Location: Sustainable Agricultural Systems Laboratory
2019 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 third 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. For Sub-objective 1B, research was conducted on soils collected from three USDA-ARS long-term agricultural research sites; one in Brookings, Missouri, and two in Beltsville, Maryland. Each long-term agricultural research 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 sampling and data analysis regarding the impact of cropping systems diversity on the soil microbial community structure. Samples have been collected from the Beltsville and Brookings sites, although due to wet weather conditions, and some crop failure in fall of 2018, a complete set of samples was not taken. Most of the samples have been processed and data will be analyzed over the next year with possible additional targeted resampling and resequencing at both locations. One manuscript describing a portion of this work has been submitted to the journal Applied and Environmental Microbiology and a second manuscript is in preparation. A researcher on this project is co-PI on a funded National Science Foundation (NSF) research coordination network grant “Research Coordination Network (RCN): AgMicrobiomes: An Interdisciplinary Research Network to Advance Microbiome Science in Agriculture.” This scientist will host an RCN sponsored symposium at the 2019 Tri-Societies meeting featuring ARS scientists working on the NP212 and associated projects. The goal of this network is to bring together researchers from around the world who conduct microbial research within agricultural systems. In other work associated with Sub-objective 1B, we developed techniques for sequencing genomes of biological control agents which have had key genes tagged with markers that allow labs to conduct comparative genomics. This facilitates the identification of key bacterial gene products that are responsible for successful biological control of root diseases in soil. This work was conducted in collaboration with scientists from Universidade Federal de Lavras, Lavras, Brazil.
Progress on research under Objectives 2 and 3 has been slowed due to the retirement of the scientist responsible for work on these objectives.
All milestones were met or partially met under Objective 4. The final screening of compounds (analytes) commonly found in biosolids was reduced from the originally proposed 53 to 27 for which methods were possible. Method testing for determination of concentration of these compounds was conducted at six wastewater treatment plants. Sixteen of these compounds were detected in samples from at least one of the wastewater treatment plants. A manuscript draft describing this work has been prepared. A bioreactor system was used to model degradation of two widely used bacteriostats, triclosan (TCS) and triclocarban (TCC), that are naturally present in biosolid materials, allowing temperature maxima to be determined. The anaerobic digestion-thermal hydrolysis processing method (CambiTM) processing method used at certain wastewater treatment plants was evaluated in another set of experiments. While the biosolids resulting from the CambiTM process are otherwise cleaner (i.e. type A vs B biosolids), there was a higher associated buildup of phthalate residues. This appears to be related to high solids adsorptivity of phthalates and the reduction in solids concentration by the thermal hydrolysis step in the CambiTM system compared with the traditional lime treatment. Comparison of changes in phthalate residues in samples from three different wastewater treatment plants indicated that aerobic processes generally lowered concentrations of these compounds while thermal hydrolysis followed by anaerobic digestion appeared to increase concentrations due to solids removal. Bioreactor vessels were run under nitrifying conditions and TCS was observed to degrade to methyltriclosan while TCC did not appear to be altered. A specialized bioreactor vessel was used to follow TCS and TCC degradation. These experiments demonstrated that increased hydraulic retention time, sludge retention time, and temperature all resulted in enhanced removal of TCS and TCC from wastewater during the activated sludge process. Furthermore, a substantial conversion of TCS into methyltriclocarban was observed. Recent progress was made on redirected research under Objective 4 with a goal to measure additional compounds in biosolids and manure that are related to antimicrobial resistance. Priority for selection was based on quantitities used and likelihood to activate genetic alterations in bacteria. We have developed analytical methods for 12 antibiotics that are widely used in animal husbandry. Progress has been made on establishing a nationwide network to utilize MESA as a marker for age dating stream transport of nitrate from agricultural sources. This project has been elevated to the Conservation Effects Assessment Project (CEAP) program and Long Term Agroecosystem Research Data (LTAR) project as well and coordinated with National Resources Conservation Service (NRCS). To expedite this effort we utilized passive sampling with a commercially available device marketed as a polar organic integrative sampler.
Accomplishments
1. Farming practices impact gene abundance of soil bacteria responsible for nitrous oxide emissions. Agricultural soils are the dominant source of nitrous oxide, a greenhouse gas and catalyst of stratospheric ozone decay. The dominant source of nitrous oxide in many agricultural soils is denitrification, a process carried out by soil microbes. In a long-term study in Beltsville, Maryland, ARS scientists showed that the abundance of denitrification genes was affected by the specific crop in a crop rotation, time of year, and farming system (no-till, conventional till or organic). However, gene quantities did not correspond to nitrous oxide emissions patterns. This information is important in the on-going search for reliable indicators of microbially mediated soil greenhouse gas emissions and will be important for scientists to improve models predicting soil microbial community dynamics and greenhouse gas emissions.
2. Low cost anaerobic digester for reduction of antibiotics and xenobiotics in farm waste. Waste management on farm (manure, carcases, plant residue) is an important issue as accumulated waste can be a source of pollution and source of potential human pathogens. ARS scientists in Beltsville, Maryland, in collaboration with scientists at the University of Maryland, College Park tested an anaerobic digestion system developed for small farms for reduction of antibiotic compounds in farm waste. This anaerobic digestion system removed seventy percent of the antibiotic monensin, used widely in animal husbandry, from waste. Once implemented anaerobic digestion systems such as this will have the potential to reduce point source pollution runoff from farms into the Chesapeake Bay and other important watersheds. This information will be important to policymakers and scientists developing methods to reduce on-farm waste.
Review Publications
Buyer, J.S., Vinyard, B.T., Maul, J.E., Selmer, K.J., Lupitskyy, R., Rice, C., Roberts, D.P. 2019. Combined extraction method for metabolomic and PLFA analysis of soil. Applied Soil Ecology. 135:129-136.
Reddy, K.N., Cizdziel, J.V., Williams, M., Maul, J.E., Rimando, A.M., Duke, S.O. 2018. Glyphosate resistance technology has minimal or no effect on maize mineral content and yield. Journal of Agricultural and Food Chemistry. 66:10139-10146. https://doi.org/10.1021/acs/jafc.8b01655.
Williams, A., Wells, M.S., Dickey, D.A., Hu, S., Maul, J.E., Raskin, D.T., Reberg-Horton, S.C., Mirsky, S.B. 2019. Establishing the relationship of soil nitrogen immobilization to cereal rye residues in a mulched system. Plant and Soil. 426:95-107.
Dangi, S.R., Banuelos, G.S., Buyer, J.S., Hanson, B.D., Gerik, J.S. 2017. Microbial community biomass and structure in saline and non-saline soils associated with salt- and boron-tolerant poplar clones grown for the phytoremediation of selenium. International Journal of Phytoremediation. 20(2):129-137. doi:10.1080/15226514.2017.1337073.
Armstrong, D.L., Rice, C., Ramirez, M., Torrents, A. 2018. Fate of four phthalate plasticizers under various wastewater treatment processes. Journal of Environmental Science and Health. https://doi.org/10.1080/10934529.2018.1474580.
Armstrong, D.L., Lozano, N., Rice, C., Ramirez, M., Torrents, A. 2019. Fate of triclosan, triclocarban, and their transformation products in wastewater under nitrifying conditions. Journal of Water Process Engineering. 28:144-151.
