Progress 10/01/23 to 09/30/24
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. 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. Artificial Intelligence (AI)/Machine Learning (ML) Artificial Intelligence (AI) and Machine Learning (ML) software (such as Alpha-fold) has been implemented on the high-performance computing clusters CEReS and ATLAS to accelerate the information discovery rate for ARS researchers. ARS scientists working on this project participated in the artificial intelligence training module offered by SciNet that enabled scientists to begin using machine learning models on ATLAS. This has led to the development of an interagency AI user forum to be sponsored by the national program staff planned to take place at two locations (Washington, D.C., and Denver, Colorado) in December 2024. Members of this project have begun collaborating with a colleague from the University of Maryland Computer Science Department, focusing on using long term agricultural yield, soil chemistry, and weather data to predict changes in indicators of sustainable agriculture. The cultivation of these concepts has resulted in two submissions to the ARS headquarters post doc competition. One scientist on this project has been asked to become an advisor to the ARS polyfluoroalkyl (PFAS) enterprise work group, which is focused on understanding the impact and remediation potential of PFAS in agricultural systems. This scientist is advising national program staff on using machine learning and artificial intelligence for PFAS remediation in soils and irrigation water. ACCOMPLISHMENTS 01 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.
Impacts
(N/A)
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.
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Progress 10/01/22 to 09/30/23
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. This report covers year two of this project. All 24-month milestones were met, and nine publications submitted. The recently hired project scientist was integrated into daily research activities as well as project stakeholder and collaborator groups. The new scientist completed a hiring search for a Physical Science Technician. The successful candidate has advanced experience in geochemical and agricultural systems, enhancing research capabilities. Project scientists served on the SciNet Scientific Advisory Committee and lead the Long-Term Agroecosystem Research (LTAR) Soils Working Group. The Soils Working Group created a common language data inventory of soils data from all LTAR sites and developed a web-based tool that enables users to harmonize datasets. This web-based tool is paired with a protocols and attributes tool that collects meta-data on protocols and procedures. Both tools will be utilized for the LTAR common experiment. Project scientists also provided leadership for the nationwide Soil Biology Network (SBGx). A project scientist served as scientific advisor to the NPS Microbiome Working Group and author on two budget initiatives submitted to REE. One initiative outlined an Agency microbiome research road map. The other initiative was in response to Executive Order 14081, Advancing Biotechnology and Biomanufacturing Innovation for Sustainable, Safe and Secure American Bioeconomy. For Objective 1, project scientists completed analysis of soil microbial and biochemical indicators of nitrogen fixation. Primers were designed to target genes contained within the nifH operon which is responsible for biological nitrogen fixation. In collaboration with the University of Maryland, relationships among common phylogenetic marker genes (16S and ITS rRNA) and specific functional genes involved in soil nitrogen and carbon cycling (nifH, nosZ, nirK, lacZ, lcc1) were explored. Predictable relationships among these genes were shown that differed with cropping system and the presence of the herbicide glyphosate. These relationships will be used to predict more accurately the impact of cropping systems on microbial soil nitrogen and carbon cycling. For Objective 2, improvement of protocols for cross-site comparison of soil biological attributes continued. Soils collected from Jornada, New Mexico, Pendleton, Oregon, Ft. Collins, Colorado, Columbus, Ohio, Ithaca, New York, and Beltsville, Maryland. were extracted and assessed for DNA quality and quantity using common protocols. These soils represent the regional diversity of LTAR Network agroecosystems. High-throughput, multiplexed-amplicon sequencing pipelines were developed to compare microbiomes based on relative abundance of assigned sequence variants (ASVs). This was achieved via creation of the app, Qseq, that performs statistical analysis and synthesis of multiplexed-amplicon-sequencing raw data and outputs formatted data for use in complementary downstream algorithms. This freely available app and other Scinet-based bioinformatic tools were used to complete two studies within the Farming System Project (FSP) LTAR site. One study showed that the herbicide Glyphosate does not impact the microbial community structure at plot scale but may impact some microbial functions, such as nitrogen fixation, under some conditions. The second study demonstrated that 26 years of farming systems management resulted in differences in microbial community structure and function corresponding to system scale differences at 0 to 15 cm soil depth. Below 15 cm depth soil type and physiochemical attributes were more predictive determinants of soil microbial community than farming system.The use of synchrotron µ-X-ray diffraction provided by the Brookhaven National Laboratory enabled project scientists to identify the distribution of minerals within manganese and iron hard concretions for the first time. These concretions are common in soils and accumulate substantial quantities of trace elements, including rare earth metals and plant nutrients, where they are removed from the bulk system. Furthermore, manganese is a powerful oxidizing agent in soils that can polymerize organic matter and alter contaminant and nutrient cycling. This study increased our understanding of natural forms of manganese and how it may impact critical geochemical cycles. For Sub-objective 3A, a new method to extract and quantitate antibiotics from various stages of processed and unprocessed manure was finalized. The resulting extract is subsequently cleaned and concentrated using solid phase extraction. The concentrated extract is then analyzed by use of this method has been validated for 10 antibiotics from four antibiotic classes. A manuscript detailing this method has been published. This new extraction method for antibiotics was applied to samples collected from a Bedding Recovery Unit (BRU) used to recover clean bedding from cow manure. Four manure types were sampled and extracted at sites along the BRU-processing line: unprocessed source material, a liquid fraction isolated by screw press separation, and the remaining solids from the screw press both before and after rotary drum heat treatment. Three antibiotics were detected in the manure samples: tetracycline, tulathromycin, and penicillin-G. Antibiotic concentrations ranged from 0.436 ⿿ 4.10 µg/kg. With animal-hospital farm manure containing incurred antibiotics, mass flow analysis of the sequential processing was determined by including corn kernels that followed the manure as it moved through this BRU device. Calculated mass flow rates indicated that 95% of the manure mass was fractioned with the separated liquid fraction. The remaining 5% of the manure mass was in the separated solid faction which contained 11% to 20% of tetracycline and tulathromycin antibiotics. No significant reduction of either antibiotic was found following BRU processing of the separated solids. Biochemical Methane Potential (BMP) testing was carried out at each BRU process sampling site to see if subsequent anerobic methane recovery caused destruction of antibiotics. Such methane recovery practices are popular on many dairy farms. Samples were spiked with oxytetracycline, ampicillin, and erythromycin and sampled and analyzed at five timed intervals up to 43 days. There was a significantly higher decrease in oxytetracycline with the heated versus the room-temperature incubations. Complete destruction of erythromycin and ampicillin occurred at room temperature and not under heated incubations. A lab-scale anaerobic digestion experiment was conducted to monitor antibiotic degradation within dairy manure based on temperature. Three antibiotics (oxytetracycline, erythromycin and ampicillin) were spiked into manure and monitored throughout a 43-day digestion under mesophilic (35°C) and thermophilic (55°C) conditions. Ampicillin was almost completely removed under both mesophilic and thermophilic conditions, while erythromycin was completely degraded (100%) under mesophilic conditions by day 36 and oxytetracycline had greater degradation under thermophilic conditions. Both conditions achieved > 30% degradation across all antibiotics throughout the digestion period. For Sub-objective 3B, there was a significant reduction in viable antibiotic-resistant bacteria in solids recovered from BRU- processed bedding material and complete elimination of pathogens. Solid, liquid separation prior to BRU heat processing, however, resulted in most of the mass staying with the separated liquid located in a storage lagoon; this material continuing to be a risk when released to the environment. Both mesophilic and thermophilic anaerobic treatment (BMP) of the final BRU solids were effective at eliminating spiked fecal indicator species (Enterococci and E. coli) by Day 9. Gene sequencing of the 16S ribosomal RNA gene is under way for comparative analysis of bacterial community diversity following the 43-day digestion of the final bedding material. Quantitative PCR (qPCR) was used to determine the relative gene abundance of eight antibiotic resistance genes (ARGs) and the 16S gene in samples from BRU and anaerobic digestion experiments. Genes included macrolide (ermB), beta-lactam (bla-2), sulfonamides (sul-1), tetracycline (tetX, tetM, tetW, tetQ), mobile genetic element (intl1), and 16S DNA for measuring bacterial populations. BRU processing resulted in significant reductions (>95%) of intl1, sul1, tetQ, tetX, and tetM while tetW, ermB and bla2 were unaffected. Thermophilic conditions had significantly lower bacterial populations compared to mesophilic conditions and both conditions reduced ARGs with specific gene reduction being temperature and condition dependent. There was evidence for some ARG enrichment throughout digestion under both conditions. For Sub-objective 4A, trials comparing approved MESA (metolachlor ethane sulfonic acid) extraction methods for the extraction of MOXA (metolachlor oxanilic acid) were completed and a methods paper published. MESA and MOXA were investigated as markers for monitoring nitrogen loss from agricultural fields. MESA and MOXA are dominant soil degradation products of the herbicide metolachlor. For Sub-objective 4B, chemical separation of MESA and MOXA was improved to allow separation of the four significant trans-isomers of both MOXA and MESA. Samples from the Choptank River Watershed were analyzed to quantitate and compare the four isomers of MESA and MOXA over three years (2007 to 2009). Lag-time calculations showed that MOXA is less persistent than MESA as a dating marker for groundwater transport of nitrogen. At the isomer-specific level, variations of the isomer pairs were closely linked to hydrologic variations which will allow development of predictive models describing flow paths for nitrogen based on soil properties. A manuscript on these results has been published. ACCOMPLISHMENTS 01 Soil depth is a more significant determinate of soil microbial community than farming system below 15 cm. The soil microbial community is important in agriculture as it functions in transformation and storage of soil carbon and plant nutrients. Models of stocks and flows of carbon and availability of nutrients currently use outdated estimates of soil metabolic kinetics; these estimates do not consider how farming systems regulate and impact transformation of carbon and nutrients. USDA-ARS scientists in Beltsville, Maryland, extracted and analyzed DNA and RNA from fungal, bacterial, and archaeal communities in 1-meter-deep soil cores from three different farming systems at the 26-year-old Farming Systems Project in Beltsville, Maryland. Results showed differences in soil microbial community at 0 to 15 cm among the three different farming systems. Below 15 cm depth, soil type and physiochemical attributes were more predictable determinants of soil microbial community than farming system. Results from this study are important to scientists and will be used to improve models of soil carbon dynamics which are needed to improve soil carbon sequestration and plant nutrient availability assessments. 02 Glyphosate application does not significantly alter microbial community structure but can impact certain traits. The impacts of the herbicide glyphosate on the plant and soil microbial community structure are unclear and there are concerns regarding non-target ecosystem effects. A variety of farming systems styles using Round-up Ready® corn and soybean at three USDA-ARS locations nationally were analyzed for microbial community structure and function to resolve these issues. Glyphosate impacted nitrogen fixing metabolism, resulting in increased biological nitrogen fixation in some cropping systems and decreased nitrogen fixation in others. This indicates that herbicides can have non-target impacts on the soil microbial community involved important agroecological functions such as nitrogen fixation. Other findings, reported in a series of seven papers, were that in modern corn and soybean farming operations use of glyphosate does not significantly change crop metabolic profiles or populations of pathogenic and endophytic fungi associated with the crop.
Impacts
(N/A)
Publications
- Fischel, M.H., Clarke, C.E., Sparks, D.L. 2023. Synchrotron resolved microscale and bulk mineralogy in manganese-rich soils and associated pedogenic concretions. Geoderma. 430: Article e116305. https://doi.org/10. 1016/j.geoderma.2022.116305.
- Porell, M., Cushman, M., Fischel, J.S., Fischel, M.H., Sparks, D.L., Grayburn, R. 2023. Scanning x-ray fluorescence spectroscopy and micro-x- ray absorption near-edge structure analysis as a guiding tool for the conservation treatment of two eighteenth-century Philadelphian portraits. X-Ray Spectrometry. Article e3345. https://doi.org/10.1002/xrs.3345.
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Progress 10/01/21 to 09/30/22
Outputs
PROGRESS REPORT Objectives (from AD-416): 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 (from AD-416): 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. This Annual Report covers the first year of this project. A new Sustainable Agricultural Systems Laboratory (SASL) scientist hired to work on this NP212 project completed onboarding, new scientist orientation, and required training. The soil chemistry skillset of the new scientist will add significant breadth to the research capability of the SASL NP212 Team. The addition of soil chemistry expertise and synchrotron X-ray techniques enables analysis of the atomic composition of soils from a novel perspective. Integrating this skillset will increase the impact and utility of future research. Collaboration has been established among ARS laboratories in Ft. Collins, Colorado; Pendleton, Oregon; and Lubbock, Texas, that has resulted in multiple, multi-area projects established in support of research initiated under Objectives 1 and 2. Supporting cross-National Program initiatives, SASL scientists have served on the SciNet Scientific Advisory Committee and as liaison to a new NPS ARS Microbiome working group. Additionally, scientists on this project continue to lead the Long- Term Agroecosystem Research (LTAR) Soils Working Group which has created a common language data inventory of soils data from all LTAR sites and developed a web-based tool that enables users to harmonize datasets among sites. This web-based tool is paired with a protocols and attributes tool that collects meta-data on protocols and procedures. Both tools are currently available on-line to the LTAR community and will be utilized in the LTAR cropping systems common experiment being implemented this fall. Two SASL NP212 scientists provided leadership for the nationwide Soil Biology Network (SBGx). SBGx works with the LTAR Network to facilitate implementation of a unified set of standardized techniques and protocols across all LTAR Network sites. For Objective 1, SASL scientists began analysis of soil microbial and biochemical indicators of nitrogen fixation. Specifically, primers were designed to target genes contained within the nifH operon (gene cluster) which is responsible for microbial biological nitrogen fixation. In collaboration with the University of Maryland, SASL scientists conducted analyses of relationships among common phylogenetic marker genes such as 16S and ITS rRNA as well as more specific functional genes involved in nitrogen and carbon cycling (nifH, nosZ, nirK, lacZ, lcc1). Predictable relationships among these marker genes were shown that differed with cropping system and the presence of the herbicide glyphosate. These relationships, now validated, will be used to more accurately predict the impact of cropping systems on functional microbial activities in soil, such as soil nitrogen and carbon cycling. For Objective 2, improvement of protocols for cross-site comparison of soil biological attributes continued. DNA and RNA were extracted from contrasting soil types representing the regional diversity of the agroecosystem in the LTAR Network. Soils collected from Jornada, New Mexico; Pendleton, Oregon; Ft. Collins, Colorado; Columbus, Ohio; Ithaca, New York; and Beltsville, Maryland, were extracted and assessed for DNA quality and quantity using common protocols. For Sub-objective 3A, a new method to extract and quantitate antibiotics from various stages of processed and unprocessed manure was finalized. The method consists of two-steps involving ultrasonic and mechanical mixing with two separate solvent extractions, an aqueous EDTA-McIlvaine buffer solution followed by methanol. The resulting extract is subsequently cleaned using solid phase extraction. The final concentrate is then subjected to LC-MS/MS analysis. To date, this method has been validated for analysis of 10 antibiotics covering 4-antibiotic classes. Performance of the method achieved beta-lactam recoveries between 5% and 74%, tetracycline recoveries between 54% and 108%, sulfadimethoxine recovery of 49%, and macrolide recoveries between 50% and 97%. A manuscript detailing this method has been submitted for publication. This extraction method was applied to samples collected from a Bedding Recovery Unit (BRU) operating on a farm in upstate New York to measure antibiotic destruction after thermal treatment to recover clean bedding from cow manure. Antibiotics were measured as the manure moved through a rotary drum BRU system. Four manure types were sampled and extracted at sites along the processing line: unprocessed source material, a liquid fraction isolated by screw press separation, and the remaining solids from the screw press both before and after rotary drum heat treating to isolate clean bedding material. Three antibiotics were detected in the manure samples: tetracycline, tulathromycin, and penicillin-G. Antibiotic concentrations ranged from 0.436 � 4.10 �g/kg. With hospital farm manure containing incurred antibiotics, mass flow analysis of the sequential processing was determined by including corn kernels that followed the manure as it moved through this BRU device. Calculated mass flow rates indicated that 95% of the manure mass was fractioned with the separated liquid fraction. The remaining 5% of the manure mass was in the separated solid faction which contained 11% to 20% of tetracycline and tulathromycin antibiotics. No significant reduction of either antibiotic was found following BRU processing of the separated solids. Biochemical Methane Potential (BMP) testing was carried out at each BRU process sampling site to see if subsequent anerobic methane recovery caused destruction of antibiotics. Such methane recovery practices are popular on many dairy farms. These tests were carried out using replicated lab- scale reaction flasks containing measured samples of the manure. Samples were spiked with oxytetracycline, ampicillin, and erythromycin and sampled and analyzed at five timed intervals up to 43 days. There was a significantly higher decrease in oxytetracycline with the heated versus the room-temperature incubations. Complete destruction of erythromycin and ampicillin occurred at room temperature and not under heated incubations. Anaerobic processing assists in removal of antibiotic from contaminated manure. For Sub-objective 3B, there was significant reduction in viable antibiotic-resistant bacteria in solids recovered from bedding material processed with the BRU. There was also complete elimination of pathogens from this material. Therefore, the BRU heating process successfully eliminated pathogenic and antibiotic-resistant bacteria in bedding material. Solid, liquid separation prior to heat processing, however, resulted in most of the mass staying with the separated liquid which accumulated in a storage lagoon. Therefore, this material continues to be at risk for release to the environment. Both mesophilic and thermophilic anaerobic treatment (BMP) of the final BRU solids were effective at eliminating spiked fecal indicator species (Enterococci and E. coli) by Day 9. Gene sequencing of the 16S ribosomal RNA gene is under way for comparative analysis of bacterial community diversity following the 43- day digestion of the final bedding material. For Sub-objective 4A, trials comparing approved MESA (metolachlor ethane sulfonic acid) extraction methods for the extraction of MOXA (metolachlor oxanilic acid) were completed and a methods paper is in preparation for submission this year. MESA and MOXA are being investigated as markers for monitoring nitrogen loss from agricultural fields. These two compounds are dominant soil degradation products of the chiral herbicide metolachlor. For Sub-objective 4B, chemical separation of MESA and MOXA was improved. All 4 significant trans-isomers of both MOXA and MESA were separated. Unfortunately, attempts to reliably measure the 4 isomers in a single injection has not yet been achieved. Lacking one injection for both MESA and MOXA, two injections (~822 sample runs) were performed on 15 sub- watershed samples from the Choptank River Watershed. The goal was to quantitate and compare all 4 isomers of MESA and MOXA for three years of samples (2007 to 2009). Lag-time calculations showed that MOXA is less persistent than MESA as a dating marker for groundwater transport of nitrogen. At the isomer specific level, it was found that variations of the rotamer pairs for each of the S and R enantiomers were closely linked to hydrologic variations in the different sub-watersheds. With this knowledge, predictive models can be developed to assist in describing flow paths for nitrogen based on soil properties. Another important result from this last year is the significant reduction in grab sample collection sizes required for MESA and MOXA. The new method requires only 50 mL of sample compared to 1-L required for the prior method. The new method makes use of new technology where larger volume injections can be introduced onto LC columns. We have validated the method for 4-peak separation of the trans isomers of both MESA and MOXA. There are several advantages to using smaller sample collection sizes; ease of collections, shipping, and storage (freezing is possible). Plans are underway to collect increased quantities of these small volume samples over flood events to look for correlations of the MESA and MOXA isomers as a function of flow. ACCOMPLISHMENTS 01 Soil depth can be a more significant determinate of soil microbial community than farming system. The soil microbial community is important in agriculture as it is responsible for transformation and storage of a large proportion of soil carbon and nutrients. Models of stocks and flows of carbon and availability of nutrients to plants currently use outdated estimates of soil metabolic kinetics that do not take into consideration how land use decisions and farming systems regulate and impact transformation of carbon and nutrients. USDA-ARS scientists in Beltsville, Maryland, extracted and analyzed DNA and RNA from fungal, bacterial, and archaeal communities in 1-meter-deep soil cores from three different farming systems at the 26-year-old Farming Systems Project in Beltsville, Maryland. Results showed differences in soil microbial community at 0 to 15 cm among farming systems, for example Organic systems contained a higher density of arbuscular mycorrhizal fungi than conventional tilled and no-till farming systems. Below 15 cm depth soil type and physiochemical attributes were more predictable determinants of soil microbial community than farming system. Results from this study are important to scientists and will be used to improve models of soil carbon dynamics which are needed to improve soil carbon sequestration and plant nutrient availability assessments.
Impacts
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Publications
- Schmidt, D., Dlott, G., Cavigelli, M.A., Yarwood, S., Maul, J.E. 2022. Soil microbiomes in three farming systems more affected by depth than farming system. Applied Soil Ecology. 173:104396. https://doi.org/10.1016/ j.apsoil.2022.104396.
- Yan, J., Tang, Z., Fischel, M.H., Wang, P., Siebecker, M.G., Aarts, M.G., Sparks, D.L., Zhao, F. 2022. Variation in cadmium accumulation and speciation within the same population of the hyperaccumulator Noccaea caerulescens grown in a moderately contaminated soil. Plant and Soil. https://doi.org/10.1007/s11104-022-05373-w.
- Kaushik, A., Roberts, D.P., Ramaprasad, A., Mfarrej, S., Nair, M., Lakshman, D.K., Pain, A. 2022. The pangenome analysis of the soil-borne fungal phytopathogen Rhizoctonia solani and development of a comprehensive web resource: RsolaniDB. Frontiers in Microbiology. https://doi.org/10. 3389/fmicb.2022.839524.
- Nimis, V., Rattner, B., Lockhart, M.J., Hulse, C.S., Rice, C., Kuncir, F., Kritz, K. 2022. Toxicological responses to sublethal anticoagulant rodenticide exposure in free-flying hawks. Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-022-20881-z.
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