Location: Sustainable Agricultural Systems Laboratory
2020 Annual Report
Objectives
Objective 1: Analyze the effects of agricultural management systems on soil biodiversity and functions.
Sub-objective 1.A: Validate combined soil PLFA/metabolomics method for analysis of microbial community structure and function.
Sub-objective 1.B: Analyze soil microbial community structure, diversity, metabolomic profile, and functional diversity in different cropping systems.
Objective 2: Develop improved management practices to reduce emissions of ammonia and greenhouse gases, and reduce pathogens during manure composting.
Objective 3: Develop technologies and practices that improve anaerobic digestion of animal manures and other feedstocks, contributing to improved system economics, recovery of nutrients, and water quality.
Objective 4: Improve the ability to quantify organic contaminants released during the process of water resource recovery, treatment, and reuse of resulting biosolids.
Sub-objective 4.A. Use bioreactors as a model system to measure xenobiotic degradation losses using a newly implemented CAMBI system.
Sub-objective 4.B. Study two specific soluble source tracers, artificial sweeteners for urban sources and metolachlor ethane sulfonic acid for agriculture sources, in order to model nitrogen loading to impacted watersheds.
Approach
We are developing a new method to simultaneously extract phospholipids and metabolites from soil. Phospholipid fatty acids are measured by gas chromatography while metabolites are measured by gas chromatography-mass spectrometry. Our methods will be tested in a greenhouse experiment using 3 soil types and 3 crop species. We will then analyze soil microbes and their activity using DNA sequencing, transcriptomics, metabolomics, and PLFA analysis in 3 different replicated field trials: the Beltsville Farming Systems Project (FSP), the Beltsville Cover Crop Systems Project (CCSP), and a cover crop field experiment at the ARS lab in Brookings, South Dakota (SD). Composting studies will be conducted at the BARC composting facility. Initial experiments will be conducted outdoors using replicate pilot-scale compost piles composed of manure and bedding from the BARC dairy. Subsequent large-scale experiments will be conducted using extended static piles and windrows of the manure/bedding. Experimental variables include aeration and compost covers. Gases and compost pile temperatures will be monitored. Results will be validated using large-scale extended static piles. Six identical pilot-scale anaerobic digesters will be operated using solids-separated manure effluent from the BARC dairy. For H2S removal experiments, duplicate digesters will be randomly assigned to one of three treatments: no air injection; air injection, low rate; air injection, high rate. Depending on the results, additional experiments may be conducted to evaluate other aeration rates or recirculation of biogas or manure in order to optimize H2S removal. Experiments during the second year of operation will evaluate manure pre-heating as a means to maintain digester temperature and improve overall energy use. The first task will be to establish analytical methods using liquid chromatography-mass spectrometry for up to 53 pollutants. Incubation studies of samples obtained at different stages in the CAMBI process will then be carried out. Based on these results, compounds that appear to be degraded will be singled out for separate individual incubation studies. The goal will be to better describe their degradation rates and formation of metabolites in the CAMBI system. An artificial sweetener will be used as a tool to track urban pollution from wastewater treatment plants while MESA will be used to track agricultural pollutants for rural sources. A liquid chromatography-mass spectrometry method for assessment of both MESA and the most easily detected sweetener will be developed. The second step will be to test the method by analyzing selected real samples. The final step will be to apply the method to base-flow fed streams in the Choptank and Bucks Branch watersheds in Delaware in order to measure groundwater residence times.
Progress Report
This report is for the fourth full year of research as the project was initiated in July of 2016. Two scientists on this project have retired and one support scientist left ARS for other employment. One SY position and the support scientist position were abolished and hiring for the remaining vacant scientist position is going forward.
Both Milestones for Objective 1 were met. Work for Sub-objective 1A was completed and detailed in the Annual Report from a prior year. For Sub-objective 1B, research was conducted on soils collected from USDA-ARS long-term agricultural research (LTAR) sites: one in Brookings, South Dakota, and one in Beltsville, Maryland. Each LTAR site was designed to compare at least two conventional corn-soybean-wheat cropping systems (till, no-till) and an aspirational set of cropping systems (cover crop-based till, no-till, organic). We completed analysis regarding the impact of cropping systems on soil microbial community structure on samples from these LTAR locations. Samples were evaluated for quantity of bacterial ribosomal (16s) and fungal internal transcribed spacer (ITS) genes and functional genes for nitrogen fixation (nifH). In collaboration with scientists at the University of Maryland on work associated with Sub-objective 1B, we isolated and genotyped a novel dark septate fungus that associates with grasses and imparts varying degrees of salt tolerance, dependent on the host/endophyte genotypes. For this work, a variety of marsh grasses were grown in native soils and subjected to a salinity gradient. From this process we were able to use growth characteristics of the plant and associated endophytic fungi to identify fungal/plant pairs that resulted in improved salt tolerance by the plant. A successful Ph.D. dissertation and the manuscript “Dark septate endophyte improves salt tolerance of native and invasive lineages of Phragmites australis” was written.
Progress on Objectives 2 and 3 was slowed due to the retirement of the Scientist responsible for these objectives.
Milestones for Objective 4 were met or partially met. We measured additional compounds in biosolids and manure that were related to antimicrobial resistance. We added two antibiotics to the previously reported 12 and finalized the method for all 14 antibiotics. The finalized method was used for analysis of manure processed through an anaerobic digester located on a farm in upstate New York. The timed processing of these 14 antibiotics was followed over 24 hours to assess the degree of degradation of the antibiotics. Aside from the beta-lactam antibiotics, no degradation was observed. Biochemical methane production (BMP) tests were conducted on the same manures in the laboratory and followed for 40 days at varying temperatures. Results from the BMP tests indicated that longer periods of exposure were needed to metabolize the antibiotics and antibiotic degradation rates increased at higher temperatures. Tests are also underway to examine for existence of antibiotic resistance by targeting key antimicrobial genes including the genes for ampicillin and tetracycline resistance (int1, ermB, tetX, sul1). Approximately eleven years of Choptank subwatershed samples were analyzed for metolachlor ethane sulfonic acid (MESA). Improvement in the analytical method for chiral separation of metolachlor oxanilic acid (MOXA), another abundant metabolite of metolachlor, has been achieved. The new MOXA method separates all 4 isomers while with the MESA method only 3 of the 4 isomers can be separated. As with MESA, we can age-date the occurrence of MOXA in stream water since it appears to transport similar to MESA as a groundwater-fed material. Comparisons are underway with 3 years of samples (total of 378) from the 12 subwatersheds of the Choptank River. Samples were collected at approximately monthly intervals. The results for MESA and MOXA are being compared for their age signals and concentration fluctuations.
Accomplishments
1. Glyphosate does not increase abundance of Fusarium Root Rot on Round-up Ready® corn or soybean. An ARS scientist, located in Beltsville, Maryland, led a multi-area team that included ARS locations in Stoneville, Mississippi, and Urbana, Illinois, which determined that applications of glyphosate on Round-up Ready® corn and soybean did not increase abundance or risk of Fusarium Root Rot. Metabolic profiling of the grain showed that the glyphosate application did not change the amino acid profile. This research informs farmers and extension agents that the commonly used herbicide glyphosate does not enhance the important disease Fusarium Root Rot.
2. Standards measurements for soil health and soil microbiology. An ARS scientist, located in Beltsville, Maryland, was co-Principle Investigator on a National Science Foundation (NSF) research coordination network that developed and published standards and technical bulletins for soil health and soil microbiology measurements. The technical bulletin is a key tool used by NRCS conservationists and non-profit groups when making recommendations to landowners concerned with improving soil health.
Review Publications
Rice, C., Hively, W.D., McCarty, G.W., Hapeman, C.J. 2020. Fluxes of agricultural nitrogen and metolachlor metabolites are highly correlated in a first order stream in Maryland, USA. Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2020.136590.
Plummer, R.E., Hapeman, C.J., Rice, C., McCarty, G.W., Schmidt, W.F., Downey, P.M., Moorman, T.B., Douglass, E.A., Strickland, T.C., Pisani, O., Bosch, D.D., Elkin, K.R., Buda, A.R. 2020. Method to evaluate the age of groundwater inputs to surface waters by determining the chirality change of metolachlor ethanesulfonic acid (MESA) captured on a polar organic chemical integrative sampler (POCIS). Journal of Agricultural and Food Chemistry. 68(8):2297-2305. https://doi.org/10.1021/acs.jafc.9b06187.
Delgado, J.A., Short, N.M., Roberts, D.P., Vandenberg, B.C. 2019. Big data analysis for sustainable agriculture. Frontiers in Sustainable Food Systems. https://doi.org/10.3389/fsufs.2019.00054.
Roberts, D.P., Mattoo, A.K. 2019. Sustainable crop production systems and human nutrition. Frontiers in Sustainable Food Systems. https://doi.org/10.3389/fsufs.2019.00072.
Kepler, R., Epp Schmidt, D.J., Yarwood, S.A., Cavigelli, M.A., Buyer, J.S., Duke, S.O., Reddy, K.N., Williams, M., Bradley, C.A., Maul, J.E. 2020. Soil microbial communities in diverse agroecosystems exposed to glyphosate. Applied and Environmental Microbiology. https://doi.org/10.1128/AEM.01744-19.
Dundore-Arias, J.P., Eloe-Fadrosh, E., Schriml, L.M., Beattie, G.A., Brennan, F.P., Busby, P.E., Calderon, R.B., Castle, S.C., Emerson, J.B., Everhart, S.E., Eversole, K., Frost, K.E., Herr, J.R., Huerta, A.I., Iyer-Pascuzzi, A.S., Kalil, A.K., Leach, J.E., Leonard, J., Maul, J.E., Prithiviraj, B., Potrykus, M., Redekar, N.R., Rojas, J.A., Silverstein, K.T., Tomso, D.J., Tringe, S.G., Vinatzer, B.A., Kinkel, L.L. 2020. Community-driven metadata standards for agricultural microbiome research. Phytobiomes Journal. 4:115-121. https://doi.org/10.1094/PBIOMES-09-19-0051-P.
Gonzalez Mateu, M., Baldwin, A.H., Maul, J.E., Yarwood, S.A. 2020. Dark septate endophyte improves salt-tolerance of native and invasive lineages of Phragmites australis. The ISME Journal: Multidisciplinary Journal of Microbial Ecology. https://doi.org/10.1038/s41396-020-0654-y.
