Location: Sustainable Agricultural Systems Laboratory
2024 Annual Report
Objectives
Objective 1: Determine the dispersal and activity patterns of fungi, bacteria and archaea with depth and across environmental gradients in agricultural systems and determine their impacts and influence on soil organic matter sequestration to inform better soil health management decisions.
Objective 2: Develop a quantitative understanding of the impact of crop Genetics x Environmental context x Management strategies (G x E x M) on crop productivity as influenced by enhanced biological nitrogen fixation (BNF) and a fuller understanding of the soil and plant - microbiome symbiosis in leguminous cash and cover crop systems at local, long-term study sites and through LTAR collaborations.
Sub-objective 2A: Study LTAR sites where legumes are grown in rotation with commodity crops to determine the factors that control regulation and efficiency of BNF and the net contribution of BNF nitrogen (N) to agroecosystems. Evaluations of the BAU and ASP cropping systems will be conducted.
Sub-objective 2B: Establish fundamental understanding of BNF in the context of plant genotype by environment interactions in the commodity crop cowpea, Vigna unguiculata, and Soybean, Glycine max.
Sub-objective 2C: Develop a standardized protocol for portable and low entry cost DNA sequencing platforms to evaluate critical sources of variability and error in analyses of biological transformations of soil carbon(C) and N.
Objective 3: Assess thermal and anaerobic treatment processes of manure and in water resource recovery and treatment to reduce antibiotics in wastewater streams and develop effective approaches for treatment and monitoring materials of concern.
Sub-objective 3A: Measure antibiotic removal during anaerobic processing of dairy manure and biosolids with small and large-scale processing methods.
Sub-objective 3B: Develop protocols for anti-microbial gene detection in agricultural systems consistent with current recommendations from the EPA and One Health Initiative.
Objective 4: Improve the ability to track the loading of nitrate from agricultural sources by using time dated metabolites of metolachlor to address N management strategies and to improve environmental and water quality.
Sub-objective 4A: Redesign sampling and analysis protocols for metolachlor ethane sulfonic acid (MESA) to include metolachlor oxanilic acid (MOXA) for collection and analysis of stream water as a tool to track nitrate sources from groundwater.
Sub-objective 4B: Determine isomer composition of both MESA and MOXA in watershed networks in order to describe groundwater nitrate loading from agriculture sources.
Approach
A molecular ecological approach will be taken to bridge gaps in understanding of biogeochemical stocks and flows in agroecosystems. Using classic chemistry, metabolomics, molecular biology, and plant physiology for analysis of samples from different cropping systems at the Farming Systems Project site critical issues in soil carbon sequestration and soil enzyme activity, and plant-microbiome interactions in relation to nitrogen fixation in legumes will be addressed. The Farming System Project in Beltsville, MD is part of the LTAR network and is a platform for comparison of long-term impacts of five cropping systems (conventional chisel till, conventional no-till, and three organic crop production rotations) commonly used in the Mid-Atlantic region of the US and elsewhere. New techniques will be developed to investigate how to improve manure anaerobic digestion systems for increased degradation of antibiotics and other compounds of concern in animal production waste streams to minimize the effect of their release into the environment. This research will also leverage the development of novel, passive sampling devices that detect breakdown products of the pesticide metolachlor as a surrogate for nitrate release from crop production fields. This improved technique will allow quantification of conservation practices directed towards reduction of agricultural waste in the nation’s water resources. In considering the connectivity and entirety and outcomes of the efforts of this project, this project will develop best management practices that improve water resources and soil quality in the Mid-Atlantic region helping to improve the sustainability of small, mid-sized, and large farms.
Progress Report
In support of Objective 1 research continued on the dispersal and activity patterns of fungi, bacteria and archaea across environmental gradients in the Long Term Agricultural Research (LTAR) network legacy site the Farming Systems Project. Two manuscripts describe the overarching influence of soil depth in controlling the dispersal of fungi, bacteria and archaea. These results begin to define the boundaries of influence that farming systems management has on soil organic matter sequestration and may better inform models describing management decisions’ impacts on soil biogeochemistry. Leveraging the initial work carried out under Objective 1, a collaboration was initiated with Pacific Northwest National Laboratory with the award of a Molecular Observation Network (MONet) grant. The proposal leverages the ARS Farming Systems Project to answer questions on agricultural management’s influence on soil chemical, physical, and biological processes with depth and across cropping systems. Researchers collected soils from five treatments and the forest control site, which were sent to collaborators to perform a suite of cutting-edge techniques, including carbon speciation, soil pore distribution, and microbiome characterization. These soils are part of a larger multi-area project focused on analyzing the distribution of carbon in various mineral pools in soils from ARS sites across the country via the Soil Biology Network. Researchers used a series of chemical extractions to determine how carbon in the mineral-associated pools, which are the most stable in soils, varies with management across ecotypes in the United States. These projects will increase our understanding of how farm management decisions impact soil carbon reserves for soil health and carbon sequestration and will help determine targeted practices to boost long-term stable carbon in agricultural and other managed soils.
In support of Objective 2, researchers successfully used the trait of biological nitrogen fixation as a marker for determining the non-target impacts of the herbicide glyphosate on functional differences in nitrogen fixation within the diverse cropping systems of the Farming Systems Project. The results from this study resulted in the development of a new software tool, the open-source R package QSeq. The QSeq package transforms raw Deoxyribonucleic acid (DNA) sequence count data into relative abundance then scales the sequence counts using independent user-provided total abundance data of specific functional genes of interest. The test case used the nitrogen fixation nifH gene data from the Farming Systems Project study. Output from this analysis then uses public, cloud based metagenomic repositories to create weighted microbial population densities normalized for environmental conditions with user options to create probabilistic estimations of microbial community function. The multidisciplinary experiment addressing Objective 3 was conducted in collaboration with University of Maryland colleagues and successfully mentored a graduate student through to a successful PhD in January, 2023. The project successfully assessed thermal and anaerobic treatment processing of manure in water to reduce antibiotics in wastewater streams and develop effective approaches for treatment and monitoring materials of concern. A method in use is thermal hydrolysis pretreatment (THP) followed by anaerobic digestion. Lab scale studies of thermally treated and non-treated solids were subjected to lab-scale anaerobic digestion at 37 degrees Celsius for 22 days. Five compounds (two antimicrobials and three phthalic acid esters) and their metabolites were monitored along with the microbial community structures. Varying results were found for compound interactions with and without pretreatment. During digestion, the antimicrobials, triclosan (TCS) and triclocarban (TCC), both increased without pre-treatment and TCS increased with THP while TCC did not increase with pre-treatment, which was destroyed by thermal hydrolysis. Metabolites of both TCS and TCC increased with and without treatment. Researchers made significant progress to improve the ability to track the loading of nitrate from agricultural sources under Objective 4. ARS scientists developed protocols for metolachlor ethane sulfonic acid (MESA) and metolachlor oxanilic acid (MOXA) analysis of stream water as a tool to track nitrate sources from groundwater. Under Sub-objective 4B, “Determine isomer composition of both MESA and MOXA in watershed networks in order to describe groundwater nitrate loading from agriculture sources” researchers found that the two major soil derived metabolites of the herbicide, metolachlor, MESA and MOXA can change shape based on the soil type they flow through. Researchers measured these specific pollutants' isomers in 15 sub-watersheds forming the Upper Choptank Watershed. Sub-watersheds with more wetland soils have a significant difference in the metabolites' shapes compared to well-drained and drier soils. The shift in chemical configuration involved the planar isomers and not the chiral centers. This study is the first time that scientists reported pollutant isomer shape changes related to soil on a landscape scale and it is a new tool for environmental monitoring. These results impact policymakers, farmers, and scientists, who must understand the chemical shape to know how it will behave in environmental and agricultural systems.
Accomplishments
1. The new QSeq tool allows researchers to compare soil microbial data from multiple locations. Soil microbial communities are critical to the functioning of agricultural systems, mediating many processes including nutrient cycling, the production of greenhouse gases, and regulating soil carbon and nitrogen stocks. However, the diversity of methods used to characterize soil microbial community structure and functions can make comparison among studies difficult. ARS researchers in Beltsville, Maryland, developed the open source bioinformatic tool Qseq (quantitative sequencing) that allows researchers to compare soil microbial metagenomic data produced independently by different labs or at independent locations. Since the tool compares estimates to constantly expanding, public, cloud-based data, the results can be constantly improved. This tool will be of interest to soil microbiology researchers in general and to those working with NRCS and other agencies interested in climate smart agriculture.
Review Publications
Fischel, M.H., Clarke, C., Sparks, D.L. 2023. Arsenic sorption and oxidation by natural manganese-oxide-enriched soils: Reaction kinetics respond to varying environmental conditions. Geoderma. 411 Article e116715. https://doi.org/10.1016/j.geoderma.2023.116715.
Barreto, M., Wani, R., Goranov, A., Coward, E., Sowers, T., Fischel, M.H., Douglas, T., Hatcher, P., Sparks, D. 2024. Carbon fate, iron dissolution, and molecular characterization of dissolved organic matter in Yedoma permafrost thaw under varying redox conditions. Environmental Science and Technology. https://doi.org/10.1021/acs.est.3c08219.
Gu, C., Joshi, S., Fischel, M.H., Tomaszewski, E., Donald, S. 2024. Saltwater intrusion increases phosphorus abundance and alters availability in coastal soils with implications for future sea level rise. Science of the Total Environment. 931: Article e172624. https://doi.org/10.1016/j.scitotenv.2024.172624.
Izaditame, F., Lemonte, J., Seibecker, M., Yu, X., Fischel, M.H., Tappero, R., Sparks, D. 2024. Sea-level rise and Arsenic-rich soils: A toxic relationship. Journal of Hazardous Materials. 472: Article e134528. https://doi.org/10.1016/j.jhazmat.2024.134528.
Sricharoenvech, P., Siebecker, M., Tappero, R., Landrot, G., Fischel, M.H., Sparks, D.L. 2023. Chromium speciation and mobility in contaminated coastal urban soils affected by water salinity and redox conditions. Journal of Hazardous Materials. https://doi.org/10.1016/j.jhazmat.2023.132661.