The effect of flow on small-scale interactions between a benthic predator and zooplankton prey are more easily observed in a laboratory flume, where high-speed cameras can capture predator-prey events and prey type and concentration can be controlled. Knowing the flow environment in which these animals live can be used to recreate realistic flow conditions in a flume by matching the characteristics of flow observed over the organisms. Predators seek food under environmental conditions that can alter the outcome of predator-prey interactions. In the ocean, the motion of water varies due to tides, currents, waves, and turbulent eddies. How does this ambient flow impact feeding by marine organisms? Bottom-dwelling , predators that feed on small animals in the water column are dominant components of many marine communities. They play a key role in transporting material from pelagic systems in the water column down to the ocean floor .Visual predators such as burrow-dwelling fish dart out and catch passing plankton, while passive suspension feeders collect food delivered by ambient currents onto capture-surfaces. This study explores the effects of the flow of ambient water on these two contrasting modes of foraging. Passive suspension feeders rely on the motion of the surrounding water to transport prey to capture-surfaces, while active suspension feeders generate currents or actively pass a capture-surface through the water. Variations in the strength of the current can affect the amount of prey delivered to benthic suspension feeders and the ability of those predators to hold onto captured food. In response to flow, active suspension feeders can modify their feeding behavior,nft channel and passive suspension feeders can passively or actively alter their shape or orientation or grow into different configurations .

In shallow coastal habitats rapidly-changing currents, waves, and turbulence can impact feeding by benthic organisms. Currents reach maximumvelocities shoreward then seaward during flooding and ebbing tides, respectively, and minimum velocities at slack high and slack low tides. As waves approach the shore, the orbital motion of the water in the waves is compressed close to the substratum and oscillates back-and-forth on a scale of seconds . Turbulent eddies of different sizes stir the water. Many benthic zooplanktivores live in shallow coastal habitats where they are exposed to the turbulent reversals of flow associated with waves. Feeding rates by passive suspension feeders in unidirectional flow have been studied both theoretically and experimentally, e.g. in soft corals , bryozoans , sea pens , and sea anemones , but only a few experimental studies have explored the effects of waves and turbulence on rates of suspension feeding . The flow of water around benthic zooplanktivores can affect predator-prey interactions at each successive stage of the feeding process: encounter, capture, retention, and ingestion . The rate of encounters with prey is the number of prey that pass through the capture zone of a predator per time. As water velocity increases, more prey are swept past a benthic predator per time. In contrast, oscillating flow due to waves may lead to a predator resampling the same parcel of water, which could become depleted of prey. However, turbulent eddies of different sizes can stir the water and counteract depletion. Rothschild and Osborn modeled the role of turbulence in increasing encounter rates between predators and prey by such mixing, but their focus was on pelagic, not benthic, predators. Although it is informative to know how much food is available to a predator, rate of occurrences of encounters do not necessarily predict feeding rates that depend on the proportion of encountered prey that are captured , retained , and ingested.As prey pass by a predator, the escape behavior of motile planktonic prey that sense a nearby predator can reduce capture rates . Waves and turbulence can mask mechanical signals of the predator in the water and can disperse and dilute chemical signals, thereby inhibiting the ability of prey to detect and avoid the predator .

Retention is the ability of a predator to hold onto captured prey. Retention of a captured particle or organism depends on the stickiness of the predator, the contact area between the predator and prey, the size and shape of the captured item, and the speed of the water, as well as the ability of the captured prey to struggle and dislodge itself. It has been suggested and demonstrated in experiments conducted in unidirectional flow that reduced feeding rates by suspension feeders in rapidly-moving water are caused by drag forces that wash prey off capture-surfaces, but retention of prey in waves has not been analyzed. Ingestion can only occur if a predator is able to successfully retain prey. To understand the mechanisms underlying how turbulence affects the feeding rates of benthic predators that eat zooplankton, we must determine how the flow affects encounter rates , capture rates , and retention rates . If feeding rates scale with flow , rates of encounter, capture, and retention would increase proportionally. Previous studies of benthic zooplanktivorous fish showed that foraging behavior was affected by waves and turbulence . Tube blennies are small tropical fish that live in burrows within coral heads and actively dart out into the water column to capture passing zooplankton such as calanoid copepods. These suction-feeding fishes use vision to identify potential zooplanktonic prey, and then lunge towards the prey in a “predator approach”. The approach is successful when the fish swallows the prey, or unsuccessful when it misses the prey or the prey escapes and swims away. When exposed to increasing turbulence, the blennies reduced foraging effort . When exposed to waves, the blennies only tried to catch prey during the periods of slow flow that occurred as the water in the waves changed direction. However, foraging efficiency improved with increasing turbulence and stronger waves because the ability of evasive prey to detect and avoid predation declined with turbulent and wavy conditions . Although the blennies foraged less frequently, the fish were more successful at capturing prey. For these active zooplanktivores an increase in turbulence and waves interfered both with the predator’s feeding behavior and prey’s escape behavior,hydroponic nft but the net result was an increase in foraging success by the predator.

For passive suspension feeders dependent on flowing water to deliver prey, do increases in turbulence and stronger waves similarly impact capture rates and feeding efficiency? The effects of unidirectional flow on feeding rates of passive suspension-feeders are well studied . By quantifying feeding rates, only the retention or ingestion stage of the feeding process is observed, while the impacts of flow on encounter and capture of prey are obscured. Research examining the mechanisms used in passive suspension-feeding to encounter, capture, retain, and ingest prey has been carried out on non-motile “prey” and suggests that higher velocities of flow lead to higher rates of encounters and captures . Experiments with corals feeding on motile planktonic prey demonstrated that evasive swimming behavior by prey reduced capture rates in low flow and in waves . The research reported here examined how levels of turbulence and speed of waves affected each stage of the feeding process used by benthic suspension feeders eating zooplankton. The objective of this study was to measure how the trapping of motile zooplanktonic prey by passive benthic suspension feeders is affected by the “strength” of ambient flow across the predators. We addressed this question using sea anemones, Anthopleura elegantissima , which are abundant on intertidal rocky shores , and which eat a variety of zooplankton, including those with strong escape responses such as copepods . In this study we used calanoid copepods as model prey organisms because they are an important component of the diets of many benthic suspension-feeding organisms , and because their swimming behavior in response to various conditions of flow is well-characterized . We examined how the turbulent and wavy flow observed in shallow coastal habitats affect encounter, capture, and retention rates of zooplanktonic prey by a passive suspension-feeding sea anemone. Our goal was to compare the effects of turbulence and waves on predator-prey interactions between passive suspension feeders and actively-escaping zooplanktonic prey with the effects of similar ambient flow on interactions between benthic fish and such prey. All individuals of Anthopleura elegantissima were collected from Horseshoe Cove, in the Bodega Marine Reserve along the Sonoma Coast in California , during October 2012 and May 2013. Sea anemones from one clone were gently peeled from the rock using a butter knife, and each individual was placed in a separate plastic bag filled with air. The bags were kept in a cooler at 10- 15°C and transported to the University of California Berkeley . The anemones were maintained for ten days in a 19-liter aquarium where they were placed on a suspended plastic mesh substratum to prevent attachment to the aquarium walls. In a temperature-controlled cold room kept at 10-15 °C, the aquarium had recirculating filtered seawater with a salinity of 35‰.

The sea anemones were exposed to a photoregime of a 12 hours dark and 12 hours light provided by full-spectrum fluorescent bulbs . Sea anemones were fed hatched Artemia spp. nauplii once a day, but were not fed 24 hours before use in flume experiments. For flume experiments, sea anemones were transported to the University of North Carolina Wilmington via overnight delivery. Individual sea anemones were placed in plastic bags that were filled with oxygen. The bags were packed into a Styrofoam cooler over a base of ice packs and a middle cushioning layer of newsprint. Upon arrival sea anemones were removed from the plastic bags and housed under aquarium conditions identical to those previously described. Zooplankton were collected from the Bridge Tender Marina in Wilmington, North Carolina , using a plankton net . Samples were diluted in seawater, aerated, and used within 12 hours of capture. Individual calanoid copepods, Acartia spp., were selected using Pasteur pipettes, and held in beakers with bottoms made of Nitex mesh that were submerged in filtered and UV-treated seawater. Before experiments, copepods were dyed red to make the organisms easy to visualize in videos. To dye the plankton, the mesh beaker was submerged in a solution of Neutral Red for 20 minutes . Copepods were videotaped while swimming in still sea water at 15°C in an aquarium before and after being stained. The trajectories of the copepods were digitized with ImageJ , and the behaviors were categorized and measured using Python .Swimming speed, duration, and direction measured from copepod trajectories in still water were not significantly different between undyed copepods and dyed copepods . For control experiments that used dead prey, copepods were heat-shocked after the dye treatment. Laboratory experiments using an oscillating flume were conducted at the University of North Carolina Wilmington. A motor-controlled piston drove FSW back and forth through a U-shaped flume with a sealed working section that was 50 cm long, 10 cm wide, and 10 cm tall . In some cases copepods were captured on the far side of the observed tentacles. If a copepod carried in the flow “disappeared” behind an illuminated tentacle and did not re-emerge, we assumed that it was captured. When this occurred, the tentacles were observed carefully in subsequent frames of the video and in every case the captured copepod became visible when the tentacles moved, the copepods fluttered into view during peak velocities, or the copepods washed off the tentacles. In addition, aerial-view photos of each sea anemone in still water were taken directly after the experiment and captured copepods were noted. No discrepancies occurred between the total number of captured copepods counted by the end of the experiment and copepods observed on the tentacles once the experiment was complete. To quantify the vertical distribution of copepods in the water column, and thus the relative availability of prey in the sea anemone’s capture zone, a distribution ratio was calculated for prey in strong and weak wave regimes. The number of copepods per time that passed through the area above a sea anemone was counted in each video . The ratio described the rate at which swimming copepods passed above the copepod in the ambient flow, relative to the rate at which swimming copepods were carried through the capture zone.

My own combination of these three fields would not be possible without thespaces already opened by those mentioned above. As a final opening thought, I note that anthropologists and social scientists involved in contemporary productions must consider the consequences of collaboration. And they must attend to the reflexive modes that are engendered within and between institutions and disciplines. If “the essence of tyranny is the denial of complexity,” then we must also consider the question, what sort of tyrannies are perpetuated by the institutionalization of interdisciplinary complex systems approaches?This attention to and tension around the internalization of social science in the living laboratory of The Bahamas runs through this dissertation and through my own participation in scientific productions there, and it was the feeling of this tension that started me on the path to what would become this project. In the summer of 2002, long before this dissertation was conceived of, I traveled to The Bahamas for the first time to conduct research towards the completion of my undergraduate thesis in environmental biology. Out of several ongoing projects from which biology students were to choose to participate as a project assistant, I chose to join the American Museum of Natural History’s Bahamas Biocomplexity Project and their initial attempt to administer socioeconomic surveys in fishing communities in The Bahamas. I was told that this social aspect of the project would be integrated,ebb flow table after a period of years, with regional biological and environmental data in order to put together a systemic model of the relationship between local human populations and the regional marine ecosystem functioning in order to inform policy on the creation and management of a proposed marine reserve network .

It was my questioning of this notion of the possibility and promise of “integration” and scientific holism that eventually inspired my own collaborations in The Bahamas, presented here.The arena of Caribbean Studies is one example of critical scholarship which interrogates social and historical categories and forms. I engage with this work throughout this dissertation in order to consider how we might think of the laboratory of The Bahamas today and how we might come to experiment in and inhabit the world. And yet an analysis of the living laboratory of The Bahamas does not flow easily from Caribbean Studies, and this is precisely because The Bahamas both is and is not Caribbean, and because the familiar objects and orientations of Caribbean social science might not adequately speak to some of what is happening there in the contemporary moment. My work in The Bahamas has taught me about the politics of being Caribbean. “Caribbeaness” is a complex attribution with which The Bahamian state and Bahamian people grapple with continually. Historically, The Bahamas has been subject to the same wide ranging and influential events as the rest of the Caribbean region, most notably the transatlantic slave trade, European colonialism, and the 20th Century independence movement. And yet, The Bahamas has been excluded from many collections of social science on the Caribbean and is usually not listed as a Caribbean country when scholars discuss the countries of the region, though it is often categorized as part of the Caribbean Region when it comes to international state politics. For example, the United States’ Central Intelligence Bureau lists it as a Caribbean nation. This confusion results from more than the fact that The Bahama Islands are not in the Caribbean Sea . It has been written that Bahamians do not consider themselves Caribbean because their affinities and trade ties lie more with the US than with the other islands.It has also been written that The Bahamas, due to its long history of success with tourism, is too wealthy to be classed with the rest of the Caribbean, or even the Caribbean of former British colonies.

The Bahamian government has reservations about its membership with the Caribbean economic community and its subsequent inclusion in the Caribbean free market. In this vein, I am interested in the ways in which The Bahamas does and does not exercise its “Caribbeanness,” and I cannot begin with the analytic assumption that this is a Caribbean place, even if these islands share a Caribbean history. This observation has necessitated an investigation into Caribbean Studies and Caribbean Anthropology in order to gauge how to relate this living laboratory to the discipline’s themes, conversations, and tensions.The social science literature on the Caribbean is extensive and diverse, and throughout the 20th Century development of Caribbean Studies the Caribbean area has become a specific “testing ground” for social scientific research and a metaphoric representation of evolving social forms. Through the exposition of case studies, the delineation of social models, and the evocation or refutation of sociological and anthropological problems and conceptual orientations, The Caribbean has provided ground for the production and deconstruction of such notions as cultural contact, New World society, class solidarity and diversity, systems of global production, colonial history, ethnicity, race, religion, gender, nationalism, transnationalism, diaspora, identity politics, globalization, creolization, paradise, and modernity- much of this scholarship under the rubric of colonial/postcolonial studies which variously tackle the theorizing of the practices and politics of oppression and resistance. The particular contingencies of specific Caribbean places have come, variously and inconsistently, to stand for general truths about kinds of postcolonial human nature, or their refutation and/or the nature and practice of postcolonial social theory itself. It is not a stretch to say that the Caribbean has come to be understood as a sort of living laboratory for colonial and postcolonial social research. Yet, during my time in The Bahamas I encountered processes, specific events, and situations that the academic genealogy of Caribbean social science cannot quite speak to because there are many processes at work simultaneously economic, biological, anthropological, and more. This creates a situation which forces one to create cross-cutting conceptual combinations in order to tell new stories and to ask new questions which may or may not be deemed postcolonial, but which owe a debt to this scholarship in any case.

David Scott’s work provides a sense of reading diverse literatures together, and he captures how one might successfully work with postcolonial studies and build off it to create a new orientation. Antonio Benitez-Rojo’s work speaks to a postmodern understanding of the Caribbean, tracing the islands as a form of thought, discussing the mystery, ambiguity, and dynamism the region has historically presented to the world.Scott has a complex approach to the consideration of the postcolonial contemporary Caribbean. His is a critique of those authors who seek to re-imagine the colonial past in the hope of altering the present, and he notes that little consideration has been given to what it is about the present which necessitates revising the past. He writes, “the precise nature of the relation between pasts, presents, and futures has rarely ever been specified and conceptually problematized. It has tended, rather, to be assumed, to be taken for granted.”Scott notes that most postcolonial Caribbean critiques, such as those criticisms of various forms of anticolonial nationalism, take up the goals of nationalist movements,hydroponic grow table and explain how they have failed, as answers, in the present. What these critiques don’t do, however, is consider the problems that the anticolonial nationals constructed in the first place. They merely assume that the colonial problems then, classic Fanonian problems of colonial racism and oppression, are the same as the postcolonial problems now. This, for Scott, tends to lead to the exposition of the negative structures of colonial power and to the concomitant narrative description of a romanticized subaltern agency in the face of this negating power. Scott’s view is different: “it is our postcolonial questions and not our answers that demand our critical attention.” In order to rethink postcolonial Caribbean questions, Scott arrives at the conception of the temporal problem-space. This is the discursive context of dispute and intervention around which questions, answers, and stakes are posed, and this is related to the notion that criticism within a problem-space, Scott’s own goal, must be strategic and alert in order to determine whether the“questions it is trying to answer continue to be questions worth having answers to.” Such criticism poses new hope for the proposition of political alternatives in our present and for the imagination of possible futures because the re-conception of the problem opens new space for the conception of possible responses. Scott’s main example in his monograph is C.L.R. James’ The Black Jacobins, the famous anti-colonial and epic narrative of the Haitian Revolution and the tragedy of Toussaint L’Ouverture. Tragedy, Scott notes, problematizes the “view of human history as moving teleologically and transparently toward a determinate end, or as governed by a sovereign and omnisciently rational agent.”

Tragedy raises doubts about the relation between pasts, presents, and futures, it exposes the “hubris of Enlightenment and civilization” and points toward a more complex and contingent understanding of human life.With such a conceptual view of tragedy and problem-space in mind, Scott hopes to reread The Black Jacobins as a work which moved beyond the anti-colonial, a work which provides grounds with which to critique the postcolonial present. In a meditation on modernity, Scott discusses critiques of James as unaware of the diversity within modernity, stating that the Enlightenment idioms promoted by the French Revolution were an important aspect of Toussaint’s revolutionary subjectivity and that to worry otherwise is to miss the point that subaltern resistance is no longer at stake in the way that it was. The relevant questions for Scott concern the problem of modernity, understood in the Foucauldian sense of a positive formation of power that shapes the material and epistemological conditions of thought and possibility. Toussaint L’Ouverture, in this schema, becomes a conscript of modernity, not only a resisting agent. The plantation is also reconsidered in this view as a form of modern power which shaped conditions of slavery and subjectivity, and this moves the consideration of slavery away from the anti-colonial criticisms of its negative effects and the search for agency. He notes that “what is at stake here is not whether the colonized accommodated or resisted but how colonial power transformed the ground on which accommodation or resistance was possible in the first place, how colonial power reshaped or reorganized the conceptual and institutional conditions of possibility of social action and its understanding.”Thus, for Scott, Toussaint is a conscript of the founding modernity of the Caribbean, a founding modernity that continues to shape the thoughts and lives of others in the region. The lack of a visible indigenous population in the Caribbean, and the forced and brutal “civilizing”process of plantation slavery, make the Caribbean the inaugural form of modernity. In the plantation, slaves and masters were altered in modern ways and inserted into modern global processes that would come to matter for reasons because of their dehumanization and violence. The point is, for Scott, that the Caribbean put forth new conditions of life, creating the West Indian as the conscripted subject and object of a modern ethos. But how do we describe the contemporary ground that shapes these conditions of life in the Caribbean today? How do we characterize the current confluences of productivity that create the region as a particular kind of problem space? Benitz-Rojo has a complex framework for nonreductive thinking about the region which I find helpful as a frame for the discussion to follow. His analytic mode of “Chaos,” referring to the advent of disorder in the passage of time, nonetheless has an emphasis on repeating dynamic states and regularities. He writes, “I have tried to analyze certain aspects of the Caribbean while under the influence of this attitude, whose end is not to find results, but processes, dynamics, and rhythms that show themselves within the marginal, the regional, the incoherent, the heterogeneous, or, if you like, the unpredictable that coexists with us in our everyday world.” The trope of repetition, within this mode is especially salient for Benitez-Rojo, because only repetition as difference, the motion of irreducible change, can be identified in the fluidity of Chaos that is the sociocultural Caribbean.

While DCA and INA behave similar in nahG plants, these two compounds differ profoundly in their level of dependency on the transcriptional co-factor NPR1 . Although the defense inducing activity of INA is fully blocked in npr1-3 plants, DCA is only partially reduced in this mutant. Thus, with CMP442, DCA and INA a small set of synthetic elicitors is now available that has different activating effects on the SA-dependent plant defense network . These molecular probes along with additional synthetic elicitors from our screen and genetic mutations are likely to prove highly useful for the fine dissection of this complex regulatory network.Chemical pesticides currently in use typically rely on direct antibiotic or biocidal activity, which often leads to undesirable toxic environmental side effects . In response to these concerns the U.S. Environmental Protection Agency has established a program to facilitate registration of new reduced-risk pesticides that have a reduced impact on human health and other non-target organisms . Synthetic elicitors identified by our project protect plants by inducing their natural immune responses. As their primary mode-of action does not involve the inhibition of key metabolic or developmental steps in target organisms, they are likely to be less harmful for humans and the environment than conventional pesticides. Due to the continuous pollution of the environment caused by the massive use of traditional pesticides and the increasing awareness of environmental protection issues of consumers and farmers in the US, Europe and other parts of the globe,vertical grow system innovative “green” pesticides suitable for conventional farming practices are urgently needed.

A possible disadvantage of the use of synthetic elicitors for crop protection is that permanent defense activation often results in fitness costs, due to the phytotoxicity of some defensive plant products and resource allocation away from growth or reproduction. For example, as a result of its long-term activity, the synthetic elicitor 2,6-isonicotinic acid , which was developed in the 1990s by Ciba Geigy, was insufficiently tolerated by some crop plants to warrant practical use as a plant protection compound . However, we found DCA and CMP442 to be promising in this respect when contrasted to other known defense elicitors, such as INA or BTH , their defense-inducing activity is only transient and weakens within several days after application . In addition, low doses of CMP442 proved to be beneficial for plant growth. Arabidopsis and tomato grown on solid medium containing low concentrations of CMP442 developed significantly longer roots than untreated seedlings. In addition, single root drench application of CMP442 enhanced growth of aerial parts of soil-grown Arabidopsis and tomato. Thus, CMP442 appears to be uniquely suited to provide plant seedlings with both protection from diseases and enhancement of vigor. We also found several other synthetic elicitors, including DCA, that have similar effects on root growth at low concentrations. However, of those synthetic elicitors we tested so far CMP442 is the most efficient one in this respect. CMP442 strongly enhanced growth of Arabidopsis roots at a concentration of 1 µM. At this concentration CMP442 still can induce defense responses.As shown in Figure 2.3, 10 µM of CMP442 was sufficient to significantly suppress the development of HpaNoco2 spores in Arabidopsis. Despite these promising observations, further studies are needed to explore the full potential of CMP442 for simultaneous disease protection and growth enhancement for crops.

Several regulatory proteins were found to contribute to both defense and developmental processes . These include the Arabidopsis proteins SGT1b, AS1 and AtTIP49a . For example, SGT1b, a regulatory component of SCF complex ubiquitin ligases, was found to be involved in controlling stability of several R proteins as well as the activation of ETI, but also SCFTIR1-mediated auxin responses, such as root development and apical dominance . We recently reported that Enhanced Downy Mildew 2 , which is required for R-mediated resistance of Arabidopsis against the Hiks1 isolate of Hpa, positively affects floral transition . EDM2 has additional roles in plant development, such as promoting proper leaf pavement cell development and controlling the succession of leaf types formed during early vegetative stages of Arabidopsis. An increasing number of studies are reporting on similar molecular links between plant immune and developmental processes. The molecular nature and biological purpose of crosstalk between both types of processes is poorly understood at this point. CMP442, with its clear effects on both plant immunity and growth, is likely to serve as a valuable tool for the dissection of molecular crosstalk between defense and development. We are currently testing its effects on both defense induction and growth enhancement in a variety of known Arabidopsis signaling mutants. Results from these and related studies should shed light on the fascinating, but yet enigmatic, link between seemingly unrelated types of physiological processes in plants. CMP442 may also allow for the discovery of fundamental causes of the general phenomenon of hormesis. Although widely described for numerous types of organisms and physical, chemical or biological stimuli, the genetic and molecular basis of hormesis is largely unknown.

Hormesis is characterized by a biphasic dose-response to a treatment which stimulates at low doses and has an inhibitory or toxic effect at higher concentrations . Biologically, hormesis is believed to be an adaptive response at either the cellular or organismal level to stress. The exposure to low doses of herbicides to produce enhanced growth has been widely reported on . Recent research has revealed some signaling pathways and mechanisms that are responsible for specific hormetic responses. These involve certain ion channels, protein kinases, deacetylases, transcription factors, chaper ones, antioxidant enzymes, and glutathione peroxidase . Another noteworthy observation is that some inducers of hormetic responses can protect the respective cells or organisms against a variety of additional stressors later on . Although the phenomenon of hormesis has been known for several decades, our knowledge of its biological basis is fragmentary at best and much remains to be explained. In particular, it is unclear if the great variety of hormesis-like phenomena have a common functional basis, or if they are mechanistically unrelated. A comprehensive comparison of molecular responses triggered by a variety of hormesis-inducing stimuli in a single type of organism, such as the versatile molecular genetics model Arabidopsis, may allow defining common denominators for this complex phenomenon. Plant diseases can be caused by pathogens with different types of lifestyles. While biotrophic pathogens require living host tissues to complete their life cycles, necrotrophs feed off dead plant cells. The phytohormones salicylic acid , jasmonic acid , and ethylene are known to coordinate plant defense responses to combat the respective type of infecting pathogen. Currently, most documented interactions between JA- and SA-dependent signaling processes are antagonistic, but their interactions are complex and details of crosstalk between them are not fully understood. Upon recognition of necrotrophs, an increase in JA and ET synthesis occurs along with enhanced transcript levels of defense genes, such as Plant Defensin 1.2 ,mobile grow system which is often used as a marker for induction of the JA pathway. Plant defensins are small peptides that can be found throughout the plant kingdom and are encoded by small gene families. Here I report on the development of a screening procedure to identify synthetic elicitors that activate the JA-/ET-dependent branch of the defense network. Towards this end, a set of genes was identified that display SA-independent upregulation in response to infection with the biotrophic oomycete Hyaloperonospora arabidopsidis . Four of the five genes are PDF members including PDF1.2b. Additionally, efforts to create Arabidopsis thaliana lines containing RNA silencing transgenes cosilencing closely related PDF family members are described. Plants are constantly assaulted by a variety of biotic stressors, such as microbial pathogens. Most pathogens are unable to infect plants, making disease the exception, not the rule . Plant pathogens are typically divided into two main categories: biotrophs, which obtain nutrients through living tissue and necrotrophs, which must kill plant tissue to acquire nutrients .

Plants evolved the ability to recognize pathogens and tailor their defense responses to the type of infecting pathogen . They possess an inducible immune system enabling them to specifically recognize molecular features of pathogens and activate transcriptional cascades defending the plant from disease . When these mechanisms are absent or inactivated by pathogen effector molecules, plants are rendered susceptible . Pathogen effectors are proteins or small molecules secreted into host cells that attenuate defense signaling processes weakening plant immune responses. Strong immunity against pathogens can be mediated by plant disease resistance genes, which encode receptors that specifically recognize effectors from distinct pathogen races . Thus, such race-specific immunity is based on interactions of complementary R– and effector-genes . A hallmark of R-mediated disease resistance is the hypersensitive response , a programmed form of plant cell death localized to pathogen infection sites. HR is an effective defense reaction against biotrophic pathogens, which are dependent on live plant tissue . During compatible interactions, basal defense is activated, which is a weakened form of plant immunity that does not involve HR and is typically insufficient to prevent disease . R-mediated disease resistance is frequently facilitated through the SA-dependent branch of the defense network, which is often attributed to defense responses against biotrophic pathogens whereas the JA- and ET-dependent mechanisms seem preferentially to mediate immunity against necrotrophs Thus, the plant immune system is able to specifically tailor distinct responses against different types of pathogens. Fine tuning of these responses is mediated by complex crosstalk between individual signaling branches . The timing, amplitudes and spatial distributions of certain defense signals determine the individual defense reactions activated in response to a given type of pathogen. One pathogen widely utilized to study plant defense is Hyaloperonospora arabidopsidis , an oomycete and obligate biotroph known to exclusively infect the model plant species Arabidopsis thaliana. The study of this pathosystem has facilitated the identification of more gene-for-gene interactions than any other plant and pathogen combination . Thus far, SA-dependent defenses have been directly attributed to limiting Hpa growth in this pathosystem with JA/ET having no distinguishable role . The majority of plant disease research indicates that interactions between JA- and SA-signaling are antagonistic, although it has also been demonstrated that at low concentrations they can act synergistically . JA is a lipid-derived signal that has many vital roles in plants . Responses to JA are controlled by a regulatory apparatus consisting of four key components: the JA signal, the ubiquitin ligase SCFCOI1, the jasmonate ZIM-domain repressor proteins, and transcription factors that positively regulate expression of JA-responsive genes . JA-signaling is involved in complex processes such as pollen maturation, response to wounding, fruit ripening, root growth, and even tendril coiling . The role of JA in the defense response to insect wounding was first suggested in 1992 . JA- and ET-dependent regulatory processes can act cooperatively . For example, both JA- and ETsignaling contribute to resistance against necrotrophic pathogens and are knownto inhibit the formation of HR. This dual function is advantageous for the plant, since necrotrophs feed off dead tissue and may benefit from HR . Activation of JA-mediated defenses are preceded by the accumulation of jasmonates synthesized by the octadecanoid pathway . However, knowledge of the JA-signaling pathway is still incomplete. Differences exist between the JA-signaling systems studied in different plant species. For example, although the system in pathway induces systemic JA responses in tomato, no evidence has yet indicated such a pathway exists in Arabidopsis . When some plants are subjected to predation, the JA pathway is activated, requiring a 200-amino acid precursor, prosystemin. Prosystemin then produces the 18-amino-acid peptide, system in, through proteolytic processing . Systemin induces the production of H2O2, followed by the biosynthesis of JA and leading to the activation of defense-related genes . The first steps of JA biosynthesis occur in the chloroplast where membrane-derived linoleic acid is converted to 12-oxo-phytodienoic acid using multiple biosynthetic enzymes . OPDA is then transported to the peroxisome, where it is reduced to OPC-8:0 by OPDA reductase3 undergoing three rounds of β-oxidation, resulting in the production of -7-iso-JA . Studies found that a main bioactive form of JA is JA-isoleucine , which is produced by conjugation of JA to Ile by Jasmonate Resistant 1 .

Tropical and arctic ecosystems are largely under sampled. Moreover, the PFT-based root distributions have not been updated accordingly. A global-scale maximum rooting depth data set was synthesized by Canadell et al. [1996] and included 253 plant species. They also aggregated maximum rooting depth data based on PFTs, which is readily applicable to large-scale land models. The rooting depth followed the order: forest > shrub > herbaceous plants > – crops. However, within-PFT variation was quite large. For example, the maximum rooting depth of tropical species was 68 m, while the mean of tropical evergreen plant maximum rooting depth was about 15 m. Particularly for arctic tundra, a more detailed rooting depth data set was developed by Iversen et al. [2015a]. Tundra maximum rooting depth ranged from 0.7 cm for a deciduous shrub species to 100 cm for a forb species . In general, evergreen shrub tundra has the shallowest rooting depth . Grass, forb, and deciduous shrub tundra have deeper root systems , and sedge tundra has the deepest roots . This data set casts doubt on land model PFT classifications for arctic tundra. For example, CLM and ALM represent arctic tundra with only two PFTs , which substantially under represents root traits across the wide range of dominant tundra species, including arctic grasses, sedges, forbs, deciduous shrubs,nft hydroponic and evergreen shrubs [Chapin et al., 1996].The ability of plants to recognize and respond to the presence of threats is vital for their survival. Given their sessile lifestyle this defense response must be swift.

Major threats to plants include diseases caused by microbial phytopathogens. Evolution has duly equipped plants, resulting in plant disease being the exception, not the rule . However, due to extensive selective breeding and the tendency of farmers to plant monocultures, plant disease has gained a foothold and has become a multibillion dollar problem . Currently, the solution is the application of pesticides which are often not only toxic to pathogens but can affect non-target plant and animal species . The off-target effects of pesticides make the discovery of novel solutions to the plant disease problem crucial . In plants, many physical and chemical barriers exist that passively prevent pathogen infection. Physical barriers can include: a waxy cuticle, stomata, and thick cell walls. Chemical barriers include phytoanticipins, phenolics, and quinines which have antimicrobial properties, as well as lactones, cyanogenic glucosides, saponins, terpenoids, stilbenes and tannins . While passive defenses are effective against some phytopathogens, an active immune system is required to combat pathogens able to bypass passive immunity . One such form of active defense includes small basic peptides called plant defensins . PDFs can interfere with a pathogen’s ability to extract nutrients, thus delaying pathogen development . Plant-pathogen interactions are dynamic and shaped by a ‘coevolutionary arms race’ . In this arms race, there are strong selective pressures for the plant to maintain its resistance against a given pathogen, as well as pressures on pathogens to overcome plant defenses . Like mammalian organisms, plants possess an inducible innate immune system that is based on the genetically determined and inheritable recognition of molecular features of pathogens .

Unlike mammals, however, plants do not have specialized immune cells and most plant cell types are capable of efficient innate immune responses. In addition to local innate immunity acting in plant tissues subject to pathogen attack, mobile signals generated in such primary infection sites control systemic defense responses mediating long lasting broad spectrum disease resistance. This innate immune system is constantly evolving in a fashion described by the ‘zigzag model’ . According to this model, the most fundamental form of plant innate immunity involves recognition of conserved molecular signatures shared by many classes of pathogens termed microbe-associated molecular patterns . MAMPs are recognized by pattern-recognition receptors on the surface of plant cells. MAMPs are essential for a pathogen survival and fitness and cannot be discarded or altered through evolution to evade PRRmediated detection . Examples of MAMPs include: chitin and ergosterol from fungi, β-glucans from oomycetes, fungal xylanase and oomycete transglutaminase, as well as flagellin and lipopolysaccharides from gram-negative bacteria . Upon recognition of a MAMP, the plant activates a comprehensive set of defense reactions called pattern-triggered immunity . During PTI there are extensive molecular, morphological, and physiological changes . Signaling cascades link recognition and response. Within minutes of MAMP recognition, there are ion fluxes across the plasma membrane, an increase in cytosolic Ca2+, an oxidative burst, which includes the production of reactive oxygen species and nitric oxide, MAP kinase activation, protein phosphorylation, and receptor endocytosis . Protein kinases are major regulators of plant defense responses that act at various hierarchical levels within the defense network . There are more than 1000 protein kinases in the plant model organismArabidopsis thaliana . In particular, receptor protein kinases , Ca2+ dependent protein kinases and MAPKs have been extensively implicated in the regulation of plant immune responses. The plant immune responses are controlled by a complex regulatory network consisting of multiple interconnected sectors that include those regulated by salicylic acid – and others dependent on jasmonic acid and ethylene as well as other less well characterized pathways .

Over time, pathogens evolved effector molecules which are released to augment virulence by manipulating and weakening, PTI resulting in effector triggered susceptibility . Such interactions between virulent pathogens and susceptible plants are termed “compatible”. A susceptible plant still maintains low levels of defense, called basal defense. Basal defense is not sufficient to fully prevent disease, but it can slow its progression . PTI is often successful against pathogens that have not evolved the ability to specifically infect a plant; this is referred to as non-host resistance. To counteract ETS, plants evolved resistance proteins , which specifically recognize pathogen effectors resulting in a resistant plant and an avirulent pathogen . This type of innate immunity is referred to as effector-triggered immunity . ETI is a faster and more robust version of PTI,nft system and often results in a hypersensitive response at the site of infection . HR involves a programmed form of death of plant cells directly in contact with an invading pathogen. In some cases pathogens evolved additional effectors to evade ETI . ETI is active against adapted pathogens. Although, these relationships are not always set in stone and they may depend on the specific elicitor molecules present during pathogen infection .This means that they can recognize pathogen effectors if tge effects of the effector on the host target. A strong oxidative burst and HR cell death are considered hallmarks for resistance mediated via R genes. ROIs have antimicrobial properties and act as a signal for activation of defense responses, including HR . HR cell death is an efficient immune response against biotrophic pathogens . Biotrophic pathogens extract their food from living plant tissue, while necrotrophs kill and digest dead plant tissue for their nutrients. Thus, by decreasing the number of cells in contact with an invading biotrophic pathogen, plants can prevent further infection. Basal defense and some cases of ETI are controlled by the SA-dependent branch of the defense network . The molecular changes that occur after pathogen recognition during ETI also occur during compatible interactions, but with ‘slower kinetics and reduced amplitude’ . SA-dependent signaling processes involve several genetically defined defense regulators, such as EDS1 and PAD4 , which control the synthesis and accumulation of this defense hormone. Defense associated SA appears to be mainly synthesized by a plastidic pathway that involves isochorismate synthase 1, which is also known as EDS16 or SID2 .

Elevated SA levels activate a set of downstream defense responses, such as expression of pathogenesis-related genes and HR cell death . A positive feedback loop links ROI, NO and SA . These signaling molecules mutually control their production. Only strong activation of this feedback loop results in the induction of HR cell death . Typically levels of ROI, NO and SA accumulation during basal defense are too low to trigger HR . Sifficiently high levels of these signaling molecules for HR induction are typically observed during ETI . SA is also a critical signal for the activation of systemic acquired resistance , a broad-spectrum defense response that is sometimes activated throughout the entire plant in response to local recognition of either virulent or avirulent pathogens . The main role of SA in SAR induction seems to be in the systemic tissue, where it causes the transcriptional co-activator NPR1 to move from the cytoplasm to the nucleus where it interacts with transcription factors, activating SAR . The SA-derivative, methyl salicylate , acts in tobacco as a long-distance mobile signal for SAR within the plant . In addition, MeSA can also serve as the airborne signal that induces defense gene expression in neighboring plants . Recent studies have revealed that SAR can increase the fitness of pathogen-challenged plants in a field setting . Although constitutive activation of SAR has substantial fitness costs . R proteins do not confer resistance against necrotrophic pathogens, which kill plants and feed off dead host tissue. Defense against necrotrophic pathogens is mediated through the jasmonate acid and ethylene branches of the defense network. The JA/ET branches are also known to have roles in responses to wounding and herbivore attack . The SA, JA, and ET pathways interact extensively. A large body of research has indicated that SA and JA are mutually inhibitory . Recent evidence indicates that they may enhance each other’s expression at low concentrations . A plant must be able to distinguish between different types of pathogens allowing it to respond with an appropriate set of defense reactions, mediated by signaling molecules. Thus, different signaling mechanisms are required to activate immune responses against pathogens with different life-styles. Studies indicate that while sometimes ET and JA interact synergistically in disease responses, that both can act independently or even antagonistically with the SA-dependent pathway . Resistance to specific pathogens conferred through JA signaling show little overlap in transcriptional changes. This context is important to fine-tuning the JA response . ET and abscisic acid regulate different branches of the JA response . JA and ET act together to induce the expression of PDF1.2 . The transcription factors, ERF1 and ORA59 work to integrate JA and ET signaling . These transcription factors confer resistance against necrotrophs . Alternately, MYC2 works with ABA signaling to negatively regulate the JA-ET responsive branch while activating genes within its own branch, such as VSP2 . This branch is associated with the wound response and priming for pathogen defense .Arabidopsis and the oomycete, Hyaloperonospora arabidopsidis , are an effective model pathosystem in which defined R-genes mediate recognition of certain Hpa isolates . Well characterized Arabidopsis mutants allow for the fine dissection of defense pathways . While useful, traditional genetics techniques are unable to circumvent functional redundancy and lethal phenotypes. This suggests that additional experimental approaches are necessary to advance knowledge of mechanisms controlling plant immunity. Chemical genetics/genomics offers distinct advantages over traditional techniques through the use of small molecules, whose effects are often impermanent and reversible. Small molecules also provide more defined temporal control. In contrast, the timing of pathogen infections is not easily defined, as the germination of spores or pathogen growth and spread in plants is often asynchronous.As discussed above, different plant species have developed effective mechanisms to cope with pathogens. Unfortunately, contemporary crops have lost parts of their innate immune system due to breeding efforts focused mainly on increasing yield. Consequently, plant diseases cause dramatic losses in crops every year. In the United States 500 million kg of pesticides are applied annually at a cost of $10 billion to farmers to control disease. Despite this, more than a third of all food crops are still destroyed by diseases . The lingering residues of pesticides on produce is currently a major health concern of consumers . Many pesticides currently in use are carcinogenic and rely on direct anti-pathogenic activity, which often leads to undesirable side effects that can have far reaching consequences both for humans and the environment . This disquiet over the dangers of pesticides has spawned considerable interest in alternative methods of disease control .

Therefore each set of R genes incorporated into a cultivar must be evaluated systematically requiring a significant investment of time. However, it is clear that gene pyramiding offers an attractive mechanism for combining the individual specificities of R genes as well as taking advantage of their synergistic effects to generate broad-spectrum resistance.An alternate strategy to breeding is to directly introduce a cloned resistance gene into a plant via transgenic technology. Introduction of a gene by transgenic means can overcome the limitations of traditional breeding, namely inter species sterility. Additionally, transgenic technologies allows multiple genes to be inserted simultaneously. However, validation of the function of the transgene and its stability and heritability after transformation requires a significant investment of time and resources. Further, the transgenic lines must also undergo subsequent analysis for agronomic traits before release. While the creation of transgenic plants may be relatively straightforward for a number of species, the strategy has its own substantial time requirements. The greatest advantage of transgenic technology is its ability to overcome fertility barriers for the dissemination of genes originating from a different species; two examples from the Solanaceae family highlight this advance. Bs2, as mentioned above, was identified originally in pepper and its resistance has been durable in the field against isolates of X. campestris . Due to the fitness requirement associated with avrBs2 locus,ebb flow tray the incorporation of the resistance locus Bs2 via transgenic technology may offer durable resistance in a number of plant systems affected by X. campetris.

To assess this hypothesis, tomato was transformed with the Bs2 gene from pepper. Inoculations of X. c. pv vesicatoria isolates onto Bs2– containing transgenic tomato plants failed to cause disease therefore Bs2 function was conserved in tomato . Tomato and pepper when crossed cannot form a fertile hybrid and this resistance could not have been utilized with standard breeding protocols. In another example the N gene from tobacco, conferring resistance to the tobacco mosaic virus , was transferred into tomato . The resulting transgenic tomato plants, expressing the N resistance gene, were inoculated with TMV and complete resistance was observed. While TMV is not as devastating economically to tomato as is X. campestris, the conceptual notion that resistance loci can be transferred among species while retaining their function points illustrates a key advance for engineering resistance using transgenic technology. These examples demonstrate conservation in disease signaling pathways that can be exploited for cultivar improvement.Disease resistance research has largely focused on understanding the specific pathogen–host interactions mediated by R and avr loci. Recently, studies have revealed signaling components that function downstream of R genes or other pathogen sensors. Studies on broad-spectrum resistance pathways, such as the rhizobacteria-mediated, induced systemic resistance pathway and the insect-responsive pathway involving jasmonic acid are rapidly gaining momentum . However, research on the pathway transducing a broad-spectrum defense response termed the systemic acquired resistance response has progressed most rapidly. Chemical and abiotic inducers of SAR, along with inherent signaling components of this pathway identified by basic research in model plant systems, are among the initial targets being used to engineer multi-pathogen disease resistance in important crop plants.

The SAR defense response is manifested when a plant host is inoculated with a pathogen that results in a localized infection. This primary infection subsequently primes the host to resist secondary infections by viral, oomycete and bacterial pathogens . In the model plant Arabidopsis, SAR is associated with a rise of internal levels of the plant hormone salicylic acid , and is correlated with the increased expression of a set of genes termed pathogenesis related genes . Several PR genes encode proteins with antimicrobial activity and thus contribute to an overall defense response directly . Research aimed at modulating this pathway and generating broad-spectrum resistance has largely targeted three parts of this response for further study: the ability of SA to trigger the response, the increased expression of PR genes and the identification and modulation of other signaling components.Therefore, investigations into the costs of induced resistance have started by assaying the effects of using chemical inducers. Heil et al. have studied the fitness of wheat plants treated with BTH in the absence of pathogens. When plants were grown either hydroponically or in the field, water-treated control plants were able to achieve greater biomass than their BTH-treated cohorts. In field experiments, however, significant growth differences were not seen until approximately 6 weeks after treatment. The authors suggest that many of the potential fitness costs associated with induced resistance responses may be masked in laboratory experiments where growth conditions are kept optimal, and support this hypothesis with experiments performed growing plants under differing nitrogen concentrations. In addition, when the age of the plants induced for SAR was considered it was found that the growth-costs of BTH treatment could be reduced if the BTH was applied after the lateral shoot formation was complete .

These data also underscore the importance of factoring plant developmental programs into any efficient strategy to enhance plant resistance by chemical treatment or genetic engineering.Another unwanted effect that may arise from transgenic manipulation of genes involved in defense signaling pathways is spontaneous cell death. Spontaneous cell death has been uncovered in many genetic screens for enhanced disease resistance and recently, has been seen in transgenic plants. These mutants and transgenic plants are often collectively referred to as lesion-mimic mutants since they display lesions similar to those observed in a defense response even in the absence of pathogens. This form of cell death in plants is sometimes influenced by alterations in environmental conditions such as light, temperature and humidity . Therefore, both in basic research and in applied experiments, it will be important to understand the parameters controlling cell death. This research is critical not only for optimizing the situations where transgenes and chemicals will be most useful to generate disease resistance, but also to minimize negative effects on important agronomic factors such as development, fertility and yield.Many of the examples listed above,flood and drain tray may appear as substantial challenges to engineering disease resistance, however, these challenges provide opportunities to create plants that are even more resistant than plants engineered based on our current knowledge. For instance if the already identified components of a signaling pathway are not the best candidates for durable resistance in the field, technologies such as micro-arrays will help to pinpoint novel targets of interest . When mutations involved in disease resistance have already been identified, but are recessive in nature such as the mlo, edr1 and mpk4 mutants, classical breeding strategies can be employed. These mutants cannot be placed into heterologous systems using transgenic technology but, as with gene-pyramiding, they are still useful in breeding. Or, as technology continues to improve, gene knockouts and silencing of homologs may be employed to generate mutants in diverse species. If research continues to suggest crosstalk between ISR, SAR and insect defense signaling pathways, there may be great potential for additive defense effects by manipulating overlapping components. So, while limitations and cost of engineering broad-spectrum defenses warrant much attention, it is useful to look at such challenges as means for streamlining and improving upon current engineering strategies.Another promising strategy for enhancing resistance in plants is the use of RNA homology-dependent silencing to combat viral and bacterial disease . The nature of this silencing has been evaluated in a number of systems where similar phenomena are called by different names; RNAi in animals and quelling in fungi . One conserved step leading to RNA homology dependent silencing is the formation of a double stranded RNA intermediate. This dsRNA intermediate is recognized by an enzymatic complex which targets degradation of all corresponding homologous RNA transcripts . Several cases detailed below illustrate the possibilities for generating disease resistant plants by taking advantage of this inherent biological process.Viral resistance using RNA homology-dependent silencing has been successfully engineered into many plant systems. Single or multiple viral-derived transgenes can be expressed in plants leading to RNA homology-dependent silencing and subsequent viral resistance.

The use of this transgenic technology may be particularly effective in thwarting viral diseases where little or no genetic resistance has been identified. Resistance to rice yellow mottle virus is one example where traditional breeding cannot be used for improvement due to fertility barriers and genetic resistance being a poorly defined polygenic trait . The RYMV open reading frame 2 was highly expressed in transgenic rice. The resultant RYMV resistant lines carried very low or non-detectable amounts of the ORF2 RNA transcript. Conversely, transgenic lines that were susceptible had abundant amounts of the ORF2 transcript. Therefore the resistance phenotype was correlated with the loss of the viral transgene expression. This indicates that the mechanism of resistance was due to silencing of the ORF2 present as the transgene and in the RYMV RNA genome. The ORF2 sequence variation among different RYMV field isolates was found to be less than 10% at the nucleotide level suggesting that an RNA homology-dependent silencing approach may be effective in the field . Viral resistance utilizing endogenous silencing mechanisms is not restricted to using a single open reading frame from one virus. Two ORF fragments from different viruses can be fused into a chimeric expression cassette to confer resistance to both viruses. One clear example was generated from using tomato spotted wilt virus and turnip mosaic virus . The open reading frame for the N gene encoding the nucleocapsid from TSWV was fused to the coat protein of TuMV and the resulting chimeric construct was used to transform tobacco. As with the example using RYMV,resistance of the transgenic plants to both viruses corresponded with the loss of transcript accumulation from both viruses as detected by northern analysis. Transgenic plants susceptible to both viruses showed accumulation of the gene fragment transcript for both viruses. These two examples have been evaluated in greenhouse experiments; however, a well-described example of RNA homology-dependent silencing for viral resistance is presently being utilized successfully in the field.One clear commercial success of generating enhanced resistance by stable expression of a viral gene is against the papaya ring spot virus . Papaya is grown throughout the tropics and subtropics and no natural resistance has been described for PRSV. A PRSV control strategy for the Hawaiian islands was developed using RNA homology-dependent silencing by expressing a mutated open reading frame for the coat protein from PRSV . Resistant transgenic plants were generated and were found to be devoid of the CP RNA indicating the RNA homology-dependent silencing of the plant-derived transgene and PRSV gene . All PRSV strains present in Hawaii have been effectively controlled using silencing constructs derived from this mutant CP ORF. Sequence analysis demonstrated that these Hawaiian isolates had 97% or greater sequence homology to the mutant CP transgene. However, isolates of PRSV from outside of Hawaii can cause disease on the transgenic papaya lines. These geographically distinct isolates were found to have a lower sequence homology to the CP than the isolates from Hawaii. Thus, silencing of PRSV was contingent upon levels of sequence homology above 97% . Interestingly, PRSV and RYMV require different levels of homology between transgene and the endogenous gene to induce silencing. The silencing in RYMV was successful for all variations tested as compared with less than 3% divergence allowed for successful silencing in PRSV. Silencing is not only dependent upon the degree of homology but also the target sequence that is chosen. Much like the transgenic approach with R genes, each silencing construct must be carefully validated. Overall, RNA homology-dependant silencing has proven its utility in both the greenhouse and the field, and appears to be among the most versatile mechanisms currently available to engineer resistance to viruses.Crown-gall is a perennial problem in nurseries of fruit trees, nut trees and some bushy ornamental plants. Prevention of gall formation is a target for engineering resistance in these trees since breeding programs for resistance are not practical due to temporal considerations . When replanted, the trunks suffer cuts that are an entry point for the bacterium Agrobacterium tumefaciens, the causal agent of the disease, and infection becomes apparent with the formation of galls.

The fact that Sonora carries the day length sensitivity allele may seem surprising as it originates from Mexico. However, Sonora is thought to have been selected from a landrace that was brought over to the Americas from Europe with Columbus in 1492 and Shcherban et al. showed that 91% of spring wheat cultivars in Europe contain the photoperiod sensitive allele Ppd-D1b. A second consistent QTL for days to heading was identified on chromosome arm 5AL in the SF and CF populations. In SF the QTL covered a 4.4 cM region with a peak at 163 cM between markers 5A_10843 and 5A_24477 and explaining 20-21 % of the phenotypic variation. The QTL in the CF population covered a 10.4 cM region with its peak at 92 cM between the markers 5A_1737 and 5A_12135 explaining 18-28 % of the phenotypic variation. Although the markers are not identical they map within a couple of cM of one another in the consensus map of Wang et al. strongly suggesting that this is indeed the same QTL. The third QTL for days to heading was on the long arm of chromosome 5B in the SF and CF populations. In SF the QTL covers a region of 2.2 and 10.1 with peaks at 120 and 126 being that there was a slight shift between years from 5B_3483 and 5B_9459 in 2013 to 5B_80245 and 5B_3483 in 2014. This created a larger cM region and a 6 cM shift in the peak of the QTL for 2014. This QTL explains 17-20 % of the phenotypic variation seen in this population. For CF the QTL covers a 1.6 cM region with its peak around 106 cM between the markers 5B_80245 and 5B_51408 explaining 17 % of the phenotypic variation seen in this population.

These populations share the 5B_80245 marker providing validation of the QTL. Additional validation comes from Zanke et al. who located a gene on chromosome 5B related to the Hd6 gene family of rice with a major impact on heading time in wheat. They found that the marker Kukri_c10016_369 was the closest linked marker to the locus,growing tomatoes hydroponically and it maps to the same genetic position as 5B_3483 identified in our mapping experiments. This suggests that the QTL identified in two of our populations across multiple years is indeed this same Hd6 related locus. It is possible that the other QTL identified on 5A and 5D are homoeologous to the 5B QTL. This of course is only speculative and would require further inquiry. The fourth QTL was identified on the long arm of chromosome 5D in the SC and SF populations. For SC the QTL covers a 2.0 and 24.5 cM region with its peak between 78 and 75 cM respectively. A shift from 5D_17130 and 5D_502 in 2013 to 5D_4695 and 5D_17130 in 2014 cause the differences seen in QTL area and peak position, however, in both years the QTLs share marker 5D_17130. The QTL explains 45-49 % of the phenotypic variation seen in this population. In SF the QTL covers a region of 21.7 cM with a peak at 10 cM between the markers 5D_17310 and 5D_42321 and shares the 5D_17310 in common with the SC QTL. This QTL explains 29-41 % of the phenotypic variation seen in this population. Finally, the fifth QTL was located on the long arm of chromosome 5D and identified in the SC and CF populations. In the SC population it covers a 19.0 and 10.7 cM region with a peak around 150 and 156 cM, respectively. This QTL explains 40-52 % of the phenotypic variation found in the population. In 2013 the left and right markers were 5D_1682 and 5D_63558 while in 2014 the markers were 5D_63588 and 5D_5776 with marker 5D_63558 appearing in both years. The large region of this QTL is likely due to poor coverage of SNP markers on most of the D genome chromosomes. This QTL was also observed in the CF population where it covered a 7.6 cM region with a peak at 139 cM between markers 5D_63558 and 5D_5776 and explaining 22-25 % of the phenotypic variation in this population.

Both populations share markers 5D_63588 and 5D_5776 providing good validation for this QTL. When comparing days to heading in the greenhouse and the field it is apparent that the 18 hours of supplemental light given in the greenhouse greatly reduced the flowering time of the populations. This difference in treatment also enabled us to detect different flowering time loci. In the field only the day length sensitivity and insensitivity loci on 2D were detected, yet when grown under 18 hours of light all other QTLs were able to be identified. These other QTLs could potentially be Eps loci given that the photoperiod response was removed via the 18 hours of supplemental lighting provided. However, this speculation would require greater inquiry and further experiments to draw any solid conclusions.These include hybrid necrosis, hybrid chlorosis, and hybrid dwarfness with hybrid necrosis being encountered more frequently . Hermsen described hybrid necrosis as a premature and gradual death of foliage in certain hybrids. The trait is controlled by two dominant complementary genes Ne1 and Ne2 located on chromosome arms 5BL and 2BS respectively . In the three populations tested, hybrid necrosis was rated in the 2013 evaluations only and at which point all lines with unacceptable levels of necrosis were removed. Thus, QTL for hybrid necrosis were identified using the 2013 data for lines with acceptable levels of hybrid necrosis that were genotyped. Two QTLs were identified as being associated with hybrid necrosis in the CF population. The first is on chromosome arm 2BS where it covers a region of 0.8 cM with its peak at 82 cM between markers 2B_31805 and 2B_4614. It explains 22.51 % of the variation seen in the population.

The second QTL is on 5BL, covering a 1.6 cM region with a peak at 53 cM between the markers 5B_29636 and 5B_67642. It explains 31.16 % of the variation seen in the population. These two QTL may be the Ne1 and Ne2 genes but scoring would perhaps have to be repeated to verify the QTLs across years. It is likely that these QTLs were only seen in the CF population since both SF and SC had few lines expressing the trait included in genotyping, whereas CF had more lines expressing the trait that were included in genotyping.With persistent predictions of climate change and increased incidence of drought, crop root systems have gained serious attention. One of the challenges in this line of research is which root traits to focus on and in what environments these traits would be important; another one is to understand how root system traits are associated with one another and what trade-offs at the whole plant level are involved. Most root morphological traits appear to be regulated by a number of small-effect loci that interact with the environment. This becomes very apparent even at the earliest stages of experiments looking at root biomass and length. Natural plasticity induced by the environment creates large deviations that often obscure the genetic component of the observable phenotype. For these reasons de Dorlodot et al. suggested that processbased traits such as growth rate, branching frequency and tropism should be studied as opposed to “static traits” such as length, mass, and volume. Some studies have focused on incorporating traits from wild relatives or via new synthetic wheat . Others have looked at associations of root system traits and plant height and many have now begun to focus on seminal root traits. It has been suggested that, in the context of drought,ebb and flow bench roots targeting water acquisition deep in the soil profile may be especially important for smaller statured plants such as rice, wheat, and common bean . By measuring the amount of total water extracted from soil-filled root observation chambers and root growth pattern data Manschadi et al. estimated that each additional millimeter of water extracted during grain filling generated an additional 55kg ha-1 of grain yield.

Lynch proposed an ideotype for maize roots that included narrow seminal root angles with abundant lateral branching which would optimize water and nitrogen acquisition; this ideotype may also be relevant to other cereal root systems. Narrow seminal root angle generates a root system growing more downward into the soil profile, and presumably, reaching lower soil levels. In contrast, a wide angle of seminal roots appears to promote lateral root growth, a habit that may be beneficial in wetter conditions and under artificial irrigation. With frequent irrigation or rainfall, a root system distributed mainly in the upper soil layers would presumably provide quicker access to water and nutrient, without any cost to the plant for building deep-reaching roots. Oyanagi first began to investigate the inheritance of the geotropic response of seminal roots in wheat and concluded that the trait was simple, being controlled by a single locus, and his continued work contributed to the basis for our understanding of seminal root angle physiology in wheat . Those studies made observations on root distribution patterns and seminal root growth characteristics dependent upon the target environment for which specific cultivars were selected. Typically, cultivars adapted to regions with limited rainfall had narrower seminal root angle and deeper root systems; wheats adapted to environments with higher rainfall and/or irrigation tend to have wide seminal root angles which, presumably, facilitate water and nutrient acquisition from a wider sub-surface area. Following these ideas, Manschadi et al. investigated seminal root angle and discovered a large amount of genetic diversity within the panel of screened cultivars. Their cluster analysis has shown that groups of wheat with similar seminal root characteristics reflected the genetic background and environmental adaptation. Those observations are supported by other research linking root distribution to improved agronomic performance and canopy temperature depression under heat and drought stress . Seminal root traits are relatively simple to score and do not require complex experimental systems. This makes them an aspect of choice in root system studies. Drawing ideas from maize studies, Oyanagi suggested that gravitropic responses of roots would be predictive of wheat root distribution in the soil. That idea was supported by Manschadi et al. who found that root system architecture is closely linked to the angle of seminal root growth at the seedling stage. Those findings led to a suggestion that selection for the growth angle and the number of seminal roots may identify genotypes better suited for drought conditions. Measuring root traits of mature plants in the field is a daunting task; for entire mapping populations it is practically impossible. Perhaps for this reason, seminal root traits of seedlings are the favorite research target as they can be measured in several simple experimental set-ups. For all these reasons, studies of seminal root traits appear justified, by providing observations of simple parameters of root architecture, especially when dealing with hundreds of genotypes at a time. At some point all observations of such proxy indicators would have to be verified by screening in the field with a limited number of genotypes. The results presented here add to earlier foundational work, and begin to unravel the genetics behind some aspects of root system architecture. The emerging picture is far more complicated than originally suggested by Oyanagi . While seminal root angle shows high heritability, it clearly is a quantitative trait with a complicated pattern of inheritance. Seminal root angles and numbers were phenotyped in three doubled haploid populations of bread wheat. These populations were created by pair-wise crossing of three landrace cultivars with contrasting root phenotypes. Cv. Sonora has shallow seminal roots growing at wide angles, and cvs. Foisy and Chiddam Blanc de Mars have deep seminal roots with narrow angles. Crosses were made in a triangular fashion so that each of the three parents is present in two of the populations. This arrangement provides a built in system for verification of QTL identified across populations and genetic backgrounds. Detailed information about genotyping, linkage mapping and general descriptions of each population can be found in the previous chapter of this dissertation.

Phosphonates can also serve as a source of phosphorus or carbon for a variety of microorganisms and several pathways for phosphonate degradation have been characterized . For example, some bacteria can use methylphosphonate as a P source in a process that releases methane and inorganic phosphate . This process is catalyzed by the C-P lyase enzyme and involves a phosphate radical intermediate . Under mildly reducing conditions phosphate radicals can rearrange to form phosphite, making it a possible byproduct of methylphosphonate degradation in anaerobic environments . Moreover, phosphonates with carbonyl or hydroxyl groups at the α-carbon, such as phosphonoformic acid, tend to form phosphite rather than phosphate as the product of C-P cleavage even under oxidizing conditions . Given that C-P lyase enzymes are involved in the degradation of a variety of phosphonates, it is possible that these reactions are a significant source of environmental phosphite. Biological phosphate reduction has also been posited as a possible source of environmental phosphite. Devai and colleagues detected phosphine gas production in wastewater and marsh soils and showed that phosphine production was stimulated by the addition of inorganic phosphate and organic matter, leading them to conclude that phosphate was being reduced to phosphine by microorganisms present in their samples . Some of this phosphine could subsequently be oxidized to phosphite in the presence of O2or UV radiation . However,hydroponic grow kit the conclusion by Devai et al. that the phosphine they observed was derived from biological phosphate reduction has since been questioned by several researchers .

Roels and coworkers have noted that biological phosphate reduction is problematic from a thermodynamic standpoint, since there is no known biological electron donor with a low enough redox potential to make the reaction exergonic . Glindemann and coworkers have shown that phosphine can be produced during the corrosion of iron, even under sterile conditions . This is due to the fact that iron minerals often contain phosphorus impurities that can be abiotically reduced to iron phosphides during the industrial smelting process and these phosphides can then be released as phosphine gas during corrosion . Subsequent studies have likewise concluded that phosphine is released due to iron corrosion and that the higher rates of phosphine production observed in the presence of microorganisms is likely due to the microbial production of organic acids and hydrogen sulfide, which accelerate the corrosion process . Although evidence of biological phosphate reduction remains inconclusive, several theoretical mechanisms by which this process could occur have been proposed. Pasek and colleagues have suggested that in addition to being produced during phosphonate degradation, phosphite could also be formed as a byproduct of phosphonate biosynthesis in reducing environments . They determined that the reductive cleavage of phosphoenolpyruvate by H2 to form phosphite and pyruvate is thermodynamically feasible under standard cellular conditions . Given that phosphoenolpyruvate is a key intermediate in the production of phosphonates from inorganic phosphate, such a mechanism would be a way of indirectly converting phosphate to phosphite. A more direct mechanism of phosphate reduction has been proposed by Roels and colleagues, who note that the reduced molybdoferredoxin cofactor of the nitrogenase complex has a redox potential of -1.0 V, which is low enough to reduce phosphate to phosphite .

However, they question the usefulness of such a reaction since energy from ATP hydrolysis must be expended in order to achieve such a low reduction potential and the organism would gain nothing from the production of phosphite. Nevertheless, it is possible that phosphite may be formed as an unwanted product of nitrogenase function in the presence of phosphate. This sort of inadvertent phosphate reduction might also occur in photosynthetic organisms, since the redox potentials of excited reaction center chlorophyll molecules range from -0.8 V to -1.26 V . Environments dominated by anoxygenic phototrophs may therefore be potential hot spots of biological phosphite production since the absence of strong oxidants in these systems would favor the accumulation of reduced phosphorus species. produced would have to be diverted for use in anabolic reactions.FiPS-3, on the other hand, uses PtdC as its phosphite transporter instead of PtxABC. If PtdC does, in fact, function as a phosphite/phosphate antiporter as has been proposed, then there would be no energy cost associated with phosphite uptake in FiPS-3 . However, when both PtxD and PtdC were expressed in SaxT, it still did not gain the ability to grow by DPO, which indicates that an additional mechanism of energy conservation, possibly mediated by the ptdFGHI genes, is required in this organism. In contrast to P. stutzeri, FiPS-3 and SaxT growing by sulfate reduction would gain substantially less energy from NADH oxidation. During sulfate reduction 2 ATP must be initially expended in order to activate and reduce sulfate to sulfite, which can then be further reduced to sulfide in an exergonic reaction . Sulfate reducing bacteria growing on H2 typically generate 3 ATP from the sulfite reduction step for a net overall production of 1 mol ATP per mol sulfate reduced, which corresponds to the expected yield based on equation 4 .

However, if sulfite reduction were instead coupled to NADH oxidation according to equation 5 , the expected yield would only be 2 mol ATP per mol sulfite reduced, which would result in no net ATP production from the overall reduction of sulfate . In order to grow by DPO, therefore, FiPS-3 and SaxT would not only need to save energy on phosphite uptake, but also conserve more of the free energy available from the oxidation of phosphite. The NAD+ /NADH couple has a redox potential of -320 mV under standard physiological conditions , which means that the reduction of NAD+ coupled to phosphite oxidation releases 63.7 kJ.mol-1 phosphite. This additional energy is presumably lost in traditional APO-capable organisms, but there is evidence that it is conserved in FiPS-3. Schink and coworkers observed substantially higher cell yields when FiPS-3 was grown on phosphite and sulfate versus formate and sulfate . Since phosphite and formate both donate 2 electrons and the redox potential of the CO2/formate couple is actually higher than that of NAD+ /NADH , the higher yields seen on phosphite are not consistent with NADH oxidation being the sole means of ATP production during DPO. Furthermore,vertical farming racks the growth yield of FiPS-3 on phosphite and CO2 via the Wood-Ljungdahl pathway was about 10 times higher than the yields typically observed for other Wood-Ljungdahl acetogens growing on H2 and CO2, such as Acetobacterium woodiiand Acetogenium kivui . These results suggest that FiPS-3 can in fact take advantage of the extremely electronegative redox potential of phosphite, although it is unclear how this is accomplished since there are no known biological redox carriers that can accept electrons at such a low potential . Schink and coworkers have proposed that ATP is generated from phosphite oxidation by means of substrate level phosphorylation in addition to the reduction of NAD+ , thus yielding both energy and reducing equivalents for each molecule of substrate utilized . Such a reaction would be thermodynamically feasible according to equation 6 . Therefore, the function of the ptdFGHI genes may be to facilitate substrate level phosphorylation during phosphite oxidation . Relyea and van der Donk have suggested that one of the possible mechanisms of phosphite oxidation by PtxD may involve the creation of a phosphorylated enzyme intermediate that is subsequently hydrolyzed to release phosphate . PtdFGHI might interact with PtxD in order to facilitate the transfer of this phosphoryl group to ADP, either directly or by means of additional phosphorylated intermediates.

This is a promising avenue for future inquiry but more work is currently necessary in order to determine whether phosphite acts as a phosphoryl donor for ATP synthesis during DPO and what role, if any, the ptdFGHI genes play in this process. Over the last 20 years, the study of reduced phosphorus compounds and their role in nature has grown from a series of curious observations and intriguing theories into an exciting new frontier in biogeochemistry. In particular, recent discoveries regarding the geochemistry and biology of phosphite have highlighted the potential significance of this compound both as a facilitator for the emergence of life on ancient Earth and as a modern driver of microbial processes that continue to shape the global biosphere. Phosphite has been detected in several environments at concentrations that suggest the current existence of a phosphorus redox cycle occurring at short geological timescales. Several anthropogenic sources of phosphite have been identified, and there is evidence that phosphite may also be produced by natural processes such as biological phosphonate metabolism and geothermal phosphate reduction. The presence of the genes responsible for assimilatory phosphite oxidation in hundreds of microbial isolates from a variety of environments indicates that this process is widespread and may have a substantial impact on the global P cycle. Furthermore, the discovery of dissimilatory phosphite oxidation and its ability to sustain carbon fixation while providing an energetic benefit raises the possibility of phosphite as a key, though hitherto unrecognized, driver of primary productivity in the environment. Several milligrams of mineral precipitates were sampled from FiPS-3 cultures grown on phosphite with either calcium or magnesium in the media and mineral samples were ground into a powder. For SEM, a sample of the powdered mineral was suspended in several milliliters of distilled water to create a mineral slurry.A drop of the mineral slurry was fixed with 2% glutaraldehyde in 0.1 M sodium cacodylate buffer, added to the silicon wafers, and allowed to settle for 1 h. Samples were then dehydrated for 10 min in 35%, 50%, 70%, 80%, 95%, and 100% ethanol, followed by critical point drying. Dehydrated samples were mounted onto stubs, sputter coated with palladium/gold, and visualized using a Hitachi S-5000 scanning electron microscope at 20 kV. For XRD, a sample of the powdered mineral was suspended in a few drops of amyl acetate to create a mineral slurry. The mineral slurry was then analyzed with a PANalytical X’Pert Pro diffractometer equipped with a Co x-ray tube and an X’Celerator detector. In accordance with previous observations, DPO-dependent growth of FiPS-3 was accompanied by the appearance of mineral precipitates in the medium several days after the onset of phosphite oxidation . The precipitates appeared to be crystalline and varied in size from several millimeters to several centimeters in length. Typically, some of the crystals would adhere to the bottom and sides of the glass culture tubes, although most would remain suspended in the medium. No precipitates were observed in cultures grown with fumarate as the electron donor instead of phosphite . Subsequent tests showed that DPO-dependent biomineralization could be used to consolidate a fine-grained calcium carbonate matrix at standard temperature and pressure and circumneutral pH. When FiPS-3 was grown in the presence of phosphite, all of the calcium carbonate present in the media was consolidated into a hardened mineral phase that adhered to the bottom of the glass culture bottles, whereas in FiPS-3 cultures grown on fumarate or in sterile phosphite-containing media the calcium carbonate particles remained suspended in the liquid phase . SEM imaging of precipitates from FiPS-3 cultures amended with either calcium or magnesium showed different mineral morphologies depending on which cation was present in the media . Analysis of the precipitates using XRD confirmed that they were crystalline phosphate minerals and that their chemical compositions varied based on the cation present. Hydroxyapatite 26) was produced in the presence of calcium, whereas struvite was produced in the presence of magnesium. The SEM images also appeared to show that some of the cells involved in the biomineralization process became embedded in the mineral phase . Genomic analysis suggested that FiPS-3 was incapable of synthesizing phenylalanine and histidine, and addition of these amino acids to the growth media did indeed result in a drastic reduction in cell doubling time and increase in maximum OD. However, FiPS-3 was still able to grow, albeit poorly, in the absence of phenylalanine and histidine, indicating that it is still able to make these amino acids even though it appears to be missing genes in both biosynthetic pathways.

Our findings around labor in particular stand in contrast to the often-referenced benefit of urban agriculture as a job creation tool . At least in the current political economic landscape of the East Bay, urban farms do not generate enough economic revenue or city investment in order to hire many full time positions; this remains a goal of many operations and opportunity for policy intervention, especially with respect to enhancing the resilience of urban agroecosystems to economic disturbance.Farms in our case study display a strong focus on reducing hunger and promoting food equity, namely through culturally appropriate diets, and the emphasis on human and social values. Due to the plethora of produce going home with volunteers, circulating at neighborhood crop swaps, and gleaned or harvested by community members that is not weighed and tracked before it is consumed, it is understandably difficult to quantify the “food security” impacts of urban agriculture . While food security may be difficult to quantify, it is nevertheless being addressed by urban farms in unique ways . In school gardens, for example, produce that is not used for classroom cooking demonstrations sometimes goes home with students or families excited to find culturally relevant crops growing in their neighborhood. Supporting healthy, diversified and culturally appropriate diets are an important element of agroecology. The diversity and quality of produce grown, especially when it is an item that might not otherwise be available to a family in a “food desert,” contribute greatly to the value produced on urban farms. One farmer interviewed described how one school garden site serves students from Hispanic, African American, Middle Eastern, Asian, and Eastern European families.

The garden teacher spoke about the diversity of crops relevant to various cultural food traditions; for example,vertical plant growing the chayote plants were of particular interest to Latinx students excited to bring them home to their mothers, while African American students eagerly collected bunches of collards, and Middle Eastern mothers came to the garden in person to collect fava beans and figs. In this way, urban agroecology contributes to food security and nutrition as well as biodiversity.Agroecology places a strong emphasis on human and social values, such as dignity, equity, inclusion and justice contributing to improved livelihoods of [urban] communities . Our study demonstrated that the majority of farm respondents placed food security, education, and environmental sustainability above profit, sales and yield. Forty percent of respondents self-identified as “Educational” farms, and most others offer educational workshops and demonstrations as part of their focus on horizontal knowledge-sharing. Agroecology seeks to address gender inequalities by creating opportunities for women. The majority of our study respondents were also women. As a grassroots movement, urban agroecology can empower women to become their own agents of change.Our results suggest the opportunity to reconceptualize and refocus the urban food policy discussion in U.S. cities around urban agriculture in a way that includes and values their social, educational, and cultural services. Urban farms are recreational and cultural heritage sites bearing comparison to public parks and museums, while also producing invaluable healthy food in areas that most need it. They provide important respite, social connection, and stress reduction to urban residents, often particularly in need of peaceful spaces. In the words of one farmer, “Urban farms can be havens of peace, health, and community, but it requires heavy involvement and advocacy from those communities for the long term in order to be successful” .

Agroecology calls for responsible and effective governance to support the transition to just, equitable and sustainable food and farming systems. In an urban environment, this requires the creation of enabling policies that ensure equitable land access and producer control over access to land, especially among the more vulnerable and historically marginalized populations. Land access is expressed most frequently as an obstacle to scaling urban food production by survey respondents, and it is certainly more of a challenge for lower-income and minority groups interested in cultivating their own “commons” . There are examples among our East Bay survey respondents of collective governance at the farm and community level, such as one farm site which is owned cooperatively by three non-profit organizations that collectively serve minority and formerly incarcerated populations, aspiring beginning farmers, and the local community through a cooperative goat dairy, fruit tree nursery, and annual vegetable production plots. City and county governance bodies have an opportunity to strengthen the resilience of urban agriculture operations and opportunities for farmer collaboration by providing subsidies and incentives for social and ecosystem services. City-level efforts to compensate or recognize farmers for ecosystem services such as soil remediation and carbon sequestration, for example, are not yet realized. Further examples of responsible governance from our data include recommendations for public procurement programs to source food from aggregated urban produce . Our respondents are engaged in circular and solidarity economies, key features of agroecology, including bartering, sharing, and exchanging resources and produce with those in their social networks. They are also interested in collaborating in a localized effort to strengthen the link between producers and consumers by aggregating produce and sharing distribution .

As cities work to fulfill their role in providing basic services to citizens, farmers are pointing out an important opportunity to provide refrigerated transportation, storage, and organizational infrastructure to transfer all possible produce grown on urban farms to the best distribution sites. Communication platforms, transport systems, and streamlined procurement in this arena following from other regional “food hub” models could improve the landscape for urban food distribution dramatically . All urban farm respondents are also engaged in closed-loop waste cycles: through composting all farm waste onsite and collecting food scraps from local businesses, farms areinvolved in a process of regeneration,vertical farming from food debris to soil. The activities of urban farms fall naturally under definitions and descriptions of agroecology. Through extending the UAE framework from farms to urban policy and planning conversations, more efficient pathways for addressing food insecurity in part through strategic centers of urban production and distribution can emerge in cities of the East Bay and elsewhere in the United States. Finally, agroecology relies on the co-creation and sharing of knowledge. Top-down models of food system transformation have had little success. Urban planners have an opportunity to address food insecurity and other urban food system challenges including production, consumption, waste management and recycling by co-creating solutions with urban farmers through participatory processes and investing in community-led solutions. In our systematic review of the literature on whether urban agriculture improves urban food security, we found three key factors mediating the effect of UA on food security: the economic realities of achieving an economically viable urban farm, the role of city policy and planning, and the importance of civic engagement in the urban food system . A radical transformation toward a more equitable, sustainable and just urban food system will require more responsible governance and investment in UA as a public good, that is driven by active community engagement and advocacy. We believe that urban agroecology principles provide an effective framework to capture the multiple ecological, social, economic and political dimensions of urban farming, beyond yield and profits, enabling those seeking transformative food systems change in the U.S. in the U.S. a common language and opportunity to measure and communicate more clearly the multiple benefits worthy of public investment. Framing this work as urban agroecology values the knowledge creation, community building, and human well-being that are also products of urban food initiatives. Our data illustrates how urban food sites are spaces of vibrant civic engagement and food literacy development yet remain undervalued by city planners and under constant threat of conversion as well as pressures of gentrification. With the majority of operations in our study functioning as non-profits, it is questionable whether many urban farms would actually be considered a true “agricultural” operation per the USDA definition as a majority of farms earn less than $1,000 in sales annually. As such, they are largely ineligible to apply for funding or loans from many of the federal and state agencies or granting programs such as the Farm Service Agency or NRCS. The idea that the UAE framework can illuminate multiple and often hidden sociopolitical dimensions of urban food production sites is powerful.

For example, over 75% of urban farming sites in our study came into being for a multitude of reasons: including re-establishing justice and dignity into historically neglected and marginalized urban communities, fighting poverty, resisting the environmentally extractive, exploitative, racist, and obesity-inducing industrial farming system, reclaiming the ability to be self-sufficient and work with your hands, and re-educating society about the physical and emotional value of cultivating the Earth. Urban farmers aspire to many things: affirming a human right to healthy food, a food literate civil society, land tenure arrangements that favor socially beneficial rather than profit-maximizing land uses, and alternative forms of exchange and value creation outside the capitalist political economy. The term “agroecology” locates these values in a historical network of similar efforts to transform the global food system along socially just and ecologically resilient lines.Reframing UA through the lens of UAE can ultimately help U.S. policy makers and city planners better understand and support urban agroecological endeavors, and provide researchers, urban citizens and urban food producers a more inclusive mode of inquiry that can lead to transformative food system change, taking care not to dismantle, invalidate, or eliminate the revolutionary, anti-oppression elements through overly prescriptive “policy solutions.” When it comes to researching, documenting, and advancing transitions to sustainable food systems through agroecology, the urban context is an important one to consider, given the growing percentage of the global population living in cities. We acknowledge Gliessman’s call for applications of his “5 levels of food systems change,” showing in our data how East Bay urban farmers are endeavoring to scale up to Level 5: “build a new global food system, based on equity, participation, democracy, and justice, that is not only sustainable but helps restore and protect earth’s life support systems upon which we all depend” . We encourage future engaged scholarship in the U.S. that employs a UAE framework to ask and answer important remaining questions about the transition to sustainable food systems, in partnership with urban farmers, around valuation, preservation, and connectivity of diversified food production sites in the modern city. This chapter presents two examples of climate change education outside of the science classroom. Building on climate change education research identifying, validating, and applying “best practices” for developing student climate literacy and improving climate education across U.S. K-12 classrooms, the first example evaluates a year-long climate change curriculum in a 6th grade humanities context. This example develops and presents an evaluation methodology for climate literacy, drawing on a student climate literacy survey tool, teacher interviews, and classroom observations. The first example leads to the hypothesis that CCE is most effective when it is experiential and action-oriented. The second example tests this hypothesis by looking at a case of experiential CCE integrated into school garden classrooms. It uses a similar methodology to evaluate a climate change curriculum with a food-focused lens, exploring impacts on student learning and behavior. Findings indicate promising outcomes and improvements to student climate literacy. Tying in with the food and climate change nexus that unifies this dissertation, the second example concludes with recommendations for scaling an onfarm, food-focused form of climate education for a K-12 audience.The realities of climate change, both already experienced and forecast for the future, make teaching young people about the causes, consequences and solutions to climate change a national imperative for public and private education. Climate mitigating action is needed at all levels, from international to individual. Current levels of awareness and knowledge about climate change are “insufficient in leading to effective behavioral change” . Leaders in climate change education argue that “based on carefully developed evidence, the emissions gap cannot be closed without also closing the education gap—that is, the gap between the science and society’s understanding of climate change, the threats it poses, and the energy transition it demands” .

Small farms offer many forms of value that large farms are often not able to, and if these values are to be held in communities, policies must shift to allow and encourage more small farms to exist. With developments like the mobile processing unit, commercial kitchen space, and renewed interest in revitalizing a local grain economy, key infrastructure pieces are falling into place, often thanks to large private donations. In order to be transferable, the Lopez model requires further democratization and incentive alignment to allow for such infrastructure improvements in lower resourced regions. Even the relatively well-resourced and well-educated agents of change on Lopez eventually come up against entrenched political economic systems that must be revised and rehabilitated to encourage local and equitable food systems to thrive as a viable alternative to the industrial, globalized food system. Farmers and researchers working together towards goals of local production and climate mitigation often confront challenges that they alone cannot resolve. Increased dialogue and education are needed to bridge between farmer-research identified needs and the policy designs and economic restructuring needed to meet these needs. Education and training for policymakers in critical food systems challenges will be necessary to enact food system changes and “vision statements” adopted by communities through well designed policies that prevent loopholes,vertical garden growing minimize negative unintended consequences, and embrace adaptive and evolving strategies as they emerge.

Islands can be natural leaders in sustainable practices, climate resilience, and local food system adoption, often out of necessity due to longer and more expensive supply chains to the mainland. Learning from the Lopez example, mobilizing a locally appropriate combination of motivated individuals, farmers educated in agroecological practices, land trusts, academics, and supportive local elected officials is a promising first step towards transforming a community food system into one that ensures food security, addresses environmental resource constraints, and mitigates climate change. Future community food systems development should be sure to bring along low income consumers and food justice organizations as active partners.Urban agriculture has sparked growing civic interest, urban farming projects, and scholarship from academic institutions across the U.S. in the past decade . There has been a proliferation of articles citing the multifaceted array of benefits attributed to urban agriculture. These span city greening and beautification to improved nutrition, public and mental health, community food security, climate change mitigation, community building, economic development and empowerment . Those highlighting the beneficial environmental and ecological impacts of urban agriculture cite reduced urban heat island effect, improved local air quality, improved storm water quality , increased pollinator populations, and climate mitigation services, such as carbon sequestration. More recently, social-ecological systems scholars point out social-ecological memory developed through collective activities such as allotment gardening that can contribute to a city’s resilience and are vital for governance of urban food systems . Urban agriculture is often celebrated as part of the burgeoning food justice movement aimed at improving food access among low-income communities in urban areas. However, its impact on reducing food insecurity in U.S. cities remains poorly understood . In fact, there are few robust analyses that measure the actual social, economic and health impacts of urban agriculture, or the policy and governance environments and civic engagement frameworks in which UA models are effective in reducing food insecurity.

Much of the literature is theoretical, focused on the production potential of urban agriculture, while more work is needed to understand and overcome barriers to access and distribution among communities in need. Without understanding the actual links between UA and food security or which specific characteristics, models or approaches reduce insecurity, urban policymakers and advocates risk backing policies that could have unintended consequences or negative impacts on vulnerable individuals and communities. This literature review explores the intersection between UA and food security to better understand how and to what extent UA addresses food access challenges facing low-income communities in urban areas, and the conditions that either enable or inhibit UA initiatives. The landscape of what constitutes “urban agriculture” is extremely heterogeneous: UA encompasses vertical and rooftop farming, urban foraging, community and residential gardens, and commercial urban farms. Some urban farms operate as for-profit businesses, whereas others operate as nonprofits reliant on grants, subsidies and donations to sustain their operations. For the purposes of city planning, the American Planning Association defines UA as the “production, marketing, and distribution of food and other products in metropolitan areas and at their edges, beyond what is strictly for home consumption or educational purposes” . In its simplest form, UA is “growing food in cities” . We define UA broadly to encompass the full range of activities involved in urban food production including self-production and subsistence agriculture. In doing so, we follow scholars who have sought to measure the contributions of a wide range of UA activities . We see three trends in current scholarship on UA in relation to community food security: a focus on the production potential of urban lands, case studies highlighting various nutritional, health, and other community benefits or outcomes from urban gardening initiatives, and more critical analyses of UA through food justice and equity lenses. Some scholars, for example, have mapped vacant lots in Oakland and backyard gardens in Chicago , predicting yield, to illustrate the production potential of UA.

Others demonstrate, through case studies, the productivity of urban gardens and the value of the food they produce in meeting nutritional needs of low-income communities, particularly households involved in gardening directly . Robust theoretical analyses have emerged critiquing the risks of UA when approached without an equity lens, potentially reinforcing structural injustices and racism and negatively impacting the communities they purportedly serve . Deeper historical and structural challenges including poverty, racism, and divestment in specific communities and neighborhoods are increasingly being recognized as the root causes of the current problem of unequal access to sufficient supplies of safe, nutritious, affordable, and culturally acceptable food facing cities . Designating land for agricultural use in urban areas may conflict with other city planning priorities around affordable housing, gentrification, and living. Because of the persistent legacy of systemic discrimination, it is neither inevitable nor guaranteed that urban agriculture will redress food system inequities; in fact, urban farms can sometimes lead to displacement through eco-gentrification . This is a particularly acute concern in areas experiencing housing pressures and population growth, such as the San Francisco Bay area and New York City. UA can also perpetuate positions of privilege within the food system by benefiting those who already hold power . Critical food systems scholars question, “who really benefits,growing strawberries vertical system and who loses in specific efforts to promote urban farms in the ‘sustainable city’ landscape?” and, “how can white food activists reframe their work so as not to fuel displacement of residents of color?” . We examine the role of urban agriculture in addressing food insecurity from a systems perspective, one that considers the policies and institutions that govern the process in which food is produced, processed, distributed and consumed, in order to ask four central questions: How and to what extent are urban produced foods reaching low income consumers, and to what effect? What are the approaches, technologies, institutions and relationships that support or detract from UA in achieving food security goals? What are the political, institutional, cultural, historical, and civic action conditions that enable or inhibit urban agriculture to address food insecurity? Lastly, How can policies be designed to support the urban farmer in earninga living wage, and support low-income consumers in accessing affordable, locally produced healthy foods? We begin by describing our literature review methodology, followed by a review of the food access and food distribution literatures as they relate to the question of how low-income communities access urban produced food. In the food access literature, we review spatial analyses and other studies that identify challenges and opportunities for expanding healthy food access in low-income communities, with a particular focus on urban produced foods. Next, we explore what is understood about the distribution of urban-produced foods especially the challenges and  trade offs urban farmers face between securing a viable income and meeting the food needs of low-income customers. Lastly, we bring together the literatures on access to and distribution of urban produced foods to identify effective strategies urban farms employ to meet food access needs of urban communities.

Our analysis reveals three key factors mediating the effect of UA on food security: the economic realities of achieving an economically viable urban farm, the role of city policy and planning, and the importance of civic engagement in the urban food system. We seek to highlight examples from both the scholarly and gray literatures that demonstrate how UA can improve food access, distribution, and justice, in a way that supports both consumers and producers of food in cities. Results of this systematic review will guide a three-year research project to investigate and address urban food access challenges in the eastern region of the San Francisco Bay Area, where interest in UA abounds, yet levels of gentrification, food insecurity, and income inequality are growing.Our systematic review of the food access and distribution literature builds on critical food systems research in order to better understand when, where and how urban agriculture can improve food access and dismantle structures that perpetuate inequality within the larger food system. We focus on literature from the United States, in order to generate ideas relevant to the political climate surrounding city and regional planners in this country, but results are applicable for comparison or potential transferability in other countries as well. We consider both peer reviewed scholarship and gray literature from food policy organizations Urban Food Policy Institute, Detroit Food Policy Council, and Race Forward. Both theoretical scholarship and case studies are drawn out below to illustrate the question of whether UA improves food access . Building on a set of 150 articles from the researchers’ personal databases , we added an additional 200 sources from five months of Google Alerts for “urban agriculture” and from bibliographies of articles in the database. The Google Alerts provided valuable additions from new studies, local news outlets, and gray literature. In many ways, the Google Alerts service better captures current trends and innovative ideas in urban agriculture than the scholarly literature, and points out important areas for future academic study, especially with respect to novel distribution methods, technology, and food recovery efforts. For example, topics such as mobile food trucks, gleaning, “agrihood” developments, participatory urban food forest projects, online food exchanges , and food distribution apps receive better coverage in local news outlets than the current body of peer reviewed literature, where these emerging ideas are largely absent. Many of the online platforms that allow farmers and backyard gardeners to sell, donate, or receive volunteer harvest assistance represent especially promising areas for future scholarly research . Farmers, Ample Harvest, or Seed Voyage. We used this body of literature to generate a list of key terms for several Web of Science searches to systematically identify the peer-reviewed literature from 1900 to present. The dataset construction and selection criteria are summarized in Figure 11.Other searches for key terms relating to food access including “food justice”, “food security”, “food sovereignty”, “food apartheid”, and “critical food geographies” added small numbers of articles to our systematic review. Terms were chosen based off keyword lists from articles in the database and results were screened for geographic relevance and mention of urban produced foods. These terms and search results bring up important questions of who prefers and uses which terms, and why. The struggle over terminology mirrors broader struggles for control, power, and self-determination. Going beyond ‘food security’, the term “food sovereignty” originates from La Via Campesina and the predominantly rural small producers movement in the 1990s; it is applied to the urban space by scholars such as Alkon and Mares and Block et al. as a distinctly political concept that is “a transformative process . . . to recreate the democratic realm and regenerate a diversity of autonomous food systems based on equity, social justice, and ecological sustainability” . Those who use “food apartheid” aim to directly implicate the segregation that is reproduced in the modern food system and food movements with respect to who can access healthy, locally produced food along racial lines . These scholars foreground issues of race in their analyses in effort to name and dismantle racist legacies in the food system.

The chapters, with their diverse research questions and publication outlets, push back against a food system that destroys human and environmental health alike, and seek out climate friendly alternatives through collaborative, participatory research projects. The research presented in chapters 2, 3, and 4 make the case for diverse values and benefits associated with relocalizing sustainable and equitable food systems centered around small diversified farms, in places where this type of food system transformation is sought. Rather than arguing for the complete overthrow of the current industrial food system, the primary contribution of these cases is to argue that shifts to current practices are both necessary and possible yet must be supported by appropriate and enabling governance structures. There are social, ecological, and educational benefits to adopting agroecological food system practices, but it is difficult to enact these practices holistically and systemically across food system elements in the current U.S. political economy. The cases offer lessons or “pilots” that are relevant to the operations of large-scale farms and industrial processes as well as small scale, agroecological operations: through adding plant diversity and minimizing soil disturbance, for example, numerous benefits can be achieved for farmers , for local ecology, and for global climate change. Therefore, findings implicate the policy and planning domain in terms of action needed to sustain and scale positive food system reform impacts, on a variety of levels and with attention to social justice implications. The findings also make important contributions to methods of climate change communication and education: effective CCE will manifest differently in different contexts and must allow for each audience to express the environmental concerns that are most pressing, immediate, and relevant in that context.

Through considering food systems and climate systems holistically, opportunities for public health benefits,vertical home farming local environmental improvements, and educational growth can be realized. Lopez Island is situated 4 miles off the Washington State mainland in the Salish Sea, where it is Figure 3- Lopez Island Farmland a lighthouse for an alternative, agroecological model of food production at the community scale. Approximately 18,000 acres of agricultural land in the San Juan Islands chain form a network of non-GMO, non-chemical based agricultural land. The 5,000 acres of Lopez Island farms stand in direct contrast to conventional farming: they are largely small scale, human powered, diversified, educational, knowledge-intensive, reliant on natural fertilizers and integrated pest management strategies, and localized in terms of who they serve2 . The Lopez Community Land Trust lists 27 farms on their annually published “farm products guide,” on this island of 2,500 year-round inhabitants. Lopez farmers seek to optimize many outcomes besides yield and several actively cultivate seed diversity through seed saving and local exchange. Seeds are selected for drought resilience, flavor, nutrient content, ability to withstand disease and pest pressure, and general endurance and adaptability to local conditions. The resident community is invested in local farms, through school food procurement, local markets, and regular volunteer presence. The summer tourism industry can attribute some fraction of its success to the local food system, as a recent tourism survey indicated “natural/rural scenery” as the top reason and “local food” in the top half of 15 listed reasons tourists come to the San Juan Islands . However, the tourism industry simultaneously poses a challenge to the local agriculture community, as the real estate and land markets are increasingly displacing farmers due to development pressures and desires for second homes on the islands. As an island community, Lopez has unique considerations around food procurement. Importing food from the mainland is expensive and risky in the face of natural disasters, as ferry service to the islands is easily disrupted and unreliable in the face of adverse weather conditions.

Ferry service costs $47 round trip from Anacortes to Lopez per vehicle and driver in the summer season. There is an added incentive on Lopez to adopt self sufficient and soil regenerating farming practices at the community scale due to its geographic isolation in combination with rocky, relatively poor soil quality. This “island incentive” is important to factor in when considering the widespread adoption of sustainable agriculture on Lopez; as the San Juan County Agricultural Strategic Action Plan reports, “islanders naturally place a high value on food security and may benefit from their isolation to preserve genetic diversity, for example, by establishing an organic seed industry” . As food supply chains in today’s globalized food system are increasingly threatened by natural and climate-exacerbated disasters, all communities will soon have increased incentives to invest in sustainable food production as a form of resilience, food security, and climate adaptation. In the realm of food self-sufficiency, innovative production systems, and climate resilience, there is much to learn from island nations and communities that are on the front lines of adapting food systems to and mitigating climate change. Lopez is striving to create a robust, resilient, socially just local food system, a distinct and more complex goal than merely investing in and promoting local food production. Individual farmers starting to adopt and successfully deploy regenerative practices is not the same as creating a sustainable and resilient local food system. A local food system, as outlined in the previous chapter, includes not just production, but transportation, distribution, marketing, retail, preparation, consumption, waste recycling, and education across system elements. A food system that is socially just, compensating farmers fairly for their labor while balancing affordability for the consumer across income groups, requires a change in food system economic transactions from the status quo. A food system that is environmentally sustainable and mitigates climate change, storing more carbon in the soil than it releases and minimizing emissions throughout the system elements, requires transformation of the dominant industrial food system. Lopez farmers are striving to increase and quantify their soil carbon reservoir, with less progress to date on reconfiguring the economic status quo. What can this island farming community tell us about creating and scaling alternatives to the chemical-industrial farming industry? What are the key challenges, tensions, and opportunities on Lopez for building a local food system that is socially just and environmentally sustainable? What are the next steps for Lopez, and other counties or regions, in moving towards goals and vision statements for re-localized food systems? These questions, when answered, become relevant not just to farmers and researchers, but importantly, to policymakers, economists, and businesses that must implement new policies and economic structures effectively in partnership with farmer- and community-generated vision statements. Significant to the presentation of results and discussion is the supremacy of private property in the United States legal system. When comparing the Lopez agricultural case study to “idealized” visions of agroecological food systems, many steps towards the “ideal” are thwarted by private property “enclosures” of the agricultural commons,vertical growers which is more pronounced in the United States than in other geographic contexts.Thus, progress towards visioning and establishing agroecological local food systems must reconcile with unique challenges in the U.S. land tenure system, and ultimately promulgate strategies for loosening the supremacy of private property if real power is to be restored to those growing our food. Through a compilation of fieldwork, ethnographic notes, participant-observation, and immersion into the community, this chapter presents data on the Lopez Island sustainable food system case study, and constructs analysis of food system transformation framed by the paradigm of agroecology .

I draw on social science research methods including semi-structured interviews and ethnographic techniques to bring forward ideas and solutions from leaders in the agricultural community of the San Juan Islands. Research partners include the San Juan Island Agricultural Resource Committee , the San Juan Islands Agricultural Guild , the Lopez Community Land Trust , the Lopez Island Farm Education program, Washington State University San Juan County Extension, San Juan Islands Conservation District , Midnight’s Farm, Stonecrest Farm, Sweet briar Farm, and Lopez Harvest. I find that the Lopez food system transformation towards resilience, sustainability, and equity is a work in progress, requiring political and economic shifts in order for regenerative food production practices to spark regeneration and equity in other branches of the food system. Significantly, farmland transition barriers and land access challenges3 combined with new and beginning farmer training are areas requiring further investment, investigation, and institutional capacity in order to secure the progress made to date into subsequence generations of sustainable farmers.It is already well established in the agroecology and sustainable food systems literature that the chemical-industrial farming system causes adverse human health, labor, social justice, environmental and climate outcomes . Thus, alternatives to the chemical-industrial farming system are imperative to develop and advance for environmental and social justice reasons. The current dominant food system is driven towards yield-maximizing outputs enabled by increasingly consolidated, mechanized monocultures, which are in turn reliant on a potent mix of chemical fertilizers, pesticides, and fossil fuels. This system functions at the expense of human health, fair labor conditions, equitable food distribution, and environmental preservation. Furthermore, the current food system contributes significantly to the problem of climate change, emitting approximately 25% of the global greenhouse gas emissions portfolio . Conversely, regenerative agroecological food systems have the potential to store more carbon annually in the soil than what is emitted through processes like respiration and plant decay, which at scale could amount to significant global carbon offsets , buying time for the planet to adopt other necessary technological and social changes to reduce carbon emissions . Agroecological, sustainable, and organic farmers are leading the way towards demonstrating new ways to both produce sufficient quantities of food and mitigate climate change through soil C sequestration. Regenerative agriculture 4’s climate mitigation potential is highlighted in a recently released report from the Rocky Mountain Institute, stating that “negative emissions technologies—natural and engineered strategies for actively removing CO2 from the atmosphere such as agroforestry and silvopasture, biomass gasification and bio-char—deployed at scale in the United States could sequester between 0.6 and 1.4 gigatons of C annually by 2050” . A report by Terra Genesis International further breaks down the mitigation potential of regenerative agriculture practices per hectare as depicted in Figure 4. According to Silver, “plants, and the soils they live in, are tremendous resources in the battle against climate change… soils have the potential to be deep, long-term repositories of some of the carbon captured by plants, keeping it from returning to the atmosphere for years to decades or longer” . Silver and her team of researchers quantify the impact of existing “agricultural mitigation practices” as potentially lowering global temperatures by 0.26°C by 2100, under RCP 2.6 . Other researchers helped develop the “Soil C 4 per Mille” initiative, launched at the COP21 talks in Paris in 2015, calling for all nations to increase soil carbon storage on agricultural lands by 0.004%, which would create a significant global carbon drawdown effect of 2-3 Gt C annually, offsetting 20-35% of anthropogenic emissions . What are these “agricultural mitigation practices” and how exactly can they be scaled across global agricultural acreage? Undoubtedly, local geography and context matter, along with available social, intellectual, and financial resources. This chapter will explore the first half of the question and explore the application of mitigation practice in the San Juan Island geographical context. A selected list of practices most relevant to Lopez Island farms are listed in Table 1 below. It is worth noting that many of these practices, in particular no-till and cover cropping, are broadly relevant to agricultural producers in both the conventional and organic industry, offering opportunities to build a “big tent” in the agriculture sector’s response to climate change.Agroecological research often ties together the climate mitigation impacts of ecological farming with the social justice impacts of farming practices that are regenerative for both land and people, building a framework for conceptualizing and studying the health of interlinked human and natural communities. In the words of Steve Gliessman, “Agroecology is a way of redesigning food systems, from the farm to the table, with a goal of achieving ecological, economic, and social sustainability. Through transdisciplinary, participatory, and change-oriented research and action, agroecology links together science, practice, and movements focused on social change” . Thus social movements focused on poverty reduction, public health, and racial justice are linked in with the agroecology paradigm. This triple bottom line of social, economic and ecological sustainability must be investigated in each context that claims “agroecology” as its mantle.