Month: December 2024

Modern nanochemistry has developed efficient techniques to manipulate nanoscale objects with a highly advanced degree of control. Chemically engineered nanoparticles can be synthesized with a large choice of sizes, shapes, constituent materials and surface coatings, and further assembled spatially into self-assembled structures, either spontaneously or in a directed manner. Advances in particle self-assembly and the quasi unlimited range of nanostructures with controlled architectures and functions available suggest that such assemblies may also provide a simple route to meta materials at infrared and visible length scales. Indeed, nanochemistry and self-assembly strategies are able to inexpensively produce materials whose inner structure is natively in the right range of sizes for optical and infrared applications and can provide fully three dimensional structures, thus opening the way to the fabrication of 3Dmeta material samples of finite volume of the highest importance to many applications. Such meta materials may be used, for example, to create 3D homogeneous, isotropic negative index materials , with simultaneously negative permittivity and magnetic permeability, cloaking devices or light-based circuits manipulating local optical electric fields rather than the flow of electrons. In this work we investigate certain EM properties of meta materials formed by densely arrayed clusters of plasmonic nanoparticles, big round plant pot which will be referred to as nanoclusters. Nanoclusters are formed by a number of metal nanocolloids attached to a dielectric core, as in the examples shown in Fig. 1, and can be easily realized and assembled by current state-of-the-art nanochemistry techniques.

Such a kind of structure generalizes the concept of nanorings originally proposed in [2] to realize a magnetic media at visible frequencies and has been recently shown in [3] to have the potential of providing resonant isotropic optical magnetism. An approximate model based on the single dipole approach in conjunction with the multipole expansion of the scattered field is used here to evaluate the electric and magnetic polarizabilities of the nanocluster. Then, the permittivity and permeability of the composite medium are estimated by the Maxwell Garnett homogenization model. Results obtained by this approximate method will be compared with data from full-wave simulations, focusing on the characterization of the nanocluster resonant isotropic electric and magnetic responses to anincident wave field, and the possibility to realize an isotropic NIM at optical frequencies.Extreme droughts are increasing in frequency, severity, and duration in arid and semiarid regions around the world due to climate change. As a result, plant species that are typically capable of withstanding regular drought stress are exposed to conditions outside of their normal range, rendering them susceptible to opportunistic disease-causing agents. Theoretical frameworks describing the roles of environmental and biotic stressors in driving plant mortality are well established. However, there is a lack of empirical data with which to resolve how these factors interact in vivo. Furthermore, studies that document progression of stress and die back throughout the course of a multi-year drought event in situ are rare. In this dissertation, I detail a series of studies aimed at understanding mechanisms of dieback and mortality by focusing on a severe canopy dieback event in a classically drought tolerant chaparral shrub, big berry manzanita in Santa Barbara, California, during an historic California drought.

I provide strong evidence that dieback is caused by members of the fungal Botryosphaeriaceae family in conjunction with extreme drought, and that dieback is also related to increased drought stress along an elevational gradient. By conducting a field survey, I identify Neofusiccocum australe as the most prevalent and widely distributed fungal pathogen in A. glauca., and that dieback is strongly correlated with Bot. infection. Using a full-factorial design in a greenhouse experiment, I provide evidence that extreme drought and infection by N. australe can indeed act synergistically, together driving faster and greater mortality in young A. glauca than either factor alone. Lastly, by taking measurements on water availability, dark-adapted leaf fluorescence, and photosynthesis in A. glauca shrubs across an elevational gradient, I provide evidence that landscape-level factors can contribute to localized variability in water stress and canopy dieback severity in A. glauca, and may be useful in predicting vulnerabilities during future drought. Remarkably, no new mortality was observed throughout the study, suggesting extreme resiliency in adult shrubs. However, canopy dieback alone can impact wildlife and fuel loads, even when not associated with mortality. Together, these results provide strong evidence that A. glauca dieback was caused synergistic effects between extreme drought and infection by N. australe, and that lower elevations and exposed slopes may be at greatest risk for future events. According to the most conservative estimates, global mean annual temperatures are now outside the historic range of the last 1,300 years . Simultaneously, mean annual precipitation has declined in many parts of the Northern Hemisphere, resulting in increased drought events . Extreme climatic shifts are predicted to affect, both directly and indirectly, biogeochemical cycling, energy fluxes, wildlife habitat, and ecosystem goods and services on a global scale . An important component in preparing for the effects of these events is to understand how communities will change in response to them, making this a critical topic for ecological research . For species to survive in dry climates, they must have evolved drought tolerance mechanisms .

However, extreme climate events can expose species that are typically capable of withstanding regular drought stress to conditions outside of their normal range. Furthermore, physiological responses to extreme drought can also have a negative feedback on plants’ defensive abilities, rendering them susceptible to biotic attack including by insects or disease agents . Consequently, synergies between extreme climatic events and biotic attack will likely lead to more dramatic changes than would otherwise occur in historically “drought tolerant” plant communities . Future climate change is expected to exacerbate these interactions worldwide. . Widespread tree mortality from drought has been documented in forested systems around the world , and biotic attack has been associated with many of these events . However, much less focus has been given historically to understanding the consequences of extreme drought on shrubland communities like chaparral , particularly in conjunction with biotic influences. Therefore, as we face predictions of hotter, longer, and more frequent drought , it is becoming increasingly critical to hone in on the mechanisms, tipping points, and ecosystem impacts of these events. Furthermore, identifying plant mortality thresholds is of upmost importance for predicting susceptibility to extreme drought events of the future . California recently experienced a record-breaking, multi-year drought from 2012- 2018, estimated to be the most severe event in the last 1,000 years , with the 2013-2014 winter season being one of the driest on record . Drought tolerance has long been considered a common trait of shrub species in California chaparral communities where hot, rainless summers are the norm . However, round plant pot in the Santa Ynez mountain range in Santa Barbara County, the dominant and widespread big berry manzanita exhibited dramatic dieback related to multi multi-year drought along with infection by opportunistic fungal pathogens in the Botryosphaeriaceae . These observations indicate that this species may be reaching a threshold in its drought resistance capabilities. Studies have reported Arctostaphylos spp. to exhibit unusual scales of dieback during periods of extreme drought stress, , however this could be the most severe dieback event in recent history, both in terms of scale and severity. Manzanita are important members of the chaparral ecosystem, providing habitat for wildlife and food through their nectar and berries . Additionally, their structure makes them important components of historical chaparral fire regimes, and their fire-induced germination strategies contribute to post-fire successional trajectories . Large-scale mortality of this species could reduce resource availability for wildlife, as well as alter fuel composition and structure in the region, resulting in an increased risk of more intense, faster burning fires. Therefore, the potential continued dieback of A. glauca is of great concern for both ecosystem functions and human populations alike. Significant dieback of A. glauca in Santa Barbara county, California, was first observed in winter, 2014 . Preliminary observations revealed patterns of dieback occurring along an elevational gradient, with effects being most pronounced at lower elevations than at higher elevations. It was also observed that dieback was most prevalent in stands located on steep, exposed southerly-facing slopes. These observations are consistent with findings by previous studies , Since A. glauca is classically drought-tolerant and able to function at very low water potentials , it raises the question of what is driving this extreme dieback event?

Could A. glauca be reaching a tipping point as a result of extreme drought stress, presence of a fungal pathogen, or both?My dissertation research focuses broadly on the influence of drought and fungal pathogens on this classic, drought tolerant chaparral shrub species. Through a combination of methods, I explore the individual and interacting roles of water stress and opportunistic fungal pathogens in A. glauca in a major dieback event, and track the fate of individual shrubs through the progression of an historic drought. My findings are organized into three chapters based on the following questions: What are the identities and distribution of fungal pathogens associated with A. glauca dieback ; How do drought stress and fungal infection interact to promote dieback and mortality in A. glauca ; and How does A. glauca dieback progress over time during drought, and how do landscape variables and drought stress correlate with dieback ? In Chapter 2, I identify fungal pathogens in A. glauca, and discuss their distribution across the landscape in the Santa Barbara county front country region. Based on preliminary findings showing significant levels of N. australe in the field, I expected to find high incidence of this opportunistic pathogen in A. glauca across the landscape, suggesting their role in drought-related dieback. The data support this prediction, as over half of the pathogens isolated were members of the Bot. family, and the majority of these were identified as N. australe, a novel pathogen in the region. Furthermore, Bot. infection was highly correlated with dieback severity, which was greatest at lower elevations. Taken together, the results show that opportunistic Bot. pathogens, particularly N. australe, are highly associated with A. glauca dieback across the landscape, and that lower elevations may be particularly vulnerable. In Chapter 3, I address the hypothesis that extreme drought and N. australe function synergistically to promote faster and greater mortality than either factor alone. I designed a full-factorial greenhouse experiment to identify whether A. glauca dieback is driven by extreme drought, infection by the fungal pathogens, or both. The results of this experiment support my hypothesis. Young A. glauca inoculated with N. australe while simultaneously exposed to extreme water stress exhibited faster stress symptom onset, faster mortality, and overall higher morality than those subjected to either factor alone. These results provide strong evidence that the severe A. glauca dieback event observed during the 2012-2018 drought was the result of synergistic interactions between extreme drought and opportunistic pathogens, rather than the nature of the drought or particularly virulent pathogens. In Chapter 4, I explore factors that are associated with climatic stress in order to draw correlations between A. glauca stress and dieback severity. Identifying such relationships can be useful in making predictions on dieback and mortality across the landscape. By analyzing data on predawn xylem pressure potentials and net photosynthesis in shrubs along an elevational gradient, I found that patterns of water availability and physiological function both varied greatly across the landscape, and only weakly correlate with dieback severity, suggesting factors other than elevation and aspect must also be important in driving plant stress and dieback. Extreme heterogeneity across this landscape likely confounded my results, yet may also play an important role in supporting the resiliency of A. glauca populations as a whole. By measuring the progression of dieback in these same shrubs over time, I found that dieback severity throughout the drought increased most at lower elevations compared to high, providing evidence that shrubs at lower elevations may be particularly vulnerable. Unexpectedly, no new mortality was observed in surveyed shrubs as the drought progressed, even though many plants exhibited severe levels of dieback throughout the study. This result shows that high levels of dieback severity do not necessarily predict morality in A. glauca. In summary, my dissertation provides strong evidence that A. glauca dieback during the recent California drought was caused by synergistic interactions between extreme drought stress and infection by widely distributed opportunistic fungal pathogen N. australe.

Analysis in the following sections expands on previous work by including consideration of recharge water from reservoir reoperation, evaluation of recharge water sourcing, cropland characteristics and groundwater hydrology for a site-specific setting and demonstrating a hydro-economic optimization approach that simulates separate decisions for land access and water delivery in the performance of Ag-MAR.The regional-scale analysis is conducted for a semi-arid part of California, USA that has conditions fairly common for many parts of the globe. The two groundwater sub-basins in the study area are part of the much larger Central Valley groundwater system with an interfingered assemblage of alluvial and flood-basin deposits of local maximum depth exceeding 1,000 ft . Many of the sub-basin boundaries shown in Fig. 2a are arbitrarily based on surface-water features, and the southern boundary has recently been adjusted northward to accommodate governance considerations for current groundwater management efforts . The 525,000-acre study area has a mix of urban , agricultural , wetland and undeveloped rangeland land uses . Over 90% of the total water use in the study area is supplied by groundwater . Moreover, square pot plastic approximately 41% of the agricultural acreage is planted as vineyards and orchards . This investment in perennial crops hardens water demand and intensifies groundwater extraction during droughts. The spatial distribution of recent water levels indicates localized depressions from extractions far exceeding groundwater recharge . Groundwater levels have dropped as much as 60 ft over the past several decades so that surface water frequently becomes disconnected from saturated groundwater and drains into the subsurface. The lower reaches of the Cosumnes River, in the central part of the study area , are dry 85% of the time .

New regulations for sustainable groundwater management in California require that this chronic lowering of groundwater levels and depletion of storage be addressed through active measures . While restoration of surface-water base flow in the study area may not be required because impact occurred before implementation of the regulations, there is interest in maintaining, and possibly improving, groundwater support of surface-water flows . Consistent with recent analysis , local stakeholders are interested in harvesting runoff from high-precipitation events for recharging groundwater. One option is reoperation of Folsom Reservoir to release extra water in advance of significant rain events alone could achieve a potentially significant amount of aquifer recharge using some of the 140,000 ac of croplands in the study area . This work presents a planning-level analysis of what might be possible. While infrastructure construction costs are not considered, the results of this work might encourage further evaluation of necessary investments.A retrospective analysis is conducted to evaluate the range of improvements in groundwater system state that might have occurred for the study area from an Ag-MAR recharge program. Recharge water is from simulated reoperation of Folsom Reservoir with delivery through the Folsom South Canal consistent with capacity limitations over a 20-year period that covers water years 1984 through 2003 . The timing and amounts of surface water delivered to croplands for recharge application is prescribed by a linear programming model that combines available information regarding surface water and groundwater hydrology with the spatial distribution of croplands. Groundwater recharge is simulated with a groundwater/surface-water model that incorporates existing land uses, surface-water deliveries and groundwater demands over the period considered .This analysis applies a formulation of simulation-optimization to MAR.

Previous work includes Mushtaq et al. who simulated unsaturated flow from individual recharge basins and applied nonlinear programming to identify optimal loading schedules for maximizing recharge volume. Marques et al. included decisions for recharge area allocation and water volume application as part of a two stage quadratic programming analysis that maximized crop profits. Hao et al. used a genetic algorithm to maximize recharge volume while meeting constraints on groundwater elevations. To the best of the authors’ knowledge, the approach presented here is new in that it combines elements of recharge basin and groundwater hydraulics with economic considerations at a regional scale. The foundation of the linear programming approach is based on the study area hydrology which is adapted to include economic considerations regarding land use. A hydrologic formulation is presented as an explanatory step in developing the full hydro-economic formulation.The formulation objective, Eq. , maximizes the volume of water recharged over the planning horizon subject to a set of operational constraints. The total volume of water recharged in any period t cannot exceed the water available for recharge , which is derived from a reoperation of Folsom Reservoir to provide additional water during November through March each year. The reoperation is performed by maximizing reservoir releases during the aforereferenced months while maintaining expected levels of service for flood control, water supply and hydropower generation . The levels of service are maintained with a set of optimization constraints that include downstream requirements for minimum environmental flows and water supply as well as the reservoir operation rule curve. The analysis is based on a perfect foresight formulation which provides an upper bound for recharge water available from the reservoir. A static upper bound on the volume of water recharged at a particular location , is based on local infiltration capacity and field berm height through an analytical ponding and drainage model described in the Appendix. Equations and dynamically constrain the magnitude of recharge decisions as a result of a cap on groundwater elevation to avoid water-logging of soil. This constraint is tied to the buildup and redistribution of recharged water as a result of groundwater flow and is described further in the Appendix.

Negative recharge decisions are prevented with Eq. .Cropland area use for recharge as a function of funding is presented in Fig. 10a,b. These are the results of parametric analysis using Eq. . Differences between the results for hydroeconomic analyses and the reference curves occur because, as indicated by the curves for individual crop categories , some of the more expensive land is brought into use before all of the least expensive land has been used. This result is driven by variation in infiltration rate across the study area which is controlled by the shallow geology and the interconnectedness of high conductivity sediments at depth used in the ponding model of Eq. . Figure 11 shows the spatial distribution of land use for two different levels of funding. For low amounts of funding, land is brought into use where there is a combination of cheaper land and higher infiltration rates in an effort to maximize the product of decision variables RA and D. This observation is consistent with the steep slope of recharge volume as a function of funding for land use at low funding levels . Spatial distribution of the recharge water cumulative depth per year is presented for the maximum funding and land use in Fig. 13. The values are generally within a reasonable range based on currently available information on crop inundation tolerance; however, large plastic planting pots constraints could be added to control cumulative water application as necessary. Figure 14 indicates the increase in groundwater storage from recharge using all of the cropland . Recharging over the 20-year planning period used 36% of the WAR . Simulation of the optimal recharge scenario with the groundwater model indicates the most of the water remains in the groundwater system ; however, appreciable amounts exit to surface water or flow across sub-basin boundaries . Additionally,the recharge provides enough base flow to support flow in the Cosumnes River throughout the 20-year simulation except during a 5-year drought from 1987 through 1992. Table 2 presents results for a range of recharge funding levels. Volumes discharging to surface-water and flowing to other sub-basins increase with the volume recharged since head buildup from adding water to the system is more pronounced. Comparison of the recharge volume results from the hydroeconomic analysis for cost set No. 1 with reference curves from the initial capture analysis indicates the effect of including study area hydrogeology in the analysis . High infiltration rate sites are selected preferentially, even when the amount of recharge area is limited by funding, and plot on the left side of the hydro-economic curve. These sites drain quickly and the results plot above the reference curves . Only few such sites are within the footprint of the cropland and, when greater amounts of land are used for recharge, the additional sites drain slower and plot below one or both of the reference curves. The result is a recharge capture curve for the study area that is shallower in slope than the reference curves. Therefore, the spatial variability in infiltration rate magnifies the diminishing returns to scale already occurring as a results of the temporal variability of the water source. More recharge could be achieved, and the study area capture curve moved higher on the plot, if the berm heights around the cropland were increased.

The linear programming results obtained can help develop guidance on where such capital investment might be most valuable. Reformulating the Lagrange multiplier for Eq. in terms of the berm height indicates where and how much additional water could be recharged over the planning horizon if berms were raised from 1–2 ft . This result provides a high estimate of what might be possible since some perennial crops may be unable to accommodate the increased ponding depth; nevertheless, this information provides guidance for where efforts might be best spent increasing berm heights. The values for Lagrange multipliers based on increasing berm height by 1 ft are low in the northern portion of the study area because little cropland is present . Given the high infiltration rates of the deeper geology in the north , recharge potential would be much better for a gravel pit since it would provide additional land area and also penetrate the low hydraulic conductivity soil layer included in this analysis. Cropland present in one of the northern model elements with high-infiltration rate was used to simulate the potential effect of repurposing a gravel pit for recharge. A total of 570 ac in crop categories 2, 3 and 4 were used to simulate gravel pits by increasing the hydraulic conductivity of the soil layer to match the underlying geology and increasing the berm height to 20 ft . Figure 16a,b summarizes the results of gravel pit simulation at the maximum annual funding level. Recharging over the 20-year planning period uses 50% of the WAR . Most of the water remains in the groundwater system with amounts similar to the previously presented results exiting to surface-water and flowing across sub-basin boundaries . Allocation is skewed towards the gravel pits and provides enough base flow to support continuous flow in the Cosumnes River throughout the 20-year simulation including during the previously mentioned 5-year drought. This approach could entail representing cropland managers as individual profit maximizing agents along with the groundwater management agency charging fees for groundwater pumping and providing rebates for recharge. This approach would relax the assumption of uniform land use rents for each crop category and include a more likely dispersion of land use costs across the study area. It is unclear if the aggregate effect of net metering with modest pumping fees would significantly differ from the work presented here since the influence on rational profit maximizers of a net rebate, rather than a payment for using land for recharge, may be similar. However, the effect of net metering combined with a cash flow constraint applied to water management operations could impose limits on a program for improving groundwater system conditions. Given the regulatory requirement for improved groundwater system state, these changes could drive pumping fees higher and influence the behaviors of profit maximizing land managers. It may also be possible to explore improving groundwater conditions through water banking operations where capital investments and operations costs would be paid by a client, or clients, external to the sub-basins. Management policy questions would include: how much water would be left in-place to benefit the groundwater system and the longevity of withdrawal rights . Details of the policy decisions would likely have implications for the amount of infrastructure investment a water banking client might be willing to make. Either the cash flow or water banking approach might be modified to encourage recharge in areas where it is most needed.

Drawing upon Bar-Tal , we further define farmer values as a farmer’s worldview on farming – a set of social values or belief system that a farmer aspires to institute on their farm . In our study, examples of social-ecological mechanisms for farmer knowledge formation among these farmers included direct observation, personal experience, on-farm experimentation, and inherited wisdom from other local farmers. Similar to Boons’ conceptual guide, our results suggest that social-ecological mechanisms may play a central role in producing a farmer’s values and in integrating ecological knowledge into their farm operation. At the same time, results also highlight that social-ecological mechanisms may contribute to a farmer’s local ecological knowledge base, and importantly, place limits on the incorporation of social values in practice on farms. It is possible that social-ecological mechanisms may also provide the lens through which farmer values and ecological knowledge are reevaluated over time. Moreover, farmer values may also mutually inform ecological knowledge – and vice versa – in a dynamic, dialectical process as individual farmers apply their values or ecological knowledge in practice on their farm. Social-ecological mechanisms may also be key in translating abstract information into concrete knowledge among farmers interviewed. For example, experimentation may codify direct observations to generate farmer knowledge that is both concrete and transferable; or, to a lesser degree, personal experience may enhance farmer knowledge and may guide the process of experimentation. In general, large plastic pots for plants we found that farmers interviewed tended to rely less on abstract, “basic” science and more on concrete, “applied” science that is based on their specific local contexts and environment .

This finding underscores that for these farmers, their theory of farming is embedded in their practice of farming, and that these farmers tend to derive theoretical claims from their land.For example, the farmers who possessed a stewardship ethos viewed themselves as caretakers of their land; one farmer described his role as “a liaison between this piece of land and the human environment.” Farmers that self identified as stewards or caretakers of their land tended to rely most heavily on direct observation and personal experience to learn about their local ecosystems and develop their local ecological knowledge. This acquired ecological knowledge in turn directly informed how farmers approached management of their farms and the types of management practices and regimes they applied. That said, farmer values from this study did not always align with farming practices applied day-to-day due to both social and ecological limits of their environment. For example, one farmer, who considered himself a caretaker of his land expressed that cover crops were central to his management regime and that “we’ve underestimated how much benefit we can get from cover crops.” This same farmer admitted he had not been able to grow cover crops the last few seasons due to early rains, the heavy clay present in his soil, and the need to have crops ready for early summer markets. In another example, several of the farmers learned about variations in their soil type by directly observing how soil “behaved” using cover crop growth patterns. These farmers discussed that they learned about patchy locations in their fields, including issues with drainage, prior management history, soil type, and other field characteristics, through observation of cover crop growth in their fields.

Repeated observations over space and time helped to transform disparate observations into formalized knowledge. As observations accumulated over space and time, they informed knowledge formation across scales, from specific features of farmers’ fields to larger ecological patterns and phenomena. More broadly, using cover crop growth patterns to assess soil health and productivity allowed several farmers to make key decisions that influenced the long-term resilience of their farm operation . This specific adaptive management technique was developed independently by several farmers over the course of a decade of farming through long term observation and experimentation – and, at the time, was not codified in mainstream farming guidebooks, policy recommendations, or the scientific literature . For these farmers, growing a cover crop on new land or land with challenging soils is now formally part of their farm management program and central to their soil management. While some of the farmers considered this process “trial and error,” in actuality, all farmers in this study engaged in a structured, iterative process of robust decision-making in the face of constant uncertainty, similar to the process of adaptative management in the natural resource literature . This critical link between farmer knowledge formation and adaptive mangement is important to consider in the broader context of resilience thinking, wherein adaptive management is a tool in the face of shifting climate and changing landscape regimes . The underlying social and ecological mechanisms for farmer knowledge formation discussed here may have a role in informing adaptive management and pathways toward more resilient agriculture . In this sense, farmer knowledge represents an overlooked source for informing innovation in farming alternatively.

Farmer knowledge provides an extension to scientific and policy knowledge bases, in that farmers develop new dimensions of knowledge and alternative ways of thinking about aspects of farming previously unexplored in the scientific literature. Farmers offer a key source of and process for making abstract knowledge more concrete and better grounded in practice, which is at the heart of agriculture that is resilient to increased planetary uncertainties . Most of the farmers considered themselves separate from scientific knowledge production and though scientific knowledge did at times inform their own knowledge production, they still ultimately relied on their own direct observation and personal experiences to inform their knowledge base and make decisions. This finding underscores the importance of embedding theory in practice in alternative agriculture. Without grounding theoretical scientific findings or policy recommendations in practice, whether that be day-to-day practices or long-term management applied, farmers cannot readily incorporate such “outsider” knowledge into their farm operations. Farmers in alternative agriculture thus may provide an important node in the research and policy making process, whereby they assess if scientific findings or policy recommendations may or may not apply to their specific farming context – through direct observation, personal experience, and experimentation.Similar to Sūmane et al. , we found that the process for farmer knowledge formation, or precisely how farmers learn, is systematic and iterative in approach. In this study, farmer ecological knowledge was developed over time based on continuous systematic observation, personal experiences, and/or experimentation. This systematic approach that relies on iterative feedback to learning applied among these organic farmers is akin in approach to examples of adaptive management in agriculture . As highlighted in the results, it is possible for a farmer to acquire expert knowledge even as a first- or second-generation farmer. Documenting this farmer knowledge within the scientific literature – specifically farmer knowledge in the context of relatively new alternative farmers in the US – represents a key way forward for widening agricultural knowledge both in theory and in practice . This study provides one example for documenting this farmer knowledge in a particularly unique site for alternative agriculture. Future studies may expand on this approach in order to document other sites with recent but practical agricultural knowledge on alternative farms.Farmers in this study tended to think holistically about their farm management. For example, when the farmers were asked to talk about soil management specifically, several of the farmers struggled with this format of question, plastic pot plant containers because they expressed that they do not necessarily think about soil management specifically but tend to manage for multiple aspects of their farm ecosystem simultaneously. This result aligns with similar findings from Sūmane et al. across a case study of 10 different farming contexts in Europe, and suggests that farmers tend to have a bird’s eye view of their farming systems. Such an approach allows farmers to make connections across diverse and disparate elements of their farm operation and integrate these connections to both widen and deepen their ecological knowledge base.For most farmers in this study, maintaining ideal soil structure was the foundation for healthy soil. The farmers emphasized that ideal soil structure was delicately maintained by only working ground at appropriate windows of soil moistures. Determining this window of ideal soil moisture represented a learned skill that each individual farmer developed through an iterative learning process.

This knowledge making process was informed by both social mechanisms gained through inherited wisdom and informal conversations and ecological mechanisms through direct observation, personal experiences, and experimentation .As these farmers developed their ecological knowledge of the appropriate windows of soil moisture, their values around soil management often shifted. In this way, over time , farmers in this study learned that no amount of nutrient addition, reduced tillage, cover cropping, or other inputs, could make up for damaged soil structure. Destroying soil structure was relatively easy but had lasting consequences and often took years, in some cases even a decade, to rebuild. This key soil health practice voiced by a majority of farmers interviewed was distinct from messaging about soil health vis-a-vis extension institutions ), where soil health principles focus on keeping ground covered, minimizing soil disturbance, maximizing plant diversity, keeping live roots in the soil, and integrating livestock for holistic management . While these five key principles of soil health were mentioned by farmers and were deemed significant, for most farmers interviewed in this study, the foundation and starting point for good soil health was maintaining appropriate soil structure. The results of this study emphasize that the most successful entry point for engaging farmers around soil health is context specific, informed directly by local knowledge. Among farmers in Yolo County – a significant geographical node of the organic farming movement – soil structure is a prevalent concept; however, in another farming context, this entry point may significantly diverge for social, ecological, economic, or other reasons. Each farming context therefore necessitates careful inquiry and direct conversation with local farmers to determine this entry point for engagement on soil health. For this reason, in some cases it may be more relevant to tailor soil health outreach to the local context rather than applying a one-size-fits all model.The capacity to learn and pass on that learning are essential for farms that practice alternative agriculture to be able to adapt to everchanging social and ecological changes ahead . Across all farmers interviewed, including both first and second-generation farmers, farmers stressed the steep learning curves associated with learning to farm alternatively and/or organically. While these farmers represent a case study for building a successful, organic farm within one generations, the results of this study beg the question: What advancements in farm management and soil management could be possible with multiple generations of farmer knowledge transfer on the same land? Rather than re-learning the ins and outs of farming every generation or two, as new farmers arrive on new land, farmers could have the opportunity to build on existing knowledge from a direct line of farmers before them, and in this way, potentially contribute to breakthroughs in alternative farming. In this sense, moving forward, agriculture in the US has a lot to learn from agroecological farming approaches with a deep multi-generational history . To this end, in most interviews – particularly among older farmers – there was a deep concern over the future of their farm operation beyond their lifetime. Many farmers lamented that no family or individual is slated to take over their farm operation and that all the knowledge they had accumulated would not pass on; there exists a need to fill this gap in knowledge transfer between shifting generations of farmers, safeguard farmer knowledge, and promote adaptations in alternative agriculture into the future. As Calo and others point out, technical knowledge dissemination alone will not resolve this ongoing challenge of farm succession, as larger structural barriers are also at play – most notably, related to land access, transfer, and tenure .Most studies often speak to the scalability of approach or generalizability of the information presented. While aspects of this study are generalizable particularly to similar farming systems, the farmer knowledge presented in this study may or may not be generalizable or scalable to other regions in the US. To access farmer knowledge, relationship building with individual farmers leading up to interviews as well as the in-depth interviews themselves required considerable time and effort.

There are many possible reasons for why there were different results from these two studies. First of all, the difference in ages tested in these two studies could have played a role as Norman et al. found there was greater success for 28-29 day old chicks when compared to14-15 day old chicks. Additionally, the use of opaque tiers prevented the chick from seeing the reward on the tier in Norman et al. . It is possible that the inability to see the reward reduced the birds’ motivation to jump to the raised platform. Most importantly, the different rewards used could have also played a role in the different performances observed. Regardless of the reasons for the difference in results, this test poses issues when used as an evaluation of spatial cognition. The aspect of spatial cognition being measured was not specified and, more importantly, this test confounds spatial cognition with physical ability. The task increases in difficulty to reach the reward with each trial. This would explain the decrease in number of birds in both rearing treatments that were able to successfully reach the tier as the difficulty increased. Also, providing perches to pullets increases leg muscle deposition in adult hens , which could explain the different performances among the birds of the two rearing treatments. Gunnarsson et al. defended this test as a valid measure of cognition because there was “no obvious reason to believe that the physical effort required to jump from 40 to 80 cm was substantially different” . Although jumping from the ground to the 40 cm tier may not be more physically taxing than reaching the 80 cm tier from the 40 cm tier, these were not the only heights presented to the birds.

It would be reasonable to presume that reaching the 80 cm tier without the aid of an additional platform would be more difficult than reaching the 40 cm tier. The jump test may be used to evaluate differences in physical ability to reach higher tiers, square pots however this task cannot separate physical ability from spatial cognition . For these reasons, the jump test may not be an ideal test to determine if spatial cognition is impaired by lack of access to vertical space during rearing. This test involves presenting a subject with a variety of baited and unbaited holes arranged in a grid. An animal is placed in the arena and is given free choice to visit any or all of possible holes. However, revisiting a previously baited hole will not be reinforced, as the food reward will have already been consumed. Working memory keeps a small amount of relevant information readily accessible while an animal is completing a task . Spatial working memory can be evaluated by measuring how often the subjects revisit holes where they already consumed the reward or holes which have already found to be unbaited . This is measured by the ratio of rewarded visits to the number of visits to the baited holes . Alternatively, reference memory is a form of long-term memory. Spatial reference memory can be examined using the hole board apparatus by repeating the same array of baited and unbaited holes over the course of multiple trials to determine if the animals’ rate of finding baited holes improves . This is determined using the ratio of the number of visits to baited holes to the number of visits to all holes . This improvement implies the location of the food rewards is being retained in reference memory and is being successful retrieved during trials .

Tahamtani et al. investigated the impacts of rearing environment on navigation and spatial memory in laying hens using a hole board task. Chicks were housed in cages for 4 weeks after which the aviary-reared birds were released into multi-tiered aviaries while the cage-reared birds remained in cages until 16 weeks, when all birds were placed in group-housed furnished cages. The hole board task consisted of nine chalk circles with a blue cup positioned in the center, concealing a food reward of live meal worms. The birds were trained to associate the cups with a food reward and only those that readily explored the test arena and found meal worms were selected. Four phases were used for training and testing: uncued acquisition, cued acquisition, over-training, and reversal phase. Uncued training and testing involved baiting only three of the nine cups in the same configuration for all exposures without any specific cues for guidance. This acts as a baseline for the hens’ ability to learn the location of the baited cups without any specific cues. Cued acquisition followed, where hens were trained and tested on the same configuration, however red boards were placed under the baited cups to serve as an extra cue for the location of the food reward. This presents new information that may improve the birds’ ability to complete the task. For over-training, the cues were removed to reestablish their baseline performance. Finally, for the reversal phase, the hens were trained and tested on an alternate configuration of three baited and six unbaited cups. The reversal phase requires flexibility in reference memory, as the birds must override the previously learned configuration in favor of the new information.

It was found that cage-reared birds took longer to complete the hole board task during the reversal phase than the aviary-reared birds, while the aviary birds had a better score for their working memory during the reversal phase when compared to cage-reared birds. This impairment of working memory during task reversal may be due to the decreased complexity found in caged systems when compared to aviary systems. Multi-tiered aviaries provide a greater amount of variability in terms of social interaction and location of resources than caged systems,potentially aiding in the development of spatial learning and memory. The hole board task is an excellent test for evaluating spatial learning and memory, however this test is not relevant at determining if these birds are more capable of navigating vertical space, since it occurs on a flat surface, or geometric plane , and does not take into account vertical space. It offers insight on differences in the working memory of cagereared and aviary-reared birds, however these results do not suggest that chicks reared with access to vertical space have an enhanced ability to avoid colliding with structures.A radial maze is a cognitive task that is designed to evaluate spatial working memory . It involves multiple walkways, or arms, radiating out from a central chamber. A food reward is located at the end of each arm and the subject is placed in the center. The subject is then allowed to freely choose to enter the arms of the maze until all food rewards have been found. The optimum strategy for finding the food rewards would be to enter each arm only once, as previously visited arms will no longer contain a food reward. In order to efficiently solve the maze, the subject must employ working memory to retain information about which arms have already been visited. The animal does this by noting cues, typically extra-maze cues, to determine which arms they have already entered . Since this maze requires adequate spatial memory, it has been employed as a technique to evaluate spatial cognition in fowl raised in environments of varying complexity. Wichman used a radial maze to investigate spatial ability in 16 week old laying hens raised in three different rearing environments. All rearing treatments had access to perches at 20 and 40 cm of height but the control group had not additional enrichments. The floor enrichment group had the addition of wooden blocks while the hanging enrichment group had hanging discs and bottles at beak height. At 16 weeks of age, once all birds had been regularly perching, square plant pot the birds were tested on an eight arm radial maze. Each arm of the maze was baited at the end with a meal worm and birds were given 20 minutes to freely explore the maze. In order to simulate the practice of moving hens from their rearing house to the laying house, all birds were moved to larger, more complex pens at 18 weeks of age. These new pens included perches at varying heights , which could be reached from the floor or by jumping from one perch to another. It was found that there was a relationship between performance on the radial maze and propensity to perch. Birds that used perches the most during the two hours period after being released into the new, complex pens required fewer visits to the arms of the radial maze in order to find all eight of the meal worms. Wichman suggested that based on these results, there is a relationship between two-dimensional spatial ability required for performance on the radial maze and three-dimensional skills required for perching. However, there were no significant differences between the treatment groups for onset of perching or performance on the radial maze. The author suggested that the low height of the perches might have allowed for easy access to vertical space between all treatments. Therefore, there may not have been enough variation between the perching behavior of the chicks to result in clear differences between treatments.

Whiteside et al. used an eight arm radial maze to investigate the impacts of floor rearing on spatial cognition and survivability of pheasants raised in captivity and released for hunting. Whiteside et al. reared one day old chicks until 7 weeks of age in three different environments: standard commercial rearing with no access to perches; access to natural hazel boughs perches; and access to artificial perches. There were no significant differences between the natural and artificial perch groups, so these conditions were combined for analysis.At 6 weeks of age, 27 chicks were tested on an eight arm radial maze to assess their spatial working memory. At the center of the maze there was a circular starting compartment and at the end of each arm of the maze there was a barrier, which concealed a food reward. Orientation in the maze was possible using extra-maze cues as the walls of the testing room were all different in color. The birds were first habituated to the arena for four days and were tested on the task on the fourth day. To solve the maze correctly, the birds had to enter each arm only once and consume the food reward. If a bird entered an arm where they had already eaten the food reward, it was recorded as an error. Those that made the fewest errors were determined to have better spatial memory than those that made more errors. Birds reared without access to perches made significantly more errors in their first eight choices than birds reared with access to perches. This suggests that access to perches at a young age improved the spatial memory of pheasants, potentially aiding in their survival post release. It is also of interest to note that birds reared with perches roosted at night during the two weeks post-release significantly more than birds reared without perches. These two studies demonstrate that performance on a two-dimensional test of spatial memory may impact future use of vertical space. This could have implications for hens’ ability to recall the location of resources and ability to navigate complex environments as an adult .In the detour paradigm, the most direct route to a goal is blocked; the animal must walk around a barrier to reach the goal . For the initially visible goal detour task, the goal is visible at the starting point but then becomes occluded by opaque walls as the animal begins to move through the apparatus. When the goal is initially visible, spatial working memory as well as route planning must occur in order to hold the location of the goal in memory and make choices about what route should be taken. Success on this task is often interpreted as the animal making a mental representation of the location of the non-visible goal and then using this representation to determine the best route . Due to the use of route planning and the need to hold the location of the goal in working memory in order to successful solve this task, the detour paradigm has been frequently used to evaluate spatial working memory and route planning.

For organic growers, two AIs, spinosad and pyrethrins, are available to target those physiological functions. The “unknown” category, which is mostly sulfur, accounted for a significant portion of treated acreage in organic agriculture. Insecticides that target the midgut, which includes Bacillus thuringiensis and several granulosis viruses, are widely applied in organic fields. Conventional growers rarely use them due to the high cost. In 2015, acreage treated with midgut targeted insecticides was 1% of total treated acreage in conventional agriculture and 24% in organic agriculture. A detailed discussion of insecticide and fungicide use by mode of action in conventional and organic production is in the appendix.Insecticides and fungicides in the two pest management programs have different modes of action and pose different levels of environmental impact. Simply comparing treated acreage or the amount of pesticide products used does not identify the differences in environmental impacts. In this context, the PURE index serves as a consistent measure across farming systems.Figure 1.3 plots PURE indices for conventional and organic fields by year. Index values for air and soil are significantly higher than those for the other environmental dimensions in both farming systems, which means that pesticide use in general has greater impacts on air and soil quality than groundwater, pollinators, and surface water. Risk indices of conventional fields are relatively stable from 1995 to 2015, with no obvious overall changes for air or soil, despite the many changes that have occurred during this 20-year period in regulations and grower portfolios. While PURE indices decreased 16% for surface water, 26% for pollinators, grow bag for blueberry plants and 7% for groundwater over the same time period, these three were much less impacted by pesticides in 1995, the beginning of the study period.

Despite the numerous regulatory actions designed to reduce environmental impacts over this 20-year period, such as the methyl bromide phase-out, large-scale substitution of pyrethroids for organophosphates, and regulations to reduce VOC emissions from non-fumigant products, the overall environmental impacts of conventional pesticide use show only limited reductions when aggregated across all crops. PURE indices for organic fields are similar to conventional fields in that the air and soil have significantly higher index vales than the others. However, the aggregate risk indices in all five dimensions are much lower in organic fields. Compared to conventional agriculture, organic agriculture has dramatically lower PURE indices for surface water , groundwater , air , soil , and pollinators . The reduction for air varies greatly across major California crops. Large reductions in the PURE index for air are observed for table grapes , wine grapes , and processing tomatoes , while others had relatively small ones such as leaf lettuce and almonds . The reduction in the PURE index for soil varies across crops as well, ranging from leaf lettuce to carrots . For surface water, groundwater, and pollinators, the differences between the PURE index in organic and conventional fields are similar across crops. A noticeable spike in PURE indices appeared in 1998 for organic agriculture caused by a single application of copper sulfate with an application rate of 150 lb/acre, which is ten times larger than the average application rate and clearly a data abnormality. The PURE index is a measure of environmental impacts on the per acre basis.One could use the yield difference between conventional and organic agriculture to adjust values in Figure 1.3 and transfer them to a measure of impacts per unit of output. Organic agriculture is found to have 10%-20% lower yields than conventional agriculture . If we use the 15% yield loss as an average to adjust the results for all crops, organic agriculture reduced the PURE index for surface water , groundwater , air , soil , and pollinators .

The impact of organic practices on pesticide use is crop specific. This aggregate result is derived based on current crop mix in California. Each crop is susceptible to a different spectrum of pests, which are managed by a distinct pesticide portfolio as part of a broader pest management program. Comparing PURE indices for individual crops shows the benefit from pesticide use in organic agriculture varies significantly. Based on value, production region, and the acreage share of organic production, four crops are selected to illustrate this point: lettuce, strawberries, wine grapes, and processing tomatoes. Lettuce, strawberries, and wine grapes are the three highest-valued organic crops in California, with organic sales values of $241, $231, and $114 million in 2016 respectively . Production of strawberries and lettuce is concentrated in the Central Coast region. Processing tomatoes are an important crop in the Central Valley. Wine grape production occurs in a number of regions across the state. In 2015, the acreage shares of organic production are 8% , 9% , 4% , and 2% for the selected crops.For my analysis, the unit of observation is a field-year, defined as a field with one or more pesticide applications in a given calendar year. In total, more than 3 million field-year observations are included in the PUR database from 1995 to 2015. Table 1.1 provides field-year summary statistics for key variables by crop. Overall, 3% of them applied only pesticides approved in organic agriculture. For all crops, conventional farms are significantly larger in size and have higher PURE indices. The average farm size in PUR is smaller than the average number in the USDA Census . One potential explanation is that one farm could have fields in different counties and apply for multiple pesticide application permits within in each county, which classifies it as multiple “farms” in the PUR. For all crops, lettuce, strawberries, and processing tomatoes, growers who operate conventional farms have significantly more experience, measured by years they are observed in the PUR. For wine grapes, conventional growers have less experience than organic growers. Ideally, farming experience is measured directly or researchers use age as a proxy. However, the PUR database does not contain any demographic information, which limited my ability to measure experience. The PUR experience is smaller than the farming experience reported in the Census, which has many reasons. . First, the PUR database I use started in 1995. Any farming experience before 1995 is not recorded. The Census is conducted every 5 years. Farms that entered and exited within the 5 year gap are included in the PUR database but not the Census, which reduce the average experience. Conventional strawberries have significantly greater impact on surface water and less impact on groundwater, measured by the PURE indices, comparing to other conventional crops. Organic strawberries, on the other hand, had a higher PURE index for air and a lower PURE index for soil than other organic crops. Pesticides used in conventional production of wine grapes have less impact on pollinators than pesticides used in other conventional crops.To identify the effect of organic agriculture on pesticide uses and associated environmental impacts, I must address the issues of selection bias at both the grower and the field levels. Compared to growers who utilize conventional practices, growers who adopt organic ones may have different underlying characteristics, such as attitudes toward environmental issues, which can also affect their pesticide use decisions directly. If grower characteristics are time-invariant, an unbiased estimation could be achieved by including a grower fixed effect in the regression.

There is also time-variant heterogeneity that is associated with individual growers, due to factors such as farm size and experience, blueberry grow bag that simultaneously influences the adoption of organic production and pesticide use decisions. The identification concern here is that growers with more farming experience or larger farms, including both conventional and organic acreage, are more likely to operate organic fields and use less pesticides . Therefore it is not reasonable to compare environmental impacts of pesticide use for growers without considering these characteristics. For each grower, annual total acreage and experience serve as measures of time-variant heterogeneity. As shown in Table 1.1, there is a significant difference for these two variables between conventional and organic growers. There could be field-level heterogeneity as well, due to pest or disease pressure, that undermines my identification strategy. Fields with less pest or disease pressure need less pesticides and are more likely to be converted into organic production at the same time. Including field fixed effects in the estimation is one approach to address these issues. Organic fields tend to be concentrated spatially to avoid pesticide drift from nearby conventional fields . Spatial relationships are not considered here because the PUR database does not have information on the distance between fields.For all five PURE dimensions, pesticides used in organic agriculture reduced environmental impact. The reduction, captures by the variable Organic, is significant at the 1% level for five environmental dimensions. Relative to the intercept, organic practices reduced environmental impacts for surface water by 86%, for groundwater by 93%, for soil by 60%, for air by 53%, and for pollinators by 76% on a per acre basis holding other variables fixed. The relatively small impact on air is linked to the facts that natural AIs do not have less VOC emissions in general. Regulations regarding high VOC-emitting pesticide AIs also contribute to this result partially because they do no affect two systems evenly. In 2015, the sale and use of 48 pesticide products were restricted due to their VOC emissions, which accounted for 5% of treated acreage in conventional agriculture and 1% of treated acreage in organic agriculture. Although reductions in PURE index values do not translate directly into dollar values or health outcomes, results from Table 1.2 suggest that pesticide use in organic fields substantially reduced environmental impacts. The coefficient for Organic × t represents the change of the difference between two farming systems over time and is positive for all environmental dimensions, which supports the hypothesis that, comparing with conventional agriculture, the environmental impacts associated with pesticide use in organic agriculture have grown over time. Air has the largest coefficient among the five environmental dimensions, which is consistent with previous figures that environmental impacts increased the most for air across all crops. The variable t is the common time trend for all conventional fields and t is negative for surface water and groundwater, which means the environmental impacts from pesticide use decreased in conventional agriculture on those dimensions. The environmental impact on soil and air increased. The combination of variables t and Organic × t shows the time trend for organic fields alone, which is upward sloping for groundwater, soil, air, and pollinators, and downward sloping for surface water. Two variables Acreage and Exp, capture time-invariant grower heterogeneity. Although the variable Organic dominates the overall effect, coefficients for both Acreage and Exp influence the environmental impact associated with crop production. For the same grower-crop combination, a larger farm size is associated with pesticide application pro-grams that pose more negative impacts for all five environmental dimensions. Meanwhile, more experience is correlated with the environmental impacts on soil, air, and pollinators. The PURE indices for surface water and groundwater are positively correlated with experience. This is partially due to the fact that experienced farmers use less organophosphate insecticide per acre, which are more toxic to earthworms and honeybees than alternative AIs.The sub-sample estimation yields similar results . Namely, in conventional agriculture, the environmental impacts on surface water and groundwater associated with pesticide use decreased over time, pesticides used in organic agriculture significantly reduced the environmental impacts measured by the PURE index, the difference between conventional and organic pesticide use decreased.The intercept is smaller than the coefficient of Organic occasionally because the crop and time fixed effects are oftentimes positive and significant and the impacts on those dimensions in organic fields are small. For the sub-sample with fields that have transitioned between production systems, total farm acreage is no longer significantly associated with impacts on groundwater, soil, and pollinators and the environmental impact on surface water is negatively correlated with farm acreage. The main reason for this seemingly dramatic difference, comparing to the full sample estimation, is that there are more wine grape vineyards and fewer almond orchards and alfalfa fields in the sub-sample. Although the organic price premium is limited for wine grapes, the organic farming practices are associated with high quality of grapes, which encourage growers to adopt organic production .