Progress 10/01/10 to 09/30/15

Outputs
Progress Report Objectives (from AD-416): Objective 1: Measure effects of management, climate, and soil conditions on microbial processes (herbicide degradation, nitrogen cycling, and weed seedbank dynamics) in corn/soybean ecosystems. Objective 2: Evaluate the effects of management and climate change on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bioenergy crops, in Midwestern cropping systems. Objective 3: Identify effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. Approach (from AD-416): Each objective of the proposed work seeks to advance knowledge of specific topics that directly or indirectly relate to weed-crop competition for resources, providing a basis to identify tactics of routine management that shift the competitive advantage to the crop. We examine the ecology of microorganisms and plants, and combine these efforts into a synthesis that applies research findings toward practical solutions. Each objective utilizes the whole scientific team, and regardless of scale, experiments include samples from a common group of sites, providing extensive metadata support. Studies under Objective 1 address microbial activities that are influenced by agricultural management, climate, or soil conditions. Primary climatic factors to be addressed are temperature and rainfall. In Objective 2, management and climate change will be evaluated as to effects on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bio- energy crops, in Midwestern cropping systems. A particular focus will be on spatiotemporal variation in demographic parameters and population growth rates at multiple levels of scale. As a means of unifying observations, whole life cycles of weeds will be the unit of study whenever possible. Objective 3 identifies effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. This 5-year project began in 2011 with the overall aim of improving understanding of the ecology and management of weedy and invasive plant species in the upper Midwest under variable environmental conditions. The project activities are complete, with all milestones fully met. Below are specific reports on the final year of progress for different components of the project. Multi-tactic weed management practices continue to be developed and tested in Midwest vegetable crops, specifically sweet corn (which the U.S. dominates development and production globally) and edamame (a popular nutraceutical soybean food crop largely imported from Asia). In sweet corn, a new research method was developed to more easily identify crowding stress tolerant hybrids; manuscript in press. On-farm experiments continue to be utilized to determine underlying genetic, environmental, and management drivers to crowding stress tolerance. A manuscript was prepared (currently in press) from in-house research on integrating competitive hybrids with various tillage practices for weed management in organic sweet corn production. Field trials assessing the effects of the glyphosate-resistance transgene, glyphosate use, and Goss�s wilt on crop performance were completed; manuscript in preparation. Multi-institution project successfully identified weed management alternatives to atrazine; manuscript in internal review. Regarding edamame, specific seed treatments show improved edamame emergence and work is ongoing. Preliminary experiment to identify cover crop/residue management systems for weed suppression has been initiated. Most recent research on crop tolerance to 5 herbicides has resulted in a federal label (bentazon, fomesafen, imazamox, and linuron) and a 24c label (sulfentrazone) for use of these products for weed control in edamame; manuscript published. Analysis of a 3-year, 136-cultivar dataset on edamame establishment, growth, and development traits revealed specific areas of future research and crop development; manuscript published. Investigations of weed management in a changing climate, begun in FY 11, were completed in FY 15. Competition of Palmer amaranth genotypes from the southern U.S. with soybean was measured in southern, central, and northern Illinois, following strict protocols to avoid introducing a seed bank for this species. A manuscript on common garden study data was prepared and published, providing farmers with necessary information to keep Palmer amaranth from invading their fields in the northern U.S. corn belt. Data were analyzed from the completed field study on the demography and growth of the energy crops Miscanthus giganteus and Miscanthus sinensis in old field and forest environments in central Illinois; manuscripts submitted. A landscape-scale simulation model was developed to quantify the potential impact of cooperative weed management associations on the evolution and spread of herbicide resistant weeds. Finally, a manuscript on understanding and guiding the collaborative process necessary for designing and implementing multitactic integrated weed management systems was published. A substantial body of new knowledge about the microbiology of nitrogen cycling has been recently reported, but remains incomplete about important processes that either result in N-loss or N-retention in soils, particularly in agricultural systems. Our work completes a three year study at two agricultural field sites where we tracked changes in the microbial populations involved in nitrification, denitrification, and ammonification, all key N-cycling processes that impact the availability and loss of N in soil. This study is unique in its length of time and spatial dimension, including effects within soil depth and field-scale differences, and takes place across multiple seasons and years. Climate data and soil properties were collected along with the biological data and analysis is underway to show how these factors may control microbial populations involved in N-cycling and which populations are most important in soils. A manuscript is in preparation on our findings of N- cycling genes involved in ammonification, a process that retains N in the form of ammonium, once thought to be a rare process in agricultural soils. A method of analysis to use in new gene sequencing technology was developed with collaborators (manuscript in review) using data collected by in-house research that revealed new N-cycling genes (previously published manuscript), which significantly advances microbial studies in soil systems. Laboratory-scale experiments were set up this year to specifically test a new hypothesis resulting from the field study that large diurnal temperature changes occurring in soil, especially surface layers, largely control microbial N-cycling (study in progress) and includes plant community effects (corn crop, velvetleaf weed) typical in our agricultural systems. Accomplishments 01 Overcoming a barrier to U.S. edamame. Little known among American consumers just a decade ago, edamame is now available in supermarkets and chain restaurants throughout the U.S. Moreover, U.S.-grown edamame is on the rise. This vegetable-type soybean, is a nutritious food that has strong growth among U.S. consumers; however, nearly all edamame consumed in the U.S. is imported. In order to feed a growing market and make sure food safety standards are met, the U.S. vegetable industry is interested in growing edamame domestically, yet weeds are a major problem. ARS researchers in Urbana, Illinois found crop tolerance to herbicides that have been used in grain-type soybean for decades. Up from a single registered herbicide in 2010, now a total of eight herbicides are federally registered for use on edamame to provide control of many grass and broadleaf weeds. The safe, proven herbicides greatly reduce the need for handweeding, which can add $500/A to the overall cost of edamame production. 02 Keeping Palmer amaranth out of the northern U.S. corn belt. Palmer amaranth is a weed species that evolved in the Sonoran desert and that has expanded its range into crop fields throughout much of the south central and southeast U.S. In fields infested by Palmer amaranth, it is highly competitive, causing complete crop yield losses in many cases. As Palmer amaranth moves north, following a warming climate, farmers in the upper Midwest have asked for help in understanding how to keep their farms from being invaded. ARS researchers in Urbana, Illinois found that the main barrier to further northward migration of Palmer amaranth is low seed movement of this species into farmers� fields. Once its seeds have arrived at a location in the upper Midwest, most Palmer amaranth genotypes are able to reduce crop yields and set enough seed to keep their population going. Growers now have specific recommendations (such as keeping machinery clean, using certified crop seed, and composting animal manure from outside farms prior to field application) to help them keep Palmer amaranth from becoming a problem in their fields.

Impacts
(N/A)

Publications

• Kane, D.A., Snapp, S.S., Davis, A.S. 2014. Ridge tillage concentrates potentially mineralizable soil N in the crop row, facilitating maize N uptake. Soil Science Society of America Journal. 79:81-88.
• Karki, T.B., Sah, S.K., Thapa, R.B., McDonald, A.J., Davis, A.S., Khadka, Y.G. 2014. Weeds and their effect on the performance of maize and fingermillet in the mid-hills of Nepal. International Journal of Applied Sciences and Biotechnology. 2:275-278.
• Williams II, M. 2015. Phenomorphological characterization of vegetable soybean germplasm lines for commercial production. Crop Science. 55:1274- 1279.
• West, N.M., Matlaga, D., Davis, A.S. 2015. Vegetative dispersal of perennial bioenergy crops as a potential invasion route. Invasive Plant Science and Management. 7:517-525.
• West, N.M., Matlaga, D.P., Davis, A.S. 2014. Quantifying targets to manage invasion risk: light gradients dominate the early regeneration niche of naturalized and pre-commercial Miscanthus populations. Biological Invasions. 16:1991-2001.
• DeDecker, J.J., Masiunas, J.B., Davis, A.S., Flint, C.G. 2014. Weed management practice selection among Midwest U.S. organic growers. Weed Science. 62:520-531.
• Ward, S.M., Cousens, R.D., Bagavathiannan, M., Barney, J.N., Beckie, H.J., Busi, R., Davis, A.S., Dukes, J.S., Forcella, F., Freckleton, R.P. et al. 2014. Agricultural weed research: a critique and two proposals. Weed Science. 62:672-678.
• Zalamea, P.C., Sarmiento, C., Arnold, A.E., Davis, A.S., Dalling, J.W. 2015. Do soil microbes and abrasion by soil particles influence persistence and loss of physical dormancy in seeds of tropical pioneers? Frontiers in Plant Science. DOI: 10.3389/fpls.2014.00799.
• Guo, J., Riggins, C.W., Hausman, N.E., Hager, A.G., Riechers, D.E., Davis, A.S., Tranel, P.J. 2015. Non-target-site resistance to ALS inhibitors in waterhemp (Amaranthus tuberculatus). Weed Science. 63:399-407.
• Evans, J.A., Tranel, P.J., Hager, A.G., Schutte, B.R., Wu, C., Chatham, L., Davis, A.S. 2015. Managing the evolution of herbicide resistance. Pest Management Science. DOI: 10.1002/ps.4009.
• Davis, A.S., Schutte, B.J., Hager, A.G., Young, B.G. 2015. Palmer amaranth (Amaranthus palmeri) damage niche in Illinois soybean is seed-limited. Weed Science. 63:658-668.
• Jordan, N.J., Davis, A.S. 2015. Middle way strategies for sustainable intensification of agriculture. Bioscience. 65(5):513-519.
• Karki, T.B., Sah, S.K., Thapa, R.B., McDonald, A.J., Davis, A.S. 2015. Identifying pathways for improving household food self-sufficiency outcomes in the hills of Nepal. PLoS One. doi: 10.1371/journal.pone. 0127513.

Progress 10/01/13 to 09/30/14

Outputs
Progress Report Objectives (from AD-416): Objective 1: Measure effects of management, climate, and soil conditions on microbial processes (herbicide degradation, nitrogen cycling, and weed seedbank dynamics) in corn/soybean ecosystems. Objective 2: Evaluate the effects of management and climate change on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bioenergy crops, in Midwestern cropping systems. Objective 3: Identify effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. Approach (from AD-416): Each objective of the proposed work seeks to advance knowledge of specific topics that directly or indirectly relate to weed-crop competition for resources, providing a basis to identify tactics of routine management that shift the competitive advantage to the crop. We examine the ecology of microorganisms and plants, and combine these efforts into a synthesis that applies research findings toward practical solutions. Each objective utilizes the whole scientific team, and regardless of scale, experiments include samples from a common group of sites, providing extensive metadata support. Studies under Objective 1 address microbial activities that are influenced by agricultural management, climate, or soil conditions. Primary climatic factors to be addressed are temperature and rainfall. In Objective 2, management and climate change will be evaluated as to effects on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bio- energy crops, in Midwestern cropping systems. A particular focus will be on spatiotemporal variation in demographic parameters and population growth rates at multiple levels of scale. As a means of unifying observations, whole life cycles of weeds will be the unit of study whenever possible. Objective 3 identifies effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. Plant and environmental interactions useful for devising new weed management systems in vegetable crops continues to be studied in sweet corn, one of the most widely grown vegetables (~700,000 acres). A journal article documents the extent to which climate region (Midwest versus Pacific Northwest), cytochrome P450 genotype in sweet corn, and herbicide tank-mix influenced crop tolerance to HPPD-inhibiting herbicides. Field trials also were conducted throughout the Midwest and Pacific Northwest to develop integrated weed management alternatives to atrazine � a widely used corn herbicide that is being phased out of several sweet corn production areas. New studies are quantifying tolerance to crowding and nitrogen stresses among processing sweet corn hybrids, as measured by yield, recovery, and profitability. In addition, on-farm experiments are being utilized to determine intraspecific competitive ability, based on optimum plant population density, of a crowding stress-tolerant hybrid. Finally, ARS researchers in Urbana, Illinois are collaborating on a multi- site ARS project investigating the impact of glyphosate and glyphosate- resistant crops on rhizosphere microorganisms and crop susceptibility to disease. Investigations of weed management in a changing climate, begun in FY 12, were continued in FY 14. Competition of Palmer amaranth genotypes from the southern U.S. with soybean was measured in southern, central, and northern Illinois, following strict protocols to avoid introducing a seed bank for this species. Common garden study data were analyzed and presented. Data were analyzed from the completed field study on the demography and growth of the energy crops Miscanthus giganteus and Miscanthus sinensis in old field and forest environments in central Illinois. Finally, a manuscript highlighting management and environmental risk factors associated with the evolution and spread of glyphosate resistant waterhemp in Illinois grain crops was prepared for submission. Denitrification has heretofore been thought to be the primary mechanism of nitrate (-ite) losses in agricultural soils under anoxic conditions. Microbial populations that mediate the reduction of the greenhouse gas N2O (N-loss) or reduce N-oxides to ammonium (dissimilatory nitrate reduction to ammonia or DNRA; N-retention) have been underestimated in soils largely due to insufficient molecular tools available to detect these populations. Using newly developed probes to target a broader range of functional genes associated with N-cycling processes, the spatiotemporal dynamics of these populations along with nutrient fluxes in two contrasting field sites that differ in characteristics of water drainage and C/N nutrient retention are being monitored. We completed Year two of a three-year study and are currently in Year three to uniquely demonstrate seasonal and diurnal shifts in bacterial populations associated with denitrification and non-denitrifier-mediated N2O reduction, and dissimilatory nitrate reduction to ammonia according to soil depth and in response to diurnal temperature cycles. Extramural funding with university collaborators extends work associated with this parent project to sequence the metagenomes over the same spatiotemporal scales at both field locations. This year, high throughput sequencing of the nrfA gene associated with DNRA provided novel data showing the high potential of DNRA present in soils, contrasting decades of previous conventional thought about the low significance of this process in agricultural soils. Accomplishments 01 Quantifying risk factors for evolution of herbicide resistance in agricultural weeds. Evolution and spread of herbicide resistance in weeds is rapidly accelerating. More than just an inconvenience to growers, increased prevalence of herbicide resistance threatens global food security at the level of production as well as consumption, as higher production costs are passed on to consumers. An analysis by ARS researchers (at Urbana, Illinois) of over 500 site-years of empirical data provides compelling evidence that a common management recommendation (rotation of herbicide modes of action over time) to growers for delaying or preventing herbicide resistance is not only ineffective, but may also actually exacerbate the problem. In contrast, this work highlights the importance of increased chemical complexity of single applications as a short-term method for delaying evolution of herbicide resistance while highly diversified weed management practices are put in place to create a more sustainable solution to the problem. This finding will have broad impact across the field crop acreage of the U.S., influencing the way producers and custom applicators design the chemical control portion of their weed management programs. 02 Predicting variables important to processing sweet corn. Measurement of yield is critical in research aimed to improve crop production. For most agronomic crops, grain yield directly relates to both productivity of the plant and revenue to the grower. In contrast, important �yield� metrics in processed vegetables differ between the processor, who makes several important crop production decisions, and the grower, who is contracted to produce the crop. In processing sweet corn, nearly all published field studies report number or mass of freshly harvested ears; metrics of limited usefulness to the processor. ARS researchers (at Urbana, IL) showed that fresh kernel mass, though rarely measured, is a far superior measurement of yield in processing sweet corn. The work's impact is seed companies are now retooling to collect crop performance data that is most relevant to development of competitive sweet corn hybrids. 03 Underestimated microbial-mediated nitrous oxide reduction and N- retention in soil. The microbial process of nitrate consumption leading to production of either nitrous oxide [N2O] or nitrogen [N2] gases (denitrification) was traditionally held accountable for the primary losses of N from soils, especially in N-fertilized agricultural soils. Current greenhouse gas (GHG) flux models require input of biological variables that accurately account for production and consumption of N2O, a potent greenhouse gas, yet predictions of N-gas emissions based on a few previously well-studied denitrifying bacteria (denitrifiers) are often inaccurate and do not account for other N- cycling processes that impact nitrate, nitrite, or ammonium pools. ARS researchers (at Urbana, IL) demonstrated that genes encoding N2O reductases in both non-traditional denitrifiers and non-denitrifiers able to reduce N2O to N2 dominate in abundance over the conventionally studied denitrifiers currently in use to inform models of N-cycling and GHG emissions and applies to a wide range of soil types. Further, the potential for direct reduction from nitrate to ammonium (a process known as dissimilatory nitrate reduction to ammonium or DNRA) as a N- retention process is now known to be high in agricultural soils and other environments. This research has identified new microbial targets related to N2O reduction and DNRA, and fills a significant gap in microbial N-cycling processes that can now aid more accurate predictions of N-fate in soil systems. This year�s information will also go to the current datacall by USDA-ARS GRACEnet (NP212), making available new biological data that can aid larger objectives for development of sound and sustainable agricultural practices.

Impacts
(N/A)

Publications

• Schutte, B.J., Tomasek, B.J., Davis, A.S., Andersson, L., Benoit, D.L., Cirujeda, A., Dekker, J., Forcella, F., Gonzalez-Andujar, J.L., Graziana, F. et al. 2014. An investigation to enhance understanding of the stimulation of weed seedling emergence by soil disturbance. Weed Research. 54(1):1-12.
• Schutte, B.J., Davis, A.S., Peinado, S.A., Ashigh, J. 2014. Seed coat thickness data clarifies seed size-seed persistence tradeoffs in Abutilon theophrasti (Malvaceae). Seed Science Research. 24:119-131.
• Lou, Y., Clay, S., Davis, A.S., Dille, A., Felix, J., Ramirez, H., Sprague, C., Yannarell, T. 2014. An affinity-effect relationship for microbial communities in plant-soil feedback loops. Microbial Ecology. DOI: 10.1007/ s00248-013-0349-2.
• Liebman, M., Miller, Z., Williams, C., Westerman, P., Dixon, P., Heggenstaller, A., Davis, A.S., Menalled, F., Sundberg, D. 2014. Fates of Setaria faberi and Abutilon theophrasti seeds in three crop rotation systems. Weed Research. DOI: 10.1111/wre.12069.
• Clay, S., Davis, A.S., Dille, J., Lindquist, J., Ramirez, A.H.M., Sprague, C., Reicks, G., Forcella, F. 2014. Common sunflower seedling emergence across the U.S. Midwest. Weed Science. 62:63-70.
• Williams, M. 2014. Few crop traits accurately predict variables important to productivity of processing sweet corn. Field Crops Research. 157:20-26.
• Tiansawat, P., Davis, A.S., Berhow, M.A., Zalamea, P., Dalling, J.W. 2014. Investment in seed physical defence is associated with species' light requirement for regeneration and seed persistence: evidence from Macaranga species in Borneo. PLoS One. 9(6):e99691.
• Schutte, B.R., Davis, A.S. 2014. Do common waterhemp (Amaranthus rudis) seedling emergence patterns meet criteria for herbicide resistance simulation modeling? Weed Technology. 28:408-417.
• Williams, M. 2014. A bioenergy feedstock/vegetable double-cropping system. Industrial Crops and Products. 59:223-227.
• Choe, E., Williams, M., Boydston, R.A., Huber, J., Huber, S.C., Pataky, J. K. 2014. Photosystem II-inhibitors play a limited role in sweet corn response to 4-hydroxyphenyl pyruvate dioxygenase-inhibiting herbicides. Agronomy Journal. 106:1317-1323.
• Welsh, A., Chee Sanford, J.C., Loeffler, F., Sanford, R. 2014. Refined NrfA phylogeny improves PCR-based nrfA gene detection. Applied and Environmental Microbiology. 80:2110-2119.
• Orellana, L.H., Rodriguez-R, L.M., Higgins, S., Chee-Sanford, J.C., Sanford, R.A., Ritalahti, K.M., Loeffler, F.E., Konstantinidis, K.T. 2014. Detecting nitrous oxide reductase (nosZ) genes in soil metagenomes: method development and implications for the nitrogen cycle. mBio. 5(3):e01193-14.

Progress 10/01/12 to 09/30/13

Outputs
Progress Report Objectives (from AD-416): Objective 1: Measure effects of management, climate, and soil conditions on microbial processes (herbicide degradation, nitrogen cycling, and weed seedbank dynamics) in corn/soybean ecosystems. Objective 2: Evaluate the effects of management and climate change on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bioenergy crops, in Midwestern cropping systems. Objective 3: Identify effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. Approach (from AD-416): Each objective of the proposed work seeks to advance knowledge of specific topics that directly or indirectly relate to weed-crop competition for resources, providing a basis to identify tactics of routine management that shift the competitive advantage to the crop. We examine the ecology of microorganisms and plants, and combine these efforts into a synthesis that applies research findings toward practical solutions. Each objective utilizes the whole scientific team, and regardless of scale, experiments include samples from a common group of sites, providing extensive metadata support. Studies under Objective 1 address microbial activities that are influenced by agricultural management, climate, or soil conditions. Primary climatic factors to be addressed are temperature and rainfall. In Objective 2, management and climate change will be evaluated as to effects on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bio- energy crops, in Midwestern cropping systems. A particular focus will be on spatiotemporal variation in demographic parameters and population growth rates at multiple levels of scale. As a means of unifying observations, whole life cycles of weeds will be the unit of study whenever possible. Objective 3 identifies effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. Investigations of weed management in a changing climate, begun in FY 12, were continued in FY 13. Competition of Palmer amaranth genotypes from the southern U.S. with soybean was measured in southern, central and northern Illinois, following strict protocols to avoid introducing a seed bank for this species. Pure line seed increase of these genotypes was performed to support an additional study year in FY14. We completed a final year of monitoring and measuring the demography and growth of the energy crops Miscanthus giganteus and Miscanthus sinensis in old field and forest environments in central Illinois, again with special procedures to minimize invasion risk. Finally, statistical analysis of management and environmental risk factors associated with the evolution and spread of glyphosate resistant waterhemp in Illinois grain crops was completed. Retooling weed management systems using new and existing knowledge that exploits useful plant and environmental interactions continue to be examined in vegetable cropping systems. Sweet corn - one of the most widely grown vegetable crops (~700,000 acres) - serves as a model crop. We completed field trials quantifying the extent to which climate region (Midwest versus Pacific Northwest), cytochrome P450 genotype in sweet corn, and herbicide tank-mix influenced crop tolerance to HPPD-inhibiting herbicides. The data have been analyzed and a manuscript is in preparation. Extramural funding was secured to develop integrated weed management alternatives to atrazine - the most widely used herbicide in corn production. Field trials throughout the Midwest, and a few locations in the PNW, are being initiated. Finally, several manuscripts on biological factors contributing to weed escapes in sweet corn have been published, including crop disease incidence (maize dwarf mosaic) and crop population density. Molecular probes developed for detection of new bacterial genes associated with the reduction of the greenhouse gas N2O were applied to monitor the spatiotemporal dynamics of populations in two contrasting field sites that differ in characteristics of water drainage and C/N nutrient retention. We completed Year one of a three-year study and are currently in Year two to demonstrate seasonal and diurnal shifts in bacterial populations associated with denitrification and non-denitrifier- mediated N2O reduction (both N-loss mechanisms), and dissimilatory nitrate reduction to ammonia (DNRA, N-retention process) according to soil depth and in response to diurnal temperature cycles. Extramural funding was obtained to extend this work to sequence the metagenomes at both field locations associated with this project, particularly genes associated with N-cycling processes. Additional work was added this year to obtain high throughput sequencing of the nrfA gene associated with DNRA to provide novel data supporting a high diversity of nrfA genes in wide-ranging soil types. Significant Activities that Support Special Target Populations: Summer agricultural research experience for minority students. Mentored Latino agroecology student from Northeast Illinois University in weed ecology and management research and production practices. Recruited student for graduate studies in Crop Sciences at University of Illinois. Accomplishments 01 Management guidelines for preventing bioenergy crop escapes. Herbaceous perennial grasses grown for bioenergy purposes can provide huge amounts of biomass, but also have the potential to become invasive if natural areas surrounding plantations are not monitored carefully for escapes. Such escapes can influence species composition in non- agricultural areas, potentially reducing wildlife habitat and forest productivity. ARS researchers at Urbana, IL, addressed the need for streamlined monitoring procedures for land managers to detect bioenergy crop escapes by conducting controlled studies of factors influencing the establishment of Miscanthus seedlings. This work demonstrated that light gradients control Miscanthus seedling establishment success, with little seedling recruitment in deep shade areas. For detection of potential escapes in forests and other low-visibility sites, land managers should focus search efforts on large canopy gaps. 02 Atrazine significance and need for alternatives. Despite extensive use of atrazine herbicide, weeds continue to cause crop loss in most sweet corn fields. Regulatory changes are reducing atrazine availability; therefore, information concerning crop loss due to weed pressure without atrazine is needed. Research by ARS scientists (Urbana, IL) documented that greater weed escapes and crop losses are likely when atrazine is removed from current weed management systems. These results stimulated research aimed to identify economically viable alternatives to standard atrazine-based weed management systems. This will reduce the environmental risks from atrazine use while safe-guarding the production of America�s most popular vegetable � sweet corn. 03 Identification of understudied microbial nitrogen (N)-cycling populations in soil. The microbial process of nitrate consumption leading to production of either N2O or N2 gases (denitrification) was traditionally held accountable for the primary losses of N from soils, especially in N-fertilized agricultural soils. Current greenhouse gas (GHG) flux models require input of biological variables that accurately account for production and consumption of N2O, a potent greenhouse gas, yet predictions of N-gas emissions based on a few previously well- studied denitrifying bacteria (denitrifiers) are often inaccurate. Research by ARS scientists (Urbana,IL) demonstrated significant microbial populations common to agricultural soils that include both non-traditional denitrifiers and non-denitrifiers able to reduce N2O to N2. These newly identified populations are as abundantly present as many of the conventional and well-studied denitrifying populations used as the previous focus in N-cycling and in GHG emissions models. The importance of this research is the identification of new microbial populations that have functional significance related to N2O reduction and identifies these as important targets of biological N-cycling to monitor in agricultural soils. This accomplishment has further led to the development of an important and growing database (>150 new gene sequences identified) used by ARS researchers in Urbana along with university collaborators to aid identification of important functional microbial populations using the newest technology to sequence and identify genes present in whole soil metagenomes (i.e. all the genetic material from an environment). Collectively, the end-product of this research will provide more comprehensive identification of the biological factors leading to more efficient N-fertilizer use and more accurate predictive scenarios of GHG emissions.

Impacts
(N/A)

Publications

• Matlaga, D.P., Davis, A.S. 2013. Minimizing invasive potential of Miscanthus � giganteus grown for bioenergy: identifying demographic thresholds for population growth and spread. Journal of Applied Ecology. 50:479-487.
• Williams, M., Pataky, J.K. 2012. Maize dwarf mosaic can reduce weed suppressive ability of sweet corn. Weed Science. 60:577-582.
• Davis, A.S., Hill, J.D., Chase, C.A., Johanns, A.M., Liebman, M. 2012. Increasing cropping system diversity balances productivity, profitability and environmental health. PLoS One. 7(10):e47149. DOI:10.1371/journal.pone. 0047149.
• Williams, M.M. II, Schutte, B.J., Yim, S. 2012. Maternal corn environment influences wild-proso millet (Panicum miliaceum) seed characteristics. Weed Science. 60:69-74.
• Liu, J., Davis, A.S., Tranel, P.J. 2012. Pollen biology and dispersal dynamics in waterhemp (Amaranthus tuberculatus). Weed Science. 60:416-422.
• Wortman, S.E., Davis, A.S., Schutte, B.J., Lindquist, J.L., Cardina, J., Felix, J., Sprague, C.L., Dille, J., Ramirez, A., Reicks, G., Clay, S.A. 2012. Local conditions, not regional gradients, drive demographic variation of giant ragweed (Ambrosia trifida) and common sunflower (Helianthus annus) across northern US maize belt. Weed Science. 60:440-450.
• Davis, A.S., Clay, S., Cardina, J., Dille, A., Forcella, F., Lindquist, J., Sprague, C. 2013. Seed burial physical environment explains departures from regional hydrothermal model of giant ragweed (Ambrosia trifida) seedling emergence in U.S. Midwest. Weed Science. 61(3):415-421.
• Williams, M.M. II, Boydston, R.A. 2013. Crop seeding level: implications for weed management in sweet corn. Weed Science. 61(3):437-442.
• Williams, M.M. II, Boydston, R.A. 2013. Intraspecific and interspecific competition in sweet corn. Agronomy Journal. 105(2):503-508.
• Chee Sanford, J.C., Krapac, I.J., Yannarell, A.C., Mackie, R.I. 2012. Environmental impacts of antibiotic use in the animal production industry. In: Norrgren, L., Levengood, J., editors. Ecosystem Health and Sustainable Agriculture. Book 2. Uppsala, Sweden: The Baltic University Programme. p. 228-368.
• Davis, A.S., Taylor, E., Haramoto, E., Renner, K. 2013. Annual post- dispersal weed seed predation in contrasting field environments. Weed Science. 61:296-302.
• Hauer, K., Meisinger, D.B., Pavlekovic, M., Thomas, S.H., Kniggendorf, A.K. , Chee Sanford, J.C., Sanford, R.A., Lebron, C.A., Liebl, W., Loeffler, F. E., Lee, N. 2012. Novel tools for in situ detection of biodiversity and function of dechlorinating and uranium-reducing bacteria in contaminated environments. Geochimica et Cosmochimica Acta. 73:A502.
• Sanford, R.A., Wagner, D.D., Wu, Q., Chee-Sanford, J.C., Thomas, S.H., Cruz-Garcia, C., Rodriguez, G., Massol-Deya, A., Ritalahti, K.M., Nissen, S., Konstantidis, K.T., Loeffler, F.E. 2012. Unexpected nondenitrifier nitrous oxide reductase gene diversity and abundance in soils. Proceedings of the National Academy of Sciences. 109:19709-19714.
• Brainard, D., Haramoto, E., Williams, M.M. II, Mirsky, S.B. 2013. Towards a no-till no-spray future? Introduction to a symposium on nonchemical weed management for reduced-tillage cropping systems. Weed Technology. 27:190- 192.

Progress 10/01/11 to 09/30/12

Outputs
Progress Report Objectives (from AD-416): Objective 1: Measure effects of management, climate, and soil conditions on microbial processes (herbicide degradation, nitrogen cycling, and weed seedbank dynamics) in corn/soybean ecosystems. Objective 2: Evaluate the effects of management and climate change on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bioenergy crops, in Midwestern cropping systems. Objective 3: Identify effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. Approach (from AD-416): Each objective of the proposed work seeks to advance knowledge of specific topics that directly or indirectly relate to weed-crop competition for resources, providing a basis to identify tactics of routine management that shift the competitive advantage to the crop. We examine the ecology of microorganisms and plants, and combine these efforts into a synthesis that applies research findings toward practical solutions. Each objective utilizes the whole scientific team, and regardless of scale, experiments include samples from a common group of sites, providing extensive metadata support. Studies under Objective 1 address microbial activities that are influenced by agricultural management, climate, or soil conditions. Primary climatic factors to be addressed are temperature and rainfall. In Objective 2, management and climate change will be evaluated as to effects on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bio- energy crops, in Midwestern cropping systems. A particular focus will be on spatiotemporal variation in demographic parameters and population growth rates at multiple levels of scale. As a means of unifying observations, whole life cycles of weeds will be the unit of study whenever possible. Objective 3 identifies effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. Degradation of the herbicide, metolachlor, in flooded soil exhibited biphasic degradation with significantly faster degradation occurring when soil microorganisms began using iron for respiration. This resulted in irreversible binding of the metolachlor residues to soil. We observed similar results with the herbicide, trifluralin in previous reports. These results suggest that the predicted increased frequency of transient flooding in the Midwest may affect the function of soil applied herbicides. We increased seed, under carefully controlled field conditions, of accessions of Palmer amaranth collected from throughout the southern U.S. for use in common garden competition experiments. Special care was taken to avoid introducing a seedbank for these species. We also monitored and measured the demography and growth of the energy crops Miscanthus giganteus and Miscanthus sinensis in old field and forest environments in central Illinois, again with special procedures to minimize invasion risk. Finally, we continued our work on the management and environmental risk factors associated with the evolution and spread of glyphosate resistant waterhemp in Illinois grain crops, beginning database construction and statistical analysis. Several experiments concerning weed management in sweet corn were conducted. Organic weed management systems in Illinois and Washington were examined, whereby combinations of competitive crop cultivars and mechanical weed management tactics were tested. In other work, integrated weed management alternatives to atrazine� the most widely used herbicide in corn production � were tested in Illinois and Minnesota. Finally, we quantified the extent to which climate region (Midwest versus Pacific Northwest), cytochrome P450 genotype in sweet corn, and herbicide tankmix influenced crop tolerance to HPPD-inhibiting herbicides. Processing pumpkin productivity and weed community characteristics also are being quantified in different production systems, including a bioenergy- vegetable double-cropping system. Biomass feedstock (rye+vetch) was fall- planted and spring-seeded; processing pumpkin is grown in different tillage and residue treatments. We have been successful in cultivating processing pumpkin, which has required some new field equipment and an aggressive fungicide application schedule. At the request of vegetable industry stakeholders, new agronomic and weed management research in vegetable soybean (edamame) is underway. One set of experiments is being used to quantify the shortcomings of current weed management systems built around the small number of herbicides being considered for use in the crop. Another set of experiments has been deployed to characterize important agronomic traits, including disease susceptibility, herbicide sensitivity, and weed suppressive traits, among new and old commercial and public cultivars. Significant Activities that Support Special Target Populations: Mentored Latino agroecology student from Northeast Illinois University in weed ecology and management research and production practices. Accomplishments 01 Breeding considerations for safe bioenergy crop production. Herbaceous perennial grasses grown for bioenergy purposes can provide huge amounts biomass but also have the potential to become invasive if germplasm is n selected carefully. ARS researchers at Urbana, Illinois, provided technical support for the improvement of bioenergy crop germplasm, identifying Miscanthus giganteus demographic rates associated with more rapid rates of invasive spread. The resulting simulation models of Miscanthus population dynamics and spread will provide targets for futur genetic selection of Miscanthus giganteus bioenergy crop cultivars with less risk of becoming invasive. This advance will support the safe production of renewable energy, while protecting natural areas. 02 Optimal plant populations for processing sweet corn. Determining plant population density for optimal crop growth and yield is a critical decision in crop production; however, practitioners have no research-bas information to support this decision in sweet corn. Plant population densities that maximized profits to the grower and vegetable processor were identified by an ARS researcher in Urbana, Illinois. By comparing results of field experiments to surveys on farms throughout the Midwest, it was learned that grower and processor gross profit margins could be improved (as much as $1,500 per acre) if higher plant populations were used with certain hybrids. The impact of this work is that it provides sweet corn growers and vegetable processors the first research-based analysis of a critical crop production decision, that is, determining th best population density for the crop. In addition, the research showed t seed industry that targeted breeding efforts to improve interplant competitive ability will improve greatly the yield potential of sweet co The sweet corn industry is using this research to change how it develop hybrids and grow sweet corn in North America. 03 Effective management of pests in sweet corn will benefit from an improve understanding of herbicide tolerance and disease resistance in this vegetable crop. An ARS researcher in Urbana, Illinois, in collaboration with a University of Illinois professor, summarized 27 years of data on disease resistance, and 8 years of data on herbicide tolerance in sweet corn. Key observations included 1) new hybrids have largely shifted away from sugary (su1 endosperm) to supersweet (sh2 endosperm) types; 2) the basis for sweet corn resistance to the rust Puccinia sorghi has come to largely based on a single class of genes (Rp gene = resistance to Puccin ; and 3) there is considerable potential for improving sweet corn tolerance to herbicides, given that 20% or more of the hybrids evaluated since 2002 are able to detoxify many herbicidal compounds metabolically (using the cytochrome P450 pathway). This research has become the primar source for the sweet corn industry (growers, processors, seed companies, crop protection companies) to determine hybrid tolerance to herbicides a resistance to prevalent diseases.

Impacts
(N/A)

Publications

• Pataky, J.K., Williams, M., Headrick, M.M., Nankam, C., Du Toit, L., Michener, P.M. 2011. Observations from a quarter century of evaluating reactions of sweet corn hybrids in disease nurseries. Plant Disease. 95:1492-1506.
• Williams, M.M. II, Pataky, J.K. 2011. Interactions between maize dwarf mosaic and weed interference on sweet corn. Field Crops Research. 128:48- 54.
• Williams, M.M. II. 2011. Agronomics and economics of plant population density on processing sweet corn. Field Crops Research. 128:55-61.
• Davidson, A.N., Ho, C., Chee Sanford, J.C., Lai, H.Y., Klenzendorf, J.B., Kirisits, M.J. 2011. Characterization of bromate-reducing bacterial isolates and their potential for drinking water treatment. Water Research. 45(18):6051-6062.
• Williams, M., Boydston, R.A., Peachey, R.E., Robinson, D. 2011. Significance of atrazine as a tank-mix partner with tembotrione. Weed Technology. 25(3):299-302.
• Bicksler, A., Masiunas, J., Davis, A.S. 2012. Canada thistle (Cirsium arvense) suppession by sudangrass interference and defoliation. Weed Science. 60:260-266.
• Davis, A.S., Ainsworth, E.A. 2012. Weed interference with field-grown soybean (Glycine max) decreases under elevated [CO2] in a FACE experiment. Weed Research. 52(3):277-285.
• Matlaga, D.P., Schutte, B., Davis, A.S. 2012. Age-dependent population dynamics of the bioenergy crop Miscanthus x giganteus in Illinois. Journal of Invasive Plant Science and Management. 5:238-248.
• Davis, A.S., Daedlow, D., Schutte, B.J., Westerman, P. 2011. Temporal scaling of episodic point estimates of weed seed predation to long-term predation rates. Methods in Ecology and Evolution. 2:382-692.
• Davis, A.S., Landis, D.A. 2011. Invasive species in agriculture. In: M. Rejmanek and D. Simberloff, editors. Encyclopedia of Introduced Invasive Species. Berkeley, CA: University of California Press. p. 7-11.
• Sims, G.K., Kanissery, R. 2012. Transformation of herbicides under transient anoxia. In: Casteneda, S.F., Emerson, M.L., editors. Xenobiotics: New Research. Hauppauge, New York: Nova Science Publishers. p. 67-84.
• Matlaga, D.P., Quinn, L.D., Davis, A.S., Stewart, R. 2012. Light response of native and introduced Miscanthus sinensis seedlings. Biological Invasions. 5:363-374.
• Evans, J.A., Davis, A.S., Raghu, S., Raghavendran, A., Landis, D., Schemske, D. 2012. The importance of space, time and stochasticity to the demography and management of Alliaria petiolata. Ecological Applications. 22:1497-1511.

Progress 10/01/10 to 09/30/11

Outputs
Progress Report Objectives (from AD-416) Objective 1: Measure effects of management, climate, and soil conditions on microbial processes (herbicide degradation, nitrogen cycling, and weed seedbank dynamics) in corn/soybean ecosystems. Objective 2: Evaluate the effects of management and climate change on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bioenergy crops, in Midwestern cropping systems. Objective 3: Identify effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. Approach (from AD-416) Each objective of the proposed work seeks to advance knowledge of specific topics that directly or indirectly relate to weed-crop competition for resources, providing a basis to identify tactics of routine management that shift the competitive advantage to the crop. We examine the ecology of microorganisms and plants, and combine these efforts into a synthesis that applies research findings toward practical solutions. Each objective utilizes the whole scientific team, and regardless of scale, experiments include samples from a common group of sites, providing extensive metadata support. Studies under Objective 1 address microbial activities that are influenced by agricultural management, climate, or soil conditions. Primary climatic factors to be addressed are temperature and rainfall. In Objective 2, management and climate change will be evaluated as to effects on the biology and ecology of weedy and invasive species, including potential weedy cellulosic bio- energy crops, in Midwestern cropping systems. A particular focus will be on spatiotemporal variation in demographic parameters and population growth rates at multiple levels of scale. As a means of unifying observations, whole life cycles of weeds will be the unit of study whenever possible. Objective 3 identifies effective combinations of weed management components through application of both new and existing knowledge that exploit useful plant and environmental interactions in vegetable cropping systems. We made substantial progress initiating investigations of weed management in a changing climate in FY 11. Design for laboratory soil microcosms for use in assessing herbicide biodegradation and microbial N-cycling under varying flooding/drainage cycles was established for use in parallel with in-situ studies at our two designated field locations. Biomarkers for reductive dehalogenating populations (which may contribute to herbicide degradation) and genes involved in nitrous oxide reduction have been validated. Over 40 new bacterial nosZ gene sequences (encoding variations of a denitrification enzyme) and ten 16s rDNA gene sequences of phenol- degraders (used for identification) were submitted to National Center for Biotechnology Information GenBank. New velvetleaf and giant ragweed seed studies are underway. Experiments were conducted to determine the ecology of organisms that degrade organic pollutants structurally related to herbicides at different depths in the profile of a major landfill in Medellin, Columbia. This site had unique features that allowed measurements to be made in aerobic and anaerobic environments as well as to relate the microbial results to chemical analyses of the soil matrix. The novel method of DNA-based stable isotope probing was used to determine the identities of organisms degrading pollutants at different depths. The potential impacts of more frequent soil saturation (due to climate change) on stability of soil-applied herbicides were explored using radioisotope techniques. Working with research partners throughout the southern U.S., we collected numerous seed accessions of Palmer amaranth and shattercane and grew them in a common environment in Urbana, IL, for seed increase to support weed-crop interference experiments. Special care was taken to avoid introducing a seedbank for these species. We also planted Miscanthus giganteus and Miscanthus sinensis in old field and forest environments in central Illinois, again with special procedures to minimize invasion risk, for the purpose of studying the demography and spread of these bioenergy crop species in non-crop environments. Finally, we continued our work on the management and environmental risk factors associated with the evolution and spread of glyphosate resistant waterhemp in Illinois grain crops, screening dozens of accessions for glyphosate resistance, and recording management histories for the farms from which they came. The results of work done thus far puts the research on track to deliver solutions for emerging questions in weed management due to exploitation of new biofuel feedstocks, climate change, and weed adaptation to existing management strategies. Significant Activities that Support Special Target Populations Summer agricultural research experience for minority students. Mentored one Latino student (crop sciences) from Northeast Illinois University, one Asian American student (MCB) from UIUC, and one female student (MCB) from UIUC in weed ecology and management research and production practices. Accomplishments 01 Stewardship guidelines for safe bioenergy crop production. Herbaceous perennial grasses grown for bioenergy purposes can provide huge amounts biomass, but also have the potential to become invasive if not managed carefully. ARS researchers at Urbana, IL, provided technical support to the MFL A Aloterra Company and Biomass Crop Assistance Program (USDA-Far Services Agency) that was based on ARS research on the invasive potentia of bioenergy crop species. ARS researchers measured vital rates and dispersal characteristics of Miscanthus and used this information to hel guide the design of bioenergy plantations and surrounding buffer areas. Production issues addressed by the plan included guidelines for safe siting of production plantations, specifications for the width of buffer zones surrounding production fields, and eradication of plantings, among others. These suggestions were taken into consideration and incorporated into the conservation plan for a new 50,000 acre pilot project in the Midwest supported by the USDA Farm Services Agency through its Biomass Conversion Assistance Program. This is the first large-scale production effort of herbaceous perennial biomass crops for bioenergy production. There has been considerable concern that these crops may become invasive so the ARS effort to ensure safe production of these crops help protect the public and public lands from unwanted biological invasions. 02 Degradation of aromatic pollutants at different depths in the soil profi The Moravia Hill landfill site at Medellin, Columbia was a long-term mixed waste site (industrial and municipal waste) that has been home to thousands of human inhabitants for decades. The population is being resettled and the site being remediated. Part of the criteria for remediation of the organic contaminants at the site was the presence of diversity of organisms that could degrade the pollutants, a question whi can best be addressed with the use of DNA-based stable isotope probing. Developed in the past decade, SIP has made it possible to identify organisms responsible for particular activity in soil. The ARS lab at Urbana is among a few laboratories world-wide suited to conduct this research, and the research questions to be addressed at the site are highly relevant to research objectives on the effects of water regime on microbial degradation processes. Clear differences in the dominant group of degraders were observed as a function of depth and the presence of oxygen at the site. Stable isotope probing demonstrated multiple groups degraders at each depth, and the differences in dominant organisms were well correlated to chemical conditions at each depth. These findings wer used to determine the manner in which the site would be remediated, and are being applied to understand the impact of water regime on the ecolog of herbicide degradation. The impact of organic carbon buried at a depth of 20 meters was in good agreement with the only published article on th microbiology of paleosols (buried soils), which occur throughout the Midwest, where they contribute to subsurface nitrogen contamination through organic matter decomposition. These results show how dominant pollutant-degrading microorganisms will be expected to shift with environmental conditions, and have great potential to explain microbial transformations of groundwater pollutants at paleosol sites in the Midwe

Impacts
(N/A)

Publications

• Duniway, M.C., Herrick, J.E., Pyke, D., Toledo, D.N. 2010. Assessing transportation infrastructure impacts on rangelands: Test of a standard rangeland assessment protocol. Rangeland Ecology and Management. 63:524- 536.
• Williams, M.M. II, Boydston, R.A., Peachey, R.E., Robinson, D. 2011. Performance consistency of reduced Atrazine use in sweet corn. Field Crops Research. 121:96-104.
• Williams, M., Pataky, J.K. 2010. Factors Affecting Differential Sweet Corn Sensitivity to HPPD-inhibiting Herbicides. Weed Science. 58:289-294.
• Davis, A.S. 2010. Cover Crop Roller-Crimper Contributes to Weed Management in No-Till Soybean. Weed Science. 58(3):300-309.
• Raghu, S., Spencer, J., Davis, A.S., Wiedenmann, R.N. 2011. Ecological considerations in the sustainable development of terrestrial biofuel crops. Current Opinion in Environmental Sustainability. 3:15-23.
• Evans, J., Davis, A.S. 2011. Consequences of parameterization and structure of applied demographic models: a comment on Pardini et al. (2009) . Ecological Applications. 21(2):608-613.
• Dalling, J., Davis, A.S., Schutte, B.J., Arnold, E. 2011. Seed survival in soil: interacting effects of predation, dormancy and the soil microbial community. Journal of Ecology. 99(1):89-95.
• Thinglum, K., Riggins, C.W., Davis, A.S., Bradley, K., Al-Khatib, K., Tranel, P. 2011. Wide distribution of the waterhemp (Amaranthus tuberculatus) delta-G210 PPX2 mutation, which confers resistance to PPO- inhibiting herbicides. Weed Science. 59(1):22-27.
• Gomez, A.M., Yannarell, A.C., Sims, G.K., Resterpo, G.C., Moreno, C.X. 2011. Characterization of bacterial diversity at different depths in the Moravia Hill landfill site at Medellin, Colombia. Soil Biology and Biochemistry. 43:1275-1284.
• Johnson, T.A., Sims, G.K. 2010. Introduction of 2,4-Dichlorophenoxyacetic Acid Into Soil With Solvents and Resulting Implications for Bioavailability to Microorganisms. World Journal of Microbiology and Biotechnology. 27(5):1137-1143.
• Quinn, L.D., Matlaga, D.P., Stewart, R., Davis, A.S. 2011. Evaluating the influence of wind speed on caryopsis dispersal of Miscanthus sinensis and Miscanthus x. giganteus. Journal of Invasive Plant Science and Management. 4(1):142-150.
• Wortman, S., Davis, A.S., Schutte, B.J., Lindquist, J. 2011. Integrating management of soil nitrogen and weeds. Weed Science. 59(2):162-170.
• Schutte, B.J., Hager, A.G., Davis, A.S. 2010. Respray Requests on Custom- applied, Glyphosate-Resistant Soybeans in Illinois: How Many and Why? Weed Technology. 24(4):590-598.