Tag: agriculture

Compared to the placebo group, participants consuming the antioxidants plus zinc and copper showed a 28% reduction in progression to advanced AMD after five years. Subsequently, the AREDS2 was conducted with a newer formulation that included vitamins C and E, either 10 mg of L plus 2 mg of Z, and either 350 mg of docosahexaenoic acid plus 650 mg of eicosapentaenoic acid , or both. Patients were also given either 25 or 80 mg of zinc, each with 2 mg of copper. Beta-carotene was eliminated from the supplement due to a potential increased risk of lung cancer among smokers, who were already at high risk for AMD. Primary analyses of the AREDS2 formula found no additional benefit in reducing progression to advanced AMD, in comparison to the original AREDS formula. However, in a secondary analysis of combined data from AREDS and AREDS2, the progression risk in those receiving L and Z was significantly lower than in other groups. Neither formulation reduced the progression from early to intermediate AMD. These clinical trials did not monitor the MPOD status over time, thus limiting our understanding of the link between L and Z intake, retinal accumulation, and AMD development or progression. To date, dutch buckets the AREDS2 formula remains the standard of care for management of patients with intermediate AMD.The accumulation of L and Z in the macula starts in utero in primates and plays a critical role in visual development and maturation later in life.

Lutein and Z were detected as early as 20 weeks of gestation in macular tissue from human fetuses inspected at autopsy. Unlike fully matured human eyes, L is the dominant macular pigment in infants under the age of two regardless of eccentricities. The retina is less mature at birth compared to other eye structures, with complete differentiation requiring four to five years. The maturation of the macula is associated with a change in the L:Z ratio over the first four years of life, which correlates with the development of cone photoreceptors. Studies in premature infants illustrate the importance of these L and Z in visual development. In preterm human neonates, extremely low levels of serum L and Z are associated with an undetectable MPOD.79 When a carotenoid-fortified formula containing 211 µg/L of combined L and Z was given to preterm infants, plasma carotenoid levels became comparable to breastfed preterm infants, and were significantly higher than those fed formulas without L or Z fortification. In a small study that monitored the concentration of L and Z in various infant formulas and breast milk from different mothers, Z was not detected in any formula but was present in all breast milk samples, while L was consistently higher in breast milk. Serum L was also noted to be six-fold higher in breastfed infants compared to those fed with a formula devoid of L. Further studies are warranted to assess the prospective effects of L- and Z-fortified formula on MPOD and visual development in infants as they enter adulthood. Lutein and Z may also protect against oxidative damage in premature infants, especially those with retinopathy of prematurity . Premature infants with ROP usually have poor visual acuity, even after laser treatment or intravitreal injection of anti-vascular endothelial growth factor agents.

In a model of oxygen-induced retinopathy, mouse pups given L showed less vessel leakage and lower avascular area compared to those given a L-free control. The authors suggested that the anti-oxidant properties of L may have contributed to these results, although ROS levels were not measured. Studies that investigate L and Z supplementation in ROP babies have produced inconsistent results. In a multi-center, double-blind, randomized controlled trial of very-low-birth-weight infants, no difference was found in the incidence of ROP between those supplemented with daily oral L and Z or placebo. However, the progression rate of threshold ROP showed a lower trend in the supplemented group. No adverse events were noted with L and Z supplementation, suggesting that they were well-tolerated. Another study examining the effects of daily oral L and Z supplementation in preterm infants from the seventh day after birth until 40 weeks of age or until hospital discharge found no change in the rate or severity of ROP compared to placebo. Further, a meta-analysis of three randomized controlled trials also found no protective association between L and Z supplementation and the risk of ROP. Additional studies are needed to assess the role of prenatal L and Z supplementation in pregnant women at risk for premature delivery.During development, L and Z are not interchangeable. Serum Z in newborns and in their mothers is strongly correlated with the MPOD of the babies, but no relationship was noted for either maternal or infant levels of L.

During delivery, a high maternal plasma Z, but not plasma L, was significantly associated with a lower risk of visual acuity problems in children at three years of age. Further investigations that can accurately distinguish and quantify dietary and plasma Z from L are needed to better understand the role of these two carotenoids in visual performance during development. The L and Z in human milk is particularly important for infant eye and brain development, and may provide long term benefits to vision and cognition. Since humans cannot synthesize carotenoids, the fetus and breastfed infants must obtain these compounds from the mother through the placenta and the breast milk. During gestation, maternal lipoprotein synthesis increases, which accelerates the transport of carotenoids to the fetus. This transfer may deplete maternal stores if the dietary intake of carotenoids in general, and L and Z specifically, is inadequate to maintain body stores. Low maternal skin and serum carotenoid levels have been reported in mothers of newborn infants. The prevalence of AMD is higher in women than in men, even though on a global basis more men smoke. At the same time MPOD levels are lower in females. The potential reasons for an increased lifetime risk for AMD in women are complex and multi-factorial in nature and may include maternal depletion of L and Z during pregnancy and lactation . Importantly, the average dietary consumption of L and Z among females in the US is far below the amount of 10 mg/d known to increase MPOD. Therefore, either the intake of supplements containing L and Z, or increased intake of foods rich in these two carotenoids for the duration of pregnancy and lactation may be of value.The concentration of β-carotene, lycopene, L and Z, the main carotenoids in breast milk are associated with maternal dietary intake over the first six months of lactation. Daily maternal supplementation of either 6 mg of L with 96 µg of Z, or 12 mg of L with 192 µg of Z, over six weeks resulted in a dose-dependent increase in L and Z levels in the breast milk and of the mothers and their infants when assessed three to four months postpartum. Another study reported that more carotenes were present than xanthophylls in maternal plasma, whereas more xanthophylls such as L and Z were presented in breast milk, in comparison to carotenes. These findings support the notion that maternal-infant transfer of carotenoids may occur, possibly at the expense of the mother. Future studies are needed to clarify if breastfeeding or L and Z intake may impact their AMD risk. The L-ZIP supplementation trial is currently exploring whether prenatal supplementation of 10 mg of L and 2 mg of Z will maintain maternal body stores, prevent potential macular pigment depletion during pregnancy, or enhance systemic and ocular carotenoid stores for both mothers and infants. Clinical trials on the long-term effects of perinatal L and Z intake on MPOD changes among mothers and infants are also warranted.100 Unfortunately, longitudinal studies on AMD in females often do not include breast-feeding history. A useful study design would be to investigate MPOD levels and relative risks of AMD between multiparous and nulliparous women, and in mothers practicing breastfeeding compared to formula feeding. Dietary intake of L and Z would be important to assess. Recognizing that such a study would take decades, shorter term studies could be conducted in non-human primates. Another challenge in retrospective studies is that breastfeeding history may not be accurate. Therefore, studies on the maternal transfer of L and Z during pregnancy and lactation with MPOD changes in infants and throughout the lifespan, grow bucket could be important but difficult to conduct. Future research should also focus on the measurement of L and Z status and MPOD in mother-infant pairs of twins or short birth intervals. Last, when accessing AMD risk in women, reproductive hormone status may be a confounding factor.

Estrogen has been shown to reduce oxidative stress and inflammation in RPE cells as well as systemically. Lifetime estrogen exposure such as the number of pregnancies, menopause, reproductive period, oral contraceptive use, and hormone replacement therapy may all influence the risk of developing AMD. Current evidence regarding estrogen exposure and risk of AMD is inconsistent. One study reported that postmenopausal hormone use decreased the risk of neovascular AMD but increased the risk of early AMD, while parous women showed a reduced risk of early AMD but not neovascular AMD. Two nationwide studies from South Korea among postmenopausal women noted that exogenous estrogen exposure was not a protective factor for AMD. A cohort study found that hormone replacement therapy and a longer reproductive period was associated with an increased risk of neovascular AMD. A cross sectional study showed that oral contraceptive use was associated with an increased risk of late AMD.106 In addition, a review summarizing the effect of estrogen exposure and the risk of all age-related eye diseases concluded that HRT, or the use of oral contraceptives, could be either positively or negatively associated with the risk of AMD.103 In contrast, some studies have reported that a longer duration of breastfeeding may be protective from late but not early AMD, even when the estrogen level was low during lactation. Future studies on the interaction of different reproductive and estrogen exposure histories and AMD risk are needed.Humans cannot synthesize carotenoids, and the best dietary sources are fruits, vegetables, egg yolks, and dairy products. Consuming a diet rich in green leafy vegetables and fish is recommended by the National Eye Institute for the high carotenoid and DHA and EPA contents. Nevertheless, in the carotenoid group, L and Z are not yet considered essential, or even conditionally essential, so no dietary reference intakes for these two compounds exists. The US intake of L and Z has been decreasing. According to the U.S. National Health and Nutrition Examination Survey , the average intakes of L plus Z were 2.15 mg/d in males and 2.21 mg/d in females in 1987, and 2.15 mg/d in males and 1.86 mg/d in females in 1992. In NHANES 2013-2014, the average intakes of L and Z in males and females was 1.58 mg/d and 1.76 mg/d, respectively. Moreover, based on data from NHANES 2003-2004, the reported intake of L was significantly higher than Z in all age groups and ethnicities. Importantly, the Z to L ratio was also lower in females than males older than 31 years of age, which may result in a higher risk of AMD in women than in men. However, due to difficulties in analyzing dietary L and Z separately, most studies analyze both carotenoids together. Since the amount of L in most foods is significantly greater than Z, precise quantification of Z has been a challenge. The amount of L and Z in foods and dietary supplements appears to be safe.112 No adverse events were found in clinical trials giving L at 30 mg/d for 120 days or 40 mg/d for 63 days. The only reported adverse effect after a daily supplementation of 15 mg L in a 20-week trial was a single case of self-reported carotenodermia, a reversible condition of orange skin color. Although a higher amount has been used in human studies, after assessing the potential risks, the observed upper safety level for L has been proposed as 20 mg/d. The European Food Safety Authority concluded safe upper limits for L and Z for use in dietary supplements were 1 mg/kg body weight/d and 0.75 mg/kg body weight/d, respectively. In primate models, rhesus monkeys fed a xanthophyll-free diet for 3 to 6.5 years developed extremely deficient or absent macular yellow pigment and drusen-like bodies. 

Larger roots were left in the oven for 4 days. Stumps were considered part of the root system for this analysis.In vineyard ecosystems, annual C is represented by fruit, leaves and canes, and is either removed from the system and/or incorporated into the soil C pools, which was not considered further. Structures whose tissues remain in the plant were considered perennial C. Woody biomass volumes were measured and used for perennial C estimates. Cordon and trunk diameters were measured using a digital caliper at four locations per piece and averaged, and lengths were measured with a calibrated tape. Sixty vines were used for the analysis; twelve vines were omitted due to missing values in one or more vine fractions. All statistical estimates were conducted in R.The present study provides results for an assessment of vineyard biomass that is comparable with data from previous studies, as well as estimates of below ground biomass that are more precise than previous reports. While most studies on C sequestration in vineyards have focused on soil C, some have quantified above ground biomass and C stocks. For example, a study of grapevines in California found net primary productivity values between 5.5 and 11 Mg C ha−1—figures that are comparable to our mean estimate of 12.4 Mg C ha−1 .

For pruned biomass, hydroponic nft channel our estimate of 1.1 Mg C ha−1 were comparable to two assessments that estimated 2.5 Mg of pruned biomass ha−1 for both almonds and vineyards. Researchers reported that mature orchard crops in California allocated, on average, one third of their NPP to harvestable biomass, and mature vines allocated 35–50% of that year’s production to grape clusters. Our estimate of 50% of annual biomass C allocated to harvested clusters represent the fraction of the structures grown during the season . Furthermore, if woody annual increments were considered this proportion would be even lower. Likewise the observed 1.7 Mg ha−1 in fruit represents ~14% of total biomass , which is within 10% of other studies in the region at similar vine densities. More importantly, this study reports the fraction of C that could be recovered from winemaking and returned to the soil for potential long term storage. However, this study is restricted to the agronomic and environmental conditions of the site, and the methodology would require validation and potential adjustment in other locations and conditions. Few studies have conducted a thorough evaluation of below ground vine biomass in vineyards, although Elder field did estimate that fine roots contributed 20–30% of total NPP and that C was responsible for 45% of that dry matter. More recently, Brunori et al. studied the capability of grapevines to efficiently store C throughout the growing season and found that root systems contributed to between 9 and 26% of the total vine C fixation in a model Vitis vinifera sativa L. cv Merlot/berlandieri rupestris vineyard.

The results of our study provide a utilitarian analysis of C storage in mature wine grape vines, including above and below ground fractions and annual vs. perennial allocations. Such information constitutes the basic unit of measurement from which one can then estimate the contribution of wine grapes to C budgets at multiple scales— fruit, plant or vineyard level—and by region, sector, or in mixed crop analyses. Our study builds on earlier research that focused on the basic physiology, development and allocation of biomassin vines. Previous research has also examined vineyard-level carbon at the landscape level with coarser estimates of the absolute C storage capacity of vines of different ages, as well as the relative contribution of vines and woody biomass in natural vegetation in mixed vineyard-wildland landscapes. The combination of findings from those studies, together with the more precise and complete carbon-by-vine structure assessment provided here, mean that managers now have access to methods and analytical tools that allow precise and detailed C estimates from the individual vine to whole-farm scales. As carbon accounting in vineyard landscapes becomes more sophisticated, widespread and economically relevant, such vineyard-level analyses will become increasingly important for informing management decisions. The greater vine-level measuring precision that this study affords should also translate into improved scaled-up C assessments . In California alone, for example, there are more than 230,000 ha are planted in vines. Given that for many, if not most of those hectares, the exact number of individual vines is known, it is easy to see how improvements in vine-level measuring accuracy can have benefits from the individual farmer to the entire sector.

Previous efforts to develop rough allometric woody biomass equations for vines notwithstanding, there is still a need to improve our precision in estimating of how biomass changes with different parameters. Because the present analysis was conducted for 15 year old Cabernet vines, there is now a need for calibrating how vine C varies with age, varietal and training system. There is also uncertainty around the influence of grafting onto rootstock on C accumulation in vines. As mentioned in the methods, the vines in this study were not grafted—an artifact of the root-limiting duripan approximately 50 cm below the soil surface. The site’s location on the flat, valley bottom of a river floodplain also means that its topography, while typical of other vineyard sites per se, created conditions that limit soil depth, drainage and decomposition. As such, the physical conditions examined here may differ significantly from more hilly regions in California, such as Sonoma and Mendocino counties. Similarly, the lack of a surrounding natural vegetation buffer at this site compared to other vineyards may mean that the ecological conditions of the soil communities may or may not have been broadly typical of those found in other vineyard sites. Thus, to the extent that future studies can document the degree to which such parameters influence C accumulation in vines or across sites, they will improve the accuracy and utility of C estimation methods and enable viticulturists to be among the first sectors in agriculture for which accurate C accounting is an industry wide possibility. The current study was also designed to complement a growing body of research focusing on soil-vine interactions. Woody carbon reserves and sugar accumulation play a supportive role in grape quality, the main determinant of crop value in wine grapes. The extent to which biomass production, especially in below ground reservoirs, relates to soil carbon is of immediate interest for those focused on nutrient cycling, plant health and fruit production, as well as for those concerned with C storage. The soil-vine interface may also be the area where management techniques can have the highest impact on C stocks and harvest potential. We expect the below ground estimates of root biomass and C provided here will be helpful in this regard and for developing a more thorough understanding of below ground C stores at the landscape level. For example, Williams et al. estimated this component to be the largest reservoir of C in the vineyard landscape they examined, but they did not include root biomass in their calculations. Others have assumed root systems to be ~30% of vine biomass based on the reported biomass values for roots, trunk, and cordons. With the contribution of this study, the magnitude of the below ground reservoir can now be updated.In plants, a fruit is the seed-containing section, which is formed from the ovary after flowering. Fruits have their vivid colors due to the presence of phytochemicals as pigments, which are natural compounds that protect against threats and insults such as insects and ultraviolet sunlight. Bright colors of fruits also attract animals and human beings for seed dispersing purposes. For instance, cocoa beans and blueberries have been used traditionally as therapies among indigenous people in North America. The fruit, leaves, seed, nft growing system and bark of the mango plant have been used as traditional medicine in Southeast Asia, Oceania, Africa, and Central America. Goji berries have been used as traditional Chinese medicine for two thousand years. Phytochemicals can be classified primarily as terpenoids, phenolics, alkaloids, nitrogen containing plant constituents, and organosulfur compounds. Examples of major phytochemical groups that are abundant from dietary sources and related to human health include carotenoids and polyphenols. Carotenoids are a type of terpenoid. Carotenoids can be classified as carotenes and xanthophylls. Phenolics can be classified as phenolic acids and polyphenols. Two primary subclasses of phenolic acids are hydroxybenzoic acid and hydroxycinnamic acid. Polyphenols include flavonoids, tannins, stilbenes, lignans, and xanthones. As one of the most studied categories of polyphenols, subclasses of flavonoids can be categorized to flavanones, flavones, anthocyanins, flavanols , chalcones, flavonols, and isoflavonoids.6Among the thousands of phytochemicals that have been identified in plants, both health promoting and toxic compounds exist.

For instance, some tannins decreased the activity of digestive enzymes or the bio-availability of protein or minerals and have been considered as antinutrients. Phytochemicals that exist in plant-based dietary sources and have value in human health maintenance and prevention of diseases are defined as phytonutrients. Fruits, vegetables, legumes, spices, nuts, wine, cocoa, tea, and olive oil are examples of foods rich in bioactive phytonutrients. The consumption of these dietary components has been related to decreased risk of developing chronic diseases, including cardiovascular diseases , age-related eye diseases, type II diabetes, cancers, and all-cause mortality. Observational studies also have reported that the total dietary polyphenol intake was inversely associated with the risk of hypertension, hypercholesterolemia, and cardiovascular events. Polyphenols under different categories may play various roles in reducing CVD risk. In the United States, the estimated flavonoid intake is 345 mg/day, with flavanols as the most abundant source. The three most consumed flavanols are catechin, epicatechin, and their polymers. Subanalyses of a cohort study indicated that dietary intakes of flavanols along with lignans, dihydrochalcones, and hydroxybenzoic acids showed a stronger inverse association with the risk of overall CVD events than other phenolic compounds. Another cohort study reported that the dietary intakes of anthocyanins, dihydrochalcones, dihydroflavonols, proanthocyanidins, catechins, flavonols, hydroxybenzoic acids, and stilbenes were significantly associated with decreased risks of total CVD. Blueberries and cranberries contain high amount of anthocyanin and proanthocyanidin, respectively, with moderate concentration of flavonoids. Cocoa is rich in flavanols,especially epicatechin and catechin. Mango, as the fourth leading fruit crop worldwide, is high in carotenoids, phenolic acids, and mangiferin, a polyphenol classified as a xanthonoid. Carotenes exist in dietary sources primarily as α-carotene, β-carotene, and lycopene. Major xanthophylls that exist in dietary sources include lutein , zeaxanthin , and β-cryptoxanthin. Epidemiological studies report inconsistent results on the relationship between dietary L and Z intakes and the risk of age-related macular degeneration. However, clinical studies have shown that the supplementation of L and Z was able to increase the level of these compounds in the retina, suggesting their protection against age-related macular degeneration . A major dietary source of L and particularly of Z is goji berry, which also have other in carotenoids, as well as phenolic acids, and flavonoids. While many examples of fruits used traditionally for health promotion exist, this literature review focuses on the evidence of mango, cocoa, blueberries, and cranberries in cardiovascular health, and goji berries in eye health. The application of modern scientific methods to assess traditional remedies is important because evidence-based data is necessary to transfer historical stories and ancient wisdom to contemporary life and advancement of health and human performance.Cocoa is the dried and fully fermented product obtained from the seeds of Theobroma cacao L. and is the main ingredient in chocolate products. While used traditionally in a number of cultures, one of the best examples of its medicinal use is from the Kuna Indians who have lived for centuries on remote islands off of the Caribbean coast of Panama. This group of indigenouspeople is famous the lack of hypertension, an infrequent prevalence of CVD, diabetes, and cancer, and a longer lifespan, compared to Panamanians living on the mainland. However, when these people migrate to an urban environment, the incidence of hypertension and vascular diseases increased significantly. Nutritional assessments showed that the consumption of total fruit, fish, and cocoa-containing beverages were significantly higher among Kuna Indians living on the island compared to those residing in Panama City, even though the overall dietary intake of added sugars and salt was higher in the indigenous group. 

Arguably the most momentous shift in cultural practices for strawberries was the introduction of preplant soil fumigants, beginning with chloropicrin in the 1950s and methyl bromide in the 1960s. Fumigation is a soil disinfestation practice that improves plant productivity and helps with the management of arthropods, nematodes, weeds, soilborne fungi and other plant pathogens. Some of the most difficult to control pathogens include Verticillium dahliae, Fusarium spp. and Macrophomina phaesolina. Without soil fumigation, these pathogens have the potential to completely destroy strawberry plantings. Early on, when CP and MB were mixed and applied together, the synergistic effects allowed strawberries to be produced as an annual rather than a biennial crop, and to be grown continuously on the same land without rotation to another crop, resulting in an increase in annual strawberry acreage. The use of fumigants also led to higher and more predictable yields and fruit quality, blueberry grow pot and further enabled the development of more stable markets for strawberries . Yields for strawberries statewide increased from a range of 2 to 4 tons per acre prior to the introduction of soil fumigants to 16 tons per acre by 1969 . Additional cultural improvements included the development of both UC and proprietary strawberry varieties uniquely adapted to coastal production conditions. Varieties were bred, for example, for disease resistance, yield and market potential.

Notable UC-bred strawberry varieties include Tufts , Pajaro, Douglas, Chandler, and Selva , Camarosa and Seascape , and Aromas, Albion and Monterey . Irrigation practices also evolved, shifting from furrow irrigation in the 1960s to drip irrigation in the 1980s, which led to further improvements in plant disease management and greater water use efficiency. These and other enhancements meant that by 2012, yields could exceed 35 tons per acre . More recently, the strawberry industry has focused on “fine-tuning” fertility and water management for more efficient resource use, along with additional yield and fruit quality improvements . The Santa Cruz–Monterey area is also recognized for its early experience with conversion of conventional strawberry production to organic management . Organic strawberry production was shown to result in lower yields, which, when offset by premium prices could potentially offer higher net returns to growers. The importance of crop rotation for disease management was not addressed in the initial study by Gliessman et al. but has since been the focus of additional research, as have more complete analyses of the economics of organic strawberry production . Growers and area researchers continue to collaborate and advance organic strawberry production techniques. Most notably, a long-term research commitment has been made to determine organically acceptable disease management practices such as anaerobic soil disinfestation , the use of commercially available soil-applied biological organisms and the incorporation of soil amendments such as mustard seed and its derivatives.

The area is now seen as a global leader in organic strawberry research, and in 2012 the first organic strawberry production manual was published by UC Agriculture and Natural Resources . Statistics documenting expansion of the organic strawberry industry over time are not available on a county-by-county basis, but statistics for California show prodigious growth in acreage and value of production: from $9.7 million in 2000 to $93.6 million in 2012, a 621% increase in real dollars . Caneberries Like strawberries, raspberries and blackberries have benefitted from enhancements in cultural practices. When well-managed, both types of caneberries can produce crops for up to 20 years. However, to maintain acceptable quality and yield Central Coast growers typically manage raspberries and blackberries so that they produce two and five crops, respectively, prior to removal and replanting. In Santa Cruz County, raspberry production was relatively flat in the 1960s and 1970s, but began to increase substantially in the 1980s . This can be explained by a shift from floricane, or spring-bearing varieties, to the then newly developed proprietary primocane, or fall-bearing varieties, that do not carry the productivity constraints associated with the inadequate chill requirements along the Central Coast. Primocane-bearing varieties allow growers to successfully produce a high quality raspberry crop in low- or no-chill coastal locations, and further manipulate time to harvest and yield with pruning and other management practices .

Between 1990 and 2014, the number of acres planted to Santa Cruz and Monterey area raspberries almost tripled, tons produced increased by about 350% and the value of production was up by over 400% in real dollars . Santa Cruz County raspberry growers began to experiment with and adopt field-scale semi-permanent protective structures or tunnels in the 1990s and 2000s . Initially developed in Europe, field-scale tunnels allow growers to extend their production seasons, enhance yield and fruit quality, and capture high off-season prices for fresh market fruit . The controlled environment, and resulting security of production, also allows for greater market stability. This shift away from open-field production to protected cropping, along with breeding improvements, has had lasting impacts on the raspberry industry and its expansion. Cultural improvements geared towards fresh market blackberry production are more recent and include advances in breeding for thornless varieties and quality attributes . In 2011, a public primocane-bearing blackberry variety became commercially available for the first time and is now being planted in the area. Since that time, additional public and proprietary primocane-bearing varieties have been in development; some have already become available. Open-field production was the norm until recently, but to ensure marketable fruit of high quality, and as growers have shifted additional acreage to primocane-bearing varieties, tunnel culture has been more widely adopted and, based on discussions with growers, is now estimated at roughly 80% of the acreage. Like organic strawberries, remarkable growth in the statewide production of organic raspberries and blackberries was documented between 2000 and 2012 . Acreage climbed by over 500% in both organic berry categories. Value of production was up over 3,000% in real dollars for organic raspberries and up by almost the same percentage for organic blackberries. It is important to note that although the organic raspberry and blackberry categories have demonstrated extraordinary growth, they still represent a relatively small percentage of all berry production in the area.Research points to several factors that have spurred consumer demand for all berries. Berries contain bio-active compounds, including essential vitamins, minerals, fiber and antioxidants that contribute to healthy diets, and that help to reduce the risks associated with some chronic diseases and cancers . This information has been widely shared with consumers through, for example, government programs promoting healthy eating , and more generic berry promotion programs . Per capita consumption of fresh strawberries in the United States almost doubled from 1994 to 2014, increasing from 4.1 to 8.0 pounds . U.S. per capita consumption of fresh raspberries was small by comparison, at just 0.5 pounds in 2014. Similar consumption data are not available for blackberries, but Cook notes that consumers generally view berries as complementary, and that sales for all berries have increased. Indeed, in 2014, berry sales increased 5.8% over 2013; berries were the number one produce category for U.S. grocery retailers, at $5.7 billion in annual sales . Some berry operations also benefit from their proximity to the area’s urban centers, which have sizeable cohorts of educated, high-income consumers who generally demonstrate an interest in health and wellness, hydroponic bucket local agriculture and fresh and organic products. In addition to the more traditional grower shipper and direct marketing channels, new technology-driven food marketing companies — virtual food hubs — have evolved to cater to this demographic. They promote the values of sustainable communities, local food economies and business integrity and transparency, all important attributes for new 21st century consumers . These companies form relationships with local growers, provide some technical and market support, and enhance sales and engagement with consumers. It is not yet clear what impacts these still-niche marketing businesses may have on the industry in total. However, growers have responded to the various health and market signals by ramping up production of both conventional and organic products, berries included.

Specialists and farm advisors with UC Cooperative Extension have performed economic analyses for Santa Cruz and Monterey county fresh market berry crops for decades . The studies estimate production costs for a representative enterprise based on characteristics common to the area’s farms. Data are collected from established growers, input suppliers and other industry experts so that a diversity of operations and practices are taken into account. Since 1990, UCCE researchers have used a farm budget software program to analyze the data and present results in several formats detailing costs for cultural and harvest practices, monthly cash costs and business and investment overhead costs. The studies also include an analysis estimating net returns to growers for several yield and price scenarios. Representative costs for food safety and environmental quality programs have been incorporated into more recent studies as they have evolved to become standard business practices. The resulting production and economic information is specifically designed to assist growers, bankers, researchers and government agencies with business and policy decisions.The first economic analysis of fresh market strawberry production for Santa Cruz and Monterey counties was performed in 1969; at least one subsequent analysis has been conducted every decade since then. Though the level of detail and data included in each study has changed over time, some interesting trends can be noted. Annual land rent climbed from $150 per acre in 1969 to $2,700 in 2014, representing 2.5% and 5.5% of total production costs, respectively. The cost of soil fumigation for conventional strawberry production increased from $350 per acre in 1969 to $3,302 in 2010, representing 5.5% and 6.9% of total production costs, respectively. Production year water use gradually decreased from 80 acre-inches per acre in 1969 to 36 acre-inches by 1996 as drip irrigation became the standard. The amount of water used to bring a crop to harvest has remained roughly the same since that time; however, growers and researchers continue to investigate methods to increase water use efficiency even further. In some areas, soil types and fields, growers have been able to reduce per acre water use by several acre-inches more . When the above costs and water usage are assessed on a per ton rather than a per acre basis, production practice cost increases are less notable, and water savings even greater. Labor-intensive practices such as hand weeding and harvest are consistently shown as costly line items relative to other operations. Representative yields for conventionally produced fresh market strawberries rose from 20 tons per acre in the 1969 study to 30 tons in 2010, an increase of 50%. Even higher yields are discussed for some varieties and production conditions; county production statistics confirm that higher yields are indeed possible . Representative yields for organic strawberries, studied over a much shorter time period, rose from 15 tons per acre in 2006 to 17 tons in 2014, an increase of 13%. As more research is directed towards organic agriculture in general and strawberries in particular, yields will likely increase even more with time. Recent efforts include improvements in cultivar breeding, cultural practices and disease management, especially soil pathogen management. The most recent economic analyses for conventional, second year conventional and organic strawberry production were performed in 2010, 2011 and 2014, respectively. Second year conventional strawberries, or those producing a crop for a second year after having produced the first without replanting, represent about 15% of the total strawberry acreage in the area. Similarities and differences in total, cultural and pest management costs for the three management approaches are shown in figures 1 to 3. Total costs for conventional strawberries were $47,882 per acre and include expenses for all practices from land preparation to harvest . For the second year conventional strawberry crop, total costs were lower at $32,798 per acre, reflecting a reduction in expenditures for land preparation and reduced harvest costs because of lower yield. For organic strawberries, total costs were $49,044 per acre, slightly higher than for conventional production, mostly due to higher soil fertility input costs. Harvest, a labor-intensive practice, clearly represents the lion’s share of total costs, at 58% in organic production, 60% in conventional production and 67% in second year conventional berries. Cultural costs represent 26% of total costs in the conventional and organic systems, but only 15% for second year strawberries because there were no associated planting costs, and because pest management costs were lower .

Alternatively, shrub stress and dieback may be dependent on a wider variety of variables, particularly in a landscape as heterogeneous as this. Additionally, we predicted that dieback severity and individual shrub death would increase over time in lower elevations and exposed slopes compared to upper elevations and more mesic slopes.The specific area chosen for this study is located in the Santa Ynez mountains of Los Padres National Forest . Stands of A. glauca occur from approximately 400m to 1200m elevation, and are frequently mixed with other co-dominate woody evergreen shrub species including Adenostoma fasciculatum, Ceanothus megacarpus and, at lower elevations, Malosma laurina. The landscape of this region is extremely heterogeneous, with unstable terrain composed largely of sandstone rock outcroppings and sandstone-derived soils , and steep slopes and ridges that are interrupted by deep canyons . These dramatic features, while common habitat for chaparral plant communities, were a limitation in our ability to choose field sites. Thus, we relied heavily on accessibility by road and trail in finding sites. The climate in this region is of a mediterranean-type, with cool moist winters and a hot, dry summer season. The majority of rainfall typically occurs from November to April, and mean annual rainfall, based on a 120-year average, is 47cm . 2.2 Precipitation data Three weather stations, equipped with real-time, self-recording data loggers and maintained by the Santa Barbara County Public Works Hydrology Division, nft hydroponic system were chosen to retrieve precipitation data during the drought based on proximity and similar elevation to study sites. The Trout Club , San Marcos Pass , and El Deseo Ranch stations represented low, intermediate, and high elevations, respectively.

Data from these stations were retrieved from the Santa Barbara County Public Works Hydrology website.Average rainfall at these stations, based on 54-69 year means, increases with elevation from 68.3cm to 90.4cm . Annual rainfall data for this study are presented in “rainfall years” from November 1 of one year to October 31 of the next, to reflect the seasonal wet period preceding each sampling period. Consistent with these historical trends, annual rainfall at Trout Club was lowest between the 2014-15 and 2018-19 water years . However, during this same time period, rainfall totals were generally lower at El Deseo Ranch compared to San Marcos Pass .Data on canopy dieback for each individual were collected in fall 2016. Dieback was assessed as the actual percent of “non-green” vegetation, defined as yellow, brown, and black/gray leaves, as well as bare/defoliated stems within the canopy. Percent dieback of each canopy was estimated by two-to-three researchers viewing multiple angles of each shrub, and final estimates were determined after thorough consultation. Site dieback was then calculated as the mean of all selected shrubs within a site. Entire stand dieback was also estimated using a combination of ground-level assessments and, when available, aerial drone photographs. These were used to confirm that canopy dieback of individual shrubs were collectively representative of whole stand dieback.Data were again collected approximately every 4-6 weeks throughout the summer dry season, this time from June through October. XPP measurements were taken using the same methods as described above. Additionally, we measured daytime gas exchange to gain a better understanding of plant function throughout the dry season and as water availability declined.

Anet was measured using a Licor 6400XT . CO2 was set to 400ppm, and photosynthetically active radiation was set between 1400-1800, to reflect maximum photosynthesis conditions at peak daytime hours. All measurements were taken between 9am and 11am DST, typically on the morning after the predawn measurements were made. A single fully-expanded leaf was chosen per plant, and two readings were recorded and averaged later during data processing. Leaves were traced in the field, and tracings were brought back to the lab and scanned to calculate leaf area within the chamber using ImageJ software . Our FMS 2 system broke in August, and we were therefore unable to collect any Fv/Fm data after the July fieldwork.Differences in means between sites for plant physiology and dieback were compared using one-way ANOVA with Tukey’s HSD post hoc analysis for means separations. Dieback data were square-root transformed for normality. Linear regression models were used to identify correlations of elevation and aspect between plant drought stress and dieback. Multiple regression models were developed using landscape factors and plant physiology as predictors for canopy dieback, and AIC values were calculated for choosing the best fit model. A repeated measures ANOVA was performed to compare dieback levels between sites and across four years of the study . Statistical analyses were performed using JMP Pro Statistical Software and R Studio .This study sought to understand spatial patterns of A. glauca canopy dieback across the landscape during an unprecedented drought, and track the progression of dieback and eventual mortality in this classically drought-tolerant shrub. Our data support the hypothesis that dieback is related to water stress from drought, and that this varied across the landscape, but there was considerable variation between sites and across time. While aspect was significantly correlated with dieback across all years, we found no consistent significant effect of elevation on dieback until 2019, late in drought period. Further, while dieback generally increased across all sites from 2016 to 2019, we observed no new incidences of mortality during this study, suggesting that in this landscape A. glauca individuals are resilient to this punctuated but overall prolonged drought.

Consistent with our predictions, elevation and aspect appeared to both have significant correlations with XPP and Anet. While these correlations were weak, their significance lends support to our hypothesis that plant stress is related to these landscape variables. These relationships also provide evidence that elevation and southwestness may be used as tools for identifying areas where plant canopies are more vulnerable drought. The low correlation coefficients may be due to extreme landscape heterogeneity in the study region including heterogeneity in substrate rockiness, soil accumulation and topographic concavity, confounded by a relatively small sample size within each site. There are many microclimate variables that were not included in this study and that may contribute to variations in water stress, including site temperature, vapor pressure deficit, and fog patterns. Additionally, though we did not find plant size to be correlated with drought stress or dieback, we believe this is due to our efforts to select even-aged individuals for monitoring, while previous studies have found significant effects of plant canopy diameter on dieback and mortality . Also, because A. glauca recruit from seed after fire, individuals within a stand tend to be of similar size and age. Therefore, we recommend that future studies include greater variation in stand age so that relationships between age/size class and dieback can be better evaluated.Elevation was not shown to be highly correlated with dieback in all years of the study, hydroponic nft system and there did not appear to be a correlation between dieback annual precipitation. Yet, some important landscape patterns were revealed. Our hypothesis that dieback severity is related to landscape variables associated with water availability was most strongly supported in fall 2019, when dieback increased significantly with decreased elevation and increased southwestness. Aspect was correlated with dieback severity across all years, suggesting thiscould be a significant variable to consider when generating models for future drought risk. Moreover, it was found that the increase in dieback severity from 2016-2019 was greatest at lower elevations compared to high. In other words, while most sites experienced an overall increase in dieback, the increase at lower elevations was much more dramatic. Collectively, these results suggest that while populations of A. glauca across the landscape in Santa Barbara county are susceptible to extreme drought, those occurring on exposed, southwest-facing slopes and/or at the lower edge of their range may be less capable of recovery, particularly during prolonged drought. This is consistent with studies showing that low elevations and exposed slopes can correlate with plant water stress and mortality . Interestingly, the dieback severity was greatest in fall 2019, despite the region experiencing above-average rainfall in both the 2016-17 and 2018-19 water years . Thus, a single year of above-average rainfall was not sufficient to restore shrubs to predrought canopy health levels.

One possible explanation for this is that 2011-2016 and the 2017-18 wet seasons were extremely dry, pushing A. glauca individuals towards a threshold of drought resistance that could not be counteracted by one or two wet years. Venturas et al. found A. glauca to have high levels of hydraulic failure, dieback, and whole shrub mortality in Malibu County during the drought year of 2014, and a study by Paddock et al. from an intense drought year in California yielded similarly high mortality for this species. This supports the significance of intense drought years that preceded higher rainfall years in our study. Additionally, Gill and Mahall and Mahall et al. found evidence that some chaparral shrubs do not respond to surplus water, and thus high-rainfall years may not be accurate predictors of shrub recovery. Shallow-rooted species like A. glauca may only be able to benefit from soil water availability near the surface, and/or they may be relying on water availability in rocky outcrops that is more dependent on outcrop cavity structure than on individual rain event totals. Therefore, short-term excessive rainfall may be irrelevant for the recovery of these shrubs. Another hypothesis is that opportunistic fungi, as identified in prior work , may have played a significant role in the sudden development and continuation of dieback. Biotic agents are known to exacerbate drought effects by amplifying hydraulic failure and/or carbon starvation . A. glauca, already weakened by drought, may have been further impacted by fungal pathogens emerging from their latency between 2012 and 2016. Drake-Schultheis et al. have documented synergistic interactions of drought and latent fungal pathogens on A. glauca in a greenhouse setting. However, more research is required to identify the exact role of latent fungal pathogens in A. glauca in the field. Interestingly, Mahall et al. report detailed phenological measurements of A. glauca individuals in a nearby population in the 1980s following individual leaves for up to three years. They do not report dieback or evidence of fungal disease in the canopy of any individuals despite detailed descriptions of leaf condition. Persona communication with Mahall and Thwing likewise confirm the absence of evidence for pathogenic fungi in their study plants. Drake-Schultheis et al. have evidence for the very recent introduction of the most virulent pathogen in this system, Neofusicoccum australe. While the Mahall et al. study was conducted during the drought of the late 1980s and this drought was similar in magnitude, itmay be cumulative drought and a new fungal pathogen together that are today causing canopy dieback.A surprising result of this study was that while mortality among A. glauca was noted across the landscape at the beginning of this study, no new mortality was observed over the following four years of drought, despite some very low XPP measurements in 2016. Indeed, the XPP obtained in Fall 2016 are almost twice as negative as those measured in A. glauca shrubs in this same region during an earlier drought in the late 1980s . Furthermore, a significant number of shrubs across sites reached extreme levels of canopy dieback yet survived and in some cases even showed evidence of recovery. These observations are indicative of an impressive resilience to drought stress in this chaparral shrub species. As previously reported, A. glauca are typically identified as anisohydric, exhibiting continued gas exchange during drought and high resistance to cavitation . Our data showing the continuation of gas exchange well into the dry season further supports this strategy, although Anet did shut down in the lower elevation populations. The Venturas et al. and Paddock et al. studies also found greater mortality in A. glauca than was recorded in our study, and in other chaparral shrubs with high cavitation resistance– a relationship suggested to be the result of greater susceptibility to high intensity drought. Therefore, why high mortality was not also observed in our study is unclear. It may be a result of Santa Barbara experiencing a slightly milder climate, compared to those of the aforementioned studies, which both took place in more arid regions of southern California, including in a chaparral-desert ecotone. Summer fog, a normal occurrence in Santa BarbaraCounty, may also play an important role in reducing vapor pressure deficit, thus providing critical drought stress relief during the summer months. Furthermore, our study areas were dominated by stands of relatively large, mature plants, which have been shown to exhibit greater survival rates during drought than smaller individuals .

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 .

California epitomizes the agriculture-climate challenge, as well as its opportunities. As the United States’ largest agricultural producing state agriculture also accounted for approximately 8% of California’s greenhouse gas emissions statewide for the period 2000–2013. At the same time, California is at the forefront of innovative approaches to CSA . Given the state’s Mediterranean climate, part of an integrated CSA strategy will likely include perennial crops, such as winegrapes, that have a high market value and store C long term in woody biomass. Economically, wine production and retail represents an important contribution to California’s economy, generating $61.5 billion in annual economic impact. In terms of land use, 230,000 ha in California are managed for wine production, with 4.2 million tons of wine grapes harvested annually with an approximate $3.2 billion farm gate value. This high level of production has come with some environmental costs, however, with degradation of native habitats, impacts to wildlife, and over abstraction of water resources. Although many economic and environmental impacts of wine production systems are actively being quantified, and while there is increasing scientific interest in the carbon footprint of vineyard management activities, efforts to quantify C capture and storage in annual and perennial biomass remain less well-examined. Studies from Mediterranean climates have focused mostly on C cycle processes in annual agroecosystems or natural systems. Related studies have investigated sources of GHGs, grow bag gardening on-site energy balance, water use and potential impacts of climate change on productivity and the distribution of grape production. The perennial nature and extent of vineyard agroecosystems have brought increasing interest from growers and the public sector to reduce the GHG footprint associated with wine production.

The ongoing development of carbon accounting protocols within the international wine industry reflects the increased attention that industry and consumers are putting on GHG emissions and offsets. In principle, an easy-to-use, wine industry specific, GHG protocol would measure the carbon footprints of winery and vineyard operations of all sizes. However, such footprint assessment protocols remain poorly parameterized, especially those requiring time-consuming empirical methods. Data collected from the field, such as vine biomass, cover crop biomass, and soil carbon storage capacity are difficult to obtain and remain sparse, and thus limit the further development of carbon accounting in the wine sector. Simple yet accurate methods are needed to allow vineyard managers to measure C stocks in situ and thereby better parameterize carbon accounting protocols. Not only would removing this data bottleneck encourage broader participation in such activities, it would also provide a reliable means to reward climate smart agriculture.Building on research that has used empirical data to compare soil and abovground C stocks in vineyards and adjacent oak woodlands in California, this study sought to estimate the C composition of a vine, including the relative contributions of its component parts . By identifying the allometric relationships among trunk diameter, plant height, and other vine dimensions, growers could utilize a reliable mechanism for translating vine architecture and biomass into C estimates. In both natural and agricultural ecosystems, several studies have been performed using allometric equations in order to estimate above ground biomass to assess potential for C sequestration. For example, functional relationships between the ground-measured Lorey’s height and above ground biomass were derived from allometric equations in forests throughout the tropics.

Similarly, functional relationships have been found in tropical agriculture for above ground, below ground, and field margin biomass and C. In the vineyard setting, however, horticultural intervention and annual pruning constrain the size and shape of vines making existing allometric relationships less meaningful, though it is likely that simple physical measurements could readily estimate above ground biomass. To date, most studies on C sequestration in vineyards have been focused on soil C as sinks and some attempts to quantify biomass C stocks have been carried out in both agricultural and natural systems. In vineyards, studies in California in the late 1990s have reported net primary productivity or total biomass values between 550 g C m−2 and 1100 g C m−2. In terms of spatial distribution, some data of standing biomass collected by Kroodsma et al. from companies that remove trees and vines in California yielded values of 1.0–1.3 Mg C ha−1 year−1 woody C for nuts and stone fruit species, and 0.2–0.4 Mg C ha−1 year−1 for vineyards. It has been reported that mature California orchard crops allocate, on average, one third of their NPP to the harvested portion and mature vines 35–50% of the current year’s production to grape clusters. Pruning weight has also been quantified by two direct measurements which estimated 2.5 Mg of pruned biomass per ha for both almonds and vineyards. The incorporation of trees or shrubs in agroforestry systems can increase the amount of carbon sequestered compared to a monoculture field of crop plants or pasture. Additional forest planting would be needed to offset current net annual loss of above ground C, representing an opportunity for viticulture to incorporate the surrounding woodlands into the system. A study assessing C storage in California vineyards found that on average, surrounding forested wild lands had 12 times more above ground woody C than vineyards and even the largest vines had only about one-fourth of the woody biomass per ha of the adjacent wooded wild lands .

The objectives of this study were to: measure standing vine biomass and calculate C stocks in Cabernet Sauvignon vines by field sampling the major biomass fractions ; calculate C fractions in berry clusters to assess C mass that could be returned to the vineyard from the winery in the form of rachis and pomace; determine proportion of perennially sequestered and annually produced C stocks using easy to measure physical vine properties ; and develop allometric relationships to provide growers and land managers with a method to rapidly assess vineyard C stocks. Lastly, we validate block level estimates of C with volumetric measurements of vine biomass generated during vineyard removal.The study site is located in southern Sacramento County, California, USA , and the vineyard is part of a property annexed into a seasonal floodplain restoration program, which has since removed the levee preventing seasonal flooding. The ensuing vineyard removal allowed destructive sampling for biomass measurements and subsequent C quantification. The vineyard is considered part of the Cosumnes River appellation within the Lodi American Viticultural Area, a region characterized by its Mediterranean climate— cool wet winters and warm dry summers—and by nearby Sacramento-San Joaquin Delta breezes that moderate peak summer temperatures compared to areas north and south of this location. The study site is characterized by a mean summer maximum air temperature of 32 °C, has an annual average precipitation of 90 mm, typically all received as rain from November to April. During summer time, plastic grow bag the daily high air temperatures average 24 °C, and daily lows average 10 °C. Winter temperatures range from an average low 5 °C to average high 15 °C. Total heating degree days for the site are approximately 3420 and the frost-free season is approximately 360 days annually. Similar to other vineyards in the Lodi region, the site is situated on an extensive alluvial terrace landform formed by Sierra Nevada out wash with a San Joaquin Series soil . This soil-landform relationship is extensive, covering approximately 160,000 ha across the eastern Central Valley and it is used extensively for winegrape production. The dominant soil texture is clay loam with some sandy clay loam sectors; mean soil C content, based on three characteristic grab samples processed by the UC Davis Analytical Lab, in the upper 8 cm was 1.35% and in the lower 8–15 cm was 1.1% . The vineyard plot consisted of 7.5 ha of Cabernet Sauvignon vines, planted in 1996 at a density of 1631 plants ha−1 with flood irrigation during spring and summer seasons. The vines were trained using a quadrilateral trellis system with two parallel cordons and a modified Double Geneva Curtain structure attached to T-posts . Atypically, these vines were not grafted to rootstock, which is used often in the region to modify vigor or limit disease .In Sept.–Oct. of 2011, above ground biomass was measured from 72 vines. The vineyard was divided equally in twelve randomly assigned blocks, and six individual vines from each block were processed into major biomass categories of leaf, fruit, cane and trunk plus cordon . Grape berry clusters were collected in buckets, with fruit separated and weighed fresh in the field. Leaves and canes were collected separately in burlap sacks, and the trunks and cordons were tagged. Biomass was transported off site to partially air dry on wire racks and then fully dried in large ventilated ovens. Plant tissues were dried at 60 °C for 48 h and then ground to pass through a 250 μm mesh sieve using a Thomas Wiley® Mini-Mill . Total C in plant tissues was analyzed using a PDZ Europa ANCA-GSL elemental analyzer at the UC Davis Stable Isotope Facility. For cluster and berry C estimations, grape clusters were randomly selected from all repetitions. Berries were removed from cluster rachis. While the berries were frozen, the seeds and skins were separated from the fruit flesh or “pulp”, and combined with the juice . The rachis, skins and seeds were dried in oven and weighed. The pulp was separated from the juice + pulp with vacuum filtration using a pre-weighed Q2 filter paper . The filter paper with pulp was oven dried and weighed to get insoluble solid fraction . The largest portion of grape juice soluble solids are sugars. Sugars were measured at 25% using a Refractometer PAL-1 .

The C content of sugar was calculated at 42% using the formula of sucrose. Below ground biomass was measured by pneumatically excavating the root system with compressed air applied at 0.7 Mpa for three of the 12 sampling blocks, exposing two vines each in 8 m3 pits. The soil was prewetted prior to excavation to facilitate removal and minimize root damage. A root restricting duripan, common in this soil, provided an effective rooting depth of about 40 cm at this site with only 5–10 fine and small roots able to penetrate below this depth in each plot. Roots were washed, cut into smaller segments and separated into four size classes , oven-dried at 60 °C for 48 h and weighed. Larger roots were left in the oven for 4 days. Stumps were considered part of the root system for this analysis.In vineyard ecosystems, annual C is represented by fruit, leaves and canes, and is either removed from the system and/or incorporated into the soil C pools, which was not considered further. Structures whose tissues remain in the plant were considered perennial C. Cordon and trunk diameters were measured using a digital caliper at four locations per piece and averaged, and lengths were measured with a calibrated tape. Sixty vines were used for the analysis; twelve vines were omitted due to missing values in one or more vine fractions. All statistical estimates were conducted in R.An earth moving machine was used to uproot vines and gather them together to form mounds. Twenty-six mounds consisting of trunks plus cordons and canes were measured across this vineyard block . The mounds represented comparable spatial footprints within the vineyard area . Mound C stocks were estimated using their biomass contribution areas, physical size, density and either a semi-ovoid or hemispherical model.The present study provides results for an assessment of vineyard biomass that is comparable with data from previous studies, as well as estimates of below ground biomass that are more precise than previous reports. While most studies on C sequestration in vineyards have focused on soil C, some have quantified above ground biomass and C stocks. For example, a study of grapevines in California found net primary productivity values between 5.5 and 11 Mg C ha−1 —figures that are comparable to our mean estimate of 12.4 Mg C ha−1 . For pruned biomass, our estimate of 1.1 Mg C ha−1 were comparable to two assessments that estimated 2.5 Mg of pruned biomass ha−1 for both almonds and vineyards. Researchers reported that mature orchard crops in California allocated, on average, one third of their NPP to harvestable biomass, and mature vines allocated 35–50% of that year’s production to grape clusters. Our estimate of 50% of annual biomass C allocated to harvested clusters represent the fraction of the structures grown during the season .