Location: Genetics and Sustainable Agriculture Research
2019 Annual Report
Objectives
Objective 1. Develop more sustainable long-term soil health management systems for improved yields from humid, Southeast Agroecosystems.
Sub-objective 1.1. Increase row crop yields in the upland soils of the South and Southeast by agronomic practices that improve soil physical and biological properties including application of organic- and inorganic-amendments and planting cover crops.
Sub-objective 1.2. Develop soil water management strategies to increase the capture and storage of rain water in soil, minimize yield-robbing drought effects, and increase dryland and irrigated crop production in the South and Southeast.
Sub-objective 1.3. Determine the environmental impact in soil, water, and air of proposed novel agronomic approaches on antibiotic resistance, emissions, and nutrient risks.
Objective 2. Develop improved decision support tools and technologies based on GxExM to optimize water use efficiency of rainfall and irrigation water for better yields from humid, Southeast Agroecosystems.
Sub-objective 2.1. Develop techniques that utilize and integrate high resolution row crop canopy spectral images gathered during the growing season for in-season water management in cropping systems and fields characterized by high soil variability.
Sub-objective 2.2. Implement databases, modeling tools, and decision-making paradigms for optimizing water management and crop yield.
Approach
Several multi-year field plots will be established. These include a) cover crops for the major row cropping systems in then the southeast, b) planting various configurations of mixed cover crop species, c) cropping systems for land leveled fields, d) stabilizing dryland soybean production using cover crops and poultry litter, e) deep rooted cover crops and soil amendments and, f) cover crops and water use efficiency. From these field experiments we will measure effects on environmental quality, greenhouse gas emissions, and economics of each of the systems; environmental quality and antimicrobial resistance in each of the systems; contribution of soil organic matter to plant available water content in each of the systems; we will optimize yield by managing field variability, we will utilize high resolution thermal imaging to optimize irrigation management and we will model soil water requirements in each of the systems.
Progress Report
Sub objective 1.1: A new grain drill that enables the planting of at least three cover crop species on the same pass was designed and is under construction by a contractor. A field for the study has been identified to test whether a planting pattern of two cover crop species in alternating drill rows leads to a desired species composition, a reduction in competition among the species, and a greater cover crop biomass of the weaker species. The cover crops will be planted as soon as the planter is delivered by the contractor in the fall of 2019. A land leveled degraded field low in fertility has been identified and the study was initiated to evaluate if long-term integration of cover crop and organic amendment into cropping systems can restore soil fertility level to pre-leveling conditions. Background soil samples were collected for determining the initial soil chemical, physical and biological characteristics. Cool-season multispecies cover crop will be planted early fall of 2019.
Sub objective 1.2: Experiments D, E, and F of Sub obj 1.2 have been established and currently nutrient, biological, emission, and physical data have been collected where appropriate. For Experiment E, cool-season deep rooted multispecies cover crop including winter wheat, crimson clover and daikon radish were planted in October 2018. Before cover crop termination, aboveground biomass was collected, and dry matter yield recorded, followed by corn planting. Fertilizer and soil amendment including inorganic fertilizer and broiler litter with/without FGD gypsum and lignite were applied. Litter bags were placed in field to determine cover crop residue decomposition. A total of five litter bags were left in the plots and were collected every three weeks during the corn growing season. Pen lysimeters were deployed vertically into experimental plots to monitor leachate volume as an indicator of soil infiltration following rain events. Soil samples were collected beneath each litter bag to analyze nutrient concentrations. Sensors were deployed to monitor ambient environmental conditions. Corn growth parameters were recorded and harvested. Soil enzyme and genomic DNA has been collected for Exp E. Initial screening for DNA based gene indicators and microplate analysis of enzymes have been conducted. Emission (soil CO2 flux via LiCor survey chamber) measurements have been taken every 3 weeks to coincide with litter bag collection as well as soil nutrient and biological measurements. For Experiment D, cover crop and fertilizer treatments were imposed according to plan. In the fall of 2018, five different cover crop species were planted with three different fertilizer treatments followed by cover crop termination and soybean planting. Soil and plant samples have been collected and have been processed for laboratory analysis. Samples were collected to measure initial conditions of soil physical properties, soil moisture and nutrients before the spring planting of the soybeans. Sensors were installed at multiple depths in the majority of plots to monitor water potential and moisture level. Sensors were installed to measure canopy temperatures to monitor crop water stress. Cover crop dry biomass was measured. Plant height and cover, soil water content, and plant physiological measurements were made throughout the growing season. Soil and plant samples were collected and measured 7 times since February 2019. For Experiment F, a furrow-irrigated field with clay soil was established with experimental plots and irrigation treatments were imposed. Winter wheat cover crop was planted in cover crop treatment plots. Cover crop biomass was measured prior to cover crop burn down. Soil moisture and water potential sensors were installed at multiple depths. Soybean was planted on schedule and soybean canopy temperature sensors were installed. A water balance was calculated to determine cover crops effect on soil moisture and soybean water consumption. Plant phenology and plant height were measured throughout the growing season.
Sub objective 1.3: Background DNA has been extracted from field plots associated with Experiment H for Sub obj 1.3. Initial screening for antibiotic resistance genes has been conducted on selected samples and DNA archived for high throughput sequencing as well as further PCR based analyses. A growth chamber-based study was initiated to determine influence of abiotic factors on antibiotic resistance development. For Experiment I, a bench was constructed to begin the greenhouse study, as well as ordering of parts for the Giddings probe to begin soil core collection.
Sub objective 2.1: New plots have been established to quantify the degree of cotton water stress using high resolution crop thermal maps acquired by unmanned aircraft system for purposes of irrigation management. Thermal imagery will be collected on cotton plots with three irrigation levels. A weather station has been secured to determine daily evapotranspiration to determine irrigation treatment levels. Current summer weather has prevented any irrigation due to an abundance of precipitation.
Sub objective 2.2: Sample data was collected for all relevant experimental sites (A-F, J, K). Historical weather data from the previous 100 and future 50 years was collected for Brooksville, Macon, N. Farm (Mississippi State), Verona, Pontotoc, Coahoma-Clarksdale, Onward, Sidon Leflore, and Stoneville, Mississippi. Soil data was collected from a cotton growth simulation model. Soil data was compiled from a national soil survey database with a focus on Mississippi, while locally collected data was added to the system. A weather and soil database for experimental sites (A-F, J, K) is currently in development for the location.
Outgoing Agreement 58-6064-8-023 with North Dakota State University: To date, the principal investigators have hired 2 research assistant professors, 2 research specialists, 4 graduate students, and 3 undergraduate research assistants. With these hires, the project has established a research team with a broad set of expertise that includes plant science, agronomy, robotics, software, electrical control systems, artificial intelligence, big data, image analysis, and geographic information systems. In addition, collaborations are established or are being developed with experts across the university in weed science, soil science, nutrient management, chemical application, and spray technology.
Achievements for Objective 1 include the acquiring and testing of equipment, and establishing and planting fertility field trials. Three unmanned aircraft (two DJI Matrice 600 Pro and one Phantom 4 RTK), two multispectral cameras (MicaSense RedEdge-RX), and one thermal camera (DJI Zenmuse XT2) were purchased for the purpose of remote sensing. Also, experimental designs were finalized and implemented for the nitrogen fertility trials for corn and wheat. Research plots were recently planted at three locations across North Dakota. Additionally, protocols were developed for data collection and organization in order to ensure metadata is recorded and retained properly during campaigns.
The major accomplishment for Objective 2 was the construction of an automated data acquisition platform that utilizes multiple optical sensors to collect image
data (Figure 1). This platform allows for more efficient image acquisition as it enables automated positioning of the sensors to desired locations in 3D space. The hyperspectral imagery is being investigated for unique spectral signatures that may help differentiate plant groups of interest. The RGB video data is being used to construct 3D point-clouds to distinguish weed species in soybean fields. Thermal images will be used to evaluate resistant and susceptible weed populations, and to identify susceptible versus resistant individuals after herbicide application. Figure 1 presents the 3D point cloud, thermal, and hyperspectral images collected in the greenhouse.
Outgoing Agreement 58-6064-9-007 with Mississippi State University: The agreement was only finalized late in the year and there have been several seminars where we brought together ARS and MSU scientists and engineers to discuss and select areas for the collaborator to interface with the ARS scientists. Mississippi State University Geosystems Research Institute will work in the area of remote sensing, image analysis, machine learning, and algorithm development.
Accomplishments
1. Integration of mixed winter cover crop into no-till dryland cotton sustains yield and improves soil health. Rapid decomposition of low cotton residue under a no-till system in the sub-humid southeastern USA enhances the potential of nutrient loss and limits the benefits of a no-till system. Offsite movement of nutrients is a great concern, as it represents an economic loss of applied fertilizers, loss of soil fertility, and downstream environmental degradation. Addition of cool season mixed (grasses and legumes) cover crops to no-till cotton may compensate for low cotton residue, by improving soil water dynamics, soil health, no-till performance and yield. ARS scientists at Mississippi State, Mississippi evaluated the residual effect of cool season cover crops in no-till cotton and soybean fertilized with broiler litter. Results indicated the presence of cover crop residue in no-till cotton improved soil physical characteristics and increased water infiltration, retained nutrients, and increased cotton yield, particularly in drier seasons. Differences in soil moisture content and cotton lint yield between residual mixed cover crop and no cover crop in no-till cotton was more evident in drier periods, with 24.8% and 8.5% greater moisture and yield, respectively, with cover crop than no cover crop management. Additionally, percolation and evaporation during crop growth periods were decreased while water use efficiency increased. These results not only provide useful information for cotton farmers, who are showing interest in cover crop integration, but also provides scientific knowledge to create growers’ confidence in adopting management practices.
2. Optimizing nitrogen fertilization may be the best way to produce nutrient-rich corn grain. Enriching the corn grain with mineral elements, Fe and Zn in particular, would have human and animal nutrition implications. Currently, the most accepted approach to enriching grains of corn and other cereal crops is through biofortification by genetic manipulation or application of the mineral elements directly on the plant. Poultry litter use as a fertilizer in crops such as cotton and corn is known to enrich the soil and plant parts with phosphorus (P), potassium (K), magnesium (Mg), iron (Fe), zinc (Zn), and other mineral elements. ARS researchers at Mississippi State, Mississippi, investigated whether fertilizing corn with poultry litter increases the levels of mineral elements in the grain beyond that possible with conventional fertilization with synthetic fertilizers. The results showed that elevating the level of N and therefore protein in the corn grain by supplying optimal N fertilization, regardless of the source, was key to enriching the grain with mineral elements including P, K, Mg, Zn, Fe, and manganese (Mn). The levels of these elements in the corn grain increased in direct proportion to the level of protein or N in the grain regardless of whether these elements were added to the soil. Grain protein in turn was a direct function of the amount of N the corn plant received from poultry litter or synthetic sources. The results suggest that optimal N fertilization may be the best approach to produce not only optimal corn grain yield but also nutritious grain. The results have direct implications for corn produced for food and feed particularly in countries with chronic mineral nutrient deficiencies in human diets.
3. Traditional soil health physical parameters are not indicative of proper soil biological recovery. Recovery of degraded soil such as mine overburden have traditionally relied on soil health indicators such as addition of organic matter, pH, and physical compaction. However, these indicators are not suitable to measure soil biological recovery. Additionally, a best management practice (BMP) for mine soil recovery is to rapidly replace the lost organic matter to the surface soil. ARS researchers at Mississippi State, Mississippi, conducted this research on an active surface coal mine, whereby reclaimed mine overburden is recovered to approximate pre-mine conditions using standard and best management practices. Soil samples were collected from a chronosequence within the recovered mine and high throughput sequencing, quantitative polymerase chain reaction, nutrient analysis, and physical measurements were made. The research showed that while soil physical conditions were recovered to near pre-mine conditions, indicating suitable abiotic soil health, soil bacterial community structure was not yet recovered, and possibly will never recover to pre-mine conditions. Soil bacterial membership remained similar to pre-mine conditions, but community structure was different, even 13 years later, suggesting that reclaimed mine overburden will possess some differences in functional biology (e.g. cycling of organic matter, biogeochemical cycling) relative to reference soils. The team also determined that use of 10 ton/acre poultry litter annually improved soil fertility and supported plant establishment and growth over other forms of organic matter. This study demonstrated that soil biology should also be assessed when determining the soil health of agricultural soils, which has broad implications to recovery of degraded or marginal soils, such as those found throughout the Southeastern United States.
4. Pelletized poultry litter (PPL) provides residual nitrogen and increased moisture retention after applications cease. Sustainable agriculture is reliant upon keeping soil healthy enough to maintain water holding capacity and adequate nutrients for crop productivity. Sub-surface application of pelletized poultry litter is a relatively new and effective application method since it delivers nutrients in direct proximity of the root zone, while also maintaining a residual soil nutrient level which can be exploited in subsequent years. ARS researchers at Mississippi State, Mississippi, conducted a multi-year study to determine the impact of pelletized poultry litter on cotton lint yield, soil nutrients, and soil physical and hydraulic properties. Cotton leaf qualities were increased by applying urea to plots with residual poultry litter during boll-filling stages. Plots with residual pelletized poultry litter and applied urea increased lint yield by as much as 10% compared with standard fertilization. Annual pelletized poultry litter application also increased soil aggregate stability, plant available water, field capacity, saturated hydraulic conductivity, and infiltration. Taken in its entirety, these results indicate that pelletized poultry litter offers a sustainable practice for increasing cotton yield in the humid Southeastern United States.
5. Novel broiler chicken dietary components reduce farm gate imports of phosphorus.. Population growth, greater income and urbanization are driving the demand for animal derived food and poultry is the fastest growing agricultural sub-sector, especially in developing countries. Research around poultry production strives to meet these challenges to formulate better strategies for sustainability, requiring a combination of approaches. ARS researchers at Mississippi State, Mississippi, studied the effect of alum litter treatment and dietary inclusion of High Available Phosphorus Corn (HAPC) and Phytase enzyme on cholesterol, bone ash and yield. This study, combined with others from the same flocks of broilers, demonstrates that combining HAPC and Phytase in diets is one way to reduce farm gate imports of phosphorus and thus improve the overall sustainability of poultry production. The lack of significant differences across flocks suggests that the performance of broilers was not consistently negatively impacted by dietary modification or use of alum litter treatments. Use of clavicle ash was a novel method to determine the impact of these treatments to possible impacts on boneless meat products; however, due to issues with the fragility of the clavicle, other bones are likely to provide more complete information. The potential impact is that the combination diet (HAPC + Phytase) shows promise for sustainable broiler production by maintaining comparable cholesterol and meat yield as well as reducing excretion of water-soluble phosphorus.
6. Strategy to diminish groundwater depletion. Groundwater in the Mississippi Delta has declined to an alarming level due to irrigation, threatening irrigated agriculture sustainability. ARS scientists at Mississippi State, Mississippi, investigated alternative water resources which could be used to replace groundwater for irrigation. Rainwater deficit from the past 120 years of weather records and irrigation demand of cotton, corn and soybean were determined. The coupled Soil and Water Assessment Tool–Modular Groundwater Flow model (SWAT–MODFLOW) was used to estimate weekly amounts of surface water available in ponds and streams. It was determined that weekly surface water resources are sufficient for major crop irrigation demand. These studies suggest that the conjunctive use of surface water and groundwater for agriculture irrigation is a feasible method to maintain groundwater management in the Mississippi Delta.
Review Publications
Tewolde, H., Shankle, M.W., Way, T.R., Pote, D.H., Sistani, K.R. 2018. Poultry litter band placement in no-till cotton affects soil nutrient accumulation and conservation. Soil Science Society of America Journal. 82:1459-1468. https://doi.org/10.2136/sssaj2018.04.0131.
Miles, D.M., Moore Jr, P.A., Brooks, J.P., Smith, D.R., Stilborn, H.L., Rice, D.W., Branton, S.L. 2019. Cholesterol, yield, tibia and clavicle ash of broilers fed high available Phosphorus corn and/or Phytase with/without Alum litter treatment. International Journal of Poultry Science. 18(7)349-352.
Read, J.J., Adeli, A., McCarty Jr, J.C., Feng, G.G. 2018. Cotton response to residual poultry litter: leaf area, nitrogen removal, and yield. Agronomy Journal. 110(6):2360-2368. https://doi.org/10.2134/agronj2018.05.0348.
Tewolde, H., Sistani, K.R., Feng, G.G., Menkir, A. 2019. Does fertilizing corn with poultry litter enrich the grain with mineral nutrients. Agronomy Journal. 111:1-3. https://doi.org/10.2134/agronj2019.02.0094.
Yang, W., Feng, G.G., Tewolde, H., Li, P. 2018. Soil carbon sequestration and greenhouse gas emission from spring- and fall-applied poultry litter in corn production as simulated with RZWQM2. Journal of Environmental Quality. 209:1285-1293. https://doi.org/10.1016/j.jclepro.2018.10.251.
Read, J.J., Adeli, A., Lang, D.J., Mcgrew, N.R. 2019. Use of poultry litter, swine mortality compost, and FGD gypsum on reclaimed lignite mine soil in Mississippi. Journal of the American Society and Mining and Reclamation. 8(2):31-51.
Song, P., Feng, G.G., Brooks, J.P., Zhou, B., Zhou, H., Zhao, Z., Li, Y. 2019. Environmental risk of chlorine-controlled cloffing in drip irrigation system using reclaimed water: the perspective of soil health. Journal of Environmental Science and Technology. 232:1452-1464. https://doi.org/10.1080/08927014.2019.1600191.
Song, P., Zhou, B., Feng, G.G., Brooks, J.P., Zhou, H., Zhao, Z., Liu, Y., Li, Y. 2019. The influence of chlorination timing and concentration on microbial communities in labyrinth channels: implications for biofilm removal. BIOFOULING. 35:401-415. https://doi.org/10.1080/08927014.2019.1600191.
Lamori, J.G., Xue, J., Rachmadi, A.T., Lopez, G., Kitajima, M., Gerba, C.P., Pepper, I.L., Brooks, J.P., Sherchan, S. 2019. Removal of fecal indicator bacteria and antibiotic resistant genes in constructed wetlands. Journal of Environmental Management. 26(10):10188-10197. https://doi.org/10.1007/s11356-019-04468-9.
Brooks, J.P., Adeli, A., Smith, R.K., McGrew, R., Read, J.J. 2019. Recovery of bacterial community structure in a chronosequence of reclaimed coal mined soil under two vegetative regimes. Journal of Environmental Quality. 48:1029-1037. https://doi.org/10.2134/jeq2018.09.0349.
Adeli, A., Brooks, J.P., Read, J.J., Shankle, M.W., Feng, G.G., Jenkins, J.N. 2019. Poultry litter and cover crop integration into no-till cotton on upland soil. Agronomy Journal. 111:2097-2107. https://doi.org/10.2134/agronj2018.05.0328.
Adeli, A., Brooks, J.P., Read, J.J., McGrew, R., Jenkins, J.N. 2018. Post-reclamation age effects on soil physical properties and microbial activity under forest and pasture ecosystems. Land Degradation and Development. 50(1):20-34. https://doi.org/10.1080/00103624.2018.1546868.
Yang, W., Feng, G.G., Adeli, A., Kersebaum, K.C., Jenkins, J.N., Li, P. 2019. Long-term effect of cover crop on rainwater balance components and use efficiency in the no-tilled and rainfed corn and soybean rotation system. Agricultural Water Management. 219:27-39. https://doi.org/10.1016/j.agwat.2019.03.022.
