Research Project: Combined Management Tactics for Resilient and Sustainable Crop Production

Location: Integrated Cropping Systems Research

2023 Annual Report

Objectives
Objective 1: Evaluate the interaction of crop diversification practices (crop rotation, cover cropping) in no-till production systems with crop performance and soil properties, focusing particularly on identifying key management factors (e.g., crop identity and sequencing) that drive differential soil biological responses associated with crop performance and resilience. Sub-objective 1.A: Evaluate temporal considerations for sampling dynamic soil biological properties and associating these soil biological properties with key management factors including crop rotation, crop sequencing, crop identity. Sub-objective 1.B: Identify key crop management factors driving differences in rhizosphere microbiomes that correlate with crop performance in a no-till production system with long-term rotational treatments (established in 2000). Evaluate differential bacterial and fungal taxa for their applicability as soil health indicators in other systems within different soil-climatic regions via collaborative research. Sub-objective 1.C: Using long-term, no-till diverse crop rotations as a base crop production system, determine the influence of adding cover crop treatments on cash crop performance and soil physical, chemical and biological properties as these effects manifest with duration of treatments (cover crop treatments added in 2016). Objective 2: Integrate research data acquired on crop rotation and cover cropping within no-till production systems to advance awareness of sustainable crop production systems that are applicable regionally through a better understanding of the direct and indirect impact of these management practices on soil, water, and air resources. Sub-objective 2.A: Investigate rotational diversification (including oat) effects on crop growth and yield, soil properties, and economics to better understand the temporal influences of these outcomes and the mechanisms by which they contribute to productivity and resilience (Cote and Darling, 2010) of the whole cropping system to comprehensively demonstrate the feasibility of these practices to potential adopting producers. Subobjective 2.B: Investigate biotic and abiotic agronomic, edaphic, and climatic factors that influence the production and grain quality of oat in cropping systems.

Approach
A large proportion of commodity crop production in the Midwest has shifted to monocultures and simplified crop rotations over the past decades, resulting in unsustainable degradation of soil, air, and water resources. Furthermore, crop production is increasingly being destabilized by more frequent occurrences of extreme weather events associated with climate change. Emerging evidence indicates management practices, such as crop diversity and cover cropping, increase soil health and provide resilience to crops from stresses including drought, flooding, pests, pathogens, and weeds. Resilient crop production systems are an essential tactic to stabilize food supplies for a growing population and reduce financial liabilities in the face of variable climates. However, the specific biological characteristics of resilient soils remain unknown and the essential drivers of beneficial soil microbiomes are ill-defined. This project will examine and quantify impacts of diversified crop production systems (crop rotation, cover cropping) on crop production, soil properties, and microbial communities under the regional conditions of our research site. These crop diversification tactics are overlaid on a no-till cropping system with reduced inorganic nutrient inputs and crop residue retention; this system has been in place for 20 years. We will test, develop, and demonstrate crop management practices that provide benefits in terms of crop productivity, soil health, water use and quality, and air quality when adopted at scale. Concurrent with delineating the outcomes for crop productivity and soils, this project will elucidate prospective soil biological mechanisms underlying crop rotation effects. Demonstration of the outcomes of crop rotational diversity and understanding the drivers for these outcomes together serve as the foundation for increased adoption of these practices. This research will be applicable under similar soil-climatic regions across the globe to serve agricultural stakeholders (producers, crop consultants, agribusinesses, extension personnel, etc.), policy makers, and the general public.

Progress Report
Sub-objective 1.A. We completed the field portion of a two-year study to examine the interaction between the timing of soil sampling (spring or fall) and the effect of crop sequencing on soil biological activities and soil structure measures. The final soil sample set was collected in the fall of 2022 from field plots representing corn and soybean phases of five different crop rotations. Short-term potential carbon (C) mineralization activities were measured and analysis of soil aggregate distributions by a collaborator are underway. The first-year data demonstrated that soybean following corn produces poor soil structure and microbial activities. We are testing a hypothesis that these observations are based on the timing of soil sample collection. An intensive temporal study of soil microbial activities in these same corn plots within differing crop rotations was initiated. Temperature and water content sensors were installed and equilibrated. Biweekly sampling of these plots, activity measurements, and their correlation with temperature and moisture commenced in spring 2023. We also conducted year 2 sampling and DNA analyses to evaluate a novel approach that relies on colonization of sterile soil packets for monitoring crop rotational effects on soil microbiomes. Sequence data on the sentinels was acquired using the third-generation, handheld Minion sequencing platform. Data analyses have demonstrated differing colonization kinetics for bacteria compared to fungi. Our findings will influence sampling strategies to increase the ability to discriminate treatment effects on soil microbiomes and their influence on soil properties and crop performance. Sub-objective 1.B. To address the impacts of crop sequencing in a diversified cropping system on soil and plant health. Six unique soil microbial legacies were generated in 2022 in a newly established field experiment. Rhizosphere soil of six rotation crops at three developmental stages (seedling, flowering, and mature) was collected. DNA was extracted from those rhizosphere samples and was sent to University of Minnesota Genomic Center for sequencing. The sequencing is done; sequence data will be analyzed to characterize rhizosphere microbiome and to examine the correlation between crop developmental stage and soil microbes. Meanwhile, the crop biomass was measured from those samples. In Spring 2023, 36 soil microbial legacies of the combinations of preceding and current crops were established. Rhizosphere soil from the seedling stage of six crops and the flowering stage of three crops was collected and the rest of samples are being collected during this growing season. Sub-objective 1.C. To address the effect of cover crops on the microbiome of cash crops and soybean soilborne diseases, bulk soil was collected from the Alternate Rotation field plots in the spring of 2022 before planting. These samples represented corn and soybean phases of two-year corn-soybean rotation with and without cover crops. After testing in the greenhouse, the soil from cover crop practices reduced soybean root rot, caused by Fusarium graminearum, but did not impact the soybean cyst nematode infection. Moreover, the rhizosphere soil was collected from two crop growth stages (seedling and flowering) in two-year corn-soybean rotation with and without cover crops. DNA was extracted from those rhizosphere samples and was sent to University of Minnesota Genomic Center for sequencing. The sequencing is in process. To develop strategies to mitigate soybean cyst nematode (SCN) infection in soybean, experiments were conducted to evaluate the interaction of SCN with rhizosphere and endospheric microbiomes and the potential to recruit beneficial microbes for improving soybean performance under biotic stress. Soil was collected in the winter of 2021 from soybean-corn rotation plots. Twelve cycles of soybean plantings with SCN infection in the collected field soil in the greenhouse were completed, and SCN disease suppression was observed after multiple cycles plantings. The rhizosphere, plant roots, and cysts of SCN were harvested from each cycle. DNA extraction and sequencing are underway to characterize the microbiome. Further, 284 bacteria and 17 fungi were isolated from the cycling samples. After testing SCN J2 mortality, nine bacteria have the potential to increase J2 mortality, compared with the control. Five fungi have the potential to reduce soybean SCN infection. Repeat experiments are underway to confirm the results. The rhizosphere soil from SCN resistant soybean varieties enhanced susceptible soybean resistance to SCN infection. Rhizosphere soil DNA was extracted, and the sequencing is in process. To identify additional beneficial bacteria for controlling soybean soilborne diseases, a total of 61 wheat rhizosphere-derived bacterial strains and one cyanobacterium isolated from soil were tested for their antagonistic activities to soybean pests and pathogens. Two bacterial strains reduced soybean Fusarium root rot. Two bacterial strains and one cyanobacteria alleviated soybean from SCN infection. Two bacterial strains decreased soybean white mold disease. One bacterium protected soybean against both SCN and Fusarium root rot. The manuscript reporting this study is in preparation. Sub-objective 1.C. Long-term research plots to evaluate the impact of no-till diverse crop rotations as a base crop production system, were continued to determine the influence of adding cover crop treatments on cash crop performance and soil physical, chemical, and biological properties as these effects manifest with duration of treatments. Plot-scale research was conducted in a timely manner to ensure data collection for the corresponding research objectives associated with this long-term experiment. An additional year of crop phenology, crop yield, and fall soils samples were collected and will be processed. Sub-objective 2.A. Research was continued to investigate rotational diversification effects on crop growth and yield, soil properties, and economics to better understand the temporal influences of these outcomes and the mechanisms by which they contribute to productivity and sustainability of the whole cropping system. All long-term experiment data was evaluated for quality control and organized to ensure data is available for additional analysis. Previous crop rotational cycle (2017-2022) was organized and a collaboration with Dr. Tong Wang, Economist at South Dakota State University was continued to evaluate the economic risk associated with diversified crop rotation; a manuscript was submitted to Soil Security, review was received, and a revised manuscript submitted. In-season soybean and pea biomass samples were ground and processed for chemical analysis to evaluate in-season nitrogen dynamic. Sub-objective 2.B. Research continued on evaluating oat production and quality in response to variety choice, seeding rate, and competition with forage legumes; forage legume responses to oat variety and management; and oat-forage rotational benefits. This change in topic was selected in fiscal year 2021 after consultation with industry stakeholders. In fiscal year 2023, the second field season of samples were fully collected and processed, and the third field season was established. Existing, external collaborations were maintained to aid evaluation of grain quality and plant health. One publication, “Index-based measurement of cover crop growth and N content with RGB sensing”, was accepted for publication in Agronomy Journal. Preliminary results uncovered management choices that improve oats’ rotational value and maintain milling quality. These were shared with growers and industry stakeholders on-site as part of the Research Unit’s annual field day. Results were also shared with grower stakeholders at the Organic Growers Research and Innovation Network in January, 2023.

Accomplishments
1. Cover crop nitrogen mineralization predicts corn yield. Producers are interested in determining if fertilizer applications can be reduced following cover crops that fix nitrogen. In-season nitrogen availability following fall-seeded cover crops are difficult to predict because it depends on seasonal patterns of nitrogen transformations that are site- and year-dependent. Research was conducted in a small grain-cover crop/corn crop rotation at two sites in South Dakota to evaluate the influence of fall-planted rye, sweet clover and vetch cover crops on nitrogen mineralization and availability to the following corn crop under no-till conditions. ARS researchers at Brookings, South Dakota, found greater corn yields when corn was grown following legume cover crops (sweet clover and vetch). Soils which had legume cover crops produced the highest rates of nitrogen mineralization during times when corn demand for nitrogen was largest (V6–R3) and they had the highest seasonal amounts of mineralized nitrogen compared with rye or no cover crops. These researchers also compared numerous methods for estimating in-season nitrogen availability and found that in-season nitrogen mineralization measurement was a better indication of corn yields than were approaches that utilized pre-season soil nitrogen or cover crop biomass and nitrogen content. Results showed that the contribution of nitrogen from mineralization following legume cover crops can decrease the need for fertilizer nitrogen application while maintaining crop yields.

2. Replacing eroded topsoil can improve soil properties that increase crop yields. Soil erosion redistributes soil within a landform, generally removing soil from upper slope positions and depositing it in lower slope positions. Replacing translocated topsoil (soil-landscape rehabilitation) is one method to improve the productivity of severely eroded land. ARS researchers in Brookings, South Dakota, investigated relationships between key soil chemical, biological, and physical factors and crop growth and grain yield in eroded and rehabilitated landforms. The highest-yielding plots had lower inorganic carbon and higher organic carbon, and higher available nutrients, water infiltration rates, fungal and bacterial populations, wet aggregate stability, and other measures of soil quality compared with the lowest-yielding plots. Differences in surface soil inorganic carbon (an indicator of high soil loss by tillage and water erosion) explained 70% of the yield variability in the upper slope. Whereas adding soil to the upper slope improved yields, removing soil from the lower slope depressed crop yields where soils had high water content and low fungal and bacterial populations. Growers, land managers, consultants, and conservation professionals can use these results to design approaches to remediate severely eroded land to improve food production.

3. Estimating carbon sequestration potential of agricultural soils. ARS researchers in Brookings, South Dakota, in collaboration with others, used a benchmarking approach to estimate carbon sequestration potential of agricultural soils. Sequestering carbon in soils mitigates climate change, improves food security against weather extremes, and could provide additional income to growers but often requires changes in management. Quantifying how much carbon can be sequestered and at what location is essential to designing effective policies by governmental and non-governmental agents. The approach used high-resolution modeling predictions developed at the continental scale to extend estimates from physical sample locations. Combining physical and modeled data allowed more accurate estimates at a national scale at low cost. Applying it to smallholder farms in Malawi, which generally are smaller than one hectare, resulted in a doubling of estimated carbon sequestration potential to 4.4 Mg ha-1. Critically, the method also improved identification of smallholder fields with high sequestration potential and those fields with effective carbon-sequestering management.

4. Accelerating agricultural innovation through state-space transition modeling. ARS researchers in Brookings, South Dakota, in collaboration with others, developed a modeling framework to accelerate agricultural research. Adaptation to changing and dynamic climates and demographics is a critical agricultural research need, yet studies are limited by biophysical (e.g., seasons) and logistical (money, labor) constraints. Moreover, stakeholder interests are often challenging to incorporate, yet essential to solution adoption. Advances in computer science – specifically, the concept of transitions among states, such as rotations between crops or the genetic architecture of a breeding population across generations – allow efficient integration of multiple input types with transition costs representing stakeholder values, thus allowing experimentation in silico to hypothesize novel, likely beneficial systems for field validation. Adopting this framework should improve the benefits of agricultural research, formalize the intuition of agriculturalists, and facilitate transdisciplinary collaboration to tackle the most recalcitrant challenges.

Review Publications
Runck, B.C., Streed, A., Wang, D., Ewing, P.M., Kantar, M.B., Raghavan, B. 2023. State spaces for agriculture: a meta-systematic design automation framework. Proceedings of the National Academy of Sciences-Nexus. 2(4):1-8. https://doi.org/10.1093/pnasnexus/pgad084.
Ewing, P.M., Tu, X., Runck, B., Nord, A., Chikowo, R., Snapp, S.S. 2022. Smallholder farms have and can store more carbon than previously estimated. Global Change Biology. https://doi.org/10.1111/gcb.16551.
Yin, C., Schlatter, D.C., Hagerty, C., Hulbert, S.H., Paulitz, T.C. 2023. Disease-induced assemblage of the rhizosphere fungal community in successive plantings of wheat. Phytobiomes Journal. 7 (1):100-112. https://doi.org/10.1094/PBIOMES-12-22-0101-R.
Yin, C., Hagerty, C., Paulitz, T.C. 2022. Synthetic microbial consortia derived from rhizosphere soil protect wheat against a soilborne fungal pathogen. Frontiers in Microbiology. 13. Article 908981. https://doi.org/10.3389/fmicb.2022.908981.
Chim, B., Osborne, S.L., Lehman, R.M. 2022. Short-term corn yield response associated with nitrogen dynamics from fall-seeded cover crops under no-till dryland conditions. Agrosystems, Geosciences & Environment. 5(3). Article 320305. https://doi.org/10.1002/agg2.20305.
Brockmueller, B., Sexton, P., Osborne, S.L., Chim, B. 2023. Winter rye cover crop seeding rate and termination timing effects on cover crop biomass and quality. Communications in Soil Science and Plant Analysis. https://doi.org/10.1080/00103624.2023.2221299.
Liptzin, D., Rieke, E.L., Cappellazzi, S.B., Mac Bean, G., Cope, M., Greub, K.H., Norris, C.E., Tracy, P.W., Aberle, P.W., Ashworth, A.J., Baumhardt, R.L., Dell, C.J., Derner, J.D., Ducey, T.F., Dungan, R.S., Fortuna, A., Franzluebbers, A.J., Kautz, M.A., Kitchen, N.R., Leytem, A.B., Liebig, M.A., Moore Jr, P.A., Osborne, S.L., Owens, P.R., Sainju, U.M., Sherrod, L.A., Watts, D.B. 2023. An evaluation of nitrogen indicators for soil health in long-term agricultural experiments. Soil Science Society of America Journal. 87(4):868-884. https://doi.org/10.1002/saj2.20558.
Rieke, E.L., Bagnall, D.K., Morgan, C., Greub, K., Bean, G.M., Cappellazzi, S.B., Cope, M., Liptzin, D., Norris, C.E., Tracy, P.W., Ashworth, A.J., Baumhardt, R.L., Dell, C.J., Derner, J.D., Ducey, T.F., Fortuna, A., Kautz, M.A., Kitchen, N.R., Leytem, A.B., Liebig, M.A., Moore Jr., P.A., Osborne, S.L., Owens, P.R., Sainju, U.M., Sherrod, L.A., Watts, D.B., et al. 2022. Evaluation of aggregate stability methods for soil health. Geoderma. 428. Article 116156. https://doi.org/10.1016/j.geoderma.2022.116156.
Smith, M.E., Vico, G., Costa, A., Bowles, T., Gaudin, A.C.M., Hallin, S., Watson, C.A., Alarcon, R., Berti, A., Blecharczyk, A., Francisco, F.J., Culman, S., Deen, W., Garcia, A.G., Garcia-Diaz, A., Plaza, E.H., Jonczyk, K., Jack, O., Lehman, R.M., Montemurro, F., Morari, F., Onofri, A., Osborne, S.L., Pasamon, J.L.T., Sandstrom, B., Santin-Montanya, I., Sawinski, Z., Schmer, M.R., Stalenga, J., Strock, J., Tei, F., Topp, C.F.E., Ventrella, D., Walker, R.L., Bommarco, R. 2023. Increasing crop rotational diversity can enhance cereal yields. Communications Earth & Environment. 4(1). Article 89. https://doi.org/10.1038/s43247-023-00746-0.