N values using metagenomics in a tropical hypersaline lake system. Journal of Paleolimnology. 65:151-168. https://doi.org/10.1007/s10933-020-00157-7.
Shan, J., Sanford, R.A., Chee-Sanford, J.C., Ooi, S., Loeffler, F., Konstantinidis, K., Yang, W.H. 2021. Beyond denitrification: The role of microbial diversity in controlling nitrous oxide reduction and soil nitrous oxide emissions. Global Change Biology. 27(12):2669-2683. https://doi.org/10.1111/gcb.15545.
Landau, C., Hager, A., Tranel, P., Davis, A., Martin, N., Williams II, M.M. 2021. Future efficacy of pre-emergence herbicides in corn (Zea mays) is threatened by more variable weather. Pest Management Science. 77(6):2683-2689. https://doi.org/10.1002/ps.6309.
Choe, E., Ko, Y., Williams II, M.M. 2021. Transcriptional analysis of sweet corn hybrids in response to crowding stress. PLoS ONE. 16(6). Article e0253190. https://doi.org/10.1371/journal.pone.0253190.
Korres, N.E., Hausman, N.E., Moody, J., Kitis, E., Williams II, M.M. 2020. Integrated weed management strategies with cereal rye mulch in processing vegetable legumes. Agronomy Journal. 112(5):4264-4275. https://doi.org/10.1002/agj2.20349.
Williams II, M., Hausman, N.E., Dhaliwal, D., Grift, T., Bohn, M. 2021. Economic optimum plant density of sweet corn does not increase root lodging incidence. Crop Science. 1-10. https://doi.org/10.1002/csc2.20546.
