Nature Agriculture

Atmospheres enriched with CO2 can create fungistatic conditions, and therefore, inhibit the growth of fungi. Raspberries exposed to CO2 levels of 20 kPa or higher had delayed gray mold decay and extended shelf life . Nine red raspberry genotypes were stored in controlled atmospheres with 12.5 kPa CO2 and 7.5 kPa O2 for 50 days at 1℃, and decay development was strongly suppressed across all genotypes . Our objective was to determine the optimum atmosphere to extend raspberry shelf-life and maximize quality during transit or storage by assessing fruit response to a range of CO2 atmospheres.Freshly harvested raspberries were obtained immediately after harvest in fall 2020 and 2021. Berries were field packed into clamshells and precooled at a commercial facility in Watsonville, California. Cooled fruit were transported on the same day in an air-conditioned vehicle to the UC Davis postharvest laboratory within 3 hours. Raspberries were held at 5℃ overnight, and the next day, the baseline quality of a sample of fruit was analyzed before randomly assigning the remaining clamshells to different atmosphere treatments at 5℃. Fruit were removed from the atmosphere treatments after 6, 10 and 14 days in 2020 and 5, 10, dutch buckets and 13 days in 2021 and immediately evaluated to assess changes in the fruit’s physical quality over time in storage. The performance of fruit in each treatment atmosphere was evaluated from the perspective of raspberry shelf life and quality. Respiration rate and ethylene production were measured at 5℃ on each evaluation date. Fruit for the 0-day evaluation were cooled overnight before measurement.

After removing stored raspberries from the atmospheres, fruit were held at 5℃ in air for 18-20 hours to off-gas before being sealed inside a 10-liter container for 1 hour at 5℃ prior to headspace gas sample collection. Respiration and ethylene production rates were calculated and expressed as ml CO2/kg/hr and µl ethylene /kg/hr, respectively. One clamshell per treatment and replication was weighed before sealing in the plastic bags. Percent weight loss was calculated by deducting the measured final weight from the initial weight, dividing by the initial weight, and multiplying by 100. Leakiness was assessed subjectively on one clamshell per treatment and replication. In 2020, a single layer of paper towel was laid on a tray. The whole clamshell of raspberries was gently poured onto the tray, then the tray was shaken five times, back and forth; gently, but enough to move the berries. The raspberries from one clamshell were arranged on a white paper divided into 40 square blocks; an individual raspberry was placed horizontally on each block for leakiness evaluation. A similar paper was used to cover the raspberries and pressed very gently onto the fruit for 1 second. The top paper and the fruit were removed, and the papers’ printed square blocks were evaluated and scored for liquid stains resulting from berry leaking. The scores for each fruit were assigned based on the intensity, where 1 = none, 2 = very slight, 3 = slight, 4 = moderate and 5 = severe . The number of fruit with a score of 2 or higher were divided by the total number of fruit to determine the percentage of affected fruit. Leakiness severity was calculated by summing up the severity scores of fruit with a score of 2 or higher and dividing by the total number of leaky fruit.

Decay evaluation was done visually on the fruit from the same clamshell as leakiness. The number of fruit with a score of 2 or higher was divided by the total number of fruit and multiplied by 100 to determine the percentage of decayed fruit. Decay severity was calculated by summing up the severity scores of fruit with a score of 2 or higher and dividing by the total number of decayed fruit. The juice was used for measuring total soluble solids content with a tabletop automatic refractometer , and results were expressed as the percentage of TSS. Four grams of juice were diluted with 20 ml of dH20 and then titrated with an automatic titrator . Titratable acidity was expressed as percentage of citric acid , the dominant organic acid in raspberries.A second clamshell of raspberries from each treatment and replication was frozen with liquid N2, and immediately broken into drupelets with a mortar and pestle. Drupelets were mixed among fruit from each clamshell and stored in a –80 ℃ freezer until analyzed. These frozen raspberries were used for measuring total anthocyanin content . The TAC was measured using a microvolume UV-Vis spectrophotometer by adapting a method from Abdel-Aal & Hucl . Liquid N2 was added to the frozen raspberry drupelets and then immediately ground with a blender for 1 min and turned into a fine powder. An aliquot of raspberry powder was added to 10 mL of acidified ethanol solution and vortexed for 1 min. The solution was incubated for 30 min at 50℃ and then filtered through a 0.45-micron polytetrafluorethylene filter . The supernatant was collected and held in a –20℃ freezer until evaluated by spectrophotometry. Absorbance was measured at 530 and 700 nm on cyanidin 3-glucoside equivalence. The acidified ethanol solution was used as a blank.Firmness is an important indicator of quality in raspberry fruit, as well as many other fruit.

The decrease in raspberry firmness after harvest was inhibited or slowed by storage under increasing CO2 concentrations, and high CO2 stored fruit had significantly higher firmness than air stored raspberries. CO2 has other effects on fruit physiology, it influences ethylene biosynthesis by regulating 1-aminocyclopropane-1-carboxylic acid synthesis and oxidization. ACC synthase is inhibited by high CO2. ACC oxidase activity is stimulated by low levels of CO2 and inhibited by higher CO2 . The association of high CO2 atmospheres with the maintenance of raspberry fruit firmness was further supported by González et al. who found that raspberries stored in a continuous flow of CO2 for 14 days had higher firmness than berries exposed to CO2 for 3 days or an intermittent CO2 treatment. In strawberries, elevated CO2 has also been shown to enhance firmness . Strawberry fruit exposed to high CO2 atmospheres exhibited changes in apoplastic pH levels and in turn may have increased cell to cell adhesion by precipitation of soluble pectin . Solubilization of CO2 produces H+ and HCO3- that could influence pH . The increase in firmness following exposure to high CO2 atmospheres, as related to pectin polymerization, is mediated by calcium. In strawberry, modification of pectic polymers decreased the amount of water soluble pectins and increased the chelator soluble pectins , which is the majorfactor in firmness increase . However, in our study, we did not find any increases in raspberry firmness as a result of exposure to up to 15 kPa atmosphere for 14 days, although the rate of softening was reduced. Forney et al. found that CA did not maintain raspberry firmness during 2-3 days storage at 1℃, and resulted in fruit softening compared to air stored raspberries. The effect of the modified atmospheres in delaying further ripening, as evidenced by differences in other raspberry quality parameters such as color, may be one reason why the firmness was maintained. Bing cherries stored in low O2 maintained a higher percentage of green stems, brighter color and higher TA, indicating delayed ripening as compared to air stored cherries . However, O2 may not have had much effect in our experiment because the lowest O2 concentration we utilized was 6 kPa and the other O2 concentrations were ≥ 13 kPa. The 15 kPa atmosphere could be the one exception. Given the relatively low O2 content and the high CO2 content, the combination of 15 kPa CO2 and 6 kPa O2 may have had additional effects on fruit metabolism beyond the effects of the high CO2 alone, grow bucket strengthening the effect of the 15 kPa atmosphere on fruit quality. However, elevated CO2 atmospheres can delay ripening without the added effect of low O2. In our study we observed an increase in leakiness and a decrease in glossiness during storage. Leakiness is initiated in raspberries by physiological breakdown of the cells, a typical symptom of a plant tissues’ senescence . Physiological breakdown is evidenced by juice leakage and softness, and contributes to the fast deterioration of raspberry fruit quality . We observed a significant increase in leakiness over time after harvest; however, the rate of increase was slower with less leaky raspberries when stored in 15 kPa atmosphere. The effect of high CO2 in slowing further ripening and overripening likely contributed to the slower rate of leakiness development. When evaluating different raspberry cultivars, Harshman et al. did not detect a clear association between fruit firmness and PB resistance, indicating that initial fruit firmness is not related to PB incidence. Forney et al. reported that storage in 12.5 KPa CO2 and 7.5 KPa O2 was less effective in delaying PB than delaying decay. Perhaps, their fruit had already begun senescence prior to CA exposure. Visible decay on the fruit surface significantly reduces raspberry fruit quality. Decay incidence in our studies was reduced by storage under high CO2 concentrations, with the maximum effect achieved at 8 and 15 kPa atmosphere. In agreement with our study, Haffner et al. found significant inhibition of raspberry decay by using high CO2 atmospheres as compared to air stored fruit. High CO2 concentrations create a fungistatic effect that slows microbial activity of fungi as well as the metabolic activity of fruit. High CO2’s fungistatic effect is due to its solubility in the aqueous phase of the produce and fungi. CO2 in the intercellular environment lowers the pH, inhibiting enzyme-catalyzed processes and enzyme production, interacting with cell membranes, and affecting the physicochemical characteristics of proteins . Altered expression of proteins in both fungi and fruit tissues can therefore alter decay development . In addition, maintaining cellular integrity as a result of CO2’s firming effect may have also inhibited fungal activity. Petrasch et al. also, reported mycelium developed faster on softer strawberry fruit than on firmer fruit. In apple and pear CA storage, Von Schelhorn et al. determined that control of fungal development was a secondary impact, and the major prolongation of shelf life was due to delayed ripening of the fruit. While the atmospheres and time-frame of apple and pear storage are very different from those for raspberry, we also found some strong effects of atmosphere on raspberry senescence, apart from decay, which may have contributed to the fruit’s ability to resist decay. CA impacts on fruit physiology may promote decay resistance in addition to direct effects on fungal development. Modified atmospheres reduce respiration rates and delay fruit ripening , which is also in agreement with our findings. In addition, higher firmness can reduce fruit damage and stronger cell walls resist cell wall degrading enzymes produced by pathogens, hindering a microbe’s capacity to infect the fruit . Maintaining a bright red color is an important postharvest quality attribute for raspberries, as dark red color is associated with overripe fruit . High values of hue angle indicate more orange-red color and low values more blue-red color. Our results showed that raspberry fruit stored in 15 kPa atmosphere maintained a stable hue angle after five days, but the hue angle declined in raspberries stored in air or lower CO2 concentrations. In strawberries, holding fruit in 15 kPa CO2 and 5 kPa O2 decreased endogenous ethylene biosynthesis and resulted in a lighter, brighter hue and this finding is also aligning with our finding where high CO2 held raspberries had significantly lower ethylene production rate than air held raspberries. pH also plays a crucial role in raspberry fruit color. CO2 in the intercellular environment lowers the pH . Hydration of CO2 and the production of HCO3 − and H+ may reduce intracellular pH . In strawberry, reducing pH from 3.81 to 3.21 resulted in a 37 to 13 percent shift in flavylium form, and also increased the stability of fruit color more than any other factors . The red flavylium cation remains stable only in acidicconditions . In addition, elevated CO2 atmospheres during storage and/or transportation were found to maintain a lighter, brighter color in strawberry . Anthocyanins play a vital role in raspberry color expression.

European elderberry levels of CNGs can vary greatly depending on the growing location, such that concentrations ranged from 0.08 concentrations ranged from 0.08 ± 0.01 to 0.77 ± 0.08 µg g-1 when fruit was evaluated from various altitudes in Slovenia. 6 These concentrations are lower than those detected in elderberry juice, found to be 18.8 ± 4.3 mg kg-1 in raw juice and 10.6 ± 0.7 mg kg-1 in cooked elderberry juice, suggesting that thermal processing can reduce CNG levels in elderberry products. American elderberries have been evaluated for their concentrations of CNGs. These include amygdalin, sambunigrin , linamarin, and dhurrin. Specifically, the Ozone and Ozark genotypes were evaluated, giving better insight into how CNG concentrations may be impacted by plant genetics. While the total concentrations of the four CNGs in the two American elderberry genotypes were somewhat similar , the composition of which CNGs made up that total were quite different: Ozone elderberries had similar levels of amygdalin and sambunigrin while Ozark elderberries had much higher levels of amygdalin than sambunigrin . The flavor profile of elderberries is an important factor in the consumer sensory experience with elderberry products. Two of the most common compounds identified as drivers of elderberry aroma identified in multiple studies of the berries or elderberry juice are β-damascenone and dihydroedulan. Nonanol was also identified as a key volatile compound contributing to the characteristic elderberry aroma , hydroponic gutter while ethyl-9-decenoate was found to be important for the characteristic elderberry aroma by another study.

While these volatile compounds can be key to the unique aroma, they are not typically the most concentrated compounds. Studies have found the most concentrated compounds to be linalyl acetate, linalool, phenylacetaldehyde, benzaldehyde , hexanal, 2- and 3-methyl-1-butanol, nonanal and benzaldehyde. However, comparing concentration of compounds across studies can be difficult due to differences in sample preparation, extraction method, and method parameters, to name a few important factors. Neither American nor blue elderberry has been evaluated for their volatile aroma composition, which limits the understanding of how these subspecies may perform and be accepted by consumers in the same formats as European elderberry. Analytical assessments of the elderberries and products using the elderberries, in addition to sensory panels would be useful information for product developers and should be performed when cultivars or genotypes are being selected for cultivation and use in commercial products.Elderflowers are frequently used in beverages and food products, including but not limited to teas, syrups, lemonades, liqueurs, wines, jams/marmalades, and tonic water. They are also used for flavoring in yogurt, coated almonds, lozenges, and confectionary goods, to name a few. Furthermore, elderflower can now commonly be found in soaps, lotions, and candles, thus consumers, especially in the United States are becoming more familiar with elderflowers, which have been well-known in Europe for generations. Topical applications are also being explored for their benefits to skin. These recent studies support the long history of use of elderflower by the Lumbee tribe in North Carolina, who use elderflower as a treatment for skin cancer by soaking flowers in witch hazel for a week then applying that to the skin. The main compound in elderflowers, like elderberries, is water, and is found in similar concentrations . Glucose, fructose, and sucrose make up the main sugars found in elderflower. 

While European elderflowers have a roughly equal amount of these sugars, elderflowers of the blue elderberry have a much higher level of fructose than glucose or sucrose. However, there has only been one study to measure these compounds in elderflowers, and more studies are needed to know if this trend occurs across each of the subspecies. There is limited data on these compounds across the three subspecies of interest, such as no information on the American elderberry; thus, few comparisons can be made. Minerals and vitamins have been evaluated in European elderflowers. Minerals include calcium, magnesium, copper, zinc, and manganese. Calcium is the most concentrated mineral with an average of 2955.9 ± 272.7 µg g-1 across several wild and cultivated samples and magnesium is the next most concentrate mineral at an average of 1200.2 ± 453.6 µg g-1 . 72 Vitamin C has only been measured in elderflower syrup, ranging from 22.47 ± 0.06 mg L-1 to 46.17 mg L-1 . Elderflowers of the European subspecies have been evaluated several times for their phenolic profile. Dominant compounds in the flavonol rutin and neochlorogenic acid. Concentrations can vary greatly, just like many of the other compounds already explored in this review. Growing and harvest conditions6 or extraction parameters can impact the final concentrations reported. Significant differences in phenolic concentrations have been found between cultivars, such that the concentration of rutin ranged from 11.6 to 42.3 mg g-1 dry weightand neochlorogenic acid ranged from 10.1 to 20.7 mg g-1 dry weight among the 16 genotypes. The coefficient of variation was greater than 10% for all of the compounds measured, including nine phenolic acids and six flavonol glycosides. American elderflowers have also been studied for their concentration of rutin and chlorogenic acid which generally align with the European elderflower profile, except that the primary phenolic acid was chlorogenic acid instead of neochlorogenic acid. American elderflower appears to contain a different chlorogenic acid isomer than the European elderflower, which has mainly neochlorogenic acid. Furthermore, 12 cultivars were sampled for the study, which showed high variability in concentration of the two compounds measured. Rutin concentrations ranged from 4637 to 8111 mg kg-1 while chlorogenic acid concentrations ranged from 1180 to 3064 mg kg-1 , showing that key phenolic compounds can be more than double in some cultivars. The concentration of these two compounds did not appear correlated, as the correlation coefficient was only 0.018.While there have been several studies measuring the CG content in elderberries of different subspecies, the data available on elderflower CG content is limited. In fact, only one study has published data on this area to date and it focused on European elderflowers. A study comparing growing locations at multiple altitude levels to determine impact on phenolic compounds and cyanogenic glycosides found that CG concentrations in elderflowers ranged from 1.23 ug g-1 to 18.88 ug g-1 , generally increasing as the altitude increases. 6 Sambunigrin was the only CG measured and compared to the berries of the same plants in this study, elderflowers contained more CGs than elderberries. 6 Elderflowers from the American subspecies nor the blue subspecies have been analyzed for their CG content. As consumer concern for this toxic group of compounds remains high, it would increase confidence of consumers to utilize the elderflowers of these other subspecies if data was available on the CG concentrations of these flowers.Elderflowers and elderflower products have been investigated for their volatile profile. A direct comparison is difficult to make from the syrups, which have other ingredients like sugar or lemons, to the plain flower extracts, but due to the high popularity of elderflower syrups, the results of those studies are included here as well. In studies of the European elderflower without any additional food ingredients, linalool and linalool derivates, such as -linalool pyranoxide and cis-linalool oxide, have frequently been identified as prominent. The aroma of linalool, the main aroma compound in lavender, can be described as citrus, fruity, floral, and woody. 80 The age of the flower when harvested as well as how the flowers are stored after harvest can greatly impact the volatile profile. As expected from the other data on inter-cultivar variation, the volatile profile is heavily influenced by the cultivar. For example, wild elderflower had twice as much rose oxide and more linalool oxide than the other 12 cultivars.

While this could be a challenge for manufacturers that use elderflower in products to have a consistent aroma from batch to batch, it also allows for more selectivity to find a cultivar that matches desired organoleptic properties in the product. American elderflowers have not yet been evaluated for their volatile profile, nor have blue elderflowers.Elderberry and elderflower are becoming more common ingredients and flavoring agents in beverages and food products. However, a vast majority of the products on the market today utilize the European subspecies of this plant due its more established cultivation and a deeper understand of the composition, particularly the phenolic profile, of the fruit and flower. North American subspecies, hydroponic nft gutter the American elderberry S. nigra ssp. canadensis and the blue elderberry S. nigra ssp. cerulea, have some information available regarding composition, but further analyses are needed to understand how they may perform in the common applications that European elderberry and elderflower are used in today.As global warming and water scarcity issues continue to impact food systems, fire-resilient and drought-tolerant plants will become more important for supplying nutrient-rich foods . Wildfires throughout the western United States are becoming more common and more serious as seasons are hotter and drier. California has been experiencing unprecedented levels of wildfires, including over 1.9 million acres burned in 2018, over 4.2 million acres burned in 2020, and over 2.5 million acres in 2021. One native and fire-resilient plant is the blue elderberry , which grows wild throughout the western United States and has become a popular choice to grow in hedgerows. The blue elderberry is drought-tolerant, and the roots of the blue elderberry can survive fires to regrow the next season to continue providing valuable flowers and fruit, making it an ideal choice to plant in regions of California and American West often stricken by wildfires. While European and American elderberries have been studied for decades, there is currently little information on the subspecies native to the western region of North America, S. nigra ssp. cerulea , known as blue elderberry due to a white-colored bloom on the exterior of the berry which makes it appear blue. In California, it grows wild in riparian ecosystems near rivers and streams , but is also planted in hedgerows on farms to improve water, air, and soil quality, in addition to providing a habitat for birds, pollinators, and other beneficial insects. The plant can grow several meters tall and wide and flowers from May to August, with peak fruit ripening throughout July and August. While elderberry prefer moist soil and some hedgerows may receive some irrigation during the summer months, most are not irrigated once the hedgerow has been established, about 2-4 years. That is one of the benefits of using native and drought-tolerant plants, as they can better withstand the natural climate without excess resources. Elderberries have a long history of use by Native Americans and Europeans in foods, beverages, and herbal medicines. Research exploring links between elderberry consumption and health has increased dramatically, particularly in the past decade. Numerous in vitro and in vivo studies demonstrate that elderberries have potent antioxidant, antibacterial, and antiviral properties. Results of two randomized, double-blind, placebo-controlled clinical trials suggest that elderberry supplements reduce the duration and severity of cold symptoms. Roscheck et al. identified two non-anthocyanin flavonoids in elderberry extract that inhibited viral ability to infect host cells when bound. While most bioactivity of elderberries is assumed to result from the phenolic compounds like anthocyanins, the high-molecular weight fraction of concentrated elderberry juice was found to contain acidic polysaccharides that had potent effects against the human influenza virus. The health-promoting properties of elderberry have led to recent increases in its use in products such as supplements, syrups, gummies, and teas, as well as wine and jams. During the COVID-19 pandemic, elderberry supplements gained wide attention because of potential anti-viral activities; however, there is no strong clinical evidence that elderberry could be beneficial in preventing or treating COVID-19. The market for elderberries is expected to continue to increase, as the sales of herbal dietary supplements was over $11 billion in 2020, a 17.3% increase from 2019. Elderberry was the topselling herbal supplement, with sales over $275 million, as consumers became more interested with supporting their immune systems 9 . In addition to the interest in elderberry as an ingredient in functional foods, elderberry can be an excellent source of natural coloring agents for food and beverage applications due to the high content of red and purple anthocyanins 35 .Characterization of the chemical composition, functional properties, and impact of processing on the bioactive compounds in elderberry is largely limited to S. nigra ssp. nigra and, to a lesser extent, S. nigra ssp. canadensis. S. nigra ssp. nigra is commonly referred to as the European black elderberry, which has many established cultivars, such as “Haschberg” and “Samyl”, and it has an established market.

Therefore, the microenvironment of host fruits to which flies try to expand will have an important influence on the survival and adaptation of fruit flies. Therefore, when tephritids successfully expand their host range from ancestral host fruits to new hosts, they must adapt well to the chemical and nonchemical properties of the microenvironment from the novel host fruits, including their phytochemicals, color, and phenology. The color of the host fruit is an important cue to many fruit-infesting insects when selecting a new host . The phenology of the novel host, such as the timing of flowering and fruiting, also affects the ability of a tephritid to use a new host . Importantly, host chemicals are key drivers when herbivores encounter a novel host and serve as attractants and barriers to adaptation . Phytochemicals include volatile compounds and secondary metabolites that serve as attractants or defensive compounds to herbivores, such as tephritids. Volatile compounds allow tephritid adults to select among potential hosts while in flight, similar to fruit color. Once tephritid flies overcome the volatile chemicals of a potential new host, they eventually make contact with the host fruit, and then they must adapt to any secondary metabolites present to successfully colonize the host fruit. These chemical and nonchemical cues of a potential novel host fruit act as selective pressures on tephritids when a novel host is encountered . These selective pressures involve visual identification; behavioral selection; and physical, chemical, round planter pot and neurophysiological responses by tephritid flies to the novel host fruit . There is likely a genetic basis for each of these processes, which suggests that various genes are involved in regulating the host plant expansion of tephritids.

Therefore, increasing our knowledge of the categories and roles of these genes in regulating host expansion will deepen our understanding and allow for improved management strategies for tephritid fruit flies. Gene regulation of host plant expansion has been revealed in several herbivorous insects, including Subpsaltria yangi Chen , Drosophila mettleri Heed , and Chilo suppressalis Walker . For example, research on host plant expansion in a cactophilic fly, Drosophila mojavensis , revealed cytochrome P450, glutathione S-transferases, and UDPglycosyl transferases as major gene classes involved in new host use . Therefore, the present review summarizes current knowledge on the categories and roles of the genes involved in host plant expansion in tephritids and the related regulatory mechanisms and relates these findings to the development of new control methods for tephritid species. Volatile chemicals stimulate chemosensory receptors in tephritid flies when assessing a potential novel host and trying to expand . Therefore, chemosensory-related genes are involved in the initial process of host plant expansion for tephritids. Olfactory-related genes of tephritids are one type of chemosensory gene that includes several gene families of odorant-binding proteins , chemosensory proteins , odorant receptors , ionotropic receptors , and sensory neuron membrane proteins , which are primarily involved in the identification of volatile chemicals, including volatiles of host fruits. After receiving odor chemical signals, these olfactory-related genes are triggered to transduce cascades that send information to specific regions of the brain, which ultimately leads to specific behavioral responses . OBP genes play an important role in the first step of chemosensory identification of insects, including tephritids . OBP genes direct odorant-binding proteins to bind volatile odor molecules specifically by distinct expression to related olfactory receptors that are bound to olfactory receptor neurons in antennae . CSP genes are regarded as playing a similar role as OBP genes involved in the initial process of chemosensory signal transmission to corresponding receptors .

OBP and CSP genes are major gene types that lead tephritid flies to respond to different chemosensory chemicals, including volatile chemicals of host plants . Except for these two categories of genes, some odor receptor genes also play important roles in host odor recognition of tephritids, such as genes related to odor receptors and ionotropic receptors . Odorant receptors of insects are composed of at least two proteins: a conserved coreceptor as an ion channel and a specific OR subunit , which determines the ligand specificity and forms structurally ligand-gated ion channels . The OR genes mediate odorant receptors of insects transmitting the odorant molecules they receive into electric signals that are transmitted to a higher-order neural center . IR genes are related to ionotropic glutamate receptors , which are regarded as ion channels . They also play important roles in odor chemical perception . The sensory neuron membrane proteins gene encodes transmembrane domain-containing proteins that belong to a large gene family of CD36 receptors . SNMPs regulates the corresponding proteins to identify chemosensory signals, mainly pheromone chemicals . The GR family is another type of chemosensory protein that is a ligand-gated ion channel broadly expressed in gustatory receptor neurons in taste organs and is mainly involved in taste recognition of CO2 , sugar, and bitterness . When receiving taste signals, GR genes are involved in identifying taste and ingestion. Altering gene expression levels also helps tephritids respond to different host plants and realize host expansion. OR13a and OR82 expression are higher in antennae in B. dorsalis in response to 1-octen-3-ol and geranyl acetate, respectively, which are major volatile components of its host fruits, mango and almond fruit . For B. minax, increasing the expression levels of several GR genes regulate the taste process in response to different chemosensory stimuli of hosts .Once a tephritid adult identifies a potential novel host fruit for oviposition or feeding, the plant fruit must be suitable for larval development, which includes overcoming any secondary toxic chemicals in the novel host fruit . The ABC transporter superfamily belonging to phase III enzymes can be subdivided into eight subfamilies, from ABC-A to ABC-H. The cytochrome p450 gene family of phase I mainly contributes to the catalysis of numerous oxidative reactions during endogenous and exogenous metabolism . The important roles of genes in this family are the metabolism of xenobiotics, plant allelochemicals , and even insecticides. GSTs are multifunctional genes of phase II enzymes that play a crucial role in the detoxification of endogenous and xenobiotic compounds, including plant secondary metabolites and pesticides. CCE families of phase II have been shown to be involved in the detoxification of plant-derived allelochemicals as well as insecticides . The ABC transporter genes of phase III encoding membrane-bound proteins typically function in the ATP-dependent transport of various substrates across biological membranes . These genes can participate in regulating detoxification of host plant secondary metabolites of tephritid flies by coding corresponding enzymes, which help to transform toxins entering the insect system into hydrophilic compounds that can be eliminated and in the adaptability of different hosts . The major digestive-related genes include gene families of cysteine proteases, proteases, lipase, glucosidase, and serine proteases . The serine proteases are members of the supergene family, including chymotrypsin, trypsin, thrombin, subtilisin, plasmin, and elastase. subclasses . Various digestive proteases exert important roles in the nutrition digestion of tephritid flies from novel host plants that they try to expand to. Plant proteins of host plants are an important nutrition source used by tephritid flies. However, round pot for plants protease inhibitors of host plants are a widespread defense against herbivores such as tephritids. Therefore, genes coding various proteases react to protease inhibitors by regulating inhibitor-sensitive proteases or expressing proteases that are not targets of the inhibitors . When expanding to other novel hosts, tephritid flies must adapt to different chemical environments from their native hosts. In fact, nonchemical stimuli, such as color, are associated with vision-related genes that allow the identification of different hosts . The genes responsible for color discrimination in Diptera are primarily related to opsin proteins in the photoreceptor cells of the eye .

Six types of Rh opsin-expressed genes have been identified as major genes involved in color recognition and photoreception in Diptera insects. The Rh1 and Rh2 opsin genes are associated with motion detection and direction, respectively . Rh3 and Rh4 are UV-sensitive opsin genes, Rh5 is a blue-sensitive gene and Rh6 is a green opsin gene . These opsin genes lead the photoreceptor of eyes to receive various chromophore pigments and then activate a series of visual transduction cascades to launch corresponding color identification behavior. In the genome of polyphagous C. capitata, the long wavelength sensitive genes Rh1, Rh2, and Rh6 and the UV-sensitive genes Rh3 and Rh4 were found, while Rh2-4 and Rh6 were found in the photo transduction pathway of oligophagous B. minax . Moreover, the role of Rh6 in modulating green color discrimination was reported in C. capitata and B. minax . In B. minax, the function of Rh6, which is responsible for green spectral sensitivity, has been identified by knockdown of the gene B. minax in female adults, and B. minax flies significantly reduced their preference for green fruit after cutting Rh6 . Absence of a member of the bluesensitive opsin subfamily was found in both tephritid species C. capitata and B. minax, but Rh5 can be specifically expressed in Drosophila . Reports about vision-related genes directly involved in the host expansion of tephritids are still very few.Tephritid fruit fly hosts expand to other new host plants, and the phenology of the new host is another nonchemical stimulus that affects fly adaptation. The phenology of the host plant fruits includes the time of flowering, fruiting, or maturation . Many studies have revealed that dormancy plays a crucial role in assisting insects in responding to various phenological environments, including the phenology of different host fruits . The dormant state of tephritids was determined by the rate of growth and development. Therefore, genes associated with development are crucial factors that regulate the adaptation of phenology of various hosts. For example, genes related to sensing day length or photoperiodism and the central nervous system regulate chronic adaptation . Under the regulation of related genes, diapause may involve the deceleration of the developmental progress of tephritids to synchronize the phenological environment . R. pomonella of tephritids is a typical case. The ancestral host of R. pomonell is the hawthorn Crataegus mollis, but its species host expanded to the domestic apple Malus domestica and subsequently formed a new apple race . Apple fruits ripen earlier than hawthorn. The flies that infest apples and hawthorns must differentially time their life rhythms to match the differences in ripening times of their respective hosts . To realize this process, the flies of the two host races varied their time of overwintering pupal diapause. Under the pressure of different host fruit phenologies, many development-related genes are involved in regulating the adaptation to the different phenologies of two host plant fruits . Functional genes associated with cell/tissue development , metabolism , translation , and cell division are highly enriched . By increasing the expression levels of these genes, the CNS development of apple flies was elevated during their diapausing period compared to that of hawthorn flies. Adult emergence-associated genes, including key hormone signaling genes, the ecdysone receptor partner usp, the ecdysone biosynthesis protein ecd, cell cycling genes Myb and rbf, genes coding Mediator complex proteins, and various genes in the Wnt signaling pathway , etc., were enriched to regulate adult fly eclosion to match their host fruit ripeness .Genes coding for ribosomal proteins are often associated with protein translation by stably expressing ‘housekeeping’ genes. This type of gene is involved in many basic biological processes, such as digestion, detoxification, growth, and development, in most organisms . Therefore, ribosomal genes may also be involved in the host plant expansion of tephritids after receiving chemical and nonchemical stimuli. As mentioned above, ribosomal genes increased their expression level to regulate the growth of R. pomonella in response to the different phenology of its new host apple . The role of ribosomal genes involved in host expansion and new host adaptation of insects, including tephritid flies, is mainly related to the response of ribosome-inactivating proteins in host plants . RIPs have been found to have insecticidal functions in many insects, including beetles, mosquitoes, and moths . Ribosome genes can help insects such as tephritids realize host shifting by regulating their expression levels to counteract the RIPs of various host plants . In addition, ribosome genes interact with some epigenetic factors, which leads to chromatin remodeling to change gene expression and regulate different biological processes, including host plant adaptation .

Instead of fingers pointing, bad, bad, bad, how can we use the situation that has struggles from different perspectives and use it as a community engagement piece?” She gave the approval to move forward. After funds were approved and all parties had decided to move ahead, CSF hired an architect familiar with community design and conferred with the Community Advisory Council before plans for the urban farm were drawn up. In 2009, the nonprofit hired a farm manager to oversee the project, Makena Scott, who was one of very few African American CSF employees at the time. Her job description included coordination of the site construction as well as on-the-ground community outreach. City Slicker Farms attempted to solicit input from park users, especially the homeless and scavenger communities, by asking Scott to consult with them, a task she found challenging logistically. Multiple CSF staff, in later interviews, asserted that a top priority for the organization was that everyone who used the park before their development would still be able to use it. This stated goal caused some conflict with local neighborhood associations, who were concerned about crime and homelessness in the area. Yet because the garden’s initial construction took away the park’s seating area and didn’t immediately replace it, the itinerant populations who were regular users of the park also felt pushed out and angry. The nonprofit attempted to be responsive by holding community meetings, but these meetings did not completely resolve tensions. The working poor rarely have time to attend meetings, black plastic plant pots or may not feel comfortable speaking in them. Homeless and itinerant populations rarely attend such meetings. In my later conversations with the itinerant population in the parks, they did not feel included.

The project broke ground on November 1, 2009. In 2010, City Slickers held a barbeque at the site to try to bring together all sectors of the neighborhood and get them talking to one another, which several attendees reported was successful for the evening but didn’t seem to have lasting effects on community relationships. CSF at this point had run into significant problems in navigating city processes, especially in receiving a legal agreement, accessing their money when they needed it and hiring laborers and contractors. Their initial time line was delayed and neighbors and members of the Community Advisory Panel were upset by the lack of communication. Instead of conveying some of their roadblocks to the community, they remained silent. Community outreach during this time was very low. By the fall of 2010, when I spoke to homeless men in the park who were relaxing after finishing their recycling for the day, I met Antony, who was not happy about the Union Plaza Urban Farm across the street. When asked about the motivations of the nonprofit, Antony told me, “They don’t give a fat fuck.”In September 2010, Union Plaza’s raised beds were built and filled with rows of seedlings, the fence was in place and some fruit trees had been planted. City Slicker Farms felt confident enough to organize a Harvest Festival marking the Grand Opening ceremony for Union Plaza Urban Farm and Fitzgerald Park. On the day of the festival, rain was threatening but when I arrived everyone seemed to be in good spirits. I helped unload tables and chairs on the grassy triangle of land called Fitzgerald Park, and laid out fliers at an info booth for City Slickers Farm next to tables piled high with orange Baby Bear pumpkins for Jack-O-Lantern carving.

The pumpkins are small and portable – perfect for a child to carve. In the adjacent triangle-shaped park, Union Plaza, rows of raised beds were visible through the four foot high wooden fence, whose gate was propped open. I had been volunteering with City Slicker Farms for five months at the time of the Harvest Festival, watering and weeding and planting in their gardens, seeding flats in their greenhouse, feeding the chickens, and selling produce at their weekly farm stand. I helped out in the office and attended a workshop on the problem of lead in soils. From the beginning I noticed that the majority of volunteers were white and well-educated. Yet the neighborhood surrounding them was mostly African American and low-income, a disparity I grew more and more curious about as I spent more time at their garden sites. For years the nonprofit was run by a predominantly white staff, and has struggled to find ways to connect with its targeted audience in the West Oakland neighborhood that surrounds them. Much of the labor to run their farms was supplied by year-long Apprentices who are offered housing in West Oakland and minimal pay. This apprenticeship model is common among more rural organic farms, but created unique problems in an urban context, setting the organization up for further racial disconnections and barriers to relationship building with the community. Apprentices were some of CSF’s most visible faces in the community, interacting on a daily or weekly basis with neighbors and volunteers. The fact that the apprenticeship was a very low-paid position meant that they tended to be possible mostly for idealistic young people coming from a fairly affluent background, or with some sort of safety net in place; it is no surprise that most of the Apprentices ended up being white. The year-long time frame of the apprenticeships also created barriers to creating long-term relationships between CSF and the neighborhoods in which they work, because as soon as trust began to form, a new Apprentice would arrive.

Working under the Apprentices was a shifting network of volunteers, providing much of the needed labor to tend the market gardens, most of whom were also white. I spoke with Rebecca Sirna, a former Apprentice and at the time the Backyard Garden Manager, about why it has been so difficult for CSF to attract and retain volunteers and employees who are people of color. When I began my research, Rebecca was the only visibly non-white full-time staff member, although interestingly, Rebecca was raised in a predominantly middle-class, white environment. In explaining the barriers to the involvement of people of color in CSF, she mentioned the status of farm work within the African-American community, and its historical association with slavery, as well as the unattractive economics of nonprofit work.Often when I spoke with CSF employees and other volunteers about race relations, they would bring up the fact that there weren’t many volunteers from the WestOakland community in a slightly puzzled, or almost hurt, tone. They reasoned that with high local unemployment and low access to food, why wouldn’t people want to volunteer with City Slicker Farms? However, this is clearly an assumption, and one that many types of poverty alleviation programs make: that people might not have money, but they have time to give. Often poor families are working a variety of part time jobs and busy with side projects and so are actually not able to give their time away for free, and may be offended by the assumption. This trend continued during the Harvest Festival – the majority of the volunteers helping to run and staff the CSF booths were white. However, the Harvest festival was an explicit attempt to address these conflicts and involve more members of the surrounding community, park users and local residents, in the project. One way they hoped to diversify the crowd was by inviting other Oakland food justice groups to participate. Other booths around the park perimeter represented an array of other food-justice-focused nonprofits that CSF had invited to the festival. They had collaborated with Jason Harvey, black plastic garden pots the African-American founder of the Oakland Food Connection, who was offering a healthy vegetarian meal out of his food truck, with veggie dogs, cabbage salad and a chili topping. Kijiji Grows, founded by a Kenyan man, was there to promote their installations of aquaponics systems in gardens. All of the nonprofits mentioned are run by predominantly African-American or African staff for a predominantly African-American audience, and CSF seemed to be deliberately reaching out to them, thereby ensuring more visible diversity in the nonprofit workers at the site. I stopped by the face-painting booth. The tiny, cold brush tickled my cheek as a cheery pumpkin surfaced, stroke by stroke. City Slickers had set up their farm stand, as always, with fruits and vegetables for sale at a sliding rate, with flowers and herbs in vases and eggs stacked on one end of the table. They offer three categories “Free Spirit” – no money exchanges hands – “Just Getting By” – reduced rate – and “Sugar Daddy/Mama” – which they liken to Whole Foods prices for organic vegetables. Several homeless collectors of scrap metal who usually hang out in the park, all African-American, had showed up and were partaking of the free food. One of them, a thin, rather young woman named Keisha was either in a manic mood or high on something, and kept trying to talk to the City Slickers staff in rapid staccato sentences. A CSF staff member quickly wearied of the near-monologue, to the point where she said, “I am done with her.”

Walking around the edge of the park and poking my head into the booths, I ran into a white local resident who brandished a petition to close Alliance Metal, the scrap metal dealer across the street. He passionately spoke of the noise, pollution, and what he saw as the effects on crime in the area. I could see that the CSF employees nearby were respectful but hadn’t signed the petition and didn’t seem to want to be overtly supporting his cause, a stance which was later confirmed by the Executive Director. I thanked him for his perspective on the situation but did not sign the petition. By the time formal presentations began, rain hoods were up and umbrellas had sprouted around the patch of grass used as a stage. The diverse crowd was of a good size for a drizzly day, perhaps 30-50 people. Nancy Nadel spoke, the local Council member who was a strong supporter of the project. The CSF Executive Director, Barbara Finnin, spoke and then turned it over to a clown show by the kids in Prescott Circus troupe, a longtime West Oakland nonprofit. This was a huge hit with the crowd, which cheered as a trio of eight-year-olds juggled and danced. During the kids’ performance, Diedre got up and started dancing, and the laughter got a little more nervous, though still indulgent. During the break-down of the tables after the Festival ended, an African-American neighbor who hadn’t attended came out to ask if he could have a pumpkin for his kids, and since one of the main reasons for holding the festival was to reach out to the neighbors, they were more than happy to give him a few. All in all, CSF staff judged the event a success. All during the Festival, City Slicker employees had been giving tours of the actual farm space across the street. CSF employee Rebecca Sirna talked about the challenge of educating residents about how to harvest. CSF reports repeated problems with people coming in and uprooting plants, for instance collards, which nonprofit employees believe was an attempt to harvest them. The plants were pulled up while still immature, but if allowed to grow to full size and harvested by taking only a few mature leaves at a time from each plant, they will produce much more food over a longer time. Therefore CSF is attempting to ask local residents and people who want to use the food from the site to harvest only during the hours when employees are working there, which at that time was about eight hours a week, over the course of afew days. Finnin and other CSF staff repeatedly mentioned in interviews that it has been difficult to communicate this policy clearly to other users of the park. Posted signs didn’t seem to help. “People don’t read them,” says Finnin. Instead, the policy seemed to be interpreted in many different ways, passed by word of mouth, and many local residents and park users with whom I spoke seemed confused about whether they were able to harvest from the garden, or angry because they felt excluded from the space. For instance, I was told a disturbing story circulating in the neighborhood about a homeless African-American woman who was picking greens inside the fence, the gate of which was at that time only secured by a loop of rope, and easily slipped off.

In Oakland, competing groups see some urban areas as empty or blighted, which they feel leads to certain logical responses: that it should be made useful and ordered again. However, dueling definitions of both blight and order are at work. In the dense urban environment, there is never “empty space” – every place on the map is an individuated place, with a unique history and quite often current uses which may not be fully visible, or when visible, may not be legally sanctioned. As in the totemic landscape of Aboriginal Australia or the homeland of the Koyukon of Alaska , a place that some would consider wild is woven as a gathering of stories, of the comings and goings of diverse human and other-worldly beings . In the urban farming and homesteading movements, there has been a recent focus on identifying all of the areas on the urban grid which would be possible for agriculture, and setting policies and incentives to create more of a hyperlocal foodshed. Some organizations express big dreams of supplying large percentages of the food an urban area needs from its own “wasted spaces.” . My work looks at what happens next, when an urban farming group starts a farm in one of these spaces. It’s not actually uncontested space, but a particular place with childhood memories and livelihoods attached. A farming project can easily be a form of colonization, through which well-meaning organizations come in with big ideas about how to help people, but end up exacerbating neighborhood divides instead. The idea of “homesteading” itself can have overtones of racial domination, plastic grow pots hearkening back to the pioneers staking claims in the “empty land” of the Western United States, land which had prior uses and claims from indigenous groups .

We enter an urban landscape of startling juxtapositions. The West Oakland streets are a mix of houses, warehouses, and condominiums separated by an elevated freeway from a major commercial district across the border in Emeryville, a strip of Big Box stores such as Home Depot, Best Buy, and Office Max. Some houses in the area have well-kept, beautiful gardens, and some are expanses of weeds, but many contain dogs of various sizes and colors. This is the neighborhood of Dogtown, a historically low-income, African-American neighborhood in West Oakland, which one informant assured me was not due to the current ubiquity of canines but instead “because that’s where they used to have dog fights.” Small Jack Russell Terriers and white fluffy Westies on leashes skitter wide of fences emitting the resonant barks of guard dogs. The underlying conflicts of the neighborhood emerge even in the bodies of their animal proxies . Viewed from above, two small triangles of park land are an anomalous green in a sea of concrete. One triangle of park space offers an expanse of trees and lawn broken by a picnic table, a wooden platform, and small dots of humans and shopping carts filled with glinting bottles and cans moving in various configurations. A larger adjacent triangle, separated by a wide street, offers more botanical possibilities. Lemon trees and lavender plants draw a line across one side, tasty blueberry bushes along another. Moving inward is a border of wood – a fence, now locked with a combination code preventing human entry. Inside are 20 or so raised beds inside, islands of dark soil and nutrient-dense greenery amid lighter gravel paths. These parks are meant to be an oasis in the midst of what many consider to be an urban food desert. But an oasis for whom? One block away is a major raised freeway, feeding minutes later into the Bay Bridge, and emitting a dull roar at all times of day or night.

Small residential homes line two sides of the parks, and one corner holds Alliance Metal and Salvage Yard , which is the destination for all of the shopping carts nosing through the surrounding blocks. Small waterfalls of clinking glass bottles, dissonant squeals of metal on metal, and rumbles of heavy machinery can be heard at the park Monday through Saturday, and industrial-sized smells periodically waft out of the plant. At an opposite corner of the park is a sleek box of metal and glass, with professional landscaping in the small entrance way – a condominium complex built in the last ten years. Behind it, one block over, a high rise condo complex is visible. The third side of the park faces a block-long high fence of corrugated iron covering a boarded up warehouse: a development project halted by the recession. This side of the park, the north side, contains much less landscaping and the street and sidewalk are littered by discarded food wrappers. Here, vans and trucks that double as homes permanently rotate through, including an impressive creation tacked together with boards of different sizes and colors, resembling a houseboat on wheels. Many of the park’s business transactions happen on this quieter, more shaded side of the park. I have overheard conversations about cars changing hands, been offered a cell phone charger in its original packaging from a homeless man pushing a shopping cart, and witnessed drug deals. It is also at times a space of sociality: periodically, a folding table emerges from a truck, four chairs appear, and a domino game commences.

These triangular parks are Union Plaza Park and Fitzgerald Park, and since 2009 Union Plaza has been a working urban farm run by City Slicker Farms, a West Oakland-based nonprofit. This is one specific field site that became a touchstone, but I worked at mural sites and gardens in several different Oakland neighborhoods which shared many of the attributes described above: all were in predominantly low income neighborhoods with a striking mix of housing types and businesses, and holding the ever-present possibility of a condo or a Big Box store appearing. East Oakland mural sites may have had a different demographic mix with more of a Latino presence, but shared many commonalities: shopping carts, corner drug sales, foreclosed Craftsman bungalows and new Condos . Sandwiched between the sea and hills with constant demographic pressure from SF exiles, people of different classes and races live in close proximity and neighborhoods can change seemingly overnight. Material effects of various imaginations indicate the liveliness and relevance of the struggle over space, whether it be graffiti/art, scrap metal/sculptures, weeds/ nutrient-dense vegetables. All are signifiers of who belongs. People’s pathways layer on top of one another, encompassing history and habit and creating the city anew each time they are traced. This piece is about the colonization of space and how these organizations use metaphors of space in order to mark territory. Food deserts, blight and war are some of the metaphors circulating that are constantly used and countered, and I explore these metaphors in the following sections.The term blight was originally used to describe plant disease that “causes rapid and extensive discoloration, wilting and death of plant tissues.” It can be used as either a noun or a verb . In its application in an urban context, the word retained much of the original sense. Blight has a long history of use in urban contexts to signify a state of physical, social and, at times, moral illness . It was first used prominently to describe deteriorating urban conditions by the 19th Century Progressive Movement, big plastic pots which wanted to catalog and quantify urban poverty and its causes . Reformers such as Jacob Riis, author of the report on urban poverty How the Other Half Lives described blight as a disease, akin to cancer, which created slums . The passage of the Housing Act of 1949 gave the concept of blight a national spotlight, as politicians and city planners argued over the best ways to support urban redevelopment and create affordable housing. The law aimed to create “decent housing for every American family,” but its aims were in many cases at odds with its effects in the world. The types of concentrated public housing and “urban renewal” which it supported became notorious for instead creating the kind of blight which the Housing Act was created to address . It sought to increase the housing supply by offering loans for construction by developers and cities as well as underwriting home purchases for individuals.

However, the loan terms offered from the Home Owners Loan Corporation were based on a neighborhood ranking system which, although intended to protect small homeowners from foreclosure, effectively institutionalized racism in lending . “A” ratings tended to be more prosperous, all-white suburbs, while neighborhood ratings explicitly followed racial make-ups of a neighborhood – for instance, if a neighborhood became integrated, its rating could be downgraded. Today we refer to the illegal practice of refusing to make residential loans or imposing more onerous terms on any loans made in an area because of the predominant race, national origin, etc., of the residents of the neighborhood in which the property is located as “redlining.” Overall, less than two percent of the housing financed with federal mortgage insurance was made available to blacks . The policies enshrined in the 1949 law still influence our cities today. The Act’s major contribution to national urban policy was the program for urban redevelopment, which allocated over a billion dollars in loans to help local governments acquire slums and blighted land for public and private development projects. The law resulted in accelerated “blight clearance” in cities across the country by providing federal funding mechanisms to support it. These policies reached their zenith in New York City through the work of Robert Moses, an urban planner who emphasized wholesale clearance of neighborhoods he deemed blighted . The bulldozed spaces were then redeveloped to encourage one use — such as high-rise apartment towers or a district focusing on cultural institutions — with a unified modernist architecture. One criticism of his work is that he gave the needs of automobiles — and the people rich enough to own one — more weight than the needs of the poor and working class residents whom he removed by pioneering the use of eminent domain laws. Ever a pugnacious and controversial figure, near the end of his life, he said, “I raise my stein to the builder who can remove ghettos without removing people, as I hail the chef who can make an omelet without breaking eggs” . Moses utilized strategies that were replicated across the country. A 1966 National Commission on Urban Problems study noted that of 1,555 urban renewal projects funded by the Housing Act, 67% were predominantly residential before urban renewal, but only 43% were residential afterward. To many, urban renewal began to appear as a form of class and race warfare . Jane Jacobs, in her masterwork The Death and Life of Great American Cities refers to blight in a unique way – she uses the term “the great blight of dullness” . In many ways, her book was written in direct opposition to the policies of Moses, whom she saw as decimating the New York she knew and loved. One of her techniques was the subversion of the term “blight,” which Moses used as a tool to mark an area for clearance. Her book is an impassioned plea to create vibrant, diverse, active street life, which she believed is encouraged through mixed use planning – co-mingling business, light industrial and residential uses in the same neighborhood. She believed that a busy, attractive street built on a human scale is a safe street because people want to be using the sidewalk, want to be patronizing businesses there, and want to live there. She was very much against segregating uses such as creating a suburban development of only houses or a downtown filled with office buildings where all of the sidewalks are deserted after five pm. Both the suburb and the downtown described would suffer from “the great blight of dullness” in Jacobs’ eyes. Jacobs use of blight fits surprisingly well with that of the aerosol muralists I worked with. At the center of the Housing Act of 1949 was the belief that physical dwellings could change the behavior of people and thereby accomplish social goals. It was based in the belief that changes in physical environment would influence values: by placing lower-class people in improved housing, they would be motivated to “improve” themselves, or adopt middle-class behaviors .

Starch metabolism is tightly regulated by plants’ internal clock and the external day-night shifts, especially in photosynthetic organs where transitory starch turnoveroccurs on a daily basis. The transcriptional response of the SBE genes follows the circadian rhythm in photosynthetic, and, in some cases, storage tissues. Cis-elements related to circadian control and light responsiveness were universally present in all the horticultural SBEs examined . Hormones, such as abscisic acid , ethylene, salicylic acid , jasmonic acid , and sugar signals have been reported to regulate SBE activity in cereal and horticulture crops. In addition, transcription factors that belong to the WRKY, MYB, bZIP, AP2/EREBP families, may bind to their cognate cis-elements in the 5′ upstream regions of SBEs to activate or suppress transcription. However, information on the transcriptional regulations of SBE is fragmented, and putative hub genes or master regulators have not been identified. Systemwide surveys of cis-elements and TFs in combination with in vitro and in vivo experiments could shed light on, and unearth such regulatory networks.The amylose-to-amylopectin ratio influences the textural, cooking, and nutritional properties of starchy foods, and the functionality of starch-derived biomaterials. Most of this structure-function analysis has been performed on starches isolated from cereals and tubers. However, the relative proportions, and molecular structure of amylose and amylopectin in unripe fruit may have unique properties that could have specialized applications distinct from these well-characterized starches. There may be additional markets for fruit starches if premature harvest occurs, or is desirable, garden pots square due to climactic events. Starch, or the proportion of the amylose fraction of starch, is used as a common ripening biomarker for apple, banana, and pear.

This marker relies on the ability of amylose to physically interact with iodide to form a triiodide blue-black complex. Starch can also influence the quality of fruit juice. Although starch is degraded to sugars when fruit ripens, this conversion is not complete. Ripe fruit processed for juice therefore contains starch, which is treated with amylases for clarification. Further, the amylose content of the remanant starch in some fruit processed for juice, may alter juice viscosity.Prepackaged leafy greens are convenient and healthy, and are popular options for salads in western countries. Metabolism in this horticultural product can be considered over distinct phases in its lifecycle: pre- and postharvest. In developing spinach, the photosynthetic organ, i.e., the leaf, fixes carbon, and partitions a large portion ~20% to starch biosynthesis during the light period under lab conditions. Starch accumulates linearly across the daytime at an almost constant rate . During the night, the leaf starch is degraded into sugar, to maintain plant metabolism, resulting in an empty polysaccharide reserve before the next light period. In Arabidopsis, the expression of SBEs and the changes of amylopectin and amylose show a similar trend, but there is variation in when SBE transcripts peak. Although there is no information on SBE transcriptional levels in spinach during the diel, there may be some similarities with Arabidopsis because the pattern of leaf starch accumulation is comparable in spinach and Arabidopsis. The preharvest starch reserve may alter the postharvest quality of leafy greens. Harvested green produce are stored in optimized packaging under limited light exposure conditions which restricts new energy and carbon input from photosynthesis. However, respiratory activity, which is the carbon skeleton generation process for cellular metabolites, although reduced, does not stop.

In detached leaves, the starch can be broken down to glucose, and sugars become the main source of fuel for cellular metabolism and ATP generation in the early stage of respiration. In the late stage of the respiratory process, the depleted sugars will be replaced by proteins, lipids, and membranes, triggering leaf senescence and cell death . This results in undesirable produce quality and ultimately, in produce loss. Preharvest and postharvest starch content may determine postharvest energy reserves and influence the timespan that buffers the onset of senescence, thus influencing shelf-life of harvested green leaves. Correlations between leaf starch content and postharvest longevity have been found. For example, lettuce and red chard harvested at the end of the day, when leaf starch content was highest, had a longer extended shelf-life than organs harvested at other times of day. This may not be true of all varieties e.g., salad roquette. Starch also correlated with improved shelf-life quality after light exposure to detached leaves in vegetables such as Chinese kale and lettuce . The accessibility of sugars from the degraded starch may relate to leafy-green quality, and the upregulation of SBEs would convert amylose to the more catabolically available amylopectin, providing a more readily available source of sugar.The amylose-to-amylopectin ratio in Arabidopsis influences flowering time and reproductive growth, key markers of development, and fitness. Whether starch molecular structure and composition influences the preharvest growth of leafy greens in a similar way, remains unknown, but it seems likely.Potato, sweet potato, and cassava are generally considered as high glycemic index foods because the starch in their storage organs is easily digested to sugars when consumed, leading to a rapid increase in blood sugar level. It is established that high GI food exacerbate metabolic disorders such as diabetes and obesity. In contrast, multidisciplinary experimental research shows that digestion-resistant starch could increase the healthful microbial communities of the gastrointestinal tract, reducing the occurrence of constipation, and lowering the risk of colon cancer. Altering potato starch composition is a viable way to increase ‘dietary fiber’ content and to enhance colonic health. This can be achieved by either physical, chemical, or enzymatic modifications of purified starch, e.g., etherification, esterification, or by fine-tuning the activity of starch biosynthetic enzymes. Reduction or knockout of SBEs in a range of species have reliably led to an increase in the resistant starch content in various species including horticultural crops e.g., potato, sweet potato, and cassava. Interestingly, SBE2 is not the dominant isoform expressed in storage tubers and roots, but it exerts a major function in amylopectin synthesis. Very high levels of RS can be achieved by the combined suppression of SBE1 and SBE2, but with a yield penalty. The transcriptional profiles and functions of SBE3 are unclear in the developing tubers . In addition, potato tubers suffer from a postharvest disorder: cold-induced sweetening . However, sugars accumulate from starch breakdown, a process referred to as CIS. Although a problem for the potato industry, CIS could be a mechanism to allow tubers to cope with chilling stress. CIS negatively affects the quality of fried or baked potato products: reducing sugars react with free amino acids at high temperature cooking through the Maillard reaction, to form carcinogenic acrylamide. Changes in the enzymes involved in starch biosynthesis and degradation are involved in CIS. SBEs are actively expressed in CIS susceptible tubers, and in StVInv silenced, CIS-resistant tubers, SBEs transcriptional level were suppressed. Naturally occurring high RS potato varieties, also, have less susceptibility to CIS. Therefore, evidence points to a positive association of SBE activity with CIS severity in some potato genotypes.Starch is a major component of the dry mass of fruits at commercial harvesting time. Starch is transiently synthesized and stored in unripe fruits with a peak just before ripening. Starch appears to be a critical feature of climacteric fruit metabolism, known for their bursts of respiratory activity and ethylene production upon ripening. Climacteric fruits contain more starch, and, more active starch biosynthesis than non-climacteric fruit after anthesis. In tomato, square pots the functional genomics model for fleshy climacteric fruit, starch fulfilled 40% of the carbon needed for respiratory processes based on a constraint-based flux model . Experimental evidence from postharvest metabolism also supports the model: tomato fruits stored postharvest under low or chilling temperatures undergo bursts of stress-related carbon dioxide and ethylene production when allowed to recover at room temperature, with an accompanying and corresponding decrease in starch reserves. A similar inverse relationship between starch content and respiratory activity was observed in ripening banana, ginger rhizomes sunberry, apple and durian. The relationship between tissue starch content and respiration may not be perfectly linear in all species, e.g., in stored ginger, starch showed a biphasic accumulation pattern as respiration progressed, a trend not seen in other tissues examined . Furthermore, the relationship between these variables may also differ among genotypes within a species.

Apart from climacteric characteristics, after the onset of ripening, starch content plummets sharply accompanied by starch decomposition into soluble sugars, and the total soluble sugar content continues to rise proportionally . This dynamic metabolic process had been reported for both climacteric and non-climacteric species including tomato, apple, banana, plantain, mango, kiwifruit, pear, and strawberry. Adequate storage of the starch-derived solublesugars, is essential to produce an acceptably flavored horticultural produce of appropriate sweetness. Accompanying the starch-sugar dynamics, amylopectin-to-amylose ratio , also changes interactively . The difference in the AP/AM ratio in fruit development is expected to influence the structure of starch and its degradability. In the ripening tomato, the rate of decrease of amylose was greater than that for amylopectin. Thus, the AP/AM ratio increased dramatically during ripening, in concert with the increase in soluble sugar content and fruit color change from green to red. This phenomenon where the proportion of amylopectin increases relative to amylose, was also evident in ripening apple and banana . It is possible to speculate that of the available starch left during fruit ripening, the amylose, or long chained amylopectin was converted into amylopectin whose branch-like structure has a much higher susceptibility to enzyme attack, allowing the rapid process of starch degradation into soluble sugars and supply for respiration. However, this mechanism may not be universal for all fruit. For example, the changes in AP/ AM ratio in kiwifruit are similar to those in developing potato tubers, where the ratio of AP/AM almost remains constant during tuber development. In ripening tomato fruit with sharp increases in AP/AM, up-regulation of SBEs transcriptional expression is expected. Among SBEs, the class 2 SBE has the major effect on altering starch compositions. Elevated expression of SBE2 transcripts does parallel the changes in the AP/AM in ripening tomato, apples, and banana. We propose that ultimately, this change in glucan structure indirectly contributes to flavor, quality, and commodity value.Starch, in general, plays an essential role in balancing the plant’s carbon budget as a reserve of glucose that is tightly related to sucrose metabolism and sugar signaling pathways. Starch is considered as an integrative mediator throughout the plant life cycle, regulating plant vegetative growth, reproductive growth, maturation and senescence, and response to abiotic stresses. This comprehensive regulation is achieved by changes in the synthesis and degradation of starch to balance glucose levels, after developmental and environmental triggers in different organs . Transitory starch and its biosynthesis have been well studied in the model plant Arabidopsis, but little research has been conducted on postharvest leafy greens. Quality metrics such as shelf-life, flavor, color, firmness, and texture are of consumers’ choice, and they are related to the limited pools of storage compounds in detached leaves, which cells rely on to maintain basic cellular activities. A hypothesized function for the starch in packaged leaves could be presented as such: starch may act as a buffer against sugar starvation, and protect against cellular autophagy, by serving as an alternative energy source. If the biosynthesis and degradation of starch could be adjusted in a controlled way, then the modulated release of sugars may influence the postharvest shelf-life in detached leafy greens . A continuous, paced supply of sugars may preserve vacuolar nutrients and water content, leaf cellular structure and integrity, and, thus extend the ‘best by’ postharvest date of the produce. Although the eco-physiological role of amylose is poorly understood in Arabidopsis, the AP/AM ratio may set a threshold for the optimum usage of starch. SBE action in leafy crops may differ from those in Arabidopsis given the dissimilar numbers of their isoforms and domain features . Modifying the quantity and quality of the starch in leafy greens such as spinach, lettuce, and watercress, by targeting starch biosynthetic enzymes, may provide evidence to its postharvest function in terms of produce longevity. Resistant starch is a popular nutritional additive to produce food with enhanced quality attributes, i.e., higher fiber content, and starchy horticultural commodities are similarly attractive.

There are many similarities and comparatively few differences between the SAGE Plant Database design and the Natural Capital Plant Database compared to the other databases, but two differences are significant. First, the Natural Capital Plant Database does not designate a regional context for any data, making it virtually impossible for the user to know if the data apply to their context. Second, the SAGE Plant Database is designed to be open access for searching, open-source for modifying, and contain a public API whereas the Natural Capital Plant Database requires a paid membership and does not have an open API. The SAGE Plant Database’s openness will allow any community with similar activities, culture, and values to clone and adapt the database to their specific needs. SAGE Plant Database’s API will allow for any person to build agroecosystem design tools that can harness the plant data inside the SAGE Plant Database. These two differences, regional context and openness, warrant the need for the SAGE Plant Database in the presence of an otherwise similar tool.Values are a person’s or community’s judgement of what is important in life . The values implicated in the design of SAGE are likely different from those of the other databases because the other databases were designed for different use contexts. However, the results from systematically comparing the values embedded in the other databases with those in SAGE Plant Database design are tenuous because I did not have full information regarding which values were implicated in the design of those artifacts. In effort to understand the values embedded in the other databases, I employed qualitative coding and investigative techniques described in Freidman et al.’s “practical suggestions for using value sensitive design.”

I mapped out stakeholders, grow bag for tomato identified benefits and harms for each stakeholder group, and mapped the benefits and harms onto corresponding “Human Values Often Implicated in System Design” defined by Friedman, et al. and onto the community values defined in section 4.2. I also used written statements on the websites and major design decisions of the other databases to deduce their embedded human values. The result of this effort can be found in the Appendix. Although the results of this analysis are incomplete, this section presents a few key similarities in the values of the other databases and describes how they diverge in the context of grassroots sustainable agriculture. The broad notion of environmental sustainability is a value that each of these systems have. Conservation and/or restoration are explicit goals of CalFlora, USDA PLANTS, UF/IFAS EDIS, and ToLN. Likewise, sustainability in the context of agriculture are explicit values of EDIS and Natural Capital. Each artifact provides some information about a plant’s ecological context, specifically their growth requirements. However, with the exception of the Natural Capital Plant Database, the other databases provide comparatively little to no information about the supporting and regulating ecosystem services a plant provides. While the notion of environmental sustainability may be fulfilled in the other databases’ intended contexts, those without sufficient information about supporting and regulating ecosystem services are less useful in the context of agroecosystem design. Sociocultural equity is another of the participating communities’ values that is also present in the information ecology each of these systems reside in. Article 25 of the Universal Declaration of Human Rights specifies, “Everyone has the right to a standard of living adequate for the health and well-being of himself and of his family, including food…” .

Catoula, representing the UN FAO, argued that the right to natural resources is implicit to the right to food, “both through direct consumption and through providing the basis for income generating activities that enable people to purchase food.” Other organizations argue that environmental conservation supports “rights of people to secure their livelihood” , and that environmental health has a direct impact on human security . The SAGE and other plant database information ecologies work towards supporting equitable access to food, natural resources, a healthy ecosystem, and wildlife. Specifically, CalFlora and ToLN support access to environmental health by providing people with access to information about their local native and wild flora and the physical plants. USDA PLANTS and Natural Capital Plant Database support access to food, natural resources, and environmental health by providing people with access to information about agricultural and wild plants. EDIS supports ecosystem health via conservation and access to food by conducting research and publishing information about agriculture and ecology. ToLN, CalFlora, and EDIS also support access to food, natural resources, ecosystem health, and to nature and wildlife through education programs. Natural Capital directly supports a person’s ability to use the data to grow food and other resources for themselves and their community. In the context of progressing access to food in particular, most of the other database information ecologies are insufficient. CalFlora and ToLN outreach and education focus exclusively on native or wild-growing California plants, not including plants used for modern-day food consumption. The USDA PLANTS information ecology does not provide outreach or education programs and also does not have characteristic properties for most food producing plants. Natural Capital’s shortcoming is only in that it requires users to pay for a membership – even though the fee is low, it is a great enough barrier to turn many newcomers away. EDIS does support sociocultural equality in the context of food sovereignty, providing their information for free online and through outreach programs on a range of agricultural and non-agricultural plants.

The single criticism of EDIS, though, is that the information on the EDIS site is provided via academic publications, often requiring a degree of education to understand beyond what novices may have.The design of the SAGE Plant Database presented in this chapter is available for anybody to implement for their community. Implementation details can vary, largely depending on the skillset and range of knowledge of the community’s technology steward. As the technology steward for this community, I present my implementation decisions and experiences. In effort to reduce the project into a manageable scope, and given my current physical proximity with the community, only the Manzanita community engaged in the first and current implementation cycle of this research. This section presents the front end implementation, back-end implementation, and distribution model of the SAGE Plant Database for the Manzanita community. Throughout this section, I introduce the members of my development team and refer to the development team as “we” when describing the implementation details. The development team consists of ten UCI undergraduate students, one of whom graduated and continued to support this project, two UCI graduate students, and myself.The SAGE Plant Database is a Python3 web application built using the Django 2.0.7 framework with a PostgreSQL database hosted on a Heroku server. Python is an object-oriented programming language developed under an open-source license and the Python Software Foundation is a 501 non-profit organization . PostgreSQL is an open-source object-relational database system. The Django framework is an open-source Python web framework and the Django Software Foundation is a 501 non-profit organization . John Brock, Moin Aminnaseri, and I chose to work with open-source frameworks that have a long-standing history of routine maintenance and upgrades to account for rapid technological advances in the web domain so that the communities using the SAGE Plant Database can adopt, maintain, and update the system without moving platforms for the foreseeable future. In contrast, proprietary frameworks tend to have less interoperability with other frameworks, grow bag for blueberry plants making it more difficult to modify or create addons to SAGE, and tend to have associated financial expenses, for example, to use the framework or to receive tech support. Any framework that is not well established has a greater risk of being discontinued by the community or company that develops it, thus forcing SAGE to be redeveloped in a new framework. Heroku is owned and operated by Salesforce, a for-profit organization. There are many hosting services to choose from, including ones that offer “green hosting” in the form of clean-energy powered servers. The reasons I chose Heroku to host the SAGE Plant Database website are because members of the development team were already familiar with it, it supported Django web applications and a Postgres database, supported uploads of git repositories , and provides free hosting during the four-year development phase.

Heroku may also provide a form of energy savings because it shuts down our application when it is not actively used and refreshes the application once a day to reduce memory consumed by memory leaks, but I have not been able to find information indicating these actions provide energy savings. Once the SAGE Plant Database has completed development, been adopted by the community, and regularly uses bandwidth , transitioning to a comparatively expensive but green webhosting service may be favored by the community.A simple visual design was favored for readability and to maintain low network usage for visual display, as more complicated interfaces often require more data usage. Kristen Segismundo, Daniel McInnis, and I developed the front-end based on the wireframes by Sahand Nayabaziz . When the user arrives at the website, they are presented with the home page which includes a list of summaries for all plants in the database . The summaries have an image, the plant names, and available attribute data. The top-left hand corner of the page is for navigation. The top bar is for searching, filtering, and logging in. The bottom left corner is for adding a plant. When a user clicks on an existing plant or adds a new plant, the website displays the full plant card. The full plant card contains all attribute information available for that plant in the SAGE Plant Database . It separates the attribute information into characteristics, needs, tolerances, products, and behaviors. If the user is logged in, they can contribute attribute information. To modify information that has already been contributed, they click on the attribute or information . To contribute a new photo, the user can click the add photo button and search the Flickr library for images available under the creative commons license. To contribute new attribute information, the user can choose an empty attribute from the lists below . Below the plant attributes, the user can see who has contributed data to the plant and leave a comment about the plant . A user does not need to be logged into search and download information. However, we do require users to create an account to contribute information because of the crowd based decision-heuristics in place for quality control . Moin Aminnaseri and I implemented the crowd-based quality control mechanism as a weighted voting system. When a user specifies a value for a property, a vote is given to that value. If a user disagrees with a value specified in the database and change it, they will be casting a vote for a value other than the one that had the prevailing majority. At the end of each day, the database updates based on a recalculation of votes, displaying the end result in the plant card view . If the user submits a value that is not reflected by at least the majority of previous data for this value, then the user’s input is not displayed, but is recorded so it can be factored into changes made to that attribute in the future. Every change made to the database is recorded as a “transaction” and all transactions remain visible to users at the bottom of each plant page .Matthew Nguyen and I have also implemented a comma separated value importer so that users can import large amounts of data rather than using the graphical user interface which can be comparatively cumbersome if the user already has their data in a spreadsheet format. To assist users in uploading data, we created a spreadsheet template that participants can use to format their data for an automatic import. Currently, users cannot yet import the data directly, but a developer is able to import this data until the feature is implemented. Moin Aminnaseri and I have also created a series of custom scripts for importing very large data sets, such as the USDA dataset, into the SAGE Plant Database. In order to provide the large number of images needed, fellow PhD student Ankita Raturi and I co-mentored an undergraduate honors student, Xin Hu, in her creation of a stand-alone application, called “Tag Your Plants.”

Information systems for this group should support participants’ efforts to engage in “people care, earth care, and fair share,” but also work to support their resistance, technology, and long-term values. If an IT is designed to support some form of quotidian insubordination, such as producing and trading open-pollination seed and plants, and participants prefer to engage in these acts anonymously, then ITs for this group need to allow for anonymous usage and interaction. Furthermore, that IT is meant to support a community and therefore must be a community asset, not subject to heteromation. Heteromation is the occurrence of a single person or entity financially benefiting from the work of an unpaid or underpaid community . Heteromation is directly at odds with the community’s anti-consumerism and long-term equality values. The IT needs to be “open” to the community so it can “regenerate” the system to match their evolving needs in the long-term. Also, the IT needs to work across a range of platforms and operating systems, from new to very old, from mobile to desktop, and work even with intermittent internet connectivity. ITs designed for this group must also fit in with their selective use values. Overwhelmed by “technologies that reach into all corners of life” , these communities do not desire yet another complex sociotechnical solution with marginal returns. In modern times, sociotechnical infrastructures are not always well thought out solutions. Bødker explains that in the third wave of HCI, researchers rapidly designed and introduced ITs in an exploratory fashion, typically with short-lasting or little impact, to understand which questions to ask. In effect, Bødker argues, the discipline has “just dump[ed] technology on people.” Indeed, grow bag the inundation of technology has made the participating communities more critical of technology. These communities also engaged in selective use of IT due to its implications in unsustainability.

Baumer and Silberman argued that “it is not obvious that the complex conditions associated with unsustainability … are best addressed with computing technology.” Tainter explains that although complex system can be very effective at addressing social problems, such as sustainability, at some point the complexity of the system becomes so great that the returns are marginal . If the complexity is left unconstrained, Tainter argues, diminishing returns become negative, meaning the system is ineffective at problem solving, and the system is vulnerable to collapse. Considering Tainter’s argument in the context of sociotechnical systems, Raghavan and Pargman suggest simplifying system complexity through the software concept of refactoring . Refactoring software is the process of applying techniques that makes code more efficient and readable, breaking down complex functionality into simpler parts, and limiting external inputs. Applying these same techniques to sociotechnical systems, Raghavan and Pargman argue, could productively address their issues of growing complexity. They provide 22 signs of a society that could be refactored with abstract concepts of how they could be refactored. For example, Raghavan and Pargman explain that removing duplicated code, including code with variations but similar functionality, is a form of software refactoring that can be applied to sociotechnical systems in the sense that similar functionalities can be consolidated. For example, disjointed efforts within an institution to build plant data services for farmers would better serve the institution and the farmers if they were consolidated into an interoperable system. I argue that the concept of sociotechnical refactoring is particularly appropriate for permaculture communities in part because it overlaps with permaculture practices. Specifically, permaculture aims to limit external inputs to their sustainable polycultures. For example, in a polyculture, nutrients for plants should be provided by other plants in the ecosystem or from on-site compost rather than off-site fertilizer.

Therefore, an IT created for a permaculture community that curbs the external inputs into their agroecosystems or information ecology will be better at addressing the community’s complex conditions associated with unsustainability than an IT that does not. If no IT can possibly provide a refactoring service to the sociotechnical system, then, as Baumer and Silverman argued, sometimes the implication is not to design technology. I argue that another way to address complex sociotechnical conditions associated with unsustainability is to ensure the IT systems empower the communities and provide their members with agency so that they can sustain themselves in the absence of the IT. In earlier work, my colleagues and I describe a self-obviating system which renders itself unnecessary by offering some service that solves or addresses a problem . In other words, the IT’s impacts remain even after it is removed from the information ecology. For example, an IT system that teaches the community how to design sustainable polycultures could facilitate the transition of enough newcomers to full participants to encourage face-to-face social learning as the community norm, rendering the information system un- or less necessary in the long-term as that knowledge becomes a part of the community’s sociocultural capital. Though the information challenges the participants faced are in theory well-suited for technological intervention, many of these permaculture, resistance, technological, and long-term values present serious tensions with adoption of modern ITs. The next section describes those challenges and Chapter 5 explores how to address them.There are many kinds of plant information, not all of which are relevant to agroecosystem design broadly , or to sustainable polyculture design specifically. Creating a sustainable polyculture design requires a significant understanding of plant relationships and human uses, as described in 1.1. However, as described in 4.1, students struggled with creating a sustainable polyculture design that specified plants, their placement, and their function.

The permaculture community draws upon ethnobotany, agroecology, and horticulture for information. Horticulture simply means “garden cultivation” in Latin, but the discipline has a more specific characterization – “the cultivation, processing, and sale of fruits, nuts,vegetables, and ornamental plants and flowers” in addition to services such as installing and maintaining landscapes . Horticulture requires a working knowledge of the average form characteristics and growth conditions of a plant population . Permaculture plant characteristic data is most similar to the level of detail found in information resources authored by horticulturalists, such as plant nurseries, and gardening websites, and books. Ethnobotanists and anthropologists have studied ways in which people around the world have classified and used plants for medicine, food, religious ceremony, and other cultural functions. Sustainable polyculture designers use these categories of data and others to choose which plants to include in the polyculture . How people use plants or arrange mutually beneficial relationships among plants in agricultural systems is based upon observation and experience. As described in section 2.1.2 observation and experience are forms of empirical knowledge in activist research. However, such empirical knowledge cannot be found in one place—it is held by individuals or disassociated communities or cultures, or, in this case, members of the participating communities. Much empirical knowledge exists as unrecorded folk knowledge , and still more knowledge has been lost during the colonialization of indigenous farming communities . In addition to horticultural knowledge, I aim to capture the recorded and unrecorded folk knowledge of individuals in the participating communities so that it can be organized and distributed to other and new members.The intrinsic characteristics that participants most commonly used in sustainable polyculture design were plants form, structure, and seasonal characteristics. Agroecology utilizes similar characteristic data. What participants referred to as “intrinsic characteristics” are known as “functional plant traits” in formal plant sciences . Functional plant traits include physiological, biochemical, morphological , anatomical, and phenological traits . Conventional agriculture utilizes functional plant trait data that are favorable for domestication and yield , but agroecologists use functional trait data to choose species or cultivated varieties to reduce detrimental negative and increase productive ecological impacts . More recently, agroecology researchers started incorporating functional plant ecology– the study of plant ecology across scales – through the comparison of species along axes of functional traits to predict plant responses to, and impacts on, surrounding environments . For example, functional plant ecology evaluates a plants functional response to drivers of climate change – Trevathan-Tackett et al. determines the functional traits of sea grass that impacts their ability to sequester carbon. Agroecologists’ incorporation of functional plant ecology in the design of agroecosystems is similar to and has the potential to bolster the functional analysis cycles to create the ecological balances necessary to form a sustainable polyculture.Without access to functional trait, horticultural, and folk knowledge, grow bag gardening many newcomer participants to sustainable polyculture design ceased their involvement, concluding the process was too difficult and the learning curve too steep. To help members of the communities engage in sustainable polyculture design, the SAGE Plant Database captures both folk and horticultural knowledge and organizes the relationships among plants and ethnobotanical uses.The goals and requirements emerged from six forms of qualitative data discussed in Chapter 3 . For this line of inquiry, I conducted all analytical coding with the intention of determining goals and requirements for the plant database. In this analysis, I assessed the contexts that inform the goals, form, and functions of the database.

All coding entailed taking notes in a physical notebook while referencing digital and physical copies of observation notes, design workshop notes, surveys, interview transcriptions, community-authored artifacts, and community-referenced artifacts that were used in, were a product of, or which described participant’s agroecosystem design process. I conducted the first phase of coding by listing high-level agroecosystem design and the implementation activities that participants engaged in. For every occurrence of a high level activity, such as installing a grey-water system, I identified the fine-grained actions that made up the activity, the tools used in the activity, and contexts the activities occurred in. I translated each fine-grained action, tool, and context into potential goals and requirements for a plant database. The participants had many goals for the SAGE Plant Database. I identified two overarching themes within the participants’ goals: goals that support the agroecosystem design process, and goals that support the communities’ ethics and values. All of the goals are presented in section 5.2.1. The participants had many requirements for the SAGE Plant Database. I found two themes among the participants’ system requirements: those that specify the plant database’s functions and those requirements that support the communities’ values. The system requirements are presented in section 5.2.2.Participants from the design workshop and those involved in early brainstorming agreed that the SAGE Plant Database needed to represent and inform community plant knowledge, and that this knowledge should be of high quality. Its purpose should be to aggregate all the local plant knowledge into one place and allow individuals to use that information, much like their own plant lists, in their sustainable polyculture design process. Many participants were concerned about the quality of plant data in the database and observed that less knowledgeable community members sometimes confused plants because several different plants are referred to by the same common name. This phenomenon is perpetuated by the fact that many gardening resources also omit scientific name or images, which are the most uniform signposts for confirming which plant the information is about. Although, all participants envisioned the database as an electronic store-house of local plant information, many participants envisioned it doing more than just that. Some participants also envisioned the database as a computer-mediated social learning tool. They wanted to connect with and learn from their peers using the database. For example, one participant envisioned a “click here if you’re growing” widget to indicate how much of that plant was being cultivated by the community and who was growing it. Many participants wanted to see their peers’ techniques for planting, growing, and harvesting, but had varying ideas of how that would manifest. However, most participants fell somewhere in the middle of the spectrum. Some participants envisioned the database as a learning tool, but without the social component. For example, one participant wanted the database to visually display inputs and outputs of the plant and suggest which plants could provide the inputs. Others had a limited view of social-learning, where the social aspect was only the “collaborative” effort to create a knowledge base. Because participants did not all agree on these extra features of the SAGE Plant Database, most of them are not included in the baseline design presented in this chapter. Some of them, however, are under consideration for future work. On the surface, the identifiable nature of the social-learning concepts for the database, such as knowing who planted what plant in which location, appears to conflict with some participants desire for anonymity.

American political economist Gar Alperovitz argues that by eliminating mechanisms for people to work together to achieve a common goal, like with unions and cooperatives, the wealthy minority has forced the poor majority into conditions where they have to operate and survive as individuals . He argues that this phenomenon is symptomatic of corporate capitalism and that US industrial agriculture is implicated in corporate capitalism. Alperovitz further posits “the design of corporate capitalism is unable to sustain values of equality, genuine democracy, liberty, and ecological sustainability as a matter of inherent systemic architecture” . Instead of corporate capitalism, he argues for the systemic design and construction of new institutions, especially locally, that support serious longer-term transformative politics because local institutions provide a context which allows and nurtures the sustained development of an alternative political culture. Among the new institutions Alperovitz describe are cooperatives, neighborhood corporations, land trusts, municipally owned energy and broad band systems, and hybrid forms of community and worker ownership. Local sustainable agriculture institutions include grassroot cooperatives, neighborhood corporations, “permaculture guilds,” farmers’ organizations, and research extension agencies. Some of these institutions, such as cooperatives and community supported agriculture programs , square black flower bucket primarily work to exchange goods – an essential activity in security food and resource sovereignty. Others, such as permaculture guilds, farmers’ organizations, and extension agencies, work to exchange knowledge.

Agroecologist Keith Douglass Warner explains that social learning has become the chief strategy for extending more “sustainable” alternatives within conventional agriculture because expanding sustainable alternatives requires more exchange of knowledge than static expert knowledge or delivery of technology . Warner argued that practitioner-led information generators such as farmers’ organizations are critical because, in many cases, growers and farmers develop agroecological strategies and practices before agricultural scientists. While “local” is a crucial component of sustainability, local institutions alone are not effective . Sustainable agriculture efforts must connect at regional and national levels to provide food items to people and places that have limited or seasonal access to certain varieties of food due to climate, land-use, or population reasons, and sometimes all three.Alperovitz argues that achieving community sustainability, and thereby ecological sustainability, requires planning at a regional or national level because decisions made at larger scales can upend or negatively impact careful local planning . He describes this “Pluralist Commonwealth” vision as a system of public, private, cooperative, and common ownerships structured at different scales and in different sectors. In the context of agriculture, a pluralist commonwealth requires mutual collaboration between grassroots sustainable agriculture efforts and municipal, regional, national, and global efforts such as those undertaken by the USDA and the UN Food and Agriculture Organization . The FAO is one example of an international institution looking to grow support for small-scale grassroots efforts in sustainable agriculture.

At the 2 nd International Agroecology Symposium in Rome , FAO Director-General José Graziano da Silva argued that agroecology is a promising mechanism towards achieving the Sustainability Development Goals . He said “to move forward, we need the engagement of more governments and policy makers around the word” . He emphasized that “scaling-up” this initiative must maintain the involvement of family and small-scale farmers . The transition movement is one example of grassroots sustainable agriculture efforts attempting to work within a formal governing system. The transition movement is a social movement originally motivated by the permaculture social movement, aiming to promote sustainable living and build ecological resilience in the near future at local levels. A social movement is an informal network of people that share a collective identity and are aligned in their engagement of a political or cultural conflict . People who identify as members of a movement participate individually or in small groups in activities characteristic of the movement and work towards addressing the conflict. Sometimes members of a social movement form an organized, typically co-located, community that are effectively communities of practice. “Transition” is defined as “transforming the place you live from its current highly vulnerable, non-resilient, oil-dependent state to a resilient, more localized, diverse and nourishing place” . Transition towns across the world have collaborated with city councils and larger governments to create legislation in regards to climate change, peak oil, and more .

Rob Hopkins, the founder of the transition movement explains “the legal structure of a group affects its behaviour and how it is seen by others” . “Flexibility and informality,” Hopkins continues, “is fine for a young initiative, but as you grow and take on more responsibilities you will need more structure and allocation of responsibility” . Agroecology integrates modern and traditional knowledge of agriculture systems, as well as social science and natural science, and emphasizes food sovereignty and social and biological diversity . Agroecology situates human systems within natural systems, eliminating the dualism as discussed at the start of Chapter 1. In building sustainable agroecosystems, agroecology models the structure of natural ecosystems but with human derived inputs and outputs. Agroecology emphasizes environmental sustainability by mimicking natural systems via use of perennial polycultures , reducing reliance on off-farm resources, avoiding synthetic inputs, minimizing toxic materials, conserving energy, and protecting natural resources such as soil and water . In comparison, industrial agriculture emphasizes monocultures , often annuals , use of synthetic fertilizers and pesticides, and heavy machinery to till, plant, and harvest. Snapp et al. have demonstrated that polyculture systems can compete with monoculture systems in terms of yield consistency, grain quality, production profitability, fertilizer efficiency, and farmer preference. Perennial crops , including trees, minimize disturbance of the system while providing additional benefits such as carbon dioxide uptake, soil stabilization, and microclimate control . Natural and semi-natural ecosystem landscapes are ecologically more sustainable, economically more beneficial than converted systems , and are socio-culturally preferable . Maintaining economic sustainability remains a challenge for mainstream agroecology practitioners. For many existing farmers and ranchers, rapid conversion to agroecosystems is not financially practical or possible, so conversion efforts tend to proceed slowly . Most farms stall at early stagesof conversion because of the initial reduction in yield and loss of profits. The farmer’s inability to adjust the economics of the farm’s operation to the new relationships that come from farming agroecosystems, and farmer doubt of the productivity of an agroecosystem in comparison to traditional monocultures, leads to giving up on the conversion . Scientific validation of agroecosystem practices is also challenging. Martin and Isaac argue that “agroecology lacks a theoretical framework for the development and testing of general hypotheses.” Agroecologist Sarah Taylor Lovell and her research team have just established what is believed to be the first “production size” field trial that compares an agroecosystem to the traditional soy and corn rotation in southern Illinois. The 30-acre experiment at the University of Illinois has seven treatments, each repeated three times . At the time of this writing, the experiment is too young to have any preliminary or conclusive results. Such an experiment takes many years to complete, making scientific validation of agroecological practices a slow process. Mainstream agroecology is facing challenges regarding social sustainability among farmers and consumers. Not unlike modern industrial agriculture, the start-up costs for agroecosystems can be unobtainable as they often require continued education, high quality inputs and infrastructures , new or different equipment , and investment in mature plants to reduce time to yield . Unlike conventional agriculture, there are few subsidies and financial programs to support farmers transitioning to sustainable agriculture methods. Because professional agroecosystem crops are novel and in comparatively small supply to conventional crops, their high price prevents the product from being equally available to all consumers .

Social learning is a critical factor in farmers’ adoption of agroecology. Warner criticized the lack of social learning among researchers, square black flower bucket wholesale extension agencies, and farmers. Note that in this context, social learning denotes participation as a group in experiential research and knowledge exchange to enhance common resource protection . Ollivier et al. argue that social learning must engage with the plurality of ontologies, knowledge, and power distribution to effectively support agroecological transitions. Social learning networks are necessary for understanding local ecological conditions and deriving techniques that are regional and social-infrastructure specific. In the United States, land-grant universities and colleges share new research with and provide education to farmers and other residents in their local area through National Institute for Food and Agriculture supported institutions called extensions . Post-Green Revolution, Warner argued, most extensions focused on “transition of technology” with the prospect of increasing yields, giving little thought to the systemic effects that technology has on the farm. Warner attributed farmers’ slow adoption of agroecology to a decline in governmental funding in the late 1980’s and early 1990’s and private investment in extension services by conventional agriculture stakeholders . However, a recent effort in the Northwestern United States to redefine extension proprieties to address climate change and state-funded research in sustainable agriculture demonstrates that trend is changing. In contrast to industrial agroecology, grassroots agroecology largely operates outside of the markets, standards, and regulations of mainstream food and agriculture systems, and is thus able to overcome some of the socio-economic challenges professional agroecology faces. For example, grassroots agroecology is typically growing at a small scale for a personal use or a small, often informal market, and so does not have large operational and distribution costs. Grassroots agroecology movements emphasize localization, which dictates that environmental and social goals constrain economic goals .Addressing localization in only some of these ways will not yield a functioning grassroots agroecology because only marginal changes would occur. In Cleveland’s case study, farms in Santa Barbara County annually produce nine times more fruits and vegetables than the population consumes, but less than 4% of produce consumed in SBC comes from within the county . The case study demonstrated that complete localization of fruit and vegetable consumption in SBC, without any changes to farming production practices, would have a marginal reduction of greenhouse gas emissions. This was an unsurprising finding for Cleveland and his team given that “food miles” account for only 2.5% of total agrifood system greenhouse gas emissions . Cleveland, however, did suggest that a holistic localization effort, one that addresses the three spatial and structural disconnects, has great potential to improve nutrition and access to fresh fruits and vegetables for the 39.5% of the SBC population that was food insecure. Cleveland concluded that more research is needed on “how localization can be accomplished in a way that directly supports the underlying goals of grassroots localization advocates” . Food sovereignty, social learning, and moderate market values are all ways that grassroots agricultural movements can support the mainstream agroecology discipline. Agroecology has particularly gained traction in the permaculture movement . Through social learning, permaculture draws amateur farmers and gardeners into agroecosystem practice, effectively putting the power to grow and access food sustainably into the hands of the people. Many amateur permaculture gardeners are turning professional and producing a new wave of farmers, most of which are young and practice in urban or suburban settings and sell their product locally.The term “ethnobotany” was coined by J.W. Harshberger in the late 19th century to describe botanists’ study of how indigenous people used plants in their local contexts. Ethnobotany research dates back as far as the 15th century when Europeans began colonizing the Americas. Midway through the 20th century, anthropologists expanded the field of ethnobotany when they began to study how human societies, particularly those that were preliterate, understood and classified plants and animals . It became a point of fascination to ethnobiologists that non-industrialized communities of people were able to control “an extensive body of knowledge akin to the scientific fields of botany and zoology” . Beginningin the 1940’s, the ethnobotany scope of study gradually expanded from indigenous people to include the study of the relationship of all humans with plants, particularly in a local context . For example, Ford argued that folk knowledge is held even by middle class Americans that maintain their yard . Folk knowledge, sometimes called traditional knowledge, refers to what “local people know about the natural environment,” which can be contrasted to scientific knowledge which is information derived from rigorous research using formal methods . The study of ethnobotany has been integral to food sustainability research and activism since the advent of agroecology in the 1970’s. Human ecologist David Cleveland suggests that integrating traditional knowledge, technologies, and mindsets, particularly in the form of sustainable agroecosystems, is the best way to address a global food crisis in which the human carrying capacity of Earth is reached or exceeded .

In Populus species, lignin can also be further modified by acylation with phydroxybenzoate. Zhao et al. used wild type , lignin p-hydroxybenzoate deficient, and p-hydroxybenzoate overproduction plants to investigate the role of this modification in the response of plants to gravitropic/mechanical stress. This increase is correlated with a significant induction of expression of a gene encoding aBAHD family acyltransferase, namely, p-hydroxybenzoyl CoA: monolignol p-hydroxybenzoyltransferase 1 whose gene product preferentially conjugates p-hydroxybenzoate to Slignin monomer sinapyl alcohol.Plant phenylpropanoids and their derivatives are essential for plant growth, stress responses, and health benefits for humans. A comprehensive understanding of the biosynthetic mechanisms and transcriptional regulatory network of phenylpropanoid metabolism in various plant species is central for developing biotechnological approaches to produce economically desirable traits and products. Additionally, advancements in synthetic biology and biosensor technology illuminate the potential of real-time control of phenylpropanoid metabolism in the future. Ferreira and Antunes reviewed current progress on synthetic biology and highlighted the application of biosensors for re-engineering and autonomously controlling plant phenylpropanoid metabolism. Lam et al. reviewed the understanding and bioengineering of the biosynthesis of tricin, a type of plant flavonoid that is an essential plant defense chemical and a promising nutraceutical. Sullivan et al. established a de novo hydroxycinnamoyl-malate ester biosynthetic pathway in alfalfa via heterologous expression of a red clover gene and enhanced alfalfa post-harvest protein protection.

A transcriptomic study of transgenic tomato plants by Zhao et al. defined a GATA transcription factor mediating the co-regulation of drought stress response and phenylpropanoid biosynthesis. Genetic, flower buckets wholesale biochemical and physiological studies from Lee et al. found that Arabidopsis needs optimal anthocyanin content for better growth under high nitrate and high salt conditions. A study by Roldan et al. using transgenic white clover with high levels of foliar condensed tannins discovered that condensed tannins bind to forage proteins to reduce anthropogenic greenhouse gas emission. Huber et al. chemoenzymatically synthesized a series of new phenylpropanoid derivatives and studied their structures and biological effects. Using qualitative and quantitative phytochemical analyses, Gampe et al. demonstrated that Ononis hairy root cultures produce isoflavonoids with less chemical divergence and in higher quantity, suggesting a promising system for large-scale isoflavonoid production. Systems biology and biotechnology have largely contributed to enhance our understanding on the molecular mechanisms underlying the biosynthesis of phenylpropanoids in plants, as well as to manipulate the phenylpropanoid metabolism to exploit its economic, medicinal and nutraceutical potential. Articles in this volume further contribute to these goals, covering different aspects and branches of the pathway. Novel insights and exciting biotechnological strategies involving the phenylpropanoid pathway are expected in the years to come.The actinobacterial genus Nocardia, the type genus of the family Nocardiaceae emend. Zhi et al., has a long and convoluted taxonomic history mainly due to an overreliance placed on morphological properties. The application of polyphasic taxonomic procedures led to marked improvements in the classifcation of nocardiae and related mycolic acid containing actinobacteria.

In general, the genus encompasses aerobic, Gram-stain-positive, acid-alcohol-positive, nonmotile, chemoorganotrophic actinobacteria which form rudimentary to extensively branched substrate hyphae that fragment into coccoid to rod-shaped elements, aerial hyphae may only be visible microscopically; the diamino acid of the peptidoglycan is meso-diaminopimelic acid , the characteristic whole-organism sugars are arabinose and galactose; diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides are the major polar lipids; the fatty acids consist of straight-chain, saturated, unsaturated and 10-methyl components; mycolic acids have 46-64 carbon atoms and up to four double bonds; the predominant respiratory quinone is a hexahydrogenated menaquinone with eight isoprene units where the two end ones are cyclized and the DNA G+C content ranges from 63-72 mol%. Many of the 119 Nocardia species with validly published names are recognized using combinations of genotypic and phenotypic properties. Most of these taxa are composed of strains isolated from natural habitats but the best-known species contain causal agents of serious suppurative and granulomatous diseases in humans and animals, especially mycetoma and nocardiosis . In contrast, Nocardia vaccinii produces galls on blueberry plants. Soil is probably the primary reservoir for Nocardia strains as they are found in diverse soil types, including acidic forest, arid, Cerrado, karst cave, rhizosphere and saline soils. However, they have also been isolated from marine habitats, especially from sponges, as well as from the gut of fungusgrowing termites and are increasingly being isolated from plant tissue, notably from nodules of actinorhizal plants suggesting that they may have a role in promoting plant growth and inhibiting phytopathogens. Two Nocardia strains isolated from Casuarina glauca nodules induced root nodule-like structures in the original host plant.

Nocardiae are an important source of novel antibiotics, as exemplifed by the production of amicoumacin B from Nocardia jinanensis, asterobactin from Nocardia asteroides, brasilicardin A from Nocardia brasiliensis, nocardicins from Nocardia uniformis subsp. tsuyamanensis and tubelactomicin A from Nocardia vinacea. A comparative survey of nocardial genomes showed that their biosynthetic potential to produce diverse novel natural products is comparable to that of better studied actinobacterial taxa, such as Amycolatopsis and Streptomyces, thereby making them an attractive source of new drug leads. These researchers showed that Nocardia strains from diverse sources, including clinical material, were equally spread across six phylogenetic clades and found that the genomes of the more pathogenic strains were, on average, slightly smaller than those of most of the other genomes and contained fewer BGCs . Similarly, information from the genome of Nocardia cyriacigeorgica shows evidence of adaptation from a saprophytic to a pathogenic lifestyle. The present study was designed to establish the taxonomic status of Nocardia strain ncl2T, isolated from a root nodule of an actinorhizal plant, and to determine its biotechnological and ecological potential. The strain was the subject of a genome-based taxonomic study which showed that it formed a new centre of evolutionary variation within the genus Nocardia, the name proposed for this organism is Nocardia alni sp. nov. with isolate ncl2T as the type strain. The genomes of N. alni and N. vaccinii strains contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds. Statistical comparison between genomic features of the isolate and its taxogenomic neighbours were undertaken to establish any positive correlations between them. Antismash 5.0 predicts NP-BGCs based on the percentage of genes from the closest known bioclusters which show BLAST hits to the genomes of the strains under consideration. The genomes of strain ncl2T and N. vaccinii NBRC 15922T contained 36 and 29 well-defined bioclusters that are predicted to encode for a broad range of specialized metabolites albeit with low levels of gene identity, as shown in Table S2. The genomes of the strains are well equipped to synthesize non-ribosomal peptide syntethases, type I polyketides, ribosomally synthesized and post-translationally modified peptides, as well as betalactone and carotenoidlike terpene compounds. They have the genetic capacity to produce products most closely related to himastatin , an antitumor antibiotic produced by Streptomyces hygroscopicus, stefmycin D , which was initially produced by a Streptomyces strain and inhibits ras-oncogen expressed cells, and teicoplanin, a product of a Streptomyces strain that inhibits growth of Gram-positive bacteria, including Enterococcus faecalis and methicillinresistant Staphylococcus aureus strains. The strains also contain bioclusters predicted to synthesise arylpolyene-like compounds that are structurally and functionally similar to caretonoids and which show antimicrobial and antioxidant activity. They also have bioclusters predicted to encode for ectoine , flower harvest buckets a protective molecule which enables bacteria to survive extreme conditions. It can be concluded that strain ncl2T and N. vaccinii NBRC 15928T have genomes rich in NP-BGCs, notably ones predicted to express for putatively novel polyketide and non-ribosomal peptide compounds thereby providing further evidence that nocardiae are a potentially prolifc source of new bioactive compounds.

It is particularly interesting that these strains have the capacity to synthesise antifungal and antibiotics given their association with plant tissues. Clearly, nocardiae should feature more prominently in natural product discovery campaigns.Comparative genome mining of strain ncl2T and the type strains of N. jiangxiensis, N. miyunensis and N. vaccinii, its closest phylogenomic neighbours, revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. Nocardia casuarinae BMG51109T and N. pseudobrasiliensis DSM 44290T were included in these analyses to represent taxa isolated from plant and clinical sources, respectively. Microbes have a pivotal role in making phosphorus available to plants either enzymatically or by producing organic acids and siderophores and other molecules that solubilize inorganic phosphate.The genome of all of the strains, apart from that of the N. pseudobrasiliensis DSM 44290T, contained genes associated with phosphate regulation and metabolism . These included gene ppx–gppA, which is responsible for the solubilization of inorganic polyphosphate and gene pstS which encodes for phosphate binding protein PstS that is involved in the production of the phosphate ABC transporter. The pstS gene was not detected in the genome of the clinical isolate thereby suggesting a possible correlation between the environmental origin of the other strains, namely soil and plant tissues, and phosphate metabolism. The genome of all of the strains contained gene senX3 which is associated with the production of histidine kinase, a high afnity phosphate transporter which has a role in controlling the phosphate regulon. Phytohormones have a central role in plant growth, notably indole -3-acetic acid and ethylene; the levels of these and other auxins in plants can be regulated by soil microorganisms able to synthesize them. The genome of all of the strains contained genes encoding for indole-3-glycerol phosphate synthase, the precursor of IAA in the tryptophan biosynthetic pathway in plants. They also contained genes encoding for other components of this pathway, including anthranilate phosphoribosyl transferase , anthranilate synthase , and aminase. Similarly, gene trpF, which is associated with the synthesis of anthranilate phosphoribosyl transferase, was present in the genomes of all of the strains, apart from N. pseudobrasiliensis DSM 44290T. Genes pdxl and aad, which encode for pyridoxine 4-dehydrogenase and aryl-alcohol dehydrogenase and are involved in auxin signaling pathways, were found in the genomes of strain ncl2T, N. jiangxiensis NBRC 101359T, N. miyunensis NBRC 108239T and N. casurinae BMG51109T . In contrast, the genomes of all of the strains contained genes associated with tricarboxylic acid biosynthesis, as shown in Table S3. However, only the genome of strain ncl2T contains gene acc that encodes for 1-aminocylopropane-1-carboxylatedeaminase, an ACC deaminase which reduces toxicity due to high levels of ethylene in plants caused by plant growth promoting rhizobacteria. This enzyme also regulates ethylene levels produced by the plant by converting ACC to ammonia and α-ketobutyrate. Plant growth promoting microorganisms can also enhance plant growth by modulating biotic stress as they can decrease, neutralize or prevent infections caused by phytopathogens by synthesizing antibiotics and lytic enzymes. The genomes of all of the strains were equipped with genes associated with the production of chitinases and glucoamylases, as shown in Table S3. They also contained genes involved in the biosynthesis of antibiotics, as exemplifed by fabG, bacC2 and hdhA which express for 3-oxoacyl-[acyl-carrier-protein] reductase, bacitracin synthase and 7-alpha-hydroxysteroid dehydrogenase which play a role in the biosynthesis of pentalenolactone, bacitracin and clavulanic acid, respectively. Further, the genomes of all of the strains, apart from N. pseudobrasiliensis DSM 442990T, contained gene auaJ which encodes for the epoxidase LasC that is involved in the synthesis of lasalocid, a polyether antibiotic. In contrast, only strain ncl2T contained gene tcmO which expresses tetracenomycin polyketide synthesis 8-O-methyl transferase, a gene is associated with tetracenomycin biosynthesis. It can be concluded that while strain ncl2T is most closely related to the type strains of N. jiangxiensis, N. miyunensis and N. vaccinii, it can be distinguished from them as it forms a distinct branch in the phylogenomic tree, has a distinct fatty acid profle and shares low ANI and dDDH values with them. Genomic features, notably genome size and CDS numbers, show that the strain is most closely related to N. vaccinii NBRC15992T, but can be distinguished from the latter by a wealth of chemotaxonomic, genomic and phenotypic data. It is, therefore, proposed that strain ncl2T should be recognized as a new species within the genus Nocardia for which the name Nocardia alni sp. nov. is proposed.Aging can be modulated by genes and lifestyle. For instance, specific gene variants of insulin-like growth factor-1 receptor and forkhead box O3A are associated with longer lifespan in centenarians. In terms of lifestyle, one of the most studied interventions that delay aging is caloric restriction , which can increase lifespan in organisms ranging from yeasts to primates.