The LTAR Integrated Common Experiment at Upper Mississippi River Basin-Platteville.

Alternative agronomic practices are needed to address the various climatic, agronomic, edaphic, and water quality related challenges faced by the dairy farmers of the Driftless Area (DA) in the Upper Mississippi River Basin (UMRB). These practices should be innovative in nature, inclusive of regional stakeholders, and sustainable to meet the future food and climate related challenges of Wisconsin agriculture. Here, we outline our Integrated (grazing and cropland) Long-Term Agroecosystem Research Common Experiment at the University of Wisconsin-Platteville Pioneer Farm (UW-P PF) in the UMRB and describe our collaboration in this USDA network. In this field-scale experiment, we are comparing the conventional dairy production system common to this region (i.e., corn-on-corn [Zea mays L.] for 4 years, followed by alfalfa [Medicago sativa L.] for 3 years, with no cover crops) with two alternative dairy production systems-(1) soil health management with no-till, cover crops, and application of a novel manure-based nutrient-rich stable product, and (2) management intensive grazing-and rotational grazing on pastures established with diverse forage-legume mix. Meteorological, edaphic, hydrologic, and agronomic data are collected and analyzed at regular frequencies. Going forward, the experiment will continue as a form of stakeholder-driven adaptive research and receive evaluation on a regular basis to determine whether any changes are required to address the "real-world" challenges faced by the farmers in the Midwest.

Hydrologic Connectivity Regulates Riverine N2O Sources and Dynamics.

Indirect nitrous oxide (N2O) emissions from streams and rivers are a poorly constrained term in the global N2O budget. Current models of riverine N2O emissions place a strong focus on denitrification in groundwater and riverine environments as a dominant source of riverine N2O, but do not explicitly consider direct N2O input from terrestrial ecosystems. Here, we combine N2O isotope measurements and spatial stream network modeling to show that terrestrial-aquatic interactions, driven by changing hydrologic connectivity, control the sources and dynamics of riverine N2O in a mesoscale river network within the U.S. Corn Belt. We find that N2O produced from nitrification constituted a substantial fraction (i.e., >30%) of riverine N2O across the entire river network. The delivery of soil-produced N2O to streams was identified as a key mechanism for the high nitrification contribution and potentially accounted for more than 40% of the total riverine emission. This revealed large terrestrial N2O input implies an important climate-N2O feedback mechanism that may enhance riverine N2O emissions under a wetter and warmer climate. Inadequate representation of hydrologic connectivity in observations and modeling of riverine N2O emissions may result in significant underestimations.

Proanthocyanidin biosynthesis in the developing wheat seed coat investigated by chemical and RNA-Seq analysis.

The composition of proanthocyanidins in the testa (seed coat) of bread wheat was analyzed by thiolysis of PA oligomers from developing grain and found to consist of (+)-catechin monomers, with a small amount of (+)-gallocatechin. The average chain length of soluble PA stayed relatively constant between 10 and 20 days post-anthesis, whereas that of unextractable PA increased over the same period, suggesting that increases in chain length might account for the insolubility of PAs from mature wheat grain. We carried out RNA-Seq followed by differential expression analysis from dissected tissues of developing grain from red- and white-grained near-isogenic lines differing in the presence of an active R gene that encodes a MYB transcription factor involved in control of PA biosynthesis. In addition to genes already identified encoding chalcone synthase, chalcone isomerase, flavanone 3-hydroxylase, and dihydroxyflavonoid 4-reductase, we showed that wheat genes encoding phenylalanine ammonia lyase, flavonoid 3',5'-hydroxylase, leucoanthocyanidin reductase, and a glutathione S-transferase (the orthologue of maize Bronze-2) were more highly expressed in the red NIL. We also identified candidate orthologues of other catalytic and regulatory components of flavonoid biosynthesis in wheat.

Envisioning the manureshed: Toward comprehensive integration of modern crop and animal production.

The specialization and intensification of agriculture have produced incredible gains in productivity, quality, and availability of agricultural commodities but have resulted in the separation of crop and animal production. A by-product of this separation has been the accumulation of manure regions where animal production is concentrated. Enter the "manureshed," an organizing framework for integrating animal and crop production where budgeting of manure nutrients is used to strategically guide their recycling and reuse in agricultural production systems where manure resources are of highest value. To move beyond regional nutrient balance analyses into the transformational realm required to mitigate "wicked" manure problems, manureshed management requires recognition of the challenges to systematically reorganizing resource flows. In better integrating crop and livestock systems, manureshed management must account for the unique nature of managing manure nutrients within individual livestock industries, anticipate trade-offs in substituting manure for commercial fertilizer, promote technologies to refine manure, and engage extensive social networks across scales that range from the farmgate to nation and beyond.

Manuresheds offer a system-level strategy for recovering manure's fertilizer value. Manuresheds address nutrient imbalances and environmental and socioeconomic outcomes. Manuresheds scale from single operations to a "mega-manureshed" transecting the southeastern United States. Manureshed management supports the strategic alignment of technologies, markets, and networks.

Response of nitrous oxide emissions to individual rain events and future changes in precipitation.

Changing precipitation has the potential to alter nitrous oxide (N2 O) emissions from agricultural regions. In this study, we applied the Coupled Model Intercomparison Project Phase 5 end-of-century RCP 8.5 (business as usual) precipitation projections for the U.S. Upper Midwest and examined the effects of mean precipitation changes, characterized by increased early-season rainfall and decreased mid- to late-season rainfall, on N2 O emissions from a conventionally managed corn (Zea mays L.) cropping system grown in an indoor mesocosm facility over four growing seasons. We also assessed the response of N2 O emissions to over 1,000 individual rain events. Nitrous oxide emissions were most strongly correlated with water-filled pore space (WFPS) and soil nitrogen (N) status. After rain events, the change in N2 O emissions, relative to pre-rain emissions, was more likely to be positive when soil NO3 - was >40 mg N kg-1 soil and soil NH4 + was >10 mg N kg-1 soil and was more likely to be negative when soil NO3 - was >40 mg N kg-1 soil and soil NH4 + was <10 mg N kg-1 soil. Similarly, hourly N2 O emissions remained <5 nmol m- 2 s-1 when combined NH4 + + NO3 - was <20 mg N kg-1 soil or NH4 + and NO3 - were <5 and 20 mg N kg-1 soil, respectively. Rain event magnitude did not substantially affect the change in N2 O flux. Finally, growing-season N2 O emissions, soil moisture, and inorganic N content were not affected by the future precipitation pattern. Near-optimal soil WFPS combined with soil N concentrations above the identified thresholds favor higher N2 O emissions.

Challenges and opportunities for manureshed management across U.S. dairy systems: Case studies from four regions.

The manureshed represents cropland needed to safely assimilate manure nutrients from an animal feeding operation. Dairy manuresheds can be contained on-farm but may need to involve additional farms that can assimilate excess nutrients. We present case studies reviewing challenges and opportunities to manureshed management in four major dairy-producing states using available information on local manuresheds. Additionally, geographic information system software was used with data from regulated Minnesota dairies to assess cropland assimilative capacities and transport needs surrounding large dairies. Manureshed requirements vary across regions, but increased import of feed and soil phosphorus accumulation constrain on-farm manure utilization across the United States. In Minnesota, a growing proportion of Jersey cattle and differences in continuous corn (Zea mays L.) vs. corn-alfafa (Medicago sativa L.) rotations contribute to the amount of land needed to absorb dairy manure nutrients. Farm-gate budgets reveal that N-based manuresheds can be contained within Idaho dairies, but P-based manuresheds extend beyond the farm. In New Mexico, relocation of surplus manure nutrients off the farm is common via informal networks, but incentives to strengthen these networks could ensure sustainable manureshed management. Evaluation of manureshed requirements in Pennsylvania is often complicated by the need for additional nutrient management planning and greater understanding of nutrient balances on the preponderance of small dairies. Nutrient imbalances with highly concentrated dairy production often lead to the need for manure transport off-farm. However, advances in herd and cropland management offer opportunities to improve on-farm nutrient efficiencies, and emerging networks and technologies promise to facilitate manure export when needed.

Biases in open-path carbon dioxide flux measurements: Roles of instrument surface heat exchange and analyzer temperature sensitivity.

Eddy covariance (EC) measurements of ecosystem-atmosphere carbon dioxide (CO2) exchange provide the most direct assessment of the terrestrial carbon cycle. Measurement biases for open-path (OP) CO2 concentration and flux measurements have been reported for over 30 years, but their origin and appropriate correction approach remain unresolved. Here, we quantify the impacts of OP biases on carbon and radiative forcing budgets for a sub-boreal wetland. Comparison with a reference closed-path (CP) system indicates that a systematic OP flux bias (0.54 µmol m-2 s-1) persists for all seasons leading to a 110% overestimate of the ecosystem CO2 sink (cumulative error of 78 gC m-2). Two potential OP bias sources are considered: Sensor-path heat exchange (SPHE) and analyzer temperature sensitivity. We examined potential OP correction approaches including: i) Fast temperature measurements within the measurement path and sensor surfaces; ii) Previously published parameterizations; and iii) Optimization algorithms. The measurements revealed year-round average temperature and heat flux gradients of 2.9 °C and 16 W m-2 between the bottom sensor surfaces and atmosphere, indicating SPHE-induced OP bias. However, measured SPHE correlated poorly with the observed differences between OP and CP CO2 fluxes. While previously proposed nominally universal corrections for SPHE reduced the cumulative OP bias, they led to either systematic under-correction (by 38.1 gC m-2) or to systematic over-correction (by 17-37 gC m-2). The resulting budget errors exceeded CP random uncertainty and change the sign of the overall carbon and radiative forcing budgets. Analysis of OP calibration residuals as a function of temperature revealed a sensitivity of 5 µmol m-3 K-1. This temperature sensitivity causes CO2 calibration errors proportional to sample air fluctuations that can offset the observed growing season flux bias by 50%. Consequently, we call for a new OP correction framework that characterizes SPHE- and temperature-induced CO2 measurement errors.

Top-Down Constraints on Methane Point Source Emissions From Animal Agriculture and Waste Based on New Airborne Measurements in the U.S. Upper Midwest.

Agriculture and waste are thought to account for half or more of the U.S. anthropogenic methane source. However, current bottom-up inventories contain inherent uncertainties from extrapolating limited in situ measurements to larger scales. Here, we employ new airborne methane measurements over the U.S. Corn Belt and Upper Midwest, among the most intensive agricultural regions in the world, to quantify emissions from an array of key agriculture and waste point sources. Nine of the largest concentrated animal feeding operations in the region and two sugar processing plants were measured, with multiple revisits during summer (August 2017), winter (January 2018), and spring (May-June 2018). We compare the top-down fluxes with state-of-science bottom-up estimates informed by U.S. Environmental Protection Agency methodology and site-level animal population and management practices. Top-down point source emissions are consistent with bottom-up estimates for beef concentrated animal feeding operations but moderately lower for dairies (by 37% on average) and significantly lower for sugar plants (by 80% on average). Swine facility results are more variable. The assumed bottom-up seasonality for manure methane emissions is not apparent in the aircraft measurements, which may be due to on-site management factors that are difficult to capture accurately in national-scale inventories. If not properly accounted for, such seasonal disparities could lead to source misattribution in top-down assessments of methane fluxes.

Error characterization of methane fluxes and budgets derived from a long-term comparison of open- and closed-path eddy covariance systems.

Wetlands represent the dominant natural source of methane (CH4) to the atmosphere. Thus, substantial effort has been spent examining the CH4 budgets of global wetlands via continuous ecosystem-scale measurements using the eddy covariance (EC) technique. Robust error characterization for such measurements, however, remains a major challenge. Here, we quantify systematic, random and gap-filling errors and the resulting uncertainty in CH4 fluxes using a 3.5 year time series of simultaneous open- and closed path CH4 flux measurements over a sub-boreal wetland. After correcting for high- and low frequency flux attenuation, the magnitude of systematic frequency response errors were negligible relative to other uncertainties. Based on three different random flux error estimations, we found that errors of the CH4 flux measurement systems were smaller in magnitude than errors associated with the turbulent transport and flux footprint heterogeneity. Errors on individual half-hourly CH4 fluxes were typically 6%-41%, but not normally distributed (leptokurtic), and thus need to be appropriately characterized when fluxes are compared to chamber-derived or modeled CH4 fluxes. Integrated annual fluxes were only moderately sensitive to gap-filling, based on an evaluation of 4 different methods. Calculated budgets agreed on average to within 7% (≤ 1.5 g - CH4 m-2 yr-1). Marginal distribution sampling using open source code was among the best-performing of all the evaluated gap-filling approaches and it is therefore recommended given its transparency and reproducibility. Overall, estimates of annual CH4 emissions for both EC systems were in excellent agreement (within 0.6 g - CH4 m-2 yr-1) and averaged 18 g - CH4 m-2 yr-1. Total uncertainties on the annual fluxes were larger than the uncertainty of the flux measurement systems and estimated between 7-17%. Identifying trends and differences among sites or site years requires that the observed variability exceeds these uncertainties.

Source Partitioning of Methane Emissions and its Seasonality in the U.S. Midwest.

The methane (CH4) budget and its source partitioning are poorly constrained in the Midwestern United States. We used tall tower (185 m) aerodynamic flux measurements and atmospheric scale factor Bayesian inversions to constrain the monthly budget and to partition the total budget into natural (e.g., wetlands) and anthropogenic (e.g., livestock, waste, and natural gas) sources for the period June 2016 to September 2017. Aerodynamic flux observations indicated that the landscape was a CH4 source with a mean annual CH4 flux of +13.7 ± 0.34 nmol m-2 s-1 and was rarely a net sink. The scale factor Bayesian inversion analyses revealed a mean annual source of +12.3 ± 2.1 nmol m-2 s-1. Flux partitioning revealed that the anthropogenic source (7.8 ± 1.6 Tg CH4 yr-1) was 1.5 times greater than the bottom-up gridded United States Environmental Protection Agency inventory, in which livestock and oil/gas sources were underestimated by 1.8-fold and 1.3-fold, respectively. Wetland emissions (4.0 ± 1.2 Tg CH4 yr-1) were the second largest source, accounting for 34% of the total budget. The temporal variability of total CH4 emissions was dominated by wetlands with peak emissions occurring in August. In contrast, emissions from oil/gas and other anthropogenic sources showed relatively weak seasonality.

Nitrous oxide emissions are enhanced in a warmer and wetter world.

Nitrous oxide (N2O) has a global warming potential that is 300 times that of carbon dioxide on a 100-y timescale, and is of major importance for stratospheric ozone depletion. The climate sensitivity of N2O emissions is poorly known, which makes it difficult to project how changing fertilizer use and climate will impact radiative forcing and the ozone layer. Analysis of 6 y of hourly N2O mixing ratios from a very tall tower within the US Corn Belt-one of the most intensive agricultural regions of the world-combined with inverse modeling, shows large interannual variability in N2O emissions (316 Gg N2O-N⋅y-1 to 585 Gg N2O-N⋅y-1). This implies that the regional emission factor is highly sensitive to climate. In the warmest year and spring (2012) of the observational period, the emission factor was 7.5%, nearly double that of previous reports. Indirect emissions associated with runoff and leaching dominated the interannual variability of total emissions. Under current trends in climate and anthropogenic N use, we project a strong positive feedback to warmer and wetter conditions and unabated growth of regional N2O emissions that will exceed 600 Gg N2O-N⋅y-1, on average, by 2050. This increasing emission trend in the US Corn Belt may represent a harbinger of intensifying N2O emissions from other agricultural regions. Such feedbacks will pose a major challenge to the Paris Agreement, which requires large N2O emission mitigation efforts to achieve its goals.

Feasibility of Recycling Excess Agricultural Nitrate with Electrodialysis.

One of the most serious environmental problems associated with agriculture is excessive nitrate N in waters leaving fields. It is a health hazard in drinking water and a primary cause of hypoxia in ocean waters receiving drainage from agricultural regions. Recent mitigation efforts have focused on techniques that promote denitrification-conversion of excess agricultural nitrate to N. This seems inherently wasteful since industrial production of nitrate fertilizer from N requires a substantial input of energy and is a major source of greenhouse gas emissions. Thus, it is desirable to develop methods to recycle nitrate, keeping it in a form suitable for reuse as fertilizer. One possibility is electrodialysis, in which direct current is passed through alternating cation- and anion-permeable membranes, creating separate streams of dilute and concentrated water. We tested the concept under controlled conditions in a greenhouse and in a field setting on a contaminated trout stream with nitrate N concentrations consistently above 20 mg L. The solar-powered field system removed 42% of the nitrate from water passing through it and concentrated it in a tank for subsequent application as fertilizer. The upper limit of concentration was approximately 520 mg L, above which precipitation of calcite limited operation. Economic analysis indicates that in comparison to denitrification methods such as bioreactors, electrodialysis is likely to be more expensive per unit of nitrate removed. The approach will be most feasible for situations in which nitrate concentrations are well above environmental standards for extended periods, to maximize operating time and nitrate removal rate.

Impact of Kura Clover Living Mulch on Nitrous Oxide Emissions in a Corn-Soybean System.

Nitrous oxide (NO), produced primarily in agricultural soils, is a potent greenhouse gas and is the dominant ozone-depleting substance. Efforts to reduce NO emissions are underway, but mitigation results have been inconsistent. The leguminous perennial kura clover ( M. Bieb.) (KC) can grow side-by-side with cash crops in rotational corn ( L.)-soybean ( L.) systems. With biological nitrogen fixation, KC provides land managers an opportunity to reduce external fertilizer inputs, which may diminish problematic NO emissions. To investigate the effect of a KC living mulch on NO emissions, automated soil chambers coupled to a NO analyzer were used to measure hourly fluxes from April through October in a 2-yr corn-soybean (CS) rotation. Emissions from the KC treatment were significantly greater than those from the conventional CS treatment despite the fact that the KC treatment received substantially less inorganic nitrogen fertilizer. A seasonal tradeoff was observed with the KC treatment wherein emissions before strip-tillage were reduced but were surpassed by high losses after strip-tillage and postanthesis. These results represent the first reported measurements of NO emissions from a KC-based living mulch. The findings cast doubt on the efficacy of KC for mitigating NO loss in CS systems. However, if KC reduces nitrate leaching losses, as has been reported elsewhere, it may result in lower indirect (offsite) NO emissions.

Metabolite Profiling of Sugarcane Genotypes and Identification of Flavonoid Glycosides and Phenolic Acids.

Sugarcane is an important agricultural crop in the economy of tropical regions, and Brazil has the largest cultivated acreage in the world. Sugarcane accumulates high levels of sucrose in its stalks. Other compounds produced by sugarcane are currently not of economic importance. To explore potential coproducts, we have studied the chemical diversity of sugarcane genotypes, via metabolite profiling of leaves by NMR and LC-DAD-MS. Metabolites were identified via in-house and public databases. From the analysis of 60 HPLC-fractionated extracts, LC-DAD-MS detected 144 metabolites, of which 56 were identified (MS-MS and (1)H NMR), including 19 phenolics and 25 flavones, with a predominance of isomeric flavone C-glycosides. Multivariate analysis of the profiles from genotypes utilized in Brazilian breeding programs revealed clustering according to sugar, phenolic acid, and flavone contents.

Indirect nitrous oxide emissions from streams within the US Corn Belt scale with stream order.

N2O is an important greenhouse gas and the primary stratospheric ozone depleting substance. Its deleterious effects on the environment have prompted appeals to regulate emissions from agriculture, which represents the primary anthropogenic source in the global N2O budget. Successful implementation of mitigation strategies requires robust bottom-up inventories that are based on emission factors (EFs), simulation models, or a combination of the two. Top-down emission estimates, based on tall-tower and aircraft observations, indicate that bottom-up inventories severely underestimate regional and continental scale N2O emissions, implying that EFs may be biased low. Here, we measured N2O emissions from streams within the US Corn Belt using a chamber-based approach and analyzed the data as a function of Strahler stream order (S). N2O fluxes from headwater streams often exceeded 29 nmol N2O-N m(-2) ⋅ s(-1) and decreased exponentially as a function of S. This relation was used to scale up riverine emissions and to assess the differences between bottom-up and top-down emission inventories at the local to regional scale. We found that the Intergovernmental Panel on Climate Change (IPCC) indirect EF for rivers (EF5r) is underestimated up to ninefold in southern Minnesota, which translates to a total tier 1 agricultural underestimation of N2O emissions by 40%. We show that accounting for zero-order streams as potential N2O hotspots can more than double the agricultural budget. Applying the same analysis to the US Corn Belt demonstrates that the IPCC EF5r underestimation explains the large differences observed between top-down and bottom-up emission estimates.

Quantifying nitrous oxide fluxes on multiple spatial scales in the Upper Midwest, USA.

This study seeks to quantify the roles of soybean and corn plants and the cropland ecosystem in the regional N2O budget of the Upper Midwest, USA. The N2O flux was measured at three scales (plant, the soil-plant ecosystem, and region) using newly designed steady-state flow-through plant chambers, a flux-gradient micrometeorological tower, and continuous tall-tower observatories. Results indicate that the following. (1) N2O fluxes from unfertilized soybean (0.03 ± 0.05 nmol m(-2) s(-1)) and fertilized corn plants (-0.01 ± 0.04 nmol m(-2) s(-1)) were about one magnitude lower than N2O emissions from the soil-plant ecosystem (0.26 nmol m(-2) s(-1) for soybean and 0.95 nmol m(-2) s(-1) for corn), confirming that cropland N2O emissions were mainly from the soil. (2) Fertilization increased the corn plant flux for a short period (about 20 days), and late-season fertilization dramatically increased the soybean plant emissions. (3) The direct N2O emission from cropland accounted for less than 20 % of the regional flux, suggesting a significant influence by other sources and indirect emissions, in the regional N2O budget.

Global and time-resolved monitoring of crop photosynthesis with chlorophyll fluorescence.

Photosynthesis is the process by which plants harvest sunlight to produce sugars from carbon dioxide and water. It is the primary source of energy for all life on Earth; hence it is important to understand how this process responds to climate change and human impact. However, model-based estimates of gross primary production (GPP, output from photosynthesis) are highly uncertain, in particular over heavily managed agricultural areas. Recent advances in spectroscopy enable the space-based monitoring of sun-induced chlorophyll fluorescence (SIF) from terrestrial plants. Here we demonstrate that spaceborne SIF retrievals provide a direct measure of the GPP of cropland and grassland ecosystems. Such a strong link with crop photosynthesis is not evident for traditional remotely sensed vegetation indices, nor for more complex carbon cycle models. We use SIF observations to provide a global perspective on agricultural productivity. Our SIF-based crop GPP estimates are 50-75% higher than results from state-of-the-art carbon cycle models over, for example, the US Corn Belt and the Indo-Gangetic Plain, implying that current models severely underestimate the role of management. Our results indicate that SIF data can help us improve our global models for more accurate projections of agricultural productivity and climate impact on crop yields. Extension of our approach to other ecosystems, along with increased observational capabilities for SIF in the near future, holds the prospect of reducing uncertainties in the modeling of the current and future carbon cycle.

The influence of plants on atmospheric methane in an agriculture-dominated landscape.

The primary objective of this study was to clarify the influence of crop plants on atmospheric methane (CH4) in an agriculture-dominated landscape in the Upper Midwest of the United States. Measurements were carried out at two contrasting scales. At the plant scale, CH4 fluxes from soybean and corn plants were measured with a laser-based plant chamber system. At the landscape scale, the land surface flux was estimated with a modified Bowen ratio technique using measurements made on a tall tower. The chamber data revealed a diurnal pattern for the plant CH4 flux: it was positive (an emission rate of 0.4±0.1 nmol m(-2) s(-1), average of soybean and corn, in reference to the unit ground area) during the day, and negative (an uptake rate of -0.8±0.8 nmol m(-2) s(-1)) during the night. At the landscape scale, the flux was estimated to be 14.8 nmol m(-2) s(-1) at night and highly uncertain during the day, but the available references and the flux estimates from the equilibrium methods suggested that the CH4 flux during the entire observation period was similar to the estimated nighttime flux. Thus, soybean and corn plants have a negligible role in the landscape-scale CH4 budget.