Author: naturehydro

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Credible and prediction intervals in the shoot at harvest were similar for both models

However, Southern California, a region that suffers from a similar degree of water shortage, currently uses less than ~3% of municipal wastewater in agriculture, while discharging ~1.5 million acre-feet effluent per year into the Pacific Ocean . Secondary municipal wastewater effluent for ocean discharge is often sufficient to support both the nutrient and water needs for food production. Water reuse in agriculture can bring municipal water reclamation effluent to nearby farms within the city limit, thus promoting local agriculture and also reducing the rate of farmland loss to urban development. While the use of reclaimed water in agriculture offers a multitude of societal and agronomical benefits, broader adoption faces great challenges. One of the important challenges is ensuring the safety of food products in light of a plethora of human pathogens that may be present in recycled wastewater. Past studies have identified risks associated with irrigating food with recycled wastewater through the retention of the irrigation water on edible plant surfaces during overhead irrigation . With the emphasis on water conservation and reduction of evapotranspiration, subsurface drip irrigation is gaining popularity . Since there is lesser contact between water and the plant surface, the chance of surface contamination of pathogens is reduced. However, this new practice presents risk of uptake of microbial pathogens into plants. Such internalized pathogens are of greater concerns as washing, even with disinfectants, may not affect pathogens sheltered in the vasculature. Although pathogen transport through root uptake and subsequent internalization into the plant has been a growing research area, results vary due to differences in experimental design, systems tested, and pathogens and crops examined . Among the array of pathogens causing food borne illness that may be carried by treated wastewater, viruses are of the greatest concern but least studied. According to the CDC, 60% of U.S. food borne outbreaks associated with eating leafy greens were caused by noroviruses ,stacking pots while Salmonella and E. coli only accounted for 10% of the outbreaks . Estimates of global food borne illness prevalence associated with NoV surpass all other pathogens considered.

Viruses are also of concern because they persist in secondary wastewater effluents in high concentrations . They do not settle well in sedimentation basins and are also more resistant to degradation than bacteria . Therefore, in the absence of solid scientific understanding of the risks involved, the public are likely less receptive to adopting treated wastewater for agricultural irrigation. NoV internalization in hydroponic systems has been quantified by DiCaprio et al. . Internalization in crops grown in soil is considered lesser but nevertheless occurs. However, the only risk assessment that considered the possibility of NoV internalization in plants assumed a simple ratio of viruses in the feed water over viruses in produce at harvest to account for internalization. The time dependence of viral loads in lettuce was not explored and such an approach did not permit insights into the key factors influencing viral uptake in plants. In this study, we introduce a viral transport model to predict the viral load in crisp head lettuce at harvest given the viral load in the feed water. It is parameterized for both hydroponic and soil systems. We demonstrate its utility by performing a quantitative microbial risk assessment . Strategies to reduce risk enabled by such a model are explored, and a sensitivity analysis highlights possible factors affecting risk.The plant transpiration rate was adopted as the viral transport rate ) based on: 1) previous reports of passive bacterial transport in plants , 2) the significantly smaller size of viruses compared to bacteria, and 3) the lack of known specific interactions between human viruses and plant hosts . Accordingly, viral transport rate in hydroponically grown lettuce was determined from the previously reported transpiration model , in which the transpiration rate is proportional to the lettuce growth rate and is influenced by cultivar specific factors . These cultivar specific factors used in our model were predicted using the hydroponic crisp head lettuce growth experiment carried out by DiCaprio et al. described in Section 2.3 . Since the transpiration rate in soil grown lettuce is significantly higher than that in the hydroponic system, viral transport rate in soil grown lettuce was obtained directly from the graphs published by Gallardo et al. using WebPlotDigitizer . The shoot growth rate for soil grown lettuce was determined using Eq. 9 . In the absence of a published root growth model for lettuce in soil, a fixed root volume of 100 cm3 was used. In the viral transport model, viral transfer efficiency was used to account for the potential “barrier” between each compartment .

The existence of such a “barrier” is evident from field experiments where some microbial pathogens were internalized in the root but not in the shoot of plants . In addition, viral transfer efficiencies also account for differing observations in pathogen internalization due to the type of pathogen or lettuce. For example, DiCaprio et al. reported the internalization of NoV into lettuce, while Urbanucci et al. did not detect any NoV in another type of lettuce grown in feed water seeded with viruses. The values of ηgr and ηrs were determined by fitting the model to experimental data reported by DiCaprio et al. and is detailed in Section 2.3. The viral removal in the growth medium includes both die-off and AD, while only natural die-off was considered in the lettuce root and shoot. AD kinetic constants as well as the growth medium viral decay constant in the hydroponic case were obtained by fitting the model to the data from DiCaprio et al. . Viral AD in soil has been investigated in both lab scale soil columns and field studies . In our model, viral AD constants in soil were obtained from the experiments of Schijven et al. , who investigated MS2 phage kinetics in sandy soil in field experiments. As the MS2 phage was transported with the water in soil, the AD rates changed with the distance from the source of viruses. To capture the range of AD rates, two scenarios of viral behavior in soils were investigated. Scenario 1 used the AD rates estimated at the site closest to the viral source , while scenario 2 used data from the farthest site . In contrast to lab scale soil column studies, field studies provided more realistic viral removal rates . Using surrogate MS2 phage for NoV provided conservative risk estimates since MS2 attached to a lesser extent than NoV in several soil types . The viral decay rate in the soil determined by Roberts et al. was adopted because the experimental temperature and soil type are more relevant to lettuce growing conditions compared to the other decay study . Decay rates in the root and shoot were used from the hydroponic system predictions.The transport model was fitted to log10 viral concentration data from DiCaprio et al. , extracted from graphs therein using WebPlotDigitizer . In these experiments, NoV of a known concentration was spiked in the feed water of hydroponic lettuce and was monitored in the feed water, the root and shoot over time.

While fitting the model, an initial feed volume of 800 mL was adopted and parameters producing final volumes of b200 mL were rejected. To fit the model while accounting for uncertainty in the data, a Bayesian approach was used to maximize the likelihood of the data given the parameters. A posterior distribution of the parameters was obtained by the differential evolution Markov chain  algorithm,strawberry gutter system which can be parallelized and can handle multi-modality of the posteriors distribution without fine tuning the jumping distribution. Computation was carried out on MATLAB R2016a and its ParCompTool running on the High Performance Computing facility at UC Irvine.Table 3 lists the parameters estimated by model fitting and their search bounds. Fitting data from DiCaprio et al. without including viral AD to the tank walls was attempted but the results were not used in the risk estimates due to the poor fit of model to the data. The rationale behind the model fitting procedure and diagnostics are discussed in Supplementary section S1H.A summary of the model fitting exercise for viral transport in hydroponic grown lettuce is presented in Fig. 2. Under the assumption of first order viral decay, NoV loads in water at two time points did not fall in the credible region of model predictions, indicating that mere first order decay was unsuitable to capture the observed viral concentration data. The addition of the AD factor into the model addressed this inadequacy and importantly supported the curvature observed in the experimental data. This result indicates the AD of viruses to hydroponic tank wall is an important factor to include in predicting viral concentration in all three compartments .The adequacy of model fit was also revealed by the credible intervals of the predicted parameters for the model with AD . Four of the predicted parameters: at, bt, kdec, s and kp, were restricted to a smaller subset of the search bounds, indicating that they were identifiable. In contrast, the viral transfer efficiency η and the kinetic parameters spanned the entirety of their search space and were poorly identifiable. However, this does not suggest that each parameter can independently take any value in its range because the joint distributions of the parameters indicate how fixing one parameter influences the likelihood of another parameter . Hence, despite the large range of an individual parameter, the coordination between the parameters constrained the model predictions to produce reliable outcomes . Therefore, the performance of the model with AD was considered adequate for estimating parameters used for risk prediction.Risk estimates for lettuce grown in the hydroponic tank or soil are presented in Fig. 4. Across these systems, the FP model predicted the highest risk while the 1F1 model predicted the lowest risk. For a given risk model, higher risk was predicted in the hydroponic system than in the soil. This is a consequence of the very low detachment rates in soil compared to the attachment rates. Comparison of results from Sc1 and Sc2 of soil grown lettuce indicated lower risks and disease burdens under Sc1 . Comparing with the safety guidelines, the lowest risk predicted in the hydroponic system is higher than the U.S. EPA defined acceptable annual drinking water risk of 10−4 for each risk model. The annual burdens are also above the 10−6 benchmark recommended by the WHO . In the case of soil grown lettuce, neither Sc1 nor Sc2 met the U.S. EPA safety benchmark. Two risk models predicted borderline disease burden according to the WHO benchmark, for soil grown lettuce in Sc1, but under Sc2 the risk still did not meet the safety guideline. Neither increasing holding time of the lettuce to two days after harvesting nor using bigger tanks significantly altered the predicted risk . In comparison, the risk estimates of Sales-Ortells et al. are higher than range of soil grown lettuce outcomes presented here for 2 of 3 models. The SCSA sensitivity indices are presented in Fig. 5. For hydroponically grown lettuce, the top 3 factors influencing daily risk are amount of lettuce consumed, time since last irrigation and the term involving consumption and ρshoot. Also, the risk estimates are robust to the fitted parameters despite low identifiability of some model parameters . For soil grown lettuce, kp appears to be the major influential parameter, followed by the input viral concentration in irrigation water and the lettuce harvest time. Scorr is near zero, suggesting lesser influence of correlation in the input parameters.In this study, we modeled the internalization and transport of NoV from irrigation water to the lettuce using ordinary differential equations to capture the dynamic processes of viral transport in lettuce. This first attempt is aimed at underscoring the importance of the effect of time in determining the final risk outcome. The modeling approach from this study may be customized for other scenarios for the management of water reuse practices and for developing new guidelines for food safety. Moreover, this study identifies critical gaps in the current knowledge of pathogen transport in plants and calls for further lab and field studies to better understand risk of water reuse.

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Carbon captured in soil already exists and is merely captured rather than permanently destroyed

This proposed bill did not pass, but CARB is in the process of constructing a webpage that will provide information on proposed offset programs, and the agency affirmatively notes that it will be considering additional offset programs as a part of future rule making activities.Thus, an agricultural soil carbon sequestration offset program may not be far from being proposed and considered as a possible offset program under California’s cap and trade program.Ensuring that emission reductions are quantifiable, permanent, and additional are important considerations for any type of offset program but are particularly difficult in relation to agricultural soil carbon sequestration offset programs. Quantifiability and permanency are especially central concerns about offset programs, and it has been suggested that agricultural soil carbon sequestration plays such a minimal role in major carbon markets because soil carbon is considered difficult to measure, verify, and track.Deciding how to allocate offset credits can be challenging in any carbon sequestration program because it is difficult to accurately quantify how much carbon has really been sequestered.Soil carbon sequestration depends on a complicated living system that is constantly changing and not easy to directly quantify. A variety of factors determine how much carbon a unit of soil can sequester, including seasonal variations, weather, precipitation, plant species present, and the variation in soil type and quality.This problem does not arise in offset programs that decrease emissions from point sources, such as smokestacks or manure lagoons,rolling benches for greenhouse where measurement is more concentrated and accurate methods of measurement are established and verifiable. For example, a manure lagoon equipped with a BCS can use a meter to determine methane emissions from the entire lagoon. Adding to the complication of quantifiability, some studies dispute whether conservation tillage practices actually sequester carbon at all.

The goal of permanency is problematic in agricultural soil carbon sequestration programs because the carbon reduction is easily reversible.When carbon is sequestered in soil, it can be re-released into the atmosphere from a disturbance such as increased intensity of tilling, wind or water erosion, or a natural disaster such as an earthquake, fire, or disease outbreak.One agricultural soil carbon sequestration offset program incorporates a 60% discount into its program to account for the uncertainty of permanency.Compare this to destroying a unit of methane with a BCS or reducing a unit of carbon emissions from a smokestack by installing new technology. When that methane or carbon unit is destroyed or never created, that reduction is not reversible because it never existed.Simple disturbances can cause the loss of some or all of the carbon that was stored in the soil and essentially negate any climate change benefit.Additionality is also at issue with agricultural soil carbon sequestration offset programs because cropland conservation practices such as no till and conservation tillage are already widely used in at least some parts of the United States due to incentives programs set up by the USDA starting in the 1960s and 1970s.The USDA study on cropland conservation practices in the Missouri River Basin indicates that within the 95 million acres of cropland studied between 2003 and 2006, 46% of the cropland met no-till criteria and 97% of the cropland “had evidence of some kind of reduced tillage on at least one crop in rotation.”Considering that cropland conservation practices seem to be common in at least some parts of the country, it may be difficult to tell if any given offset project under an agricultural soil carbon sequestration offset program would have occurred anyway in a business-as-usual scenario for purposes of determining additionality.The checkpoints for offset programs—that the offset credits generated are quantifiable, real, permanent, and additional—do not explicitly include an analysis of the trade offs or incidental effects of an offset program. However, in agricultural soil carbon sequestration offset programs, the considerations of incidental effects caused by the offset program should be a critical checkpoint to consider.

Some of the conservation practices that most effectively sequester carbon in agricultural soil can present trade offs that bring new problems for farmers that must be fixed through alternative means. Primarily, tilling decreases weed growth, so farmers who infrequently or never till typically use more herbicide to keep weeds out of their field.Farmers using the other sequestration practices encouraged under soil carbon sequestration programs besides no-till and conservation tillage are also reported as using much larger quantities of herbicide. For example, the Kenya Agricultural Carbon Project does not address the use of herbicides, and the World Bank reported that herbicides are heavily used on farms that are involved with the project.An environmental and social monitor for a soil carbon sequestration program reported that “the herbicides are applied . . . without due regard to environmental consequences.”At least one assessment reported contrary findings, that less herbicide was used when conservation practices were employed.However, this assessment utilized many types of conservation practices including improved pesticide management practices, which could explain the decrease in herbicide use in this study. Increased herbicide use can be detrimental for reasons including environmental harm, pollutant emissions, and human health. Herbicides can migrate into the surrounding environment through soil, air, and waterways.The resulting chemical residues can negatively affect the natural surroundings, as any chemical might.The effects would depend largely on the toxicity of the chemicals used in the herbicide, the quantity used and leached, and the sensitivity of the surrounding environment. Additionally, harmful air pollutants, including greenhouse gases, are released when using herbicides.Herbicides release a large amount of nitrous oxide, a powerful pollutant with an estimated 298 times the global warming potential of carbon dioxide.This can be seen as similar to the problem of copollutants. Co-pollutants are pollutants that are released simultaneously and from the same source as the greenhouse gas or pollutant at issue. Increasing emissions of the pollutant at issue will often increase co-pollutant emissions, which can be more localized and harmful in smaller quantities. Similarly, increasing herbicide use will increase nitrous oxide emissions that would not have otherwise occurred if not for increased herbicide use. Thus, even if an agricultural soil carbon sequestration offset program is measured to be carbon neutral, it may unintentionally provide an avenue for increased nitrous oxide emissions and harm to the environment. Another incidental effect of increased herbicide use is that more chemicals will be put onto our food products and affect human uses of soil, water, and air.Herbicides have been linked to serious diseases, such as non-Hodgkin’s lymphoma, soft-tissue sarcoma, and Parkinson’s disease.Due to these health risks, some countries have started to mandate that farmers reduce the amount of herbicide used on their crops due to the harmful human health effects of herbicides.

These circumstances have led some to sharply oppose the increased use of herbicide. If CARB considers including an agricultural soil carbon sequestration offset program in AB 32’s repertoire of offset programs,cannabis grow systems the issues of quantifiability, permanency, additionality, and incidental effects of the offset projects should be addressed. Implementing a new agricultural soil carbon sequestration offset protocol under AB 32 without considering and compensating for these issues would jeopardize the purpose of AB 32’s cap and trade program and likely inflate AB 32’s carbon market with credits that do not actually represent the additional sequestration of one ton of carbon dioxide or its equivalent.These issues may be most completely and accurately addressed by using an ecosystem approach to design the offset program and to approve and implement the resulting offset projects in a case-by-case manner. An ecosystem management approach acknowledges the inter connectivity of the parts within an ecosystem and sees the environment as a single functioning landscape.This approach recognizes that considering only a single species, pollutant, or practice can be detrimental when it successfully decreases one harm but incidentally increases another harm that may be just as, if not more, harmful to the ecosystem. Accordingly, any increase in herbicide use, and subsequent nitrous oxide emissions, or any other potentially harmful externality would be accounted for in the offset program. Under an ecosystem approach, offset programs would not favor projects or regulations that induce harms of a larger or more detrimental magnitude than the harm which is to be prevented by the program. The need for an ecosystem approach, and the regulating agency’s response to this need, is illustrated by the Endangered Species Act.Certain species are listed and protected under the Endangered Species Act and a federal budget is allocated to preserving those listed species. However, many believe that the environment and society would be better served by protecting and managing ecosystems on a larger scale as opposed to individual species.Recognizing this and similar needs in different areas under their jurisdiction, the U.S. Fish and Wildlife Service published An Ecosystem Approach to Fish and Wildlife Conservation, which includes guidelines the FWS strives to use in order to incorporate the ecosystem approach into their conservation work. The Pacific Islands Forum Fisheries Agency , a group formed to help its Pacific Island members to manage, control, and develop the fisheries within the Exclusive Economic Zones, encourages its countries to utilize an ecosystem approach to manage their fisheries.The FFA’s Ecosystem Approach to Fisheries Management consists of four steps.The first step is to determine the scope of the assessment by clearly identifying what is to be managed.The second step is to identify all the issues to be assessed within five key areas and to agree on the values that are to be achieved for each issue.The third step is to determine which issues should be directly managed.The last step is to determine acceptable performance levels, what management arrangements will achieve these levels, and the review process for assessing performance.During the creation of the offset program, an ecosystem approach could be utilized to determine whether the program should be created at all. If no agricultural soil carbon sequestration offset project could ever in theory have a net benefit when considering all the greenhouse gas sources and sinks and other externalities created by an individual project, then the analysis under an ecosystem approach may indicate that the offset program should not be approved. If the analysis of the offset program under an ecosystem approach indicates that only certain types of projects could result in a net benefit to the environment, the program could be limited to those particular types of projects. The ecosystem approach could also be used to assist in determining on a case-by-case basis whether an agricultural soil carbon sequestration offset project should be approved under the offset program. Because the variables associated with each agricultural soil carbon sequestration project will be different for each project and have the potential to vary greatly, a case-bycase ecosystem approach for the approval process for each project would help decision makers to properly determine whether the offset project is quantifiable, permanent, real, and additional. Which externalities should be included in an ecosystem approach analysis of agricultural soil carbon sequestration projects would be a basis for much disagreement, and would depend on scientific and policy analysis beyond the scope of this Comment. However, at a minimum, the effects of increased herbicide use on the surrounding ecosystem and the increase of nitrous oxide emissions should be included in the analysis, as those are some of the more egregious oversights in certain existing agricultural soil carbon sequestration programs, as discussed in Part V.B. In addition to legitimizing a future offset program and resulting offset projects in general, applying case-by-case and ecosystem approaches have the potential to resolve specific issues regarding quantifiability, additionality, and incidental effects identified in Part V.At least two main methods of quantifying agricultural soil carbon sequestration for the purposes of allocating credits for agricultural soil carbon sequestration offset projects could be envisioned. One is a simpler standards-based approach and the other follows a case-by-case process. Although a case-by-case approach may be impracticable in practice, this example illustrates why a case-by-case approach would be more appropriate and crucial for an agricultural soil carbon sequestration offset program. The standards-based option is to give an offset credit per a certain acreage of land covered by an offset project.That particular acreage of land would, on average, sequester one metric ton of carbon dioxide or carbon dioxide equivalent regardless of individual features of the land.

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The main reason was a reduction in direct and indirect nitrous oxide emissions

Phase I also considered agricultural adaptation strategies that addressed regional issues such as hydrology, growers’ attitudes toward climate change, and urbanization versus preservation of farmland. These topics are explored in more quantitative ways here.Since 1960, total crop acreage in Yolo County has been declining. Vegetable and orchard crop areas have increased, while field crop acreage has declined . There has been an increase in higher‐revenue‐per‐acre crops, especially a shift out of barley, and a shift into more processing tomatoes, wine grapes, and walnuts. Many factors affect changes in acreage, including changes in market conditions , input supplies, and climate. Among factors affecting acreage decisions, we investigated whether changes in climate have affected acreage allocations across crops. If responses to climate changes in the past continue to hold in the future, we can use hisorical information to learn more about how crop acreages are likely to change in response to the forecasted Yolo County climate changes from 2010 to 2050. We developed econometric models that relate acreages of each major crop to relative prices and key climate variables . The models are applied to the data including 60 years of acreage for major crops and 100 years of local climate history. Our climate history indicates that during the past century, the increase in annual temperature appears to be mainly due to warmer winters rather than to warmer summers . There was a decrease of about 150 winter chill hours in the last 100 years. Using historical reationships between climate and acreage allows investigation of how forecasted climate changes in Yolo County may affect Yolo acreage patterns. Acreage projections use climate projections for the B1 and A2 scenarios from 2010 to 2050 with GCM data from GFDL‐BCCA. Acreage projections hold constant relevant drivers of crop acreage, except for local climate variables. Among field crops,planting gutter warmer winter temperatures were projected to cause wheat acreage to decline and alfalfa acreage to rise . Thus, future decisions to increase alfalfa acreage present an interesting implication for water use: wheat uses little irrigation; whereas, alfalfa is one of the more intense water users.

By 2050, tomato acreage is projected to increase compared to the current level . This is also related to the increase in growing degree days in the winter months. A warmer climate in late winter/early spring has allowed early planting and provided favorable conditions for establishment. The forecasted climate changes have only moderate impacts on projected tree and vine crop acreage, in part because the climate changes that have occurred have not yet affected key variables enough to induce a significant change in the acreage of perennials when market conditions have been favorable. Almond acreage is projected to increase slightly with warmer temperatures in 2035–2050 . Almonds have a relatively low winter chill hour requirement. Walnut acreage, however, would decline slightly ; it has a higher winter chill requirement. This is consistent with the finding that surveyed orchard growers express concern about a decrease in winter chill hours . These projections rely on using historical relationships between acreage change and climate variables change. They are based actual past responses of acreage to climate. However, no attempt is made to forecast the relative prices, technical changes, new markets, or other factors that will also affect acreage. Water supply vulnerabilities for agriculture and other sectors can be mediated through traditional infrastructure improvements or alternative water policies . Local stewardship that is implemented by water managers and agricultural users tends to be more economical and have less environmental impact than developing new supplies. One tool that has helped water resource managers integrate climate change projections into their decision making process is the Water Evaluation and Planning system . WEAP, a modeling platform that enables integrated assessment of a watershed’s climate, hydrology, land use, infrastructure, and water management priorities , is used here for the Yolo County Flood Control and Water Conservation District service area. It covers 41 percent of the county’s irrigated area and is located in the western and central portion of the county .Recognizing the key role that land‐use planning will play in achieving the goals of AB 32, legislators passed Senate Bill 375 in 2008, requiring sustainable land‐use plans that are aligned with AB 32 .

Local governments must address GHG mitigation in the environmental impact report that accompanies any update to their general plan or carry out a specific “climate action plan” . Emissions of GHG from agriculture are often missing from existing inventory tools geared to local planners. The local government of Yolo County was among the first in California to pass a climate action plan . This project contributed to this climate action plan, and developed a set of guidelines to estimate GHG emissions from agriculture within a local inventory framework . The Tier 1 methods used here have been adapted for local activity data largely from three main sources: the California Air Resources Board Technical Support Document for the 1990–2004 California GHG Emissions Inventory ; the U.S. Environmental Protection Agency Emissions Inventory Improvement Program Guidelines ; and the 2006 IPCC Guidelines for National GHG Inventories . In Yolo County, total agricultural emissions declined by 10.4 percent between 1990 and 2008 .Lower fertilizer use was driven by two important land use trends: a 6 percent reduction in the county’s irrigated cropland; and a general shift away from crops that have high N rates coupled with an expansion in alfalfa and grape area, which require less fertilizer . In both years, emissions of CO2, N2O, and methane from diesel‐powered mobile farm equipment were responsible for 20.0 to 23.0 percent of total agricultural emissions in Yolo County between 1990 and 2008 . Fuel consumption per unit area for several important crops offset the small decline in irrigated cropland. Using the Tier 1 method prescribed by ARB, emissions of CH4 from rice cultivation were estimated to increase from 25.9 to 31.2 kilotons carbon dioxide equivalent between 1990 and 2008, entirely due to an expansion in the area under rice cultivation. Studies also suggest that cultivation practices that combine straw incorporation and winter flooding tend to generate more CH4 emissions than burning rice straw . Thus, estimates generated using the DeNitrification‐DeComposition model showed a larger increase in emissions over the study period because the Tier 3 method accounted for changes in residue and water management made in compliance with the state air quality regulations that have phased out rice straw burning, and the increase in cultivated area . 

Many agricultural practices to mitigate GHG emissions offer agricultural co‐benefits. For example, economic factors are prompting local farmers to shift more of their land to crops that happen to require less N fertilizer and diesel fuel, and to adopt practices that reduce these inputs. Growers cite rising cost and market volatility of inputs, rather than mitigation per se, as a more immediate motivation to use fertilizer and fuel more efficiently. In 1990, emissions sources associated with urban areas accounted for approximately 86 percent of the total GHG emissions countywide,gutter berries while unincorporated areas supporting agriculture were responsible for 14 percent . If calculated on an area‐wide basis the county’s urban areas emitted approximately 152.0 tons CO2e per hectare per year . By contrast, this inventory results indicates that in 1990 Yolo County’s irrigated cropland averaged 2.16 t CO2e ha‐1 yr‐1 and that livestock in rangelands emitted only 0.70 t CO2e ha‐1 yr‐1 . This 70‐fold difference in the annual rate of emissions between urbanized land and irrigated cropland suggests that land‐use policies that protect existing farmland from urban development are likely to help stabilize and or reduce future GHG emissions, particularly if they are coupled with “smart growth” policies that prioritize urban infill over expansion .Many factors affect farmers’ perceptions and response to climate change; for example, characteristics of the individual farmer and their farm; social networks and involvement in programs run by local institutions, agricultural organizations, and extension services; and views on government programs and environmental policies. The goal of this sub-project is to: examine Yolo County farmers’ perceptions of climate change and its risks to agriculture; and develop a better understanding of how such factors might influence farmers’ adoption of proposed adaptation and mitigation practices. We conducted semi‐structured interviews with eleven farmers and two agricultural extension workers in the fall of 2010. The sampling strategy recruited respondents from a cross section of farm sizes, local cropping systems, and market orientations. Interviewers followed a set of open‐ended questions to minimize prompting and interviewer bias, and were used to develop a quantitative survey which was mailed to farmers in Yolo County during February and March of 2011. The survey sample was drawn from a list of 572 individuals who have submitted conventional or certified organic pesticide use permits to the Yolo County Agriculture Commissioner’s office. The final response rate was 34.0 percent. Results of the survey indicated that 54.4 percent of farmers agreed to some extent with the statement “the global climate is changing” . A minority indicated that local summer temperatures had decreased over time, while only 5.6 percent observed an increase. While contrary to statewide mean temperatures, this corresponds with local climate records which show little change in maximum summer temperature over the last century . A majority of farmers indicated that rainfall, drought, and flooding had not changed over the course of their career, but a sizable minority reported water availability had decreased and <1 percent said it had increased. In 1976, the newly constructed Indian Valley Reservoir began supplementing the District’s surface water supplies to local growers.

However, a recent drought in 2009 and 2010 reduced water releases in those years to less than 40 percent of the average for the preceding decade . The memory of this recent a drought may therefore occupy a central place in farmers’ perception of water related trends. Respondents with greater concern for drought and less reliable water were more likely to pump groundwater, drill new wells, and adopt drip irrigation . A farmer’s views on climate change affected the inclination to implement voluntary mitigation practices. More specifically, farmers who disagreed with the statement “The global climate is changing” were less likely to adopt mitigation practices than those who agreed with the statement. Likewise, skepticism that human activities are an important cause of climate change meant less inclination to adopt mitigation practices. Farmers who had frequent contact with local agricultural organizations were more likely to implement mitigation strategies Farmers are often more concerned about the future impact of government regulations than they are about the direct impacts of climate change. This ranking of concern is not surprising given the gradual nature of climate change. However, it does underscore the importance of understanding how farmers view environmental regulations and the information needed to influence their likelihood to adopt mitigation and adaptation practices. Strategies to expand the reach of local agricultural organizations and government conservation programs by improving farmer participation in their activities are thus seen as an important way to strengthen adaptation and mitigation efforts.UPlan relies on a number of demographic inputs . Attractors are given a positive value . Discouragements are given negative values . A system of weights is used to rank the attractive or discouraging property of each variable. We modified UPlan to allow development within existing urban areas, on the assumption that a significant urban redevelopment is likely within the 2010–2050 time frame. The A2 scenario loses two times more acreage of high quality soils to urbanization compared to B1 . One of the most striking findings is just how little land is required to house future populations at higher densities. The B1 and AB 32+ scenarios require 44 percent and 7 percent of the urbanized land of the A2 scenario, respectively. Even holding population increase constant at B1 levels, these scenarios use 63 percent and 38 percent of the land of the A2 scenario, most or all of it within existing urban areas, and also greatly reduce GHG emissions from transportation. These results suggest that the most important climate change mitigation policy that Yolo County could adopt would be to restrict urban development to infill locations within existing cities, and to keep existing farmland in agriculture.

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Many ecological processes governing agricultural pest abundance occur over a large spatial scale

Additionally, as the amount of land in cropland increases, opportunities for invasion or refuge from pesticide applications may be reduced, thus leading to a negative effect of landscape simplification on pesticide use. Three recent reviews of empirical, landscape-scale ecological studies evaluating the effect of landscape complexity on insect pests reported similarly equivocal results, with some studies finding reduced pest pressure, pest abundance, or pest diversity, whereas others find no relationship or the opposite relationships . The variability in the literature may reflect the inadequacy of current study designs to disentangle the net effect of landscape simplification on pesticide use. Confounding variables, such as crop type, or endogenously determined variables, such as farm size or income, could give misleading results if not properly controlled for. Alternatively, studies that are small scale or over short time periods may miss important underlying drivers of pest abundance. Pests disperse large distances, both naturally and aided by the movement of people and goods. Agricultural pests are thus likely governed in large part by meta population processes . Within an agricultural landscape pests may go locally extinct from crop patches because of pesticide use or because of stochasticity influencing small populations, only to be recolonized from a persistent meta population existing in the surrounding agricultural matrix or from a new invasion into the system. Natural enemies too may require resources outside of individual crop fields for alternative prey and shelter for overwintering or from disturbances, such as pesticide application or harvest . Furthermore,dutch buckets the periodic disturbance of crop fields may disrupt predator–prey dynamics by reducing natural enemies directly or by temporarily reducing pest populations to the level below which predators can be supported.

As a result of pest and natural enemy dispersal and immigration, the effect of local processes on regional abundances may be small, despite large effects on within-field abundances. Thus, small-scale studies that fail to account for the landscape-scale dynamics of agricultural pests and their natural enemies could result in spurious associations of what promotes or limits pest abundance. For these reasons, landscape-scale studies provide the best insight into the effect of habitat simplification on pests . Beyond meta population dynamics and trophic interactions, invasion and spread of insect pests and natural enemies are partly stochastic processes influenced by yearly environmental conditions and by the timing of insect pest and natural enemy arrival . Thus, temporal scale may be equally as important as spatial scale to disentangle the effects of landscape simplification on pest abundance. For example, a heat wave at the right time of the growing season may result in widespread pest mortality and high crop yields, whereas a heat wave at a different time of the season may stress crops, making them more susceptible to pest outbreak but having little effect on the pests themselves. This variability over time could appear like ambivalent results of landscape simplification when it is instead the result of the interaction between insect pests and weather. If we are to mitigate the effects of pesticide use on both human health and ecological systems, it is necessary to understand the underlying abiotic or biotic factors resulting in differences in pesticide use. Here I take advantage of longitudinal data from the US Department of Agriculture Census of Agriculture to revisit whether landscape simplification is a consistent driver of insecticide use. I perform cross-sectional analyses for five USDA census years in seven Midwestern US states at the county level. I follow this with a panel data analysis using a fixed-effects model, which identifies the effect of landscape simplification on insecticide use using year-to-year variation within counties.

I specifically focus on insecticides in these states to compare this multiyear analysis with a recent single-year study by Meehan et al. . I check the robustness of these results by comparing data from the USDA Census of Agriculture to the National Agricultural Statistics Service Cropland Data Layer , and check different selection criteria for included counties. I compare these results to that of Meehan et al. , who used the same data sources and model specifications for 2007 only, and find that incorporating multiple years of data as I do here provides insights impossible to glean from a single data year.Annual expenditure on insecticides is over 4 billion dollars in the United States , which equates to the use of almost 100 million pounds of active ingredients . Given the many health and environmental consequences related to insecticide exposure, it is critical to understand what farm, landscape, or environmental characteristics drive the insect pests that motivate insecticide use. It has long been thought that landscape simplification is one of these characteristics. Reviews of empirical evidence for this theory have been largely inconclusive , although a recent statistical analysis of the Midwestern United States in 2007 found a strong, positive relationship between landscape simplification and insecticide use . Here I analyzed data from five USDA Census of Agriculture years using cross-sectional and fixed-effects models. The cross sectional results show that landscape simplification does not consistently drive higher insecticide use. Although the coefficient on proportion of county in cropland, my metric for landscape simplification, is positive and significant in the 2007 analyses, that relationship is absent or reversed in prior census years. Furthermore, adjacent census years, such as 2002–2007 and 1992– 1997, show large changes in the magnitude and changes in significance of the landscape-simplification coefficient.It is evident that the drivers of insecticide use may not be easily or reliably identified using single time-period studies. Using a fixed-effects model to remove unobserved characteristics, I find a non-significant relationship between landscape simplification and proportion of county in cropland. Counter intuitively, these results suggest that as cropland increases, the proportion of cropland sprayed with insecticides is unaffected.

The existence of a null relationship between landscape simplification and insecticide use is not unlike the results of Hutchison et al. , who reported large reductions in the European corn borer in non-Bacillus thuringiensis corn as a positive externality from B. thuringiensis corn plantings. Although pesticides may have negative effects on public health, biodiversity, and ecosystem services,grow bucket the application of pesticides by a nearby farm may reduce pest incidence on surrounding farms because of pesticide drift or pest suppression . Additionally, as the amount of land in cropland increases, opportunities for invasion from natural or untreated areas may be reduced. As a result of landscape simplification, natural lands have been isolated to farm boundaries, fallow lands, or wood lots . Numerous ecological studies have found that these fragmented natural or less intensively managed areas can act as a source for natural enemies and pest species that recolonize species poor crop fields . If the cost of pest invasion is greater than the benefits of natural enemy pest suppression stemming from non-crop land, these habitats can have a net negative impact on the farmer in terms of pest control. The above mechanisms may explain why a null relationship is observed in the fixed-effects model; however, they do not account for the importance of year. What could explain the wild variation in the landscape simplification coefficient in the cross sectional analyses and why year fixed effects are so important? There are a number of drivers that could be behind the year-to year variability, and deciphering which mechanism is at play is critical because different policy measures are needed to address different types of drivers. For example, a stochastic driver such as weather could be the culprit. Insect development is strongly influenced by weather conditions, such as temperature and precipitation, and thus yearly differences in these or other environmental conditions could have an important effect on insecticide demand and the relationship between landscape simplification and insecticide use. Preliminary analysis indicates that the effect of weather on this relationship is complex. [Preliminary analysis using growing season precipitation and degree days based on the National Climatic Data Center Global Historical Climatology Network Daily file does not explain the variation in the cross-sectional relationship between landscape simplification and insecticide use.] This finding may be because the timing of pest arrival relative to the growing season may determine the likelihood of pest outbreaks and the benefits of applying insecticides . Furthermore, temperature and precipitation affect the survival and development of different pests differently, and thus which pests and enemies are present may determine the effect of weather on the relationship between landscape simplification and insecticide use. Refined data on pest outbreaks or type and timing of insecticide use are currently not available for the study area examined. However, the development of such data or further empirical study focusing on abiotic conditions would greatly increase our understanding of the link between weather events and insect outbreaks, and thus increase our ability to forecast variation in insecticide use both now and under future climate change. It is also conceivable that the change in the relationship between landscape simplification and insecticide use between 2007 and all previous years reflects a systematic and predictable trend in insecticide use. For example, in 1996 there was a major change in the regulation of pesticides in the form of the Food Quality Protection Act .

FQPA prompted the reevaluation of all registered pesticides, and promoted the use of more selective, less persistent “reduced-risk” pesticides via a fast-track registration process . FQPA could affect the relationship between landscape simplification and insecticide use because insecticides that are effective against a multitude of insect pests and persist in the environment for longer periods of time may have provided higher positive externalities to surrounding crop fields, thus necessitating less insecticide use in landscapes dominated by agricultural fields. The implementation of FQPA and the resulting use restrictions took 10 y, and phasing out of certain chemicals is still in progress . Because changes in available insecticides were occurring between 1996 and 2007, it is difficult to statistically evaluate the effect of FQPA on the results reported here. Future Census’ of Agriculture or more refined insecticide data that include information on the active ingredient in use could elucidate how policy changes are interacting with the relationship between landscape simplification and insecticide use. Agriculture has vast impacts on the Earth’s environment and these impacts are only expected to grow as demand increases in the coming decades . The challenge, as Balmford et al. discuss, is how to meet the increasing demand with the least effect on native biodiversity and the ecosystem services intact ecosystems provide. There are various advantages and disadvantages to whether increased demand should be met by increased intensity of farming on current agricultural land or by increased land conversion to agriculture to be farmed with more biologically harmonious farming methods . In the Midwestern United States, it appears that land-sparing at the county level does not lead to consistent increases in the proportion of cropland treated with insecticides. However, without understanding what is behind the year-to-year variation in the relationship between landscape simplification and insecticide use, it is impossible to predict how land sharing or land-sparing as a policy initiative would affect insecticide use in the future. As suggested by this study and recent empirical reviews , the presence and direction of the relationship between landscape simplification and insecticide use can be positive, negative, or null. If this variation is driven by variation in yearly weather, whether simplified landscapes cause more or less insecticide use could flip flop unpredictably. If the variation is driven by extreme weather or weather characteristics that will be altered with climate change, perhaps there will be some directionality. If the relationship between landscape simplification and insecticide use is an indirect consequence of management policies, perhaps 2007 is a glimpse of the future. The data available are currently inadequate to decipher the underlying mechanisms. However, given the different policy implications of a stochastic driver, such as weather, versus a predictable driver, such as regulatory change, developing the necessary data sources to tease apart the underlying causes is imperative. Perhaps most importantly, this study emphasizes the need for longer-term research agendas, especially when investigating a politically, economically, and ecologically important question, such as insecticide or pesticide use.

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Terpenoid synthesis showed clear segregation into the mevalonate and the MEP/DOXP pathways

Airborne dust was ever-present while we sampled, and despite extensive containment efforts, some exposure of the apparatus to dust occurred . However, the rest of the DOM metagenome is remarkably distinct from the other samples, suggesting that, with the exception of the known contaminants, it is still representative of the deep groundwater. We eliminated all suspected contaminant genomes from further analysis.We assembled genomic bins using the following pipeline: IDBA_UD initial assembly, REAPR breaking of misassemblies, VizBin binning of contigs into draft genomes using 5-mer frequency and coverage information for visual aid, additional manual bin cleanup based on contig coverage distribution , taxonomic assignment of bins based on RAPSEARCH to the UniProt UniRef100 database. Selected bins were assembled further by PRICE targeted assembly and REAPR correction of misassemblies. Genome quality was assessed throughout using CheckM. Further details are in the methods. Overall we assembled and refined 79 unique genomic bins from the three groundwater samples . An additional 51 bins were made from the LAG sample and were used to determine probable contaminants in other samples, but no refinement of these bins was attempted, as we were interested in the properties of the groundwater communities. Contamination was only detected for the DOM sample as previously discussed. No evidence of overlap with the surface water was seen in either MW5 or MW6. The most abundant taxa in the partial genomic bins were from the CPR Parcubacteria , followed by the DPANN Woesearchaeota , and the CPR Microgenomates . While the OD1 and OP11 lineages have previously been found in association with anammox communities. The high relative abundance and diversity of CPR and DPANN genomes at over 50% of the community is notably higher than previous reports . The next highest abundance of our genomic bins were from the Planctomycete Brocadiaceae family . We made genomic bins of many of the other key members of the wastewater anammox community, including Omnitrophica , Nitrospirae , Chloroflexi , Chlorobi , Bacteroidales , Acidobacteria , and γ-Proteobacteria . Additionally, we assembled partial genomes from the Nitrospinae/Tectomicrobia group , Spirochaete , a Planctomycete from the OM190 family, an archaeon from the TACK radiation, a Firmicute that was dominant in the DOM well, a Bacteroidetes , an α-Proteobacterium, and a β- Proteobacterium. Finally, we assembled numerous phage bins.

Only one is included here ,hydroponic gutter but evidence of bacteriophage was abundant.While many potentially interesting and novel genomes were isolated from this community, we focus here on the Brocadiaceae Planctomycetes, which oxidize ammonium under anaerobicconditions in a specialized organelle called the anammoxosome that protects the cells from the toxic hydrazine intermediate products of the biochemical reaction. Anammox genomes are highly prevalent in the MW5 and MW6 samples and also occur in the DOM sample . We were able to make several near-complete assemblies of these genomes , however, the genome size of 2 Mb for many of these genomes was well below the 4 Mb seen in other members of this family. The coverage of some of these small genomes is rather high , making it seem plausible that the true genome size is reduced. In an attempt to resolve this discrepancy, we rebinned the MW5 anammox genomes using less stringent criteria, and found increased but still incomplete coverage of the Brocadiaceae reference genomes . These composite genomes were multi-strain chimeras, as indicated by conserved single copy gene occurrences increasing above one . The fact that merging multiple strains of the same species did not give complete coverage of the single copy genes is in agreement with the hypothesis that the true genome size is small but further sampling would be needed to confirm the hypothesis. In any event, we have not been able to resolve the discrepancy in genome size in the present study. The phylogenetic placement is apparent by homology with the Brocadia sinica and Jettenia caeni reference genomes . The separation of genomic bins shown by pentanucleotide clustering suggests multiple Brocadia-like genomes coexist in MW5, MW6 and DOM. A 16S phylogeny supports this observation . We refer to these genomic bins herein as MW5-59_1, MW5-59_2, MW6-02, MW6-03, MW6-13, DOM-02, DOM-03, and DOM-40 . We also assembled an 8.3 Mb Planctomycete genome with similarity to the Planctomycetaceae family within the Planctomycetes . The larger genome size indicates the genome is not of the Brocadiaceae, which have genome sizes around 4 Mb. Whole genome sequence comparison of MW6-09 to the available reference Planctomycetes showed highest similarity to Singulisphaera acidiphilus , however, the similarity even to Singulisphaera was not especially high, indicating that this genome is truly diverged from the reference genomes. Examining the 16S alignment suggests the genome could be from the OM190 group of Planctomycetaceae , a group with no sequenced genomes . We caution, however, that while we could link the EMIRGE-assembled OM190 16S gene with theMW6-09 genome using targeted assembly , multiple 16S fragments could be linked to the genome, thus our placement MW6-09 as an OM190 Planctomycetaceae should be revisited when new, related genomes are discovered.

To determine whether the anammox strains were unique to their respective bins or overlapping, we used VizBin to perform additional kmer distribution-based clustering of all the Planctomycete contigs together. Six distinct clusters are apparent , with MW5-59_1, MW5- 59_2, and MW6-13 overlapping. We next refined the genomic bins by combining the anammox genomes from MW5, MW6, and DOM and repicking chimeric bins. We then performed a single round of assembly using PRICE in order to merge the contigs. Overall, little improvement in bins was made. However, inter-strain contamination was reduced, and the DOM-02 bin was substantially improved by adding 20% more contigs from MW6 that coclustered . The 16S phylogengy indicates the bins come from three distinct lineages . The abundant MW5 and MW6 bins come from a new lineage that is intermediate between Jettenia and Kuenenia. The abundant DOM bins and one of the MW6 bins come from two different lineages within the Brocadiaceae W4 group. As there are no sequenced members of these lineages to use as reference, we aligned our bins to the closest available reference draft genomes of Brocadia, Jettenia, Kuenenia and Scalindua species . Reflecting the 16S phylogeny, the best homology was to Jettenia for the abundant MW5 and MW6 bins, and lower homology was seen for the DOM bins and MW6-02. As previous reports have noted low diversity of anammox genomes within a given sample , we find it noteworthy that as many as three distinct anammox genomes coexist within a single groundwater well. To confirm that all of these genomes were true anammox metabolizers, we checked for hydrazine conversion genes by BLASTX. Confirming that they are indeed anammox organisms, all Brocadiaceae genomes showed good coverage of the hydrazine database, and MW6-09, which is phylogenetically places as a nonanammox Planctomycete, did not have BLASTX hits.We analyzed the biochemical potential of the genomic bins in two ways focusing on pathways and modules rather than on individual proteins . This analysis was based on taxonomic placement rather than on the well of origin. First, we mapped the contigs from each draft assembly to the database of KEGG orthologs and used KEGG Mapper to visualize the results. Second, we used antiSMASH to detect potential secondary metabolite bio-synthetic gene clusters. The results reveal variation between genomic bins as well as pathways for potential community interactions linking nitrogen and sulfur metabolic pathways in the groundwater.To determine what functional genes are present in the water microbiota, we first aligned all of our contigs in each of the dairy water samples to the KEGG prokaryote database and evaluated trends at the whole metagenome level. Overall, we see enrichment of phosphotransferase systems, two-component systems, ABC transporters, and terpenoid production. The PTS systems are particularly high in the nutrient poor DOM sample,hydroponic nft channel consistent with the idea that there is a selective pressure driving acquisition of nutrients in nutrient-poor environments. However, no clear signature of different modes of nitrogen metabolism is indicated when examining the aggregated data for each sample. Thus, we examined the individual genomic bins to get a broad understanding of their biochemical potential. We focused on the KEGG pathways for nitrogen metabolism, sulfur metabolism, flagellar assembly, chemotaxis, ABC transporters, two-component systems, terpenoid synthesis, ATPase family, secretion systems, cofactor F420 , and B12 production since these pathways showed the most variability across the genomic bins. We include nucleotide synthesis as a positive control, since all of the complete bins have good coverage of the nucleotide metabolism pathways.

Because many of the genomic bins were partially incomplete, we aggregated KEGG maps from related species in order to get a more coherent picture of the pathway representation as a function of phylogeny . Overall, we see sparse coverage of nitrogen metabolism by the CPR, and DPANN genomes, while Methylomirabilis, Omnitropica, Nitrospira, Brocadia, and Nitrospinae had high coverage. The Bacteroidales also had sparse coverage of nitrogen metabolism, and the Chlorobi had intermediate coverage of the pathway, indicating that not all genomes in the community are directly involved in nitrogen metabolism. The same pattern was true of sulfur metabolism, with the exception that OP11 has the module for assimilatory sulfate reduction, which is consistent with the work of Canfield showing that sulfur and nitrogen redox pathways are coupled in the oxygen minimum zone of the oceans. Methane metabolism, indicated by presence of the coenzyme F420, was present in one DPANN bin, one OD1 bin, Methylomirabilis, and Nitrospinae. Intermediate coverage of this module was seen for Chlorobi, supporting the observations of Speth et al that species have diverse and overlapping niches within the anammox community and Shen et al that methane oxidation co-occurs with anammox. For oxidative phosphorylation, distinct ATPases were seen between the phyla. OP11, OD1, Methylomirabilis, Omnitrophica, Chlorobi, and Nitrospinae have the F-type ATPase, while DPANN, has the A-type ATPase, and Nitrospira, Brocadiaceae, and Bacteroidales have both F-type and A-type ATPases.In terms of acquiring nutrients from the environment, the CPR genomes were deficient in ABC transporters besides phosphate. The DPANN have slightly more, but the rest of the genomes each have significant coverage of  15 ABC transporters each. Coverage of two-component systems was consistent across all genomes for phosphate, while either nitrogen or nitrate was present for all except OP11. Twitching motility was indicated for OP11 as well as for OD1, and Chlorobi. High coverage of the chemotaxis pathway was seen only in the Nitrospira, Brocadiaceae, and Nitrospinae, with moderate coverage seen in the DPANN, OP11, OD1, Chlorobi, and Bacteroidales. Methylomirabilis and Omnitrophica appear to lack pathways for both chemotaxis and flagellar assembly, whereas Nitrospira, Brocadiaceae, and Nitrospinae have the complete pathways, and Chlorobi and Bacteroidales have most of the chemotaxis pathway but Chlorobi has the complete flagellar pathway and Bacteroidales lack it entirely. In terms of biosynthetic capabilities, Omnitrophica, Nitrospira, the Brocadiaceae, and Nitrospinae have complete vitamin B12 pathways, while Chlorobi and Bacteroidales have the latter half of the pathway as does one OP11 genome, while the other OP11 genomes as well as the OD1 genomes lack B12 production entirely. Methylomirabilis has sparse coverage of the pathway, and the DPANN genomes have genes for converting B12 to the active form. These results indicate that B12 sharing is likely an active part of the anammox community metabolism.Methylomirabilis, Omnitrophica, Nitrospira, Brocadiaceae, Bacteroidales, and Nitrospinae all have only the non-mevalonate pathway, whereas Chlorobi has both pathways, and DPANN use either one pathway or the other but not both. Within the CPR, OP11 has the mevalonate pathway, and OD1 has neither pathway. Wide variation was seen in the secretion systems, with the DPANN, OP11, and OD1 using only the SecSRP system, Bacteroidales using the SecSRP and Tat systems, Methylomirabilis and Omnitrophica using the SecSRP, Tat, and Type II systems, and Nitrospira using the SecSRP, Tat, Type I and II systems. The Brocadiaceae and Chlorobi use the SecSRP, Tat, Type II, IV and VI systems. And finally, Nitrospinae uses the the SecSRP, Tat, Type I, II, IV and VI systems. Comparison of KEGG pathway coverages with the available reference genomes showed similar results, supporting the hypothesis of niche specialization in a shared community metabolism.

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The tax was finally suspended indefinitely, pending a new proposal from the government

As with past reforms, the Commission’s proposal to place a cap on direct income payments was completely rejected due to widespread opposition from the member states. The final result of the Commission’s proposal income payment cap was a form of degressivity, under which payments over a certain threshold may be reduced. Degressivity was left to the member states as an option, with a very small level made mandatory . Moreover, member states could choose to garnish their total national envelope, as opposed to applying degressivity directly to their largest earnings, allowing them to reduce or entirely eliminate the loss to large farmers. Finally, greening measures were watered down, the end result being that most farmers were exempted from compliance, and overall standards were lowered. Essentially, anything that was contentious or in some way resisted by a member state was handled one of three main ways: the standards for the policy were lowered; the qualifications for an exemption were widened; or discretion for what standards to set and how to enforce the policy was given to the individual member state. In the end, nearly 50% of arable land covered by the CAP and just under 90% of arable goods farmers were exempted from the new greening rules and standards. The remaining more minor elements of the initial reform proposal were also adjusted in the final agreement. Those member states whose direct income payments were 90% or more below the EU average were afforded more flexibility in transferring funds between Pillar 2 and Pillar 1 . The proposal to more rigorously define who counts as a farmer and thus what land can be considered agricultural was significantly weakened. The Commission’s effort to restrict a base payment to individuals engaged in farming as their primary source of income was also completely defeated,hydroponic grow systems meaning anyone with agricultural land could receive this payment, even if they were a non-farmer. A.2.3 which summarizes the changes for these small proposals can be found in the Appendix.

The MFF agreement, which fixed the budget and also included some CAP provisions shaped the course of the CAP negotiations that operated concurrently and ultimately subsequent to the battle over the budget. This effect was perhaps most profound in the area of greening. Greening measures to support the environment and battle climate change were, at least at one point, considered an essential part of justifying the increasingly criticized direct payment scheme. In the initial stages of the CAP reform, when the process began in 2010 before the MFF talks were underway, it was expected that farmers would be required to provide a direct, clear, “public good” in the form of following particular environmental practices in exchange for the receipt of direct payments. However, once the MFF was agreed, the greening push was fatally weakened. With the budget fixed, the threat of imposing cuts if greening standards were not raised was no longer credible. The greening case was hurt more broadly by the fact that there was general uncertainty of the extent to which these measures would deliver real, significant environmental benefits. In addition, many worried about the added financial costs for farmers and more broadly the bureaucratic cost of administering these programs. In the end, the final agreement fell well short of initial proposals. A perhaps overly pessimistic view was expressed by multiple DGVI officials who lamented that rather than making the CAP fairer, greener, and simpler, reform left the CAP still unfair, barely greener, and far more complex . This characterization understates the reform. In fact, there were meaningful changes to reduce systemic inequalities. That said, the reform did make the CAP far more complex and also did little to improve greening. The previous four chapters have explored the major rounds of CAP reform, illustrating my claims about the conditions that affect policy reform, the nature of farmer power, and the links between welfare state reform tactics and agricultural policy reform, including the key strategy of pairing compensation with reform. These chapters have demonstrated that reforming agricultural policy is an exercise in navigating farmer power.

Theories of welfare state retrenchment help to explain how and why the process of agricultural policy unfolds in the manner that it does. Most often, reformers rely on the kinds of strategies described by Paul Pierson in his analysis of welfare retrenchment: compensating farmers, making smaller adjustments to correct existing policies , and introducing changes that may open the door to more far-reaching shifts down the road . When CAP reform is initiated at a time of disruptive politics, like trade negotiations or enlargement, it is much more likely to succeed. The 1992 MacSharry and 2003 Fischler reforms occurred at times of disruptive politics and the end result was major reform to the operation of the CAP payment system. Of course, as my argument requires, these reforms 1) were paired with generous compensation and 2) largely consisted of recalibration, in which the modes of payment were changed, but the amounts remained the same. Under politics as usual, reform proposals are almost always defeated. The 1999 and 2013 CAP reforms occurred in “normal” times- no trade negotiations were occurring and enlargement was not looming. In both cases, despite proposals for extensive change, the CAP remained virtually unchanged. Any minor reforms that did occur were either accompanied by extensive compensation or qualified by massive exemptions. The previous four chapters have demonstrated how theories of welfare state retrenchment, combined with an awareness of the broader context of the reforms, can help explain the process and outcome of the CAP reform. The question remains, however, if the analytical efficacy of welfare state retrenchment theories stems from circumstances particular to the CAP and the EU or if this approach can be applied more broadly. In order to assess the analytic usefulness of my approach, I test it under a variety of different conditions and circumstances in three mini-cases: austerity-driven domestic policy in Europe, domestic agricultural policy reform in Japan, and agricultural trade policy negotiations in the GATT Uruguay Round.

My claims about the politics of agricultural policy reform and farmers’ influence over policy making are not restricted to the CAP and the specific circumstances of EU politics. They can also explain agricultural reform at the domestic level. To make this case, I explore domestic politics and policy making in the wake of the 2008 financial crises. The mini case proceeds in two parts. I begin with a close look at France, focusing on domestic policy reforms, which are not specifically agricultural in nature. An “eco tax” 41, proposed in France in 2013, that was to affect truck transport of goods, including agricultural products, was abandoned due to pressure in large part from farmers. Pension-related cuts, however, went ahead despite mass protests. The second part of the mini case looks at domestic reform in Europe more broadly, and confirms that the French case is not an outlier. Indeed, I find that at the domestic level, European governments largely did not cut national discretionary spending on agriculture, while they did impose significant cuts on pensions. In the wake of the Great Recession and sovereign debt crisis, austerity programs were adopted across the European Union. Spending was cut, programs of support for those suffering financial hardship were canceled or suspended,hydroponic growing and new taxes were created to help generate revenue for cash-strapped governments. One social group that would have appeared to be particularly vulnerable to austerity-imposed policies is the agricultural community. Farmers are a tiny population that is continuing to decline. Any spending cuts or new tax burdens would therefore apply to only a small portion of the population, in theory allowing politicians and policymakers to minimize the negative backlash faced by aggrieved constituents. Moreover, farmers already receive a disproportionate share of financial support, given their share of the population, making their programs and policies low-hanging fruit for retrenchment-minded officials. Yet, since the 2008 financial crisis, farmers have felt little if any of the budgetary pressure that austerity has brought to bear on communities across Europe. As is observed in EU policy making, farmers at the domestic level successfully resist the imposition of new costs that are not paired with compensation. The parallels between the ways that farmers defend their policies and thwart unwanted policy changes at the domestic and EU levels can be made clear by looking at a case in which a national government attempted to impose new costs on their agricultural community without offering compensation. In 2013, Socialist French President François Hollande attempted to implement the so called “eco tax” first put forward by his conservative predecessor, Nicolas Sarkozy. The eco tax was intended to promote greener commercial transportation by imposing a tax on heavy vehicles. Under the plan, any vehicle over 3.5 tons would be taxed a flat rate of .13€ per kilometer traveled on 15,000 kilometers of roads included in the scheme. The government expected the tax to generate over €1 billion in revenue annually. The eco tax was slated to come into effect beginning 1 January 2014. The government’s proposal was immediately met with criticism from the main French farmers’ organization, the FNSEA. The organization described the tax as an “usine à gaz”, a situation where pipes are going everywhere and the system is overly complex. Through thus turn-of-phrase, the FNSEA meant to convey that the eco tax was a complicated procedure with little actual value or payoff. The FNSEA argued that the tax would place a significant burden on the agricultural community, particularly farmers in Brittany, who had suffered significantly from the financial crisis, and demanded that it be suspended immediately.

Other critics raised concerns that Breton farmers might be driven out of business as a result of higher transportation costs. In addition to the concerns about its effects on Breton farmers, the FNSEA warned that French goods would pass through the tax gates more often than trucks carrying foreign goods, putting French farmers at a disadvantage compared to farmers’ goods arriving from abroad. Xavier Beulin, the leader of the FNSEA, promised immediate action against the proposal, directing members to target the “portiques” that were intended to scan the trucks as they passed underneath. Beulin called on farmers from other parts of France, even from those areas without the tax scanners, to join the protests. The call for action was successful, as a wave of angry protests erupted in Brittany and across France. In Brittany, the heart of the demonstrations, protesters gathered in main town squares, many wearing red caps, or bonnets rouges in a reference to a 17th-century protest against a stamp tax proposed by Louis XIV. Some protestors threw stones, iron bars, and potted chrysanthemums at riot police, while others destroyed the electronic scanners intended to collect the fee from passing trucks. The protesters included not just farmers, but also the broader public, who were rallying to oppose taxes, with some also supporting the farmers specifically. In addition to the violent actions in Brittany, farmers elsewhere blocked roads with their tractors, including around Paris. Despite the disruptions these protests caused to the daily life of the average French citizen, the farmers did not face any negative public backlash, a further indication of the deep support and connections between farmers and urban France. Indeed, public polling concerning the image of farmers revealed that the public has a strong, positive image of farmers. According to a 2014 survey, shortly after the mass protests by farmers, just 26% of respondents were willing to describe farmers as selfish and only 16% of respondents agreed that farmers were violent. A resounding 80% agreed with the statement that farmers were trustworthy42 . After Prime Minister Jean-Marc Ayrault met with local officials from Brittany, the government proposed to “suspend” the tax until January. This concession, though it was expected to cost the government €800 million in revenue, was seen as insufficient, and tens of thousands of protesters continued to gather in the epicenter of resistance to the proposal, the town square of Quimper in Brittany.France’s eco tax then, like to efforts to change CAP income support systems or greening policies, demonstrates that it is nearly impossible to impose new costs on farmers, without some degree of compensation or widespread exemptions. For example, new CAP greening standards that are costly for farmers to adhere to are typically coupled with subsidies for compliance.

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Fischler truly viewed his task in these reforms as saving the CAP from collapse

Germany also took action, replacing its SPD farm minister, Karl-Heinz Funke, with Green Party member Renate Künast, a Fischler ally and vocal advocate of CAP reform. Künast advocated strict standards for animal welfare, tough environmental regulation, and greater oversight of and limitations on industrial farming. Prior to the MTR, commitments to meaningful environmental measures were tepid at best. Environmental policies were optional, and implementation was left to the discretion of member states, who mostly ignored them due to farmer resistance. The series of food scares increased pressure on the CAP from consumers, environmentalists, and animal welfare advocates. Public opinion of the CAP in these matters was quite negative. While 90% of respondents in a 2001 Eurobarometer poll expressed a belief that the CAP should “ensure that agricultural products were healthy and safe”, only 36% thought that “food bought could be safely eaten” and just 34% felt that “food bought is of good quality” . As a result, Fischler saw an opening to push for meaningful, mandatory reforms that would increase food safety and security, including the adoption of environmental and animal welfare regulations. There was also a growing recognition among the public that farmers were significant polluters . According to Eurobarometer surveys in 2001 and 2002, just under 90% of respondents stated that the CAP should be used to “promote respect for the environment” while only 41% of respondents across the EU 15 felt that the current version of the CAP actually “promoted respect for the environment” . The environmental goal was second only to the objective of “ensuring the agricultural products are healthy” . The CAP bore the brunt of the blame for agricultural pollution,hydroponic container system given that it allowed for the industrialization of agriculture and by extension tacitly promoted the use of environmentally damaging farming practices, designed to extract the highest possible yields. A final problem confronting the CAP concerned the distribution of benefits. The CAP directed most of its support to only a small number of farmers. For example, in France, 40% of all aid went to fewer than 10% of French farmers, overwhelmingly the large cereal cultivators .

This problem, known variously as the 80/20 problem or the “Queen of England Problem” had plagued the CAP for a number of years. Reformers were under pressure to, if not correct this imbalance in support distribution entirely, at least attenuate it. The unequal allocation of CAP benefits, and reports in the press about disparities in payments received by large and small farmers, led Fischler and his associates to be concerned that public opinion would turn against the CAP. Declining public support was a real worry because EU officials, particularly other Commissioners, already questioned why such a large sum of money was being spent on an increasingly small faction of the population. The challenges and opportunities posed by enlargement, WTO negotiations, and poorly operating CAP programs offered Fischler and his associates an opportunity to propose far reaching reforms of the CAP under the auspices of the MTR. Such reforms were seen by Fischler and his team as necessary to “reduce the ammunition of those demanding large budget cuts and [to] create a new support base for the CAP” . If the CAP remained unreformed, unsustainable spending and environmental destruction would make it an easy target for other commissioners and member states who preferred a much slimmer CAP budget. Their case would be helped by increasingly negative attitudes from the general public. As Pirzio-Biroli, Fischler’s deputy, noted, “[we] concluded that, if we wanted to preserve the CAP, we needed to change it” . Fischler’s agenda was not just about cutting spending . Rather, he sought to reform the CAP to save the CAP- most notably by making it financially sustainable, viable under enlargement, compatible with WTO rules, and responsive to public concerns about food safety and the environment. Some critics saw Fischler as a bean counter, looking to make cuts wherever he could to get CAP spending under control. While it is true that Fischler was attempting to radically restructure CAP spending, these critics misread the motives behind his actions. Fischler was himself a former agricultural minister. He was seeking to reform the CAP and to make cuts not to please his colleagues in Brussels, but rather to make sure the CAP continued to be viable.

Fischler benefited from a high degree of personal credibility within the Commission, having been a minister of agriculture and the leader of Austria’s accession negotiations. He was considered to be both an expert on agricultural policy and a reform-minded official, who was willing to pursue the tough changes necessary for preserving the overall health of the CAP, no matter the criticism he might face from farmers or their member state representatives. As evidence of the high regard in which Fischler was held, Commission President Romano Prodi completely devolved agenda-setting competency to Fischler and reportedly “had no firm ideas one way or the other about agriculture and issued no directive to Fischler about how or whether to reform” . Although the MTR was intended only to be a health check and not a revision of existing CAP policies, Fischler believed that the CAP needed much more than a status report on the functioning of existing programs. A program that could neither work within the EU budget nor meet basic environmental and health standards ran the risk of being cut drastically by European technocrats, if not entirely eliminated. In addition, without reform, the CAP would stand to be an anchor inhibiting the EU’s ability to negotiate in the Doha Round of WTO negotiations. Fischler thus constructed his reform objectives around making those changes necessary to ensure the CAP’s long-term survival. If he did not reform the income payment system, new member states would explode the budget beyond sustainability. If the CAP remained an obstacle for European services and manufacturing in trade negotiations, these external actors would force deep and unpleasant changes to CAP programs such that European agriculture no longer tied their hands. In other words, failure to reform the CAP could spell the end of the CAP. Fischler’s central goals were to decouple CAP payments from production and to expand the environmental scope and standards of CAP policy . The first goal, decoupling, would help reduce the vast disparity in CAP income payments, whereby 80% of CAP income payments went to only 20% of eligible farmers. It would also put CAP spending into conformity with WTO rules. The second goal, improving environmental standards, would address growing public dissatisfaction with the effects of CAP policy on food safety and the environment. Decoupling would go a long way towards ensuring that the CAP remained financially viable in an enlarged Europe,planter pots drainage while mandatory environmental standards and regulations would make certain that newly-added agricultural land was protected as well as guarantee that food produced in Eastern Europe would meet the higher quality and safety standards already in place in the West. While there had recently been high-profile incidents of food-borne illnesses, overall safety and quality standards and rules in the West were much higher than those in the East. Without these changes, the CAP would be overwhelmed by the financial strain of supporting the new member states, would be challenged by Europe’s trading partners, and would lose public support due to its social and environmental consequences. Fischler had learned several lessons from the Agenda 2000 negotiations. During Agenda 2000, the early publication of reform proposals allowed vested interest groups the opportunity to mobilize and undermine initiatives before they could even be launched .

Farmers in particular, once tipped off about the contents, had moved to lobby their governments to oppose reforms before any discussion or formal presentation and explanation of the proposals could occur. Fischler, therefore, resolved to develop the MTR behind closed doors, like MacSharry had done with his 1992 reform. By working first in secret, Fischler would be able to propose a reform that called for dramatic and far-reaching change—more than was expected under the MTR. A more open development process would leave the agricultural directorate susceptible to interference from the member states. Given that a number of member states wanted the MTR to be nothing more than a review, Fischler opted to keep his proposals under wraps until the time was right. Secrecy also gave Fischler and the Commission a research advantage: they could collect and gather evidence so that when the reform proposal was presented, Fischler would be able to provide data to support his proposals . The member states would then be forced to play from behind in order to mount specific, evidence based criticisms of the Commission’s reform package. Because the content of proposals would be a surprise to the member states, they would be unable to make specific, detailed claims about the effects of reform, and any general reactions, like claiming the reforms would hurt farmer incomes, could quickly be refuted by the Commission, armed with data and evidence. Another key and more personal lesson that Fischler had learned was to be wary of French President Jacques Chirac. When speaking about his adversaries in CAP negotiations, Fischler stated, “my biggest opponent was Mr. Chirac” . The two had tangled multiple times in the past. Fischler described Chirac as an “intelligent and crafty politician who knew a great deal about agriculture and could manipulate political rules to his advantage” . Fischler recounted that at the Berlin Summit, where Agenda 2000 would be formally adopted by the European Council , Chirac “used a trick” to reopen and revise the agreement . First, Chirac exploited his personal relationship with German Chancellor Gerhard Schröder who held the rotating presidency at the time. Because the CAP was part of the new Multi-annual Financial Framework , the summit chair could open any component of the MFF for debate and reform. Second, Chirac used a complicated rule in the operation and calculation of the CAP budget to compel other member states to abandon a dairy reform that Chirac did not like29. Fischler “was furious because the reform was already agreed to, but Chirac went back and undid the work” . Fischler learned the hard lesson that even when the agreement was concluded in the Council of Ministers, he still needed to make sure the holder of the rotating presidency did not reopen the CAP portion of the MFF at the European Council summit meeting. Fischler’s rocky relationship with Chirac continued after the Berlin Summit. Following the Agenda 2000 reform, Chirac unsuccessfully appealed to Commission President Prodi to not renew Fischler’s post as agriculture commissioner for a second term. When asked specifically about the MTR, Fischler again identified Chirac as one of his biggest adversaries . During the MTR negotiations, Fischler, however, benefitted from the lessons he had learned from the Agenda 2000 reform process and was better positioned to manage and respond to Chirac.Fischler’s initial plan was sent to the Commission on 10 July 2002 after months of study and work conducted largely in secret by Fischler and a small group of associates, including his Deputy Director, Corrado Pirzio-Biroli. The small group included only the top officials at DGVI. These officials relied on studies and analyses by experts within the DGVI administration, who conducted preparatory analysis and calculated potential effects of the reforms but were not fully informed of overarching agenda. Otherwise, Fischler and his associates preferred to keep the civil servants in the dark. Because CAP reform would force DGVI civil servants to change how they worked and adopt new, often complex and cumbersome systems, Fischler thought it unwise to reveal the extent of the plan to them. Fischler was also concerned that the civil servants might leak aspects of the program to their permanent representations, allowing the member states to begin to mount a defense before he could announce his reform package . Retrenchment-minded welfare state reformers are also known to work in secret. Keeping potential reform proposals out of the public debate and masking the costs of new policies and reforms are strategies commonly used by welfare state reformers to avoid resistance from those who stand to lose.

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A quota system would potentially cost France market share both internally and externally

France believed in general that the Commission had far exceeded the negotiating mandate that had been agreed to prior to the start of GATT negotiations. French representatives were particularly upset with the extent to which EU negotiators were willing to reduce or even eliminate export subsidies. The informal deal between Mitterrand and Kohl helped each side advance an interest of particular importance. This agreement was made possible by a meeting in September of 1991 of the Quadrilateral that confirmed that the terms of the MacSharry proposals could unblock the stalemate in GATT agricultural negotiations. Shortly thereafter, the German cabinet formally announced that it would not veto the CAP deal over a cereal price cut . An announcement from the French government in favor of the CAP reform quickly followed. To get to this point each government had to come to some hard realizations about the CAP reform under discussion. Germany was facing a domestic fiscal crisis induced by the costs of reunification. In addition, its farming sector had changed dramatically. While small farms had dominated in the West, the East German model was the factory farm. East German farms lagged in production, but they were expected to rapidly become more efficient with access to improved technology and information. Any surpluses produced by the East would, under the current model, add to CAP costs and expenditures. Germany was already one of the main underwriters of the CAP budget and was confronted with having to pay even more to fund the CAP. These budgetary increases would also come in addition to the growing costs of reunification. While some of the new money from added CAP costs would be filtered back to the East German farmers, Germany’s overall contribution to the CAP would likely increase at a higher rate than its return,blackberry cultivation as CAP costs continued to grow rapidly. It was therefore more economically advantageous for Germany to advocate for a smaller and less expensive CAP, which would reduce Germany’s overall contribution, leaving more money to be deployed as needed domestically. Germany also desired a successful conclusion of the GATT round, which would benefit its industry tremendously.

The MacSharry Reform marked the first time that Germany faced significant resistance to agricultural policy from industrial and economic circles, with the Federation of German Industry stating a preference for agricultural policy reform, albeit cautiously . This opposition from industry marked a major change, given that industrial and agricultural interests had been bonded in a close alliance dating back to Bismarck . A GATT deal could not be reached without progress in the agricultural sector, and a reduction in price supports would go a long way towards making GATT progress possible. Kohl therefore broke with Germany’s traditional stance against price cuts, announcing that “the EC agricultural reform was not possible without substantial price cuts, especially for cereals” . France’s acceptance of reform was made possible by four developments. First, there was recognition that a structural change needed to be made. Production that continued unchecked would lead to increasing expenditure and thus an endless cycle of budget crises. Second, French officials realized that the structural reform on the table, price cuts paired with compensation, favored the French production profile. At the time, France was not only an efficient producer but also Europe’s leading exporter of agricultural goods and the world’s second leading exporter of cereals, a position the French were bent on maintaining. Given the strong position of the agricultural sector, particularly in cereals, the French government and the French Grain Farmers Association recognized that France could remain competitive, if not gain market share, under a system of price cuts while less efficient farmers in other countries would not be able to compete with the French. The status quo in the CAP, with its system of export subsidies, high prices, and import tariffs allowed even small and inefficient producers to sell their goods competitively alongside those of the largest and most efficient producers. If prices were cut, large grain producers would remain competitive, due to their efficiency, but the smaller farmers would be rendered uncompetitive. With these producers driven out of the market, the larger and more efficient French farmers could then gain market share. The third development that pushed France toward accepting the reform was the acceptance that for some products, the status quo was no longer tenable.

The AGPB was warned by Guy Legras, DGVI director and part of the EU’s GATT team, that new GATT rules were likely to require duty free importation of PSCs, or “products to substitute for cereals” and that, without a cereals price cut, French farmers would be unable to compete with PSCs . Cereals producers grow grains for both human and animal consumption. If the system of high prices was maintained and the GATT agreement proceeded as expected, grains produced for animal feed would be far more expensive than the PSCs, and French grain growers would lose market share and revenue as livestock farmers turned to alternative food sources for their animals. So, while the main French farmers’ union, the FNSEA maintained its “no reform and no discussion of reform” position, the powerful grain farmers, represented by the AGPB broke with the FNSEA and lent their formal support to the French government’s acceptance of the MacSharry Reform. The fourth factor that led to France swinging to support the reforms was the fear of the consequences of a failed reform. Specifically, what was most feared was a quota system, a possible alternative way to check spending and production if price cuts failed. In other words, while the possibility existed to impose reform via price cuts now, the failure to adopt reform would put the CAP into a position where the only possible alternative to control CAP spending would be to impose a quota system. At this point, a quota system existed, but only for the dairy sector. It was controversial, because it placed a strict limit on production, dividing up “shares” among producers and prohibiting production beyond the specified amount, even if it could be done more cheaply and efficiently than a competitor. In terms of the internal market, if demand exceeded production limits in France, milk would have to be brought in from producers in countries where quota limits exceeded domestic demand. Externally, efficient French producers would be unable to produce and sell milk beyond their strict quota limit, restricting their ability to expand their market share. A quota system would place a hard limit on production, continuing to prop up smaller and less efficient producers by guaranteeing them a market while restraining the ability of the efficient producers to expand into and serve new markets.

While French farmers were split over price cuts, they were united in their opposition to a quota system. In sum, on this first core issue of the negotiations, price cuts, Denmark, the Netherlands, and the United Kingdom were in favor of them from the start. The southern bloc of Greece, Spain, Portugal, and Italy were not opposed, as these proposed cuts did not affect their main agricultural products. The final three member states took a more circuitous path to support for the price cut element of the reform. Germany, though traditionally in favor of high prices, ultimately supported price cuts in an effort to ameliorate a domestic financial crisis brought on by the costs of reunification and to help clear the way for a hugely beneficial GATT agreement. Though initially opposed, France ultimately accepted the proposed price cuts thanks to support from the AGPB, an acceptance that reform had to happen in order to preserve the CAP,plastic plant pot sizes and a recognition that the reforms on the table favored the existing French production profile. Finally, Ireland’s stake was only in the beef sector- it did not grow cereals, and its cattle were all grass fed. As in France, support from the Irish Farmers Association led to support for these measures from the country’s representatives. The second major issue under discussion concerned the measures to redirect support to small farmers. The support of the pro-market countries, Denmark, the Netherlands, and the UK, was won with two key concessions. While none of these countries opposed price cuts, they all opposed modulation. Home to some of the largest farms in Europe, these countries felt that their farmers would be disproportionally punished by a system that reduced compensatory payments for large farmers and redirected those savings to smaller farmers. The Commission ultimately dropped all systems that would modulate income payments to the benefit of small farmers. This concession was necessary for reasons that again echo welfare state reform. Under modulation, it was very clear which farmers would be subjected to financial loses but it was far more uncertain which farmers would benefit, how much, and when. With certain losers but uncertain winners, it was easy to rally opposition to the program. The lackluster defense of the program was exacerbated by the wide variation in production size and style in the member states. The clear losers could rally their leaders against the reform, but winners, not knowing who they would be, did not mobilize. Finally, it was broadly understood that the inclusion of modulation was a deal breaker for Denmark, the Netherlands, and the UK. In order for negotiations to proceed, it had to be dropped. Denmark, the Netherlands, and the UK also won a concession over their other major sticking point. They objected to the compulsory land set-asides, which would require only farmers with the largest holdings to remove land from production. Under the proposal, farmers would not receive any compensation for this set-aside land. As they were home to some of the largest farms in the EU and thus also the farmers who would be subjected to this set-aside policy, Denmark, the Netherlands, and the UK staunchly opposed this program, arguing that it was unfair to their farmers.

To quell these objections over compulsory land set-asides, and the “inequity” of small farmers being exempted from them and thus being eligible to receive some form of income support for all of their land, the Commission offered a further concession that all set-aside land would be eligible to receive compensatory payments. The third core issue in the negotiations was the milk quota. While the proposed reform called for a reduction in milk quotas, Italy, Spain, and Greece demanded an increase. This demand was strongly opposed by Belgium, Denmark, Luxembourg, the Netherlands, and the UK. These “northern bloc” countries were upset that the southern European countries were not respecting the system already in place . These countries, and Italy in particular, were singled out for demanding an increase its quota while not respecting the existing quota. Italy, for example, had still not implemented or adhered to the quota system adopted by the EU in 1984. An agreement was reached that included a guarantee not to cut quotas and an offer for a quota “adjustment” once the previous quotas had been applied satisfactorily . Though not directly specified as such, an “adjustment” was understood to be an increase. The final reform package included four central components. The first component was price cuts for the three sectors most affected by overproduction: cereals, beef, and dairy. These sectors were subjected to price cuts of 29%, 15% and 5% respectively. These cuts were to be lagged, coming into effect gradually over a period of roughly five years. Within dairy, milk production, which is regulated via quotas rather than price controls, was not subjected to any alteration of quota amounts, despite proposals to reduce their levels. The second component of the agreement was the adoption of a series of payments to compensate farmers for revenue lost due to the price cuts. Instead of being paid based on output through a series of high, fixed prices and export subsidies, farmers would now be paid a direct payment that had no connection to current production levels. The direct income payment would be calculated based on the historic yield of a given crop for that region. At this stage, the direct payment based on historic regional yields would only be applied to a portion of the farmer’s land.

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Three key policy instruments supported the price guarantee system

The most commonly used have been compensation and vice into virtue. Such is the farmers’ influence that is is nearly impossible to impose new costs on them without offering some form of compensation in return. Vice into virtue, meanwhile, has facilitated the successful overhaul of major CAP systems by presenting the task as correcting a malfunctioning program as opposed to simply shutting it down. In sum, the first part of my argument shows why CAP reform is so difficult by revealing both how farmers have managed to retain political influence despite losses in demographic and economic power and by using welfare state theories to identify key obstacles to retrenchment. The second part of my argument identifies the circumstances that may permit systemic reform. The third enumerates the welfare state retrenchment tactics policymakers use to navigate and manage the influence of the farmers. Taken together, my argument accounts for when and why CAP reform occurs as well as the final outcome of CAP reform.Chapter Two describes the history and operation of the CAP leading up to the contemporary period of reform covered in the dissertation’s empirical chapters. The chapter focuses on three main periods of the early CAP: its creation in the 1960s, including early successes and challenges, the failed Mansholt Plan of the 1970s, and the limited changes of the early 1980s. I show that even in these early periods of reform, disruptive politics were a necessary condition for reform and that policymakers utilized welfare-style tactics to achieve what limited success they could. This overview provides the background necessary to understand contemporary challenges to the CAP and obstacles to reform. Chapter Three focuses on the 1992 MacSharry Reform of the CAP. The MacSharry reforms marked the first major overhaul of the Common Agricultural Policy since its adoption in 1962. The MacSharry Reform took place under conditions of disruptive politics,blueberry container size as the negotiations overlapped with the GATT Uruguay Round. The landmark reform paired vice into virtue with compensation in order to transform the CAP’s primary function from production to income support.

Specifically, the MacSharry Reform introduced, in a limited form, a direct payment system that paid farmers regardless of how much they produced, essentially “decoupling” payments from production. Overall, the chapter demonstrates that even when reform was urgently needed, reformers still had to employ a number of welfare retrenchment tactics to overcome farmer opposition and were ultimately unable to cut spending. Chapter Four explores the so-called Agenda 2000 reform. Agenda 2000 was intended to further the objectives outlined in the MacSharry round. However, Agenda 2000 was not negotiated during a time of disruptive politics. The surplus crisis had been resolved by the MacSharry Reform, no GATT/WTO negotiations were scheduled, and the next round of enlargement was far enough in the future that no immediate reform action was required. The Agenda 2000 reform thus allows for the dissertation argument to be tested on a reform that took place under politics as usual. I show that Agenda 2000 ultimately introduced only limited, mostly voluntary change along with substantial financial compensation to farmers. Chapter Five examines the 2003 Mid-Term Review of the CAP, also known as the Fischler Reform, which was not expected to bring about a significant change. This round of reform occurred under disruptive politics, however: the CAP confronted severe financial pressure from enlargement and contentious trade negotiations in the WTO. This round of CAP reform presented a favorable context for reformers to make changes and a challenge for farmers to prevent tough amendments to a flailing policy. Fischler’s reform continued and extended the process of decoupling, begun by MacSharry and also introduced a new version of the compensation scheme called the Single Farm Payment. In addition, Fischler was able to make mandatory environmental policies that had only been optional in previous reforms. Despite these changes, many proposed policy reforms were watered down significantly and reformers had to employ a number of tactics typically used by welfare state retrenchers to achieve their goals. For example, reformers paired a compensation program with the vice into virtue strategy to successfully introduce the Single Farm Payment. Chapter Six investigates the most recent round of CAP reform concluded in 2013, which occurred largely under politics as usual. The budget was not in crisis and the EU was not involved in any WTO negotiations. The only major reform achieved during these negotiations, the recalibration of the direct payment system, is the only one with a clear link to a source of disruptive politics, in this instance enlargement.

The CAP was still contending with the consequences of the previous rounds of enlargement, in particular issues related to an imbalance in payments made to Western and Eastern countries. In order to increase the likelihood of successful reform in at least this domain, reforms linked the policy revisions to the disruptive politics of enlargement, rather than presenting the reforms as routine policy maintenance. Other reform proposals, such as adopting strict greening standards, imposing a ceiling on direct income payments, and restricting the qualifications for receiving agricultural payments, were completely blocked. The within-case variation, then, illustrates the importance of disruptive politics for achieving CAP reform. In Chapter Seven, the conclusion, I demonstrate the applicability of the dissertation argument beyond CAP reform through three mini cases. The first analyzes national government responses to the financial crisis, the second Japanese agricultural policy, and the third farmer influence over international trade negotiations. Across all three cases, each in different institutional settings, a common theme emerges: whatever changes to agricultural policy may be enacted, it is difficult if not impossible to impose spending cuts on farmers. Finally, the conclusion considers the implications of my argument for EU policymakers, for welfare retrenchers, and for scholars of social class transformation and decline.The CAP emerged out of a political deal between France and Germany. France agreed to support the common market, which would be of great benefit to Germany industry, while Germany agreed to support a common policy for agriculture. Essentially, this promise meant that Germany would be paying for French farmer subsidies, and in exchange, France would open its market to German manufactured goods. The Treaty of Rome, signed in 1957, established the European Economic Community , and with it, the common market. It also included plans for a common policy for agriculture to be established within five years. While the Treaty of Rome did not outline the design or operation of the CAP, it defined the objectives of the CAP as follows: “to increase productivity by promoting technical progress…to ensure a fair standard of living…by increasing the individual earnings of persons engaged in agriculture; to stabilize markets; to assure the availability of supplies; to ensure that supplies reach consumers at reasonable prices” . The operational details would be worked out in a series of conferences, meetings, and negotiations that followed the signing of the Treaty of Rome in 1957, culminating in the formal launching of the CAP in 19626 . There was obviously some tension among CAP objectives, and the goal of ensuring products at reasonable prices for consumers would quickly be abandoned: the CAP would be grounded in a system of inflated prices, funded by taxpayers.When the CAP was established,raspberry planter famine was a recent memory, so there was concern for ensuring self-sufficiency in food. During WWII, Europe suffered from food crises ranging from shortages to famine. The Netherlands, for example, endured what is now known as the “Hunger Winter”, when an estimated 22,000 Dutch people died from starvation.

After the war, rationing was common as Europe struggled to feed itself. In Germany alone, the US, with support from the UK had, by 1948, provided nearly $1.5 billion in food aid. The memories of Europe’s food insecurity were, and remain, powerful. Indeed, in speaking to policymakers in the Netherlands about the importance of the CAP, nearly every official referenced the Hunger Winter, even those who would not have been alive at the time . One of the core goals of the architects of the CAP , was to ensure that Europe would always be able to feed itself by boosting agricultural productivity and output. CAP founders also had a social objective, seeking to close the income gap between farmers and industrial workers. In the years just before the creation of the CAP, a noticeable gap had developed between the average earnings of farmers and those of individuals employed in other fields, most notably industry. For example, in Germany in 1958-1959, farm incomes were equal to 76% of non-farmer incomes . The situation was equally grim in the other member states. In France in 1961, farm income was estimated at “3,280 French Francs for farm owners and 2,540 French Francs for farm workers” compared to 4,690 French Francs for industrial wage and salary earners . Policymakers feared that, without intervention, this wage gap would only worsen. The ultimate result would be an uncontrolled rural exodus, collapsing the countryside and overburdening cities, as farm workers sought more lucrative industrial jobs. The CAP sought to achieve the goals of increased production and improved earnings through a system of price guarantees, with agricultural prices set well above world market prices.The first was a set of high import tariffs and other measures to limit the import of agricultural goods. The second was a guarantee to engage in intervention buying, whereby the EU would purchase those goods in excess of EU customer demand at inflated prices. The third was a system of export subsidies that allowed the EU to dispose of the excess product on the world market. Essentially, this system guaranteed that all agricultural output would find not only a buyer, but one who was willing to pay a much higher price than what the market dictated. The CAP registered three major successes in its early years. First, food production, stimulated by high guaranteed prices, increased rapidly. The CAP enabled Europe to attain food security and self-sufficiency. The Continent would never again have to rely on the US to feed its people. The CAP generated a steady supply of core goods including cereals, milk, and butter. In addition, European consumers were provided with an abundant and diverse selection of produce. The second major achievement of the CAP was the modernization of European agriculture. The high prices that incentivized production generated capital that farmers could now reinvest in their farms. In the past, European farmers had tried and largely failed to compete with cheap imports, particularly of cereals, from the United States and Canada. European farms lagged behind the United States, and most farmers did not have the means to modernize and become competitive. The CAP’s high prices and tariff barriers sheltered European farmers from US competition. Farmers who benefited from high prices were able to reinvest their profits into both new technology and more land. New technology facilitated more and faster production at a lower cost. The third achievement of the CAP was to manage Europe’s transition from a primarily agrarian and rural society to an increasingly urban and industrial society. In other words, the CAP allowed for the peaceful management of the rural community’s transformation. The new system which offered higher guaranteed prices allowed smaller and less efficient farmers to stay on the land and eke out a living instead of abandoning it as they otherwise might have done. Thus, instead of a mass rural exodus and the subsequent collapse of countryside, this system slowed the process and cushioned the decline of agriculture. That is not to say that no one left farming under the CAP. Indeed, opportunities for early retirement facilitated the permanent exit of a small number of farmers in a controlled manner. In fact, exit from the sector was used to strengthen it, as the departure of predominantly small and inefficient farmers allowed the larger and more productive farmers to buy up more land. Essentially, exit permitted a transition to a more modern, efficient model of agriculture, grounded in large farms as opposed to small family or subsistence farms that had once dominated the European countryside. Most importantly, this goal was achieved humanely and without democratic collapse, social upheaval, or economic catastrophe.

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There are also limitations in the measurement of the variables we used for analysis

The exposure variable as well as covariates were all measured using self-reported survey data and subject to recall bias, which has been well described for exposure and disease studies. We limited recall bias in the survey by anchoring the past in memorable events such as recent rainy and dry seasons as well as holidays. While survey respondents sometimes found it difficult to precisely quantify household land area, the evidence for recall bias in agricultural surveys in sub-Saharan Africa is limited. Additionally, infection outcomes are limited by the sensitivity and specificity of available diagnostic methods: urine filtration for S. haematobium and duplicate Kato-Katz examination of two stool samples for S. mansoni. The detection methods used for S. haematobium are more sensitive compared to those used for S. mansoni , but the low sensitivity of diagnostic techniques used to detect S. mansoni infections—especially low intensity infections—may have contributed to the inconclusive results we observed for this parasite species. Our findings add a new dimension to the notion that the benefits of water resources development for food security are offset by infectious disease. While we cannot speak to the dam’s net impact, we find that schistosomiasis risk may be a result of land use for subsistence livelihoods as well as landscape-level environmental change. Residents of the lower basin of the Senegal River face an unfortunate trade-of where the prevailing economic activity may make them sick.Every bio-process in which cells are the final product or used in the production process requires suitable culture conditions for cell growth and product quality. In the rapidly growing cellular agriculture/cultivated meat industry, where cells are grown for consumption to replace carbon‐intensive and often unethical animal agriculture,plastic plant container cost‐effective media has been identified as the most critical aspect in scale‐up and commercialization .

Optimizing these conditions is difficult due to a large number of media components with nonlinear and interacting effects between cells, medium, matrix material, and reactor environment . Typically, culture media used for processes in cellular agriculture consist of a basal medium of glucose, amino acids, vitamins, and salts supplemented with fetal bovine serum for improved cell survival. FBS is an undefined, animal‐derived serum consisting of proteins, hormones, and other large molecular weight components, and contributes substantially to the cost of media . Even when enriched with additional growth factors or FBS, media is often far from optimal for all cell types and requires adaptation and/or optimization , which is difficult for media mixtures with >30 components, as is common in cell culture. To manage this complexity, design‐of‐experiments methods are often employed in which factors are set to a user‐specified value and outputs are measured . These DOE designs are arranged in such a way that statistically meaningful correlations can be found in fewer experiments than techniques like intuition, “one‐factor‐at‐a‐time” sequences, or random designs. A more advanced form of this is to use sequential, model‐based DOEs such as a radial basis function or Gaussian Process , combined with an optimizer/sampling policy, to automatically select sequences of optimal designs. These approaches are often more efficient than traditional DOE at optimizing systems using fewer experiments and allow for more natural incorporation of process priors , measurement noise , probabilistic output constraints and constraint learning , multi-objective , multi-point , and multi‐information source designs . Even with these methods available, limitations still exist. In previous work, we applied a machine learning approach to optimize complex media design spaces but had limited success due to the difficulty in measuring cell number for multi-passage growth . Therefore, in this study, we utilized a multi‐information source Bayesian model to fuse “cheap” measures of cell biomass with more “expensive” but higher quality measurements to predict long‐term medium performance.

We refer to the simpler and cheap assays as “low‐fidelity” IS, and more complex and expensive assays as “high‐fidelity” IS. While not always predictive of long‐term growth, these lower fidelity assays are at least correlated with cell health and can help in identifying interesting regions of the design space for further study with the high‐fidelity IS. We used this model, with Bayesian optimization tools, to optimize a cell culture medium with 14 components while minimizing the number of experiments, optimally allocating laboratory resources, and building process knowledge to improve our optimization scheme and model. In Section 2 we discuss the computational and experimental components of this BO method. In Section 3 we present the results of the BO method in comparison to a traditional DOE method, followed by Section 4 where we demonstrate the importance of fusing multiple sources of information to obtain relevant process knowledge and/or optimization results.The system under consideration was the proliferation of C2C12 cells. These cells are immortalized muscle cells with similar metabolism and growth characteristics as other adherent cell lines useful in the cellular agriculture industry. Cells were stored in 70% DMEM , 20% FBS , 10% dimethyl sulfoxide freeze medium at −196°C until thawed. Vials were thawed to 25°C and the freezing medium was removed by centrifugation at 1500 g for 5 min. The centrifuged cell pellet was resuspended in 17 ml of DMEM with 10% FBS and placed on 15 cm sterile plastic tissue culture dishes . Cells were incubated in a 37°C and 5% CO2 environment. After 24 h the medium was removed, the culture dish‐washed with Phosphate Buffer Solution , and fresh DMEM with 10% FBS was introduced. After an additional 24 h, cells were harvested using tripLE solution , diluted in PBS, and counted using Countess II with trypan blue exclusion and disposable slides . The process of removing cells from a plate, counting, and re‐plating them with fresh medium is called sub-culturing or passaging.

How well the C2C12 cells survive and grow after passaging is indicative of their long‐term potential in a large cellular agriculture process. The design space was comprised of the components and minimum/maximum concentrations listed in Table 1. These components were chosen because they are often used to supplement standard DMEM to improve cell growth; this represents a reasonable test case for the industrial application of these multi‐IS BO methods to the cellular agricultural industry. The composition of standard DMEM , is shown in Table 3, and should not be confused with the base DMEM “supplement” , which contains only amino acids, trace metals, salts, and vitamins and none of the other 14 components. pH and osmolarity are not controlled in this study, so act as latent variables.Production scale cellular agricultural processes will require >10 passages of cell growth so optimizing growth based on single‐passage information is not adequate . However, multi-passage growth assays are difficult/ expensive to measure, and even more difficult to optimize when given many components. We managed this complexity by coupling long‐term cell number measurements with simpler but less valuable rapid growth chemical assays in murine C2C12 cultures as a model system for cellular agricultural applications, capturing a more wholistic model of the process. We combined this with an optimization algorithm that efficiently allocates laboratory resources toward solving argmax D x for desirability function D x , a function that incorporates both cell growth and medium cost. This resulted in a 38% reduction in experimental effort, relative to a comparable DOE method, to find a media 227% more proliferative than the DMEM control at nearly the same cost. As the longer‐term passaging study suggests, our Passage 2 objective function and IS were well‐calibrated to mimicking the complex industrial process of growing large batches of cells over many passages,blueberry container with Passage 4 cell numbers well‐predicted by this objective function. The reasons for the success of the BO are myriad. The BO method iteratively refines a single process model to improve certainty in D x‐optimal regions, whereas the DOE relies on a series of BB designs where the older data sets are ignored because they were outside of the optimal factor space. The BO also used a variety of IS, whereas the DOE only used a single low‐fidelity AlamarBlue metric . Looking at Figure 8c, the AlamarBlue and LIVE tended to cluster around the point y = 1, making it difficult to distinguish between high‐quality and low‐quality media. This may be due to the deviation of linearity of the %AB and F530 metric at high biomass. The BO method also refined its multi‐IS model over the entire feasible design space, allowing it to take advantage of optimal combinations and concentrations of all 14 components over the entire domain, whereas the DOE needed to reduce the design and factor spaces to reduce the number of experiments needed, and may have identified the wrong optimal boundary locations resulting in suboptimal experimental designs. The BO method was also able to leverage information about process uncertainty to improve the model is poorly understood regions of the design space, whereas the steepest accent method used by the DOE chased after improved D x with little regard for overall noise or experimental errors.

This was worsened by the sensitivity of the polynomial model to random inter‐batch fluctuations in %AB, which may have driven the DOE to suboptimal media. Note that the success of our BO method should not be taken as generic superiority over all potential instantiations of DOE or commercial media used for C2C12 growth. While the BO method worked well at solving the experimental optimization problem, the multi‐IS GP accuracy was limited to highly sampled regions of the design space, thus limiting the efficacy of sensitivity analysis. This was a conscious decision made to trade off postfacto analysis for sampling media with high desirability D x . Accuracy was also limited by the low amount of data N available relative to the large dimensionality p, which is inherently the case in complex biological experiments where each batch of q experiments takes >1 week to evaluate. Finally, the hyperparameters θ* used in the multi‐IS squared exponential kernel were deliberately regularized with prior distributions to smooth the posterior of the prediction μ x . Regularization may have diminished the quality of the inter‐IS correlations; the model hyperparameters ignored features where IS differed in favor of a simpler correlative structure to explain the data. This is seen in Figure 8b,c, where the kernel evaluations show nearly equal inter‐IS correlative strength for most IS used. This may have “squished”/ignored features that could have provided additional information, but at the cost of sampling the design space too widely, again a deliberate choice of model skepticism towards outliers. Even with these limitations, the BO method clearly performs well on media optimization systems relevant to cellular agriculture, that is, those with multiple and potentially conflicting information sources with varying levels of difficulty in measuring. The media resulting from the BO algorithm supported significantly more C2C12 cell growth with only a small increase in cost. This algorithm performs better than traditional DOE in this case, especially in incorporating critical data from growth after the multiple passages in an affordable manner. With these results, it should be possible to implement this type of experimental optimization algorithm in other systems of importance to cellular agriculture and cell culture production processes with difficult‐to‐measure output spaces, including for optimization of serum‐free media for cell growth and for differentiation.Water management is becoming more challenging by the effects of climate change, population growth, and severe competition for water by the municipal, agricultural, industrial, and energy sectors. Accordingly, integrated water resources management focuses on water demand and supply management to achieve sustainable development. Water is a scarce resource essential for societal survival and functioning. This makes the application of integrated water resources management essential to cope with scarcity and the challenges posed by climate change and increased water demand to by expanding economies. A conceptual framework combining integrated landscape management and institutional design principles perspectives was applied to analyze cooperation initiatives involving water suppliers and agricultural stakeholders from agricultural wastewater. A national drought risk assessment for agricultural lands taking into account the complex interaction between different risk components was presented. The research showed that crop diversification, crop pattern management, and conjunctive water management can be effective in improving agricultural water.