Horticulture

When looking at the effects of CO2 the different seedling treatments were combined. When looking at the effect of CO2 on any growth or weathering parameters, only planted columns were considered. Statistical analysis was performed using JMP software version 5.01a . Two way ANOVA was used to determine treatment and interaction effects. Significant differences between CO2 treatments were assessed with a student T test, and significant differences between ectomycorrhizal treatments with Tukey’s HSD test, using a one way ANOVA.Upon harvest we observed highly variable rates of mycorrhizal colonization. We classified the seedlings as abundantly colonized , moderately colonized , or sparsely colonized . Of the 20 seedlings in the mycorrhizal treatments 6, 4, and 10 seedlings were abundantly, moderately, and sparsely colonized, respectively, at the time of harvest. While the root systems extended 12S21 cm down the 30 cm columns, no mycorrhizae were found deeper than 6 cm. There were no extraradical hyphae or ectomycorrhizae resembling Piloderma& fallax or Suillus&variegatus observed in the non mycorrhizal treatment, but there were turgid, smooth,maceta cuadrada plastico  black root tips observed in the non mycorrhizal treatments that may have been Thelephoroid mycorrhizae. Chitin analysis of roots and growing medium showed almost no chitin in our unplanted controls, and significant chitin in both mycorrhizal treatments . There were also significant amounts of chitin in the non mycorrhizal planted treatments. In both mycorrhizal treatments most chitin was found in the mineral mix, whereas in the non mycorrhizal treament most chitin was found in the rhizosphere and roots. Combining the two mycorrhizal treatments we found moderately more chitin in the elevated CO2 treatment, 86 mg chitin/column vs. 50 mg chitin / column . When the chitin content was expressed as total chitin content per gram seedling biomass , we see that the mycorrhizal treatments did have significantly more chitin than the non mycorrhizal treatment, and that elevated CO2 was associated with a higher chitin content in the Piloderma treatment.Formic, lactic, and acetic acids made up the majority of measured low molecular weight organic acids , comprising 82%, 12%, and 4% of total LMWOA’s, respectively.Much smaller amounts of malonate, oxalate, fumarate, and succinate were occasionally detected, but their occurrence in measurable quantities was not associated with any treatment. Nonplanted columns had significantly lower LMWOA levels than planted columns while P.&fallax columns had significantly higher LMWOA concentrations than non-planted, but significantly lower levels than either the nonmycorrhizal or S.&variegtus columns . These differences were driven by differences in the production of formate and lactate . Columns exposed to elevated CO2 produced significantly more total LMWOA’s , and this difference was driven primarily by significantly greater formic acid production . When amounts of LMWOA are calculated per gram seedling DW there are no significant differences between mycorrhizal or CO2 treatments .Solution pH was measured for the leachate from 7 sampling dates. Leachate pH was consistently alkaline . The nutrient solution used to water the columns was pH 5. There was no significant difference between elevated and ambient CO2 treatments nor between the non mycorrhizal treatments and the mycorrhizal treatments in leachate pH, but the leachate of the non planted controls was significantly lower in pH than the planted treatments on 5 of the 7 sampling dates and moderately but not significantly lower on the other two sampling dates. The pH of the column leachate from the planted columns did not change appreciably over time, while the leachate from the unplanted columns decreased slightly over time .The needle concentrations of Ca, K, Mg, Fe, and P were all at or above deficiency thresholds for P.&sylvestris , though P is near the lower limit of optimal growth. CO2 treatment had no effect on needle nutrient concentrations and mycorrhizal treatment only affected needle [Ca] . Neither CO2 level nor mycorrhizal treatment had a significant effect on total seedling contents of Ca, K, or Mg despite significant differences in seedling biomass between CO2 treatments. The differences in seedling Ca and K contents between treatments correlated tightly with seedling DW, while the opposite trend was found with Mg. Ectomycorrhizal colonization, particularly with Piloderma, increased seedling Mg concentration.Whole column weathering budgets for the 4 elements: Si, Ca, K, and Mg show no effect of CO2 on total weathering losses . The presence of seedlings, mycorrhizal or not, did significantly enhance weathering losses compared to nonSplanted controls.More Si and Mg were weathered in columns planted with P.&fallax inoculated seedlings, but these differences were not significant . The major pool of weathering losses for Mg, K, and Ca in the seedling treatments was uptake into the growing seedlings; losses of magnesium were particularly dominated by seedling uptake . Silica losses were fairly evenly distributed between ΔCEC and column leachate, while seedling uptake was negligible . As stated previously, ΔCEC was negative for calcium and slightly negative for some K and Mg treatments. When the nutrients added during watering were subtracted from the final budgets the net weathering losses of Ca, K, and Mg in the non planted treatment are negative or only slightly positive ,maceta 7 litros  suggesting a “missing sink” for weathering products.Elevated CO2 increased the biomass of the Pinus&sylvestris seedlings. Other studies on coniferous seedlings have generally found a growth stimulation with elevated CO2 , and this trend includes several studies on mycorrhizal Pinus&sylvestris seedlings , although some other studies have failed to find an effect of elevated CO2 on growth . We found a slight reduction in root:shoot with elevated CO2. Most studies on ectomycorrhizal P.& sylvestris seedlings which have noted a growth stimulation from elevated CO2 also found an increase in root:shoot . A decrease in root:shoot does not necessarily indicate reduced  below ground C allocation as carbon could be allocated to EM fungi rather than root biomass. If we use Ekblad and Nasholm’s estimate that 9.5% of fungal biomass is chitin, then our observed 21 mg average difference in chitin between elevated and ambient CO2 treatments would correspond to 220 mg more fungal biomass supported by seedlings in the elevated CO2 treatment. This difference would bring the root: shoot ratios of the two CO2 treatments to near parity. Additionally, a given amount of ectomycorrhizal biomass typically has a significantly higher respiration rate than the same mass of fine roots and thus represents more below ground carbon allocation This same explanation for potentially higher below ground carbon allocation despite lower root:shoot applies to our findings of slightly lower root: shoot in the two mycorrhizal treatments vs. the nonmycorrhizal treatment. Low molecular weight organic acid production was strongly associated with seedling biomass across both CO2 and mycorrhizal treatments. While EMF are often mentioned in the literature to produce significant amounts of LMWOA’s, our findings seem to fall in line with the majority of studies examining the EMF role in LMWOA production which fail to find an increase in LMWOA production when comparing EMF and nonSEMF seedlings . However, many of these studies do find that EMF significantly alter the composition of LMWOA’s produced, particularly increasing oxalic acid concentrations , which we did not. Similar to Fransson and Johansson , we did not find that elevated CO2 increased LMWOA production beyond its effect on seedling biomass. Elevated CO2 was associated with significantly increased chitin content in seedlings colonized by Piloderma&fallax, but not with seedlings colonized by Suillus& variegatus;&this increase was due to elevated chitin levels found in the growth matrix, not on the seedling roots. Increased mycorrhizal growth is commonly found in elevated CO2 treatments . Many studies show that this response is highly fungal speciesS specific . It is interesting to note that Fransson and Johansson , in which they assessed the effects of elevated CO2 on mycorrhizal growth of 5 ectomycorrhizal species, also found this strain of Piloderma&fallax responded far more to elevated CO2 than any other fungal species examined. Our finding of no increase  in seedling biomass in the mycorrhizal seedlings is not uncommon. Despite the fact that Pinus&sylvestris is considered obligately mycorrhizal, many studies have also found a growth depression of P.&sylvestris with mycorrhizal colonization when mycorrhizal and non mycorrhizal seedlings are compared . Given the high needle nutrient concentrations in our non mycorrhizal seedlings, and the very dense rooting we observed, it seems likely that high nutrient availability, and a very restricted rooting zone were the primary reasons we observed no growth stimulation by mycorrhizaeThe generally low levels of mycorrhizal colonization we observed were likely a result of nutrient levels being too high , or insufficient drainage . The significant amounts of chitin observed in the non mycorrhizal treatments may indicate either the presence of thelephoroid mycorrhizal contamination or saprotrophic fungi growing in the mineral mix. Our visual observations of shiny, turgid, smooth, black roots, and the fact that the majority of the chitin found in the non mycorrhizal treatments was found in the roots and not in the mineral mix suggests some thelephoroid mycorrhizal contamination. The larger size of the non mycorrhizal seedlings and their lower chitin levels indicates that thelephoroid infection was minor. Nutrient levels were sufficient for healthy balanced growth. Leachate concentrations of nutrient cations were steady suggesting that we increased the nutrient amounts sufficiently to keep up with the increasing nutrient demand of the growing seedlings. The fact that none of the needle nutrient concentrations were below sufficiency threshold further suggests that none of the seedlings had severe nutrient deficiencies that could have compromised carbon allocation physiology.The overall negative weathering observed for some mineral nutrients suggests a missing sink somewhere in our weathering budget. The two most likely possibilities are the formation of secondary precipitates that were not extracted upon harvest or a large pulse of weathering in the initial 3 weeks of equilibration , before seedlings were planted. We used a chemical speciation and equilibria model Visual MINTEQ to determine if secondary precipitates may have formed. Given the makeup of LMWOA’s observed, the pH’s measured and the elemental concentrations in the drainage as input parameters the only compound likely to have precipitated would have been Caoxalate, but only in very small quantities <3 uM. This leaves the initial “equilibration flush” as the likely missing sink in our weathering budget. All the columns were treated equally before planting so this missing sink should not affect the merit or interpretation of our results. Overall, and in every individual elemental flux , seedlings had a significant effect on weathering. For the nutrient cations K, Mg, and Ca, extra weathering products were taken up by the seedlings, while for Si, which was not taken up in appreciable quantities , extra weathering products were found on exchange sites in the mineral matrix. Mycorrhizal colonization did not significantly increase weathering rates or nutrient uptake, but seedlings colonized by Piloderma&fallax did exhibit a trend toward increased weathering. More Si and Mg were mobilized in the P.&fallax treatment despite the fact that P.&fallax colonized seedlings were on average smaller, though these differences were not statistically significant. P.&fallax colonized seedlings also had significantly higher Mg concentrations. Elevated CO2 had no effect on the weathering losses of Ca, K, or Si, but increased Mg losses . While seedlings grown in elevated CO2 did have higher plant and fungal biomass, and higher total seedling elemental contents, these increases in nutrient uptake were balanced by reduced leaching losses and not by enhanced mineral dissolution. Soil biota are capable of stimulating weathering of alumina silicate minerals by four distinct mechanisms. Proton&promotion: positively charged hydronium ions exuded by biota bind with partially charged negative surface sites on minerals, displacing cations from the mineral surface and destabilizing Si or Al on mineral surfaces, facilitating their release into solution. Plant growth is generally seen as a net acidifying phenomenon as a plant’s greater uptake of positively charged nutrient cations than negatively charged nutrient anions leads to a plant’s net exudation of protons. Ligand8promotion: an anion, either inorganic or organic, binds to mineral surface cations, again destabilizing the bond energy at the mineral surface stimulating release of surface cations and framework Si or Al. Removal&of&transport&limitation: the removal of weathering products from the surface boundary layer via nutrient uptake or enhanced solution flow eliminates or reduces the constant readsorption of these mineral weathering products that occurs in concert with dissolution, enhancing net dissolution.

We had a very low sequencing success rate and this appeared to be due to contamination of many samples by saprotrophic other fungal infection. Our sampling was done in mid summer, and this may be a time of high root turnover. The levels of nitrogen fertilization applied in this study termed “high” and “low” would be considered “extremely high” and “very high” in natural settings. The highest rates of nitrogen deposition in the eastern US are generally below 20 kg N/ha/yr , and many forests considered to be exhibiting nitrogen saturation associated decline are below 15 kg N/ha/yr . The high and low levels of fertilization employed here are 20 and 6 fold higher than the atmospheric deposition levels in this part of the northeast. Because there was no evidence of an interactive effect of nitrogen treatment and horizon with regards to community composition, we will first discuss our findings in the context of nitrogen addition experiments and then discuss the implications of our findings on horizon preference. There is some evidence that deciduous forests may respond differently to nitrogen deposition than coniferous forests , so, when possible, we will focus on studies done in deciduous forests. We will also not discuss studies that focus exclusively on ectomycorrhizal sporocarp  inventories. Sporocarp inventories formed the majority of early studies on the effects of acid deposition on ectomycorrhizal communities, and could be considered the canary in the coal mine that has spurred 2 decades of research following the seminal work by Arnolds . However, there is ample evidence that sporocarp abundance may not be reflective of mycorrhizal abundance . 

We will address the results of our colonization intensity measurements in the context of rooting distribution,vertical grow system  ecosystem biogeochemistry and ecosystem responses to nitrogen deposition.Our findings of a significant shift in ectomycorrhizal species composition are generally in agreement with other investigations on the effects of N deposition on ectomycorrhizal commmmunities. Avis et al. and Lucas and Casper found that nitrogen fertilization significantly impacted ECM community composition in oak forests of the eastern US, as have numerous studies in coniferous forests . Our results stand apart from those of Avis et al. and Lucas and Casper in that they observed significant effects on N fertilization on ECM community composition at N fertilization levels between 20 and 35 kg/ha/yr and in as little as two years, while we found no significant effects of 18 years of 50 kg/ha/yr of N fertilization on ectomycorrhizal community composition. Avis et al. also failed to find a significant community change after 18 years of fertilization at 54 kg/ha/yr. The majority of N addition studies on coniferous plots have found a significant impact of 30S50 kg N/ha/yr on ECM community composition , though Ishida and Nordin failed to find an effect of 12 years of 50 kg N/ha/yr on ECM community composition in a spruce forest. Wallenda and Kottke identified a general threshold for 20S30 kg N/ha/yr before marked changes in the ECM community composition are likely to be observed, although they caution that forest specific factors may change this threshold a great deal in either direction, and at the time of their review, there were no studies on the effects of N addition on ECM communities in deciduous forests.

Our findings of a marked reduction in ECM diversity with high N fertilization are also in line with the findings of Avis et al , and Lucas and Casper , which found significantly reduced ECM diversity in their high N treatments, though again, they noted significant decreases in ECM diversity at levels comparable to our “low” N treatment, while we did not. Avis et al. failed to find a significant effect of N addition on ECM diversity. Looking at studies in coniferous forests, a reduction in ECM diversity with N addition seems to be the general finding , but studies have also found no reduction in ECM diversity in forests fertilized with moderate or very high levels of N addition . We could clearly identify certain species to be nitrophilic or nitrophobic but we could not make such characterizations for any higher level phylogenetic groups other than the Clavulinaceae. We found that the Clavulinaceae were generally nitrophobic and this is in agreement with the findings of Avis et al. . Among our 5 most abundant Lactarius species, one was nitrophilic, two were more common in the low nitrogen treatment, and nitrogen had no effect on the abundance of the other two. Lactarius&quietus was also quite abundant in Avis et al.’s study on oak, but they found no consistent reaction to nitrogen fertilization. In their study across a depositional gradient in an Alaskan spruce forest Lilleskov et al. found Lactarius&theiogalus to be dramatically nitrophilic, shifting from 7% to 69% of all root tips from the low to high end of their nitrogen gradient; we found L.&theiogalus to be mildy nitrophilic, occurring in greatest abundance in the low N treatment. Cox et al.’s study across european Picea&abies forests identified the genera Lactarius and Thelepohra/Tomentella to be nitrophilic.Our most abundant species was Cenococcum&geophilum, and it was termed nitrophobic due to its sharply reduced abundance in the high N treatment. Avis et al. found Cenococcum abundance across N treatments variable, with one TRFLP type being nitrophilic and another nitrophobic. 

Lucas and Casper found Cenoccocum&geophilum abundance increased on oak roots in response to nitrogen fertilization . Avolio et al. looked at ECM community composition on pine and oak seedlings in response to nitrate fertilization and found that Cenococcum abundance increased markedly in response to N fertilization on oaks, and decreased markedly in response to N fertilization on pines. Cenococcum geophilum is widely thought to be acryptic species complex , and we examined the possibility that we had sub-taxa within C.&geophilum that might have a distinct affinity for nitrogen or horizon. Clustering our C.&geophilum sequences at different % similarities did yield different clusters,macetas cuadradas  but did not divide this large group according to any horizon or nitrogen affinity. This inability to define Cenococcum’s niche is not uncommon; in a 2007 commentary, Dickie identified Cenococcum as “one notable exception to the rule of niche differentiation”.The ECM communities in the organic and mineral soil were quite distinct, both across all treatments and within a given nitrogen treatment. Our findings of different ECM communities in the mineral and organic horizon is common to other studies which have examined the ECM communities in organic and mineral soil separately , though to date few studies have done so. We found evidence of increased diversity in the mineral soil. Rosling et al. found higher diversity in the mineral soil, while Dickie et al. found lower diversity in the mineral soil, and Scattolin et al. found moderately increased diversity of ECM species in the mineral soil. All three of these studies were done in coniferous forests. Certain species in our study exhibited clear preferences for one horizon or another, and these trends were also applicable to higher phylogenetic classifications. In particular the Russulaceae exhibited a preference for the organic horizon while members of the genus Inocybe, the order Agaricales, and the families Tricholomataceae and Clavulinaceae were significantly more abundant in the mineral soil. In contrast to our findings, Baier et al. and Scattolin et al. found that Lactarius and Russula were generally more abundant in the mineral soil, though they found individual species within both genera that were more abundant in the organic soil; both studies were done in high elevation coniferous forests. Tedersoo et al. found, as we did, that the Agaricales exhibited strong preference for mineral soil, though they also found the Clavulinaceae to be significantly more abundant in the organic horizon, in contrast to our findings. 

In general, our data suggests greater specialization in the mineral horizon than in the organic horizon. Of the 65 species we found, 31 were found only in the mineral soil, while only eight were found exclusively in the organic horizon. Rosling et al. also found a higher proportion of species occurring exclusively in mineral soil.Across all treatments, the ectomycorrhizal colonization intensity was very similar between the mineral and organic horizon, and this stands in some contrast to the published literature. Very few studies have exhaustively sampled the ectomycorrhizal community in the mineral soil , but those that have, have found as many, if not more, ECM in the mineral soil as in the organic soil . More studies have sampled the upper layers of the mineral soil, and ECM colonization intensity, measured as either percent root length colonized or percentage of fine root tips that are mycorrhizal, is generally lower in the mineral soil .However, Scattolin et al. found that the A and B horizons in a montane spruce forest in Italy had significantly higher mycorrhizal colonization intensity than the organic soil, so our finding of equal or slightly elevated colonization intensity in the mineral soil is not unprecedented. Magill et al. assessed the fine root biomass in the same plots we did two years before we sampled these stands. They found that between 55% and 62% of all fine roots were found in the mineral soil, though they only sampled the top 20cm of mineral soil. Thus, our findings of equivalent or higher colonization intensity in the mineral soil can be interpreted as equivalent or higher mycorrhizal biomass in the mineral soil.  Nitrogen addition had no effect on the colonization intensity in the low N treatment or in the organic horizon of the high N treatment, and increased the percentage root length colonized in the mineral soil in the high N treatment. According to Magill et al. , the fine root biomass in the organic horizon in these same stands is 25% and 27% lower in the low and high N treatments, respectively. Fine root biomass in the top 20 cm of the mineral horizon has not been significantly affected by nitrogen treatment, thus the percentage of fine roots found in the mineral horizon increased marginally from 55% to 62% with nitrogen addition . We can thus infer that there is a significantly higher fraction of total ectomycorrhizae in the mineral soil in the high N treatment. There is considerable variation in the literature in reported responses of ECM colonization and fine root biomass to nitrogen addition. The consensus seems to be that nitrogen addition decreases both, but the large number of reports finding the opposite suggests that characteristics of the individual forest being examined may be important to consider. In a meta analysis of 6 studies conducted in 14 forest stands, Treseder et al. found a moderate decrease in %RLC of 5.8% with nitrogen fertilization, but also noted that the responses to N were very heterogeneous. In a meta analysis of boreal forests’ responses to nitrogen addition, Cudlin et al. found a not significant decrease of 10% in percent mycorrhizal colonization. Carfrae at al. and Koren and Nylund found significantly increases in %RLC with nitrogen fertilization. Wöllecke et al. noted a sharp decrease in % RLC with nitrogen fertilization, but this was much more pronounced for the organic horizon than the mineral horizon, also indicating increased fraction of total mycorrhizal activity in the mineral soil under nitrogen addition. To the authors’ knowledge no published studies have examined the effects of nitrogen on ECM colonization intensity in deciduous forests. The literature on the effects of nitrogen on rooting activity is no more consistent. While, many micro and mesocosm studies have demonstrated a decreased ratio of root biomass to shoot biomass with increased N availability , and the mechanisms for this are well understood , the effect is generally driven by increases in above ground biomass and the effects of nitrogen fertilization on  below ground biomass in forests vary considerably. Cudlin et al. found an increase in root biomass of 10% in their meta analysis of 22 forest studies, while Ostonen et al. found a 20% decrease in specific root length in a meta analysis of 54 studies, both of these studies reported such high variation in responses to N that neither trend was significant.The altered mycorrhizal colonization we observed in the high N plot may be an adaptation to limitation or colimitation by phosphorous or base cations. 

Leaf organic d13C and d18O values support this observation, because P. piscipula showed consistently higher d13C values than G. floribundum , coupled with lower d18O indicating that the decrease in photosynthetic carbon isotope discrimination was associated with greater stomatal conductance and greater photosynthesis . Greater photosynthesis in P. piscipula is consistent with maintaining a canopy of leaves later into the dry season. Thus, our results are most consistent with maintenance plant water potential to maximize carbon gain during the onset of the dry season. The observation that P. piscipula appeared to use shallower water sources and maintained its canopy of leaves later into the dry season was not expected. Part of this pattern is driven by the capability of P. piscipula to utilize dynamic sources of water, such as the cold front precipitation during the frontal season . This makes sense, because the Laja bedrock layer was a poor source of water at all times, and soil pockets, which are available, but heterogeneous in distribution, were always better sources of water than rock layers . Water content of soil/ bedrock sources changed along the year suggesting a different seasonal contribution to plant water uptake. The hg of topsoil in the wet and frontal seasons were very similar and three times greater than values measured in the dry season. The Sascab bedrock layer could be a significant source of water in the wet and frontal seasons, but not in the dry season.

Soil pockets had two times more water than topsoil in the dry season suggesting that they could be an important source of water for trees during the dry season. In the dry season,vertical farms the rock profile had hg between 1 and 5 % but nearly all were less than 1 %. These values were slightly lower than those reported by Querejeta et al. and Hasselquist et al. in nearby areas, which suggest that the bedrock was subjected to a greater evaporation during this study. The d18O values of water in this study integrated processes ranging from evaporation of soil and bedrock water sources, transpiration of tree species, and precipitation events. In the wet season, enriched values of d18O of water in topsoil 10–15 cm and trees revealed the occurrence of a depleted precipitation event that occurred on October 21, 1 day before sampling, bringing 19.7 mm of water . Furthermore, a frontal system including cold front #3, the tropical wave #37, as well as the remnants of tropical storm Kiko that formed in the pacific, converged on the study area days before the wet season sampling in October 2007 . Hurricanes, tropical storms and cold fronts generally have lower stable isotope ratios than convective precipitation events . For example, Perry et al. recorded d18O values of 9.91 % for precipitation during tropical storm Mitch in 1998, and precipitation events ranging from 6 to 10 % for d18O have been recorded in the vicinities of the study area . Consequently, depleted oxygen values in soil 15–30 cm and P. piscipula and G. floribundum trees could be accredited to precipitation originated from these events. Soil pockets also showed more negative values than rock, suggesting that depleted rain water reached this layer.

During dry season measurements in February 2008, the d18O of topsoil 0–15 cm was more positive than groundwater suggesting another depleted source of water. Cold front #29, which occurred 4 days before sampling and brought 33.9 mm , could be the main source of water. However, the more negative value of topsoil from 0 to 5 cm could be affected by dew water since this soil sampling was done early in the morning. More negative d18O values in topsoil than ground water have also been observed by Saha et al. in similar environmental conditions in Miami, associated with water condensation occurring at night in the upper soil layers. Condensation has been shown to deplete d18O soil water 10–15 cm depth by 5 % . Condensation can also account for up to 47 % of total transpiration . Surface dew is easily generated when temperatures go below the dew point at night or in early morning . Under tropical conditions in Tahiti, Clus et al. reported average dew yields of 0.102 mm of dew during the dry season. Therefore, condensed water could be an important source for P. piscipula. Overall, our results indicate that variation in phenology between these two deciduous tropical dry forest tree species, which vary in the timing of their deciduousness, is not akin to the relatively large variation in rooting depth that can occur between tropical evergreen and deciduous species , but rather reflects the diversity of plant physiological strategies that occur in tropical forest .The excremental body has been defined by Mark Feather stone as the disposable body that is set up within US society as a foil to the formalized, white, utopian American body in order to assert the US’s global power through corporeal poetics.Furthermore, the excremental body has been demonized as a way to justify the disembodied, mechanized body of supermodernity which represents the perfect, post human body which does not break down, feel pain, or expire.

Ultimately, the excremental body is the pathologized other that feels pain and ultimately represents “the horrific real of the vulnerable body.”In regards to the US’s involvement in Vietnam during the Cold War Era, American society was, and still is, culturally and psychologically unwilling to recognize and empathize with the suffering and tortured bodies in the Global South and within its own borders. The pathologization of the “natural” body, soil, water, urine, and all that is “other” allows US society to relentlessly exercise and grow its accursed share through neo colonial agendas.As the devastating effects of the Anthropocene become ever more acute, contemporary artists Jun Nguyen Hatsushiba and Jae Rhim Lee re present the excremental body at the forefront of their respective projects in order to remediate disembodiment,vertical plant growing highlight the interdependency of all life forms, and hold the US necropolitics accountable for countless ecological atrocities. The “Anthropocene” popularized in 2000 by the atmospheric chemist Paul Crutzen and ecologist Eugene Stoermer, has been deemed by geologists to begin in the 1950s due to the dramatic effects of modern and nuclear weapons upon ecosystems during WW2 and the Cold War battles fought between communism and capitalism.The Anthropocene critically links human actions with the rapid change and depletion of earth’s systems, but its history actually begins long before the 1950s. When German biologist, Ernst Haeckel, coined the term “ecology” in 1866, it became a discipline that facilitated the domination of colonial anthropocentrism over passive, human and nonhuman worlds — effectively becoming what T.J. Demos calls the “science of empire.”A lot has changed for the worse since 1866, since ecology’s colonial origins still persist through turbo capitalism’s apathy towards the biosphere exacerbates a psychological and cultural fear of morbidity due to a “uniquely modern form of egoism [which] has broken [the] interdependence between the living and the dead. With disastrous results for the living, who now think of the dead as eliminated.”This perversion of death is further clarified by Achille Mbembe’s theory of Necropolitics as “let live and make die” which is in direct response to Michel Foucault’s concept of biopolitics defined as “live and let die.” Coined by Foucault in the 1970’s during the Cold War era, biopolitics meant to “make live and let die” in line with the capitalist liberal governmentality that specifically sought to make life “cozy” for the First World nation states.On the other hand, necropolitics delineates a management of life in the neo liberal capitalist world: let all those who hold wealth and power live, and make the rest die through systematic abandonment.

The Vietnam War is particularly relevant to the artists Jun Nguyen Hatsushiba and Jae Rhim Lee since their projects relate to the necropolitics of US chemical warfare that sparked the formation of an ecological consciousness in American society. In these works, the contaminated human and environmental “body” collide.Staged in South Korea and later shown to a Japanese audience, Jun Nguyen Hatsushiba’s film, Memorial Project Waterfield: The Story of the Stars , aims to commemorate the losses incurred by ecological, political, and economic violence during the American War in Vietnam . Focusing on the violent trauma incurred on the body, land, and water Nguyen Hatsushiba re presents the act of urinating as a way to memorialize the embodied struggles of Vietnamese people who suffer from slow ecological violence and US cultural hegemony. By creating a multidimensional space within his work, he offers a heterogeneous re presentation of Vietnamese society and suffering that has been systematically erased by hegemonic US narratives of the Vietnam War. On the other hand, Jae Rhim Lee’s Infinity Burial Project offers consumers an opportunity to remediate the imperceptible accumulation of industrial toxins within the human body through the use of mushroom mycelia in order to promote environmental stewardship and provoke the psychological structures surrounding cultural death denial . By uncovering the ubiquity of invisible chemical contamination in America and offering a green burial alternative that facilitates a physical transfer of nutrients from a decomposing human body to the soil, her work expands one’s understanding of how human death is linked to vibrant, nonhuman systems. In order to ease a people’s fear of death stoked by super modernity, her work attempts to bridge the dichotomy between “man” and “nature” with her focus on interspecies relationships within the soil. Both artists utilize alienated substances, such as dejecta and decomposing bodies, in order to probe colonial logics and animacy hierarchies that are socially and racially charged. Such matter labeled as “waste” is often steeped in logics of purity and danger that justifies necropolitical classifications of people as valuable or disposable. Residues of human life, ranging from excreta and corpses to industrial toxins and landmines, serve as important reminders of humans’ undeniable entanglement with ecological systems that lie beyond human control. Although these residues are out of sight, and often imperceptible, they are potent reminders of anthropocentric frameworks and heighten the agency and animacy of nonhuman “objects” or systems. In this paper I will show how both artists seek to halt the repetitious calamities caused by humans by transforming substances that are considered taboo –– urine and corpses –– into opportunities for ecological, psychological, and cultural remediation.In 2006, Jun Nguyen Hatsushiba staged Memorial Project Waterfield: The Story of the Stars as a performance installation at the 6th Gwangju Biennale in South Korea with the main intention of turning it into a video performance . The physical performance space was confined to a prison like structure constructed out of 8 meter tall walls that were lined with long metal poles . Visitors could only view the work from an aerial perspective provided by standing on the bridge that overlooks the courtyard and connects the Gwangju Biennale’s two gallery buildings. 26,000 plastic water bottles packed the entire ground surface of the 10 meter wide by 14 meter long space. During the live performances, there were 3 groups of 5 men and women who would alternate shifts every hour. Some performers came from Vietnam in order to assist the artist with training, while the rest of the cast consisted of Korean men and women volunteers aged 18 – 30 years old. These volunteers were cast based on their interest in contemporary art, youthful appearance, and overall good health.During shifts, the performers were tasked with drinking water, urinating into containers, injecting urine into recently emptied bottles, carefully wading through the bottles, and listening to the spontaneous orders of the shift leader to take cover, sit, or lie down .Over the span of about 20 days, these repetitive, carefully orchestrated tasks gradually formed 50 urine colored stars that were each 1 meter wide and constituted the image of the 50 stars on the American Flag hybridized with the yellow star of the Vietnamese flag . This symbolic relationship between the two flags’ stars reflects the entwined historical, cultural, and economic relationships between the US and Vietnam. Nguyen Hatsushiba attributes the chemical destruction of US and Vietnamese ecosystems to militarization and neo liberal capitalism.

Studies in EcoTrons will be increasing in the near future and will provide unprecedented insights into ecosystem functioning; for example, Roscher et al. found that the functional composition of communities is key in explaining carbon assimilation in grasslands. Mesocosms, which we call EcoPODs, are smaller versions of EcoTrons with higher experimental throughput that bridge laboratory and field studies . Existing EcoPODs have a footprint of approximately 2.1 m2 and can be filled with up to 1.23 m3 of soil of 0.8 m in depth . Using the EcoPOD lysimeter technology, intact soil monoliths can be retrieved from the field and studied under controlled conditions in the laboratory. The above ground portion is approximately 1.5 m tall and, therefore, allows the study of a number of different plants in soil with macro and microorganisms in the context of environmental changes. The contained nature of EcoPODs allows accurate mass balance calculations . EcoPODs allow precise conditioning of above and below ground temperature and moisture and, therefore, can simulate seasonal changes and enable short as well as long term experiments. They are equipped with state of the art sensor technology allowing in situ measurements of key environmental parameters,growing vegetables in vertical pvc pipe activities of organisms, and ecosystems at micrometer to meter scales.

EcoPODs can be equipped with multi and hyperspectral cameras that track plant biomass and physiological states. In conjunction with highly controlled physical and chemical conditions, researchers will be able to track the microbial activity within the system using a variety of genomic tools, including DNA or RNA shotgun metagenomics, proteomics, and metabolomics. This will facilitate tracking of microbial recruitment and activity across all life stages of the plant and can simulate seasonal changes. Broadly, this system can be used for fundamental research questions about biogeochemical cycles and the role of biodiversity in ecosystem processes, as well as applied studies that include biological or chemical components that require increased safety clearance and cannot be easily tested in the field. Because soil ecosystem and phytobiome experiments increasingly rely on in situ sensing over time, EcoPODs can also serve as a test bed for novel and improved sensing capabilities. Complimenting approaches to develop more field relevant laboratory growth systems are composed of one or more single plant chambers such as RootChips , GLO ROOT , EcoFAB , and other systems that enable detailed characterization. For example, RootChips systems provide a high throughput system for rhizosphere imaging, the GLO ROOT systems enable direct imaging of root architecture within soils, and EcoFABs are “fabricated ecosystems” that are aimed at creating model ecosystems on par with the model organisms used for genetic and biological studies. EcoFABs comprise a chamber, biological and abiotic components , and any measurement technologies .

EcoFABs allow real time microscopy for high resolution imaging of plant root architecture and are currently designed to provide sufficient materials for metabolomic, geochemical, and sequence based analyses. They are made using widely accessible 3D printing technologies to fabricate controlled microbiome habitats that can be standardized and easily disseminated between labs . This approach provides flexibility that enables scientists to add or change variables while monitoring microorganisms and their interaction with plants.EcoFABs are also envisioned to facilitate standardization of phytobiome research because construction materials are cheap and construction instructions are available . Analogous to medical drug testing pipelines, which generally begin as high throughput laboratory screens and are gradually scaled up to relevant mammal models and, finally, to human clinical trials, we envision phytobiome research studies to similarly follow a throughput versus relevance gradient from EcoFABs to EcoPODs and, finally, to field studies . Although this suite of fabricated ecosystems is not aimed at simulating the real world, the enhanced control over abiotic and biotic factors in these experimental platforms enables plant root microbiome interaction studies that are not possible in field experiments because fields generally display greater complexity and unpredictability or do not allow for manipulations. Thus, use of fabricated ecosystems can reveal important correlations and causations of individual metabolic reactions as well as biogeochemical cycles. Challenges that have been encountered or are foreseeable include the relatively short experimental durations that can be executed in EcoFABs as well as EcoPODs due to the size limitations of the respective platforms and because of potential increases in parasite pressure as a result of air and water flow limitations.

On the other hand, EcoTrons are not set up for quick turnover experiments and require expensive infrastructure to start and end experiments. Although insights obtained from greenhouse experiments have often not been replicable in the field, we expect that EcoFAB can serve as a reproducible system, in which microscopy and metabolomics can be applied to low complexity microbiomes in the context of plant roots. Data obtained from individual microorganisms can inform microbially based biogeochemical models, as discussed below. We expect EcoPODs and EcoTrons to facilitate in situ sensing,vertical greenhouse climate manipulations, and deep soil monolith access. Links and extrapolations among fabricated ecosystems and the field can be achieved by generating and testing hypotheses across platform scales. For example, field observations may be tested under replicable conditions in EcoTron or EcoPOD and promising microbial candidates could be isolated and further studied in EcoFABs. A reverse workflow is also imaginable, where promising microbial isolates or plants resulting from EcoFAB experiments may be tested in EcoPOD or EcoTron before being potentially released into field experiments. Furthermore, extrapolations could be testable beforehand by taking advantage of archived datasets from sources such as long term observatories, including Neon . Generally, challenges for extrapolating results of these fabricated ecosystems to realistic field conditions could be presented by the limited complexity in these laboratory systems; for example microbial isolates often perform predictably under laboratory conditions but may be inactivated by night temperatures or competitors. There is still a number of unknown unknowns which may significantly affect plant performance, microbial community dynamics, and soil nutrient cycling, and which vary from ecosystem to ecosystem, hence resulting in a disconnect between studies conducted in the laboratory versus in the field. Other challenges are presented by natural climate variability in the field and the uncertainty in climate change predictions, which are significantly affected by socioeconomical drivers . Although laboratory experiments may be conducted based on historic field data or even in tandem with real time field data measurements—for example, using sensor platforms coupled to edge computing —results may have limited applicability under future climate scenarios. However, this is also true for reproducibility of field experiments in general. Studying plant microbiome interactions and soil processes under defined conditions can assist in the identification and evaluation of such unknown unknowns which, in turn, will improve applicability of laboratory results to the field.Microbial communities found on healthy plants are incredibly taxonomically diverse and include bacteria, archaea, fungi, oomycetes, algae, protozoa, nematodes, and viruses.

This microbial complexity makes it impossible to definitively establish causal relationships between plant and microbial genotypes and phenotypes as well as environmental factors. Instead, representative synthetic communities of defined complexity enable systematic bottom up approaches in gnotobiotic systems under controlled and reproducible conditions to determine causal relationships . In order to systematically test plant microbial community dynamics and functions in relation to the chemical composition of the surrounding environment, comprehensive strain collections representing the phylogenetic and functional diversity of the plant microbiota have been established thanks to the cultivability of an unexpectedly large fraction of the members of the plant microbiota . This high cultivability of plant associated bacteria is likely based on low complexity food webs, continuous substrate supply by the plant, and an essentially aerobic environment . In addition to cultivation and subsequent whole genome analysis, screening SynComs of various complexity for interactions and metabolic activity in correlation with environmental parameters has been a bottleneck. Microfluidics tools such as massively parallel on chip coalescence of microemulsions enable screening of 100,000 communities per day . For example, bacterial isolates can be screened individually and in combinatory sets as SynComs for various useful properties, including plant growth promoting functions such as suppression of pathogens or degradation of harmful substrates, for their potential in bio fuel production, or as environmental remediation agents. Such tools coupled with high throughput DNA or RNA sequencing and long read sequencing platforms including PacBio and Oxford Nanopore , as well as metabolomics and various activity assays , now allow rapid profiling composition, function, and activity of SynComs as well as complex native microbial communities residing in soils and on plants.The quantity of data generated by the new technologies described above surpasses the capabilities of traditional analysis methods. Nevertheless, to gain insight, we need to integrate and fuse different data streams. To accomplish this, we must overcome the heterogeneous data types and lack of standards for data exchange. Ultimately, we need systems that can dynamically pull in diverse data from different devices and experimental modalities and intelligently interpret it using background knowledge in order to derive new hypotheses or make predictions such as being able to predict the consequences of specific environmental changes on plant health mediated by the microbiome. Machine learning methods and, in particular, deep learning have proven particularly useful for classification problems involving large datasets such as environmental data generated from technologies, including thermal sensing and LiDAR. Supervised ML techniques will learn to classify entities based on vectors of data characteristics, trained from prelabeled data. DL techniques involve the use of multilayer architecture neural networks . Different DL architectures can be applied to different problems. Convolution networks can be applied to image detection and recognition problems , whereas recurrent architectures such as long short term memory can be applied to time series data. One of the challenges of phytobiome data are the paucity of sample data or lack of resolution in imaging and instrumentation. One DL architecture designed to address this is the generative adversarial network . A GAN can generate plausible synthetic data by utilizing two NNs that are trained together in an adversarial scenario—one network attempts to distinguish real examples from fake ones, and the other creates plausible example data to fool the first. Over time, both models improve, and the generated examples become more plausible, reflecting real world characteristics of the domain without the need for explicit encoding of priors. In the context of phytobiome data, GAN could, for instance, help to synthesize and denoise imaging data . Although DL has seen tremendous gains and achieved much over the last decade, there are still a number of challenges. The input data must be in vector form, which is straightforward for sensor data; however, complex biological information must be embedded in a suitable fashion. NNs are famously inscrutable—they do not provide any explanation as to why they produce a particular result. This is particularly problematic in the face of adversarial attacks, in which the NN is deliberately fooled by fake data designed to elicit a misclassification. The burgeoning field of explainable artificial intelligence attempts to use a variety of techniques to make DL decision making less of a black box process. The field of DL and ML has seen a rapid advance in recent years but, in many cases, DL methods may not yield improvements over traditional methods. DL methods are best applied for complex multidimensional data such as imaging data or for predictions involving complex latent nonlinear mechanisms; for example, as found in ecosystem models. Some have successfully applied DL methods to modeling distinct ecosystem parameters such as soil temperature over a soil depth profile , and processes such as ice shelf melting as part of the Energy Exascale Earth System Model . DL methods will also gain importance in microbe enabled soil biogeochemical models that aim to predict links between climate change, elevated CO2 concentrations, plant–microbe interactions, and soil nutrient cycling . For example, the ecosys model allows for the incorporation of microbially based models using traits such as growth rate , optimal temperature , and resulting enzyme activity , as well as genome size. Microbial traits, which can be obtained from genomic data, help to identify and quantify trade offs .

Symbiotic relationships established between plants and bacteria such as rhizobium and some actinomycetes provide most of the nitrogen available to legumes and actinorhizal plant species. A number of studies attempted to develop new association between non legume plants and N fixing bacteria, however, these attempts were mostly unsuccessful . The discovery of endophytic diazotrophs that provided reduced N to the non legume plant species represented an alternative way of exploiting plant microbe interaction for N nutrition. Brazilian sugarcane plants harboring N fixing endophytes were grown for many years with low fertilizer inputs, and showed no symptoms of N deficiencies . Other non leguminosae plant species were also shown to benefit from association with diazotrophic endophytes, such as wheat and rice . Iniguez et al. generated a nifH mutant from Klebsiella pneumoniae and compared this to the wild type strain in order to demonstrate that the wild type K. pneumoniae strain provided N to the wheat plant thus alleviating N deficiency. The wheat plants were supplemented with stable N isotope labeled nutrients.

Mass spectrometry was used to show that less 15N was present in wheat plants inoculated with the wild type K. pneumoniae strain. Since these plants obtained a higher percentage of their N from nonisotopically labeled atmospheric N2,vertical home farming the majority of the plant nitrogen was derived from the wild type strain. In a different study, the transcript abundance of the nifH gene was measured by RT PCR in endophytic Herbaspirillum sp. during colonization of internal regions of wild rice plants . Interestingly, they showed higher nifH transcript abundance during the light period compared to the dark period. Given the tight relationship between N fixing activity and nifH gene transcription, the high level of nifH mRNA during the light period indicated that the endophytes produced higher level of reduced N at a time when they could benefit most from photosynthate production. This study described a promising avenue for non legume plants to obtain N from the reduction of atmospheric N2. It remains to be seen that similar results are achievable with soil grown plants or in the field where plants may be less limited for growth than in sand filled pots. In addition, competition from other bacteria may prevent colonization by endophytic diazotroph. Plant genetic contribution to this symbiosis is an important area of research leading to selection of agriculturally important plant genotypes with increased capacity to establish symbiosis for nutrient acquisition. Several studies have begun to pave the way in this area.

The identification of genetic loci underlying complex traits in Lotus spp and Medicago led to the sequencing of specific genes essential for the establishment of root symbiosis. Kistner et al. characterized seven mutants of Lotus japonicus that were impaired in nodulation and were also defective in arbuscular mycorrhiza formation. Kanamori et al. used a F2 mapping population established by crossing the Lotus japonicus mutant and wild type for positional cloning of a gene essential for symbiosis that encoded a plant nucleoporin gene required for Ca2+ spiking occurring after contact between Nod factor molecules and root hair cells. The combination of genetic and genomic analysis resulted in a deeper understanding of the plant genetic contribution to the establishment of symbiosis with rhizosphere bacteria. One drawback of this approach is that it may take many years, from the identification of the genetic basis for complex traits to the development of new cultivars with enhanced capacity for establishing and maintaining symbiosis. Rhizosphere bacteria and phyllosphere colonizing epiphytes have been shown to produce a range of plant growth stimulating phytohormones. A recent study by Boiero et al. evaluated the phytohormone synthesis of three commercially available strains of Bradyrhizobium japonicum grown in pure culture. They showed that the three strains have differential capability to produce the five major phytohormones: auxins, cytokinins, gibberellic acid , abscisic acid and ethylene. This is important to consider as each individual and combinations of phytohormones may have different impact on plant growth.

The auxin compound indole 3 acetic acid can be generated in bacteria through different biosynthetic pathways . Saravanan et al. reviewed the roles in plant growth promotion of two N fixing organisms, Gluconacetobacter diazotrophicus and an Acetobacteraceae strain. In particular they discussed additional roles for G. diazotrophicus, including the production of plant hormones such as IAA, and gibberellins. Idris et al. showed for the first time that the gram positive bacterium Bacillus amyloliquefaciens produced and secreted significant amounts of IAA. They also showed the positive effect of IAA on the growth of Lemna minor. Patten and Glick demonstrated the direct positive effect of IAA produced by Pseudomonas putida through the indolepyruvic acid pathway, on root development. Roots from Canola seeds treated with the wild type P. putida were longer in length than that of seeds treated with an IAA deficient mutant. However, the bacterial production of IAA may not always be beneficial for plant as it is involved in pathogenesis and that high concentration of IAA can also inhibit root cell growth . Ethylene has many physiological effects on plant growth, development and modulation of responses to biotic and abiotic stresses. Bacteria such as Pseudomonas spp., Burkholderia caryophylli, Achromobacter piechaudii were shown to lower the endogenous ethylene level in planta by producing a degradative enzyme 1 aminocyclopropane 1 carboxylic acid deaminase . The effects of ACC deaminase producing rhizobacteria on plants included increased root growth,vertical growers and improved tolerance of salt and water stress . These effects were noted in axenic conditions and more recently in field conditions. Inoculation of wheat plants with Pseudomonas spp. and B. caryophylli improved grain and straw yield by as much as 43% and 44%, respectively . However no measurements of ethylene concentration were carried out on plants in pots or in the field to show direct correlation of ACC deaminase production and ethylene degradation. It is therefore possible that other bacteria associated effects might have improved wheat plant growth. Cytokinins constitute a group of plant hormones that promote cell division in conjunction with auxin and are known to induce stomata opening. Rhizosphere bacteria and fungi associated with plants were shown to produce cytokinins. Arkhipova et al. studied the production of different cytokinins by Bacillus subtilis and showed improved growth for lettuce plants after inoculation with cytokin in producing bacteria. This was also the case when plants were grown under water stress . The authors mainly considered the production of cytokinins by B. subtilis as mechanism of plant production.

It would be interesting to investigate possible alternative mechanism by which this species is able to promote plant growth. Lettuce plants were grown in sand and the study did not address whether similar results could be obtained in the field where competition from other rhizosphere bacteria might prevent B. subtilis growth and where bacterial production of other phytohormones might interfere with the effect of cytokinins. The modulation of phytohormone by bacteria that lead to disease resistance is addressed in the Biocontrol section. Plant growth promoting bacteria have been shown to positively impact plant performance through different mechanisms. For future development of commercial inoculant, it is therefore important to consider all potential metabolic activity of the phytohormone producing bacteria. In addition, components of the inoculant growth media could be transformed into metabolites that could impact plant growth in the early stages of plant development . For successful application of plant growth promotion using bacterial inoculant, many aspects of the plant environment have to be considered in the field. In particular, it is important that the inoculant be beneficial to the crop, and do not improve the growth of the weedy species and do not render the plants more susceptible to biotic and abiotic stresses.Further development of plant growth promoting bacteria could benefit from selection, through breeding programs of plant genotypes that respond better to the plant growth promoting bacteria. The efficiency of bio control agents for plant disease has been demonstrated and some are commercially available . General mechanisms of action for plant pathogen control include competition for nutrients and space at the infection site, antibiosis, parasitism, production of cell wall degrading enzymes, induced resistance in the plant, and manipulation of bacterial signaling molecules. It is likely that several mechanisms of action are at work in many bio control agents. Compant et al. reviews the mechanisms of plant disease bio control by plant growth promoting bacteria. Here, we discuss two mechanisms of disease control: induced resistance and manipulation of signaling molecules. Interactions with bacteria can induce two types of plant defense responses that help protect against further infection. Systemic acquired resistance is a specific response that triggers both a local increase in phytohormone accumulation and the formation of phloem mobile signal. Non pathogenic free living rhizosphere bacteria and endophytes can trigger the second type of plant defense called induced systemic resistance . A major distinction between SAR and ISR is the involvement of salicylic acid , with ISR being activated via a SA independent pathway. One example of plant disease control is the use of Pseudomonas strains with biocontrol activity to induce resistance in appleagainst the pathogenic fungus Venturia inaequalis , which causes apple scab. The movement of Pseudomonas on apple leaves was studied in order to understand its antagonistic interactions against V. inaequalis . Using confocal laser scanning microscopy , it was demonstrated that P. fluorescens Bk3 localized near stomatal openings. The P. fluorescens Bk3 traversed the cuticle through secretion of cutinases, and acquired nutrient from fluid isolated from the apoplastic space. Also, isolated leaf cuticles stimulated bacterial extracellular proteins . In order to understand the interaction between the V. inaequalis and apple tree, cDNA libraries using suppression subtractive hybridization were constructed for the resistant and susceptible cultivars . Many plant defense related transcripts such as those encoding for β 1,3 glucanase, cystein protease inhibitor and metallothioneins were at higher levels in the resistant cultivar. On the other hand, more RuBisCo transcripts were found in the susceptible cultivar than in the resistant one. Similar proteins were expressed in apple trees treated with the bio control strain P. fluorescens Bk3 and V. inaequalis . The presence of P. fluorescens Bk3 was demonstrated to elevate the defense mechanisms in the apple trees and could serve as effective bio control strategy. The authors implied that low levels of RuBisCo and high levels of metallothioneins resembled that of “old leaves” and were “unattractive” to V. inaequalis . The authors did not investigate whether P. fluorescens Bk3 induced SAR or ISR type of plant resistance. Some bacteria rely on signaling molecules for the development of pathogenesis. Other microbes living in the same environment may degrade these signaling molecules. Recombinant bio control strains producing carAB, genes required for degradation of a fatty acid signaling molecule, were shown to reduce virulence caused by Xanthomonas sp. and Xylella fastidiosa . Secondary metabolites produced by plants were shown to mimic or inhibit quorum sensing molecules. M. truncatula was shown to produce more than a dozen compounds that stimulated or inhibited QS . Plants have been manipulated to produce molecules that mimic or block QS signal, and enzymes that degrade QS molecules or quorum quenching strategy. Scott et al. engineered tobacco plants to synthesize acyl homoserine lactones in the chloroplast and demonstrated that AHL was transported and secreted on the phyllosphere and in the rhizosphere. Pre treatment of potato slices with Bacillus thuriensis resulted in reduced maceration from Erwinia carotovora virulence . The authors showed that the decreased pathogenesis involved the disruption of E. carotovora quorum sensing by deterioration of QS molecules with AHL lactonase. Pre treatment of potato slices with B. thuriensis lacking the ability to produce AHLlactonase did not reduce maceration. Manipulating plants to express AHL lactonase has shown positive effect in protecting plants against pathogens . Recently, a gene called qsdA from Rhodococcus erythropolis, encoding a new type of AHL lactonase has been characterized. The gene was able to confer quorum quenching capacity to P. fluorescens that led to enhanced protection of potato tuber against the soft rot pathogen P. carotovorum . Elucidating the mechanism by which bacteria elicit ISR is important for the development of commercial bio control agent.

Furthermore, UA policy in the U.S. remains largely agnostic about the sustainability of production practices and their impact on the environment. While U.S. agriculture policy narrowly focuses on the production, distribution and marketing potential of UA, broader discussion of its activities and goals proliferate among food systems scholars from a range of fields including geography, urban planning, sociology, nutrition, and environmental studies. These scholars are quick to point out that UA is much more than production and marketing of food in the city, and includes important justice elements . In the Bay Area context, we continue to see the result of this dichotomy: thriving urban farms lose their leases , struggle to maintain profitability or even viability and encounter difficulties creating monetary value out of their social enterprises. In light of the ongoing challenge to secure longevity of UA in the United States, there is a need for an alternative framework through which food and farming justice advocates can better understand and articulate what UA is, and why it matters in cities.Agroecology is defined as “the application of ecological principles to the study, design and management of agroecosystems that are both productive and natural resource conserving, culturally sensitive, socially just and economically viable” ,vertical gardening in greenhouse and presents itself as a viable alternative to productivist forms of agriculture.

Agroecology in its most expansive form coalesces the social, ecological, and political elements of growing food in a manner that directly confronts the dominant industrial food system paradigm, and explicitly seeks to “transform food and agriculture systems, addressing the root causes of problems in an integrated way and providing holistic and long term solutions” . It is simultaneously a set of ecological farming practices and a method of inquiry, and, recently, a framework for urban policymaking ; “a practice, a science and a social movement” . Agroecology has strong historical ties to the international peasant rights movement La Via Campesina’s food sovereignty concept, and a rural livelihoods approach to agriculture where knowledge is created through non hegemonic forms of information exchange, i.e. farmer to farmer networks . Mendez et al. describe the vast diversity of agroecological perspectives in the literature as “agroecologies” and encourage future work that is characterized by a transdisciplinary, participatory and action oriented approach. In 2015, a global gathering of social movements convened at the International Forum of Agroecology in Selengue, Mali to define a common, grassroots vision for the concept, building on earlier gatherings in 2006 and 2007 to define food sovereignty and agrarian reform. The declaration represents the views of small scale food producers, landless rural workers, indigenous peoples and urban communities alike, affirming that “Agroecology is not a mere set of technologies or production practices” and that “Agroecology is political; it requires us to challenge and transform structures of power in society” .

The declaration goes on to outline the bottom up strategies being employed to build, defend and strengthen agroecology, including policies such as democratized planning processes, knowledge sharing, recognizing the central role of women, building local economies and alliances, protecting biodiversity and genetic resources, tackling and adapting to climate change, and fighting corporate cooptation of agroecology. Recently, scholars have begun exploring agroecology in the urban context. In 2017, scholars from around the world collaborated on an issue of the Urban Agriculture magazine titled “Urban Agroecology,” conceptualizing the field both in theory and through practical examples of city initiatives, urban policies, citizen activism, and social movements. In this compendium, Van Dyck et al. describe urban agroecology as “a stepping stone to collectively think and act upon food system knowledge production, access to healthy and culturally appropriate food, decent living conditions for food producers and the cultivation of living soils and biodiversity, all at once.” Drawing from examples across Europe, Africa, Latin America and Asia and the United States, the editors observe that urban agroecology “is a practice which  while it could be similar to many ‘urban agricultural’ initiatives born out of the desire to re build community ties and sustainable food systems, has gone a step further: it has clearly positioned itself in ecological, social and political terms.” . Urban agroecology takes into account urban governance as a transformative process and follows from the re emergence of food on the urban policy agenda in the past 5 -10 years.

However, it requires further conceptual development. Some common approaches in rural agroecology do not necessarily align with urban settings, where regenerative soil processes may require attention to industrial contamination. In other cases, the urban context provides “specific knowledge, resources and capacities which may be lacking in rural settings such as shorter direct marketing channels, greater possibility for producer consumer relations, participatory approaches in labour mobilisation and certification, and initiatives in the area of solidarity economy” . Focusing on the social and political dimensions of agroecology, Altieri and others have explicitly applied the term “agroecology” to the urban context, calling for the union of urban and rural agrarian food justice and sovereignty struggles . Dehaene et al. speak directly to the revolutionary potential of an agroecological urban food system,greenhouse vertical farming building towards an “emancipatory society” with strong community health and justice outcomes. Our research builds upon this emergent body of work that employs urban agroecology as an entry point into broader policy discussions that can enable transitions to more sustainable and equitable city and regional food systems in the U.S. . This transition in UAE policymaking is already well underway in many European cities . As noted, there are many dimensions of agroecology and ways in which it is conceptualized and applied. We employ the 10 elements of agroecology recently developed by the UN FAO in our discussion of urban agroecology. These 10 elements characterize the key constituents of agroecology including the social, ecological, cultural, and political elements. Despite the emancipatory goals of agroecology, a recent review of the literature by Palomo Campesino et al. found that few papers mention the non ecological elements of agroecology and fewer than 1/3 of the papers directly considered more than 3 of the 10 FAO defined elements. In an effort to help guide the transition to more just and sustainable food and agricultural systems in cities across the U.S., we propose that food system scholars and activists consider using the 10 elements as an analytical tool to both operationalize agroecology, and to systematically assess and communicate not only the ecological, but also the social, cultural and political values of urban agroecology. “By identifying important properties of agroecological systems and approaches, as well as key considerations in developing an enabling environment for agroecology, the 10 Elements [can be] a guide for policymakers, practitioners and stakeholders in planning, managing and evaluating agroecological transitions. In San Francisco’s East Bay region, urban food production proliferates in schoolyards, in half acre lots converted to urban farms, on rooftops, and in backyards reflecting a diversity of participants, goals, impacts and challenges . The San Francisco East Bay region is also experiencing rapid gentrification and a worsening affordable housing crisis coupled with high rates of income inequality and food insecurity. The challenge of urban soil contamination creates trade offs for aspiring growers between vacant lot availability and siting on the most heavily polluted plots . Specific city policies vary in the degree to which they support or discourage urban agricultural activities, and availability of arable land across the East Bay is uneven. Our case study focuses on urban farmers in the East Bay spanning over 28 miles from El Sobrante in the northeastern edge of the bay, to Hayward in the southern East Bay as shown in Figure 1.

We include both for profit and non profit farms ranging from educational school gardens to roof top farms marketing microgreens. We employed a participatory and collaborative mixed methods approach, involving diverse stakeholders from the East Bay Agroecosystem. We held two stakeholder input sessions involving over 40 urban farmers and food advocates to co create the research questions, advise on the data collection process, interpret the results, and prioritize workshop topics for the community. We administered an online Qualtrics survey to 120 urban farms in the East Bay that had been previously identified by the University of California Cooperative Extension Urban Agriculture working group and additional outreach. The survey launched in Summer 2018, which is a particularly busy time for farmers, and in response to farmer feedback was kept open until November 2018. 35 farmers responded in total, representing a 30% response rate. While there are limitations in our ability to generalize findings to the East Bay urban farming landscape as a whole due to the relatively small sample size, we obtained a fairly representative sample of the diversity of farm types in the East Bay based on our typology of the original 120 farm types . Survey questions fell into nine categories: 1) Background Info, 2) Farm Description, 3) Operating Expenses and Revenues, 4) Land Access and Tenure, 5) Production and Soil Health, 6) Distribution, 7) “Waste” and Compost, 8) Food Access, and 9) Training, Communications, and Follow Up. There were a few open ended questions allowing farmers to express what they saw as the three largest challenges facing urban agriculture operations in the area, and policy relevant suggestions for securing spaces for urban farms and increasing community food security. In addition, we interviewed five urban farmers to deepen our understanding of the social, political, economic, and ecological constraints under which their farms operate. These farmers are particularly involved in networking efforts to strengthen urban farm viability in the East Bay. Four out of five represent locally prominent non profit farms and one subject represents an alternative cooperatively run urban farm; three interview subjects are women and two are men. Our study complied with UC Berkeley’s Institutional Review Board protocol for the protection of human subjects and all participants gave consent for participation.Farmers in our study stressed the importance of producing non food related values on their farms, including education and community building. One farmer in particular emphasized their organization’s mission of “growing urban farmers growing food,” or teaching other people how to grow a portion of their food basket, thus unlocking food sovereignty and food literacy while increasing healthy food access. Another respondent reported that their farm is “highly desirable for adults with special needs that need a safe place to be outside,” echoing respondents who point out the intimate connection between food and health. Farms frequently reported hosting educational and community building workshops, cooking and food processing demonstrations, harvest festivals, and other open to the public community events enhancing the resilience and connectivity of people, communities and ecosystems. Social networks emerged as an important theme for enabling the establishment of urban farms , and sustaining operations through social connections between urban farmers and other food justice and health advocates. Farmers identified three primary challenges: revenue, land, and labor inputs. Half of all respondents reported farm earnings of $1,500 annually or less, and all four operations receiving over $250,000 in annual revenue are well funded non profit operations . Regardless of for profit or non profit status, most farms reported multiple sources of revenue as important to their continued operation , with an average of 3 revenue streams per farm. All non profit farms reported multiple revenue streams except for three, who were sustained entirely by either board donations, membership fees , and grants. The most important revenue sources for non profits include grants, grassroots fundraising, and unsolicited donations rather than sales. In addition to these monetary sources, all farms reported receiving substantial non monetary support , which adds to the precarity of operations when these informal support channels disappear.The cost of labor, and relatedly, access to capital and grant funding to pay living wage salaries, were also extremely significant challenges identified by survey respondents. The majority of respondents stated that most of their labor is volunteer rather than paid, with nonprofit respondents reporting this more frequently than for profit enterprises . The maximum number of paid staff at any operation is 20 , while the average is 4. Many farms reported the desire to be able to hire and pay workers more, but not having sufficient revenue to accomplish that goal. Annual volunteer labor participants on farms ranged from 0 to 1542 with an average of 97 volunteers, representing a significant public interest in participating in local food production. Not surprisingly, amount of paid labor and total farm income are positively correlated .

Any one of these factors might drive migration to Israel from Iquitos; together, they are a powerful motivating force. Between 2016 and 2019, I interviewed 52 adult members of the Iquitos Jewish community, a number that, according to the synagogue records, represents all but seven of the adult affiliated members of the synagogue during that time period. In that time, the average age of my respondents dropped from 45 to 38, and almost all the 2016 interviewees made aliyah. Although I interviewed 19 people in 2016 and 35 in 2019, I am sure that these averages represent a notable demographic shift, because during both visits I was assured I had spoken to the majority of adults in the community, having arrived in a habitual lull between the exodus of the recent converts and the entry of prospective converts. I was able to re-interview only three adults in 2019, as all the rest had either died, moved to Lima, or moved to Israel. Notably, in 2016, almost 90% of my interview subjects claimed Moroccan Jewish ancestry, while only half of my 2019 subjects did: the other half were the spouses of community members who did claim descendance. In general, there has been almost complete turnover in Iquitos, and the main body of congregants in 2019 was made up of younger adults, most with children below the age of 13. Individual/community-level dynamics explain this turnover.

Those that I spoke to in 2016 were either old-timers who have practiced all their lives, or in large part,potted blueberries those still dwelling in Iquitos after the 2011 conversion. Encompassing 280 children and adults, 2011 saw the largest conversion in Iquitos, almost three times the size of the conversion of 2018, which included 94. According to the Abramowitzes and my oldest respondent in 2016, who was 76 years old, almost all the converts from 2002 and 2004 made aliyah as outlined in Rabbi Bronstein’s plan. They left behind younger siblings, parents, and in some cases children. “Before 3G [cellphone networks] it was hard to stay in touch because calling was expensive, but by 2009 or around then I think we all had it, and I started calling every week,” said Angélica12, explaining how she used her cellphone to maintain contact with her older sister and eventually niece, who moved to Beersheba in 2003. She was not alone in taking advantage of technology to keep in touch with friends and family in Israel. 33 of my 35 2019 interviewees mentioned using the Internet and/or their cell phones to communicate with past olim. These technological connections make passing information between Iquiteños in Israel and in Peru much faster, cheaper, and easier. Most people use WhatsApp to message and video call, and three families showed me WhatsApp group chats that included members living in both countries, while others told me that it was common practice.

Facebook is another thread connecting the two halves of the community: individuals use Messenger and their personal pages to communicate. Some people do visit in person, especially after a death in the family. In 2016, two young women were visiting Iquitos for that reason, and one in 2019. One man maintained business interests in Iquitos and returned in person every few years to attend to his enterprises. Children will also return to visit their parents while alive: in 2019, the Abramowitzes and two other older individuals informed me that they had received at least one visit from their adult children since those children’s aliyot. Nevertheless, air travel between Israel and Peru is prohibitively expensive for most, so overwhelmingly, modern communications technology permits familial and friendship ties to persist across distance in Iquitos. These transnational ties inspire those who originally stayed behind in Iquitos to become active in the community themselves. Respondents told me that hearing family members’ and friends’ stories of their experiences with Judaism and aliyah inspired them to come to the synagogue to learn for themselves, feel closer to their distant relations, or to seek a new spiritual experience. Those who stayed universally told me that they felt that Judaism fit them or called to them in some way. The most common responses were that respondents valued Judaism’s perceived emphasis on family and education, that it made them feel closer to their family history, and that they appreciated what felt like a personal relationship with God. These responses came in response to my request that they tell me the story of their relationship with Judaism.

As conversion narratives, they may not reflect the actual course of events, but they are very real to their respondents. It also supports Lofland and Stark’s “affective bond” and “intensive interaction” steps, which Snow and Phillips accept as perhaps the most important and universally applicable steps in the model. This part of the narrative demonstrates how commonplace, practical transnational influence blends with a sense of spiritual calling for many Iquiteños. It also indicates that Lofland and Stark’s insistence that converts must sever “extra-cult bonds” , in keeping with general portrayals of conversion as intensely individual, is quite incorrect in this case. Considering that other large portion of my interviewees from 2019 were the spouses of those with Jewish ancestry, some 14 adults, 10 of whom were women, without such bonds, most of my 2019 interviewees would never have entered the synagogue. Once in the synagogue, these young families are educated about Judaism following the syllabus described earlier, which hews closely to the topics of education first suggested by Rabbi Bronstein. Students begin with lessons in elementary Hebrew, using children’s primers,square plastic pot which take place alongside classes taught in Spanish on Jewish history and culture — essentially, Ashkenazi Jewish history and culture. Moroccan Jews or Latin American Jews are not included. When classes in conversational Hebrew and the history of the modern state of Israel are required alongside classes in liturgy, the very syllabus of conversion indicates that Israeliness and Jewishness are the same, and that both those identities have little to do with Iquiteños’ own pasts. Moreover, as each wave of new converts leaves, it reinforces the idea that graduating, if you will, into Jewishness also involves leaving the Diaspora for Israel. Once again, the practical and the religious converge, each necessary to endorse the other.In 2019, 25 of 35 respondents had children under the age of 18 still living in Peru. Universally, those 25 mentioned a desire for their children to “get a Jewish education” and “grow up Jewish.” The best way to do this, they thought, was to allow them to grow up in Israel. Parental concern about children’s Jewish educations, opportunities, and identities if they continue to live in Iquitos are the primary motivating factor I found in adults’ narratives about their migration choices. Most of these children are quite young: only two sets of parents had children above the age of 15. It is indeed difficult to practice Judaism in Iquitos: seven parents told me of their children facing antisemitic taunts from their peers, and every parent mentioned that they had to choose between a higher-quality education at a Catholic school and an inferior one at supposedly secular public schools, which nonetheless often ask students to practice writing via copying prayers. There is only the one synagogue, no access to kosher food, and little in the way of Jewish life for teenagers. “I worry that my daughter will just be confused,” one mother told me. “She comes home singing these Christian songs just as much as she sings the [Jewish] prayers.” In this way, education and religion are tied together. To Iquiteño-Jewish parents, getting a “good education” has as much to do with getting an education that teaches their children how to be good Jews as it does with academic practicalities.

There is no division. If being a good Jew means being in Israel, then it stands to reason that learning to be a good Jew should take place in Israel. Some might consider this mindset purely rationalist, desiring a “better” life for one’s children. I, however, cannot help but see the inseparability of practical education and spiritual education for the parents of Iquitos. The two eighteen-year-olds I interviewed in 2019 were the most candid about the material benefits they expected to receive after migrating.Another felt that his chances of achieving enough stability to financially support his younger siblings would be better working in Tel Aviv than in economically depressed Iquitos.Both also told me that by making aliyah and becoming successful Israeli citizens , they would be proving that they were Jews, something they had felt sure of since they were young children, but which also felt like something that could be taken away from them, whether by the strictures of Iquitos’ Catholic rhythms or by the lack of recognition of their Conservative/Masorti conversions. One, who mentioned acquiring an expedited Orthodox conversion in the military, said that he wanted to be financially successful so that he could meet a Jewish Israeli woman and support her. Even these young adults, then, blended their economic interests and their spirits. However, it is vitally important to note that, although these benefits might accrue to the youngest members of the community, or perhaps their children, they will probably not accrue to the majority of Iquiteño migrants. Being middle-class in Perú is not the same as being middle class in Israel, and the hit migrants take from being unable to speak Hebrew fluently, not being certified in their professions in Israel, and other hindrances, severely hamper them. This is dealt with more thoroughly in the next chapter, but it is clear that in the absence of material benefit, some sort of religious benefit becomes a more convincing argument. When these young adults and young parents with their children migrate, they will not leave behind the rest of their families as earlier waves of converts did. The transnational social field between Israel and Iquitos, which has been self-sustaining for almost two decades, may continue in a diminished way, but it is running out of potential converts, and therefore potential migrants. Sra. Abramowitz does not believe there will be another conversion anytime soon, and does not wish to continue classes aimed at emigration. She wants to build a community, if possible, in Iquitos, though she doubts there are enough people to make it viable long-term. Sr. Abramowitz told me, in his jocular way, “Eventually there simply aren’t any more Levy’s out there in the jungle to find.” Rather than a give-and-take or circular model, the migration dynamic in Iquitos is one of suction, where people leave and do not return. As families reunite in Israel and stay there, and as fewer people with Moroccan-Jewish heritage exist in Iquitos to rediscover their roots, migration to Israel may peter out along with the base community. I could, of course, be incorrect. Perhaps this latest wave will begin to pull more, previously unaffiliated people without Jewish ancestry towards Israel, but there is no evidence of such a dynamic yet. It is inaccurate to describe Iquiteño Jews as solely motivated to convert by practical or religious concerns. Iquiteño Jews are motivated by both practical and religious concerns, and often do not see a difference between the two. Individuals may fall differently on a spectrum between material and religious interests, but all exhibit at least some blending behaviors. Because of this blending, the choice to emigrate is often seen as simply a part of the choice to convert. This fusion is a result of early state/institutional-level influence on the Iquitos congregation in a global atmosphere that has all the hallmarks of standard migration. Given a situation that is ripe for migration in general, and offered a way of learning Judaism that emphasizes the role of Israel and once even required aliyah, it is unsurprising that recent converts continue to migrate to Israel at such a high rate. This transnational activity is both a sign of and a reason for the changes to Iquiteño self-identification as Jews and as members of a diaspora.

Through the view of agricultural systems as ecosystems, agroecology combines these disciplines and has subsequently incorporated further disciplines of cultural, human, and social sciences in a wider systems approach. It has existed as an explicit concept since the 1930s, evolving through the 1970s by increasing awareness of practices, focusing on indigenous knowledge and emerging social movements. These tenets position agroecological paradigms as both an alternative to chemical, mono-cultural or industrial farming, and as a catalyst for conventional agriculture to adopt more sustainable approaches. Agroecological systems are considered to be built on the principles of natural ecosystems and are seen as multifunctional and functionally integrated systems of complementary and dynamic relations between livingorganisms and their environments. In Table 1, some well-explored key characteristics related to agroecology are listed. The functions of natural ecosystems, in terms of energy and nutrient flow, as well as the dynamics of adjusting and being resilient to constantly changing surroundings and regulating populations,dutch bucket for tomatoes clearly are different from an agroecosystem.

The latter are altered by and reacting to human dominance, or at a more extreme end, are disconnected or isolated from pre-existing energy and nutrient flows. Over the past decades, many academic agroecologists have increasingly stressed the importance of considering the human and social systems as integrated parts of the agroecological system. Building complex systems involves extensive human knowledge, experience, and community collaboration. Blay-Palmer and co-authors point to how the benefits of sharing place-based knowledge and good practices can help in joining forces for transforming food systems at a wider scale. The scale of an agroecological system can be large or small, but the scope of agroecological farming activities is wide; the majority of the population of smaller-scale family farmers are often considered to be applying agroecological farming approaches, and are currently estimated to produce food nourishing 50–70% of the global population, and supply up to 80% of the food in Sub-saharan Africa and Asia. With regard to human livelihood and scale related to agroecological systems, Walter Goldschmidt found that rural communities with more, smaller farms saw higher human well being than those with fewer, larger farms in settings of North-American farming in the middle of last century. This has been questioned by modernist scholars, but has also seen numerous studies supporting its conclusions over time, and it certainly has never been strongly refuted. As the example above on research in New York’s Chinatown produce economy showed, the diversity of production was found directly related to the proximity of supply and lower cost of healthy food.

Another argument for how the resilience of an agroecosystem includes environmental elements as well as social and institutional elements is raised by Gonzales De Molina who refers to Holling, Berkes, and Folke and Holt-Giménez : “The resilience of an agroecosystem does not depend solely on its productive arrangements. State institutions, responsible for managing natural and socioeconomic disasters, can create favorable or adverse conditions for the recovery of the productive capacity of an agroecosystem. In this respect, there are institutions that favor the resilience of an agroecosystem more than others. In contrast to private or simply state property, communal forms of ownership, characteristic of traditional rural cultures, result in management approaches that adapt more easily to surprises or changes experienced by ecosystems.”This emphasis on institutions and the resilience dimension suggests stronger links between agroecology and fundamental environmental, ethical, political, and governance related questions and issues about the right and access to land and other natural resources and ecosystem services, such as water, soil, forests, and pollinators. It also underlines the importance of wider disciplinary and practical perspectives, such as landscape agroecology and the process of landscape planning in rural as well as linked rural–urban settings. Wezel and co-authors emphasize the relevance of working with “agroecology territories” in a more holistic framework combining sustainable agriculture and food systems as well as addressing biodiversity conservation, as places actively engaging in transition to sustainable farming and food systems.The agroecosystem concept and the science of agroecology provide a foundation for examining and understanding the interactions and relationships among the diverse components of the food system. 

How can a food system be characterized as agroecological? There is a clear and undisputable link between how food is produced and how it goes into the food system. Stassart and co-authors emphasized ways in which agroecological systems could expand to a broader level, suggesting greater valorization of agrobiodiversity and the underlying diversity of knowledge found in both farming and food system, while providing broader perspectives of agroecology both in farming and food systems. Logically, food cannot be claimed to be “sustainable,” even when being produced in a “sustainable way,” if it feeds into and contributes to food systems which are fundamentally unsustainable, for example, are contradicted by the use of huge amounts of fossil fuels or packaging material, or increase social inequity, or are wasteful of other tangible and intangible resources.The linkages between agroecology and food sovereignty receive wide acknowledgement and detailed explanation by agroecological and food sovereignty movements , viewing agroecology as a major catalyst for enabling the realization of the agrarian reform called for by the food sovereignty movements. These movements focus upon principles of low-input use, resilience,blueberry grow pot sustainability as well as its prioritization of smallholders or peasant farmers. Food sovereignty and agroecology are also strongly united through their agency for and common defense of what are claimed as the common inheritances of humanity in terms of natural resources. Altieri and Nicholls demonstrate how different dimensions of sovereignty including food, energy, and technological sovereignties are all critical to agroecology and contribute to its resiliency. Table 1 suggests how linkages between key features of agroecology on a wider scale can be brought into important functions and structures of entire food systems. Multi-functionality and resilience are highlighted by numerous agroecological scholars and address agroecological systems’ capacities and aims. These scholars assess system properties such as ability to absorb shocks, and other inherent capacities to undergo relevant transformations, transitions, and processes of stabilization under changing and new conditions through feedback loops and iterative development processes. Resilience is a relevant key concept which potentially informs the design and maintenance of an agroecological food system, which can build upon local structures of markets, linking reciprocal flows, for example, between urban and rural landscapes, preserving food cultures and nourishment, and opening new possibilities for processing, storing, and retailing. In an agroeco logical farming system, “health” is crucial at all levels of the system. This holistic understanding of health and the importance of maintaining a high-immunitylevel is also relevant for food systems, where the juxtaposition of feedback loops, like immune system response, are imagined to help regulate the resource flows and stimulate the social connectedness in the food system, and emphasize the nourishment aspect of the food which is produced, exchanged and eaten in the food system.Potentials in the agriculture and food systems that link urban and rural areas need to be maximized as a normal part of a balanced development process. 

In this article, we understand a city-region context for food systems as a landscape which includes rural, urban, and peri-urban areas, the two latter varying from a few thousand persons to many million people , which of course will call for widely different place-based and context relevant solutions. The increasing and partly unplanned urbanization has led to significant changes in diets, consumption patterns, and food trade , and in many urban areas, food markets are detached from local or domestic food production. In addition,huge amounts of so-called waste are produced, both in terms of food waste from processing and ensuring availability of a wide range of food at all times for eaters, as well as waste based on non-renewable resources. The fact that we talk about “waste” underlines the detachment from food production and farming, soil management, animal keeping, and resource cycles which were not present just 100 years ago These issues are addressed by the first two points in Table 1, which are strongly interlinked and enforce minimal external inputs and recycling of resources and biomass. In a city-region context, this clearly calls for a reorganization of resource cycles and avoidance of losses of energy, water, and nutrients in a combined rural–urban landscape. Where the linkages between rural and urban areas in some cases are facilitated by local governance systems in terms of markets linking, for example, smallholder farmers with urban markets , creation of full resource cycles including, for examples, compost material from cities to the soil and the rural areas, seem to be rarely addressed. Such cycles could involve human food waste being converted into animal feed and compost, energy in terms of biofuels produced from what normally would be considered as organic waste, minimization of plastic and packaging, and systems involving human urine and feces being composted and/or recycled in safe and responsible ways. Indeed, such agro-waste-recycling systems enabled Paris to rely on its local foodshed for over 1,000 years. The system boundaries in a city-region food system cannot be clearly defined, and a “completely closed food system” would be unlikely, even a contextualized food system, shaped, and iteratively co-created by multiple involved actors, and based on recycling and closed loops principles. Referring to the four-dimensional sustainability concept including environmental, social, economic, and institutional levels, as described by Valentin and Spangenberg , Spangenberg and FAO , an agroecological food system in a city-region context will consist of a complex web of smaller food systems, for example, involving CSAs, urban, and peri-urban farming and a number of different supply chains and levels of organization, which interact and overlap internally as well as with surrounding landscapes and food systems. Most likely, products from other geographic and climatic zones, for example, coffee and spices, will be involved, and inclusion of surrounding marine or other landscape elements further blur apparently clear systems boundaries. Furthermore, vulnerability to local shocks raises the general idea of crisis-preparedness and will always call for a certain ability of all food systems to step in and assist others, in case of failing harvests or natural disasters, and make wider connections between food systems desirable. Trade and transport between different food systems can be organized in ways which are equitable and environmentally not burdening, and can supplement local food systems rather than displace local produce. These aspects need to be considered if the aims and characteristics of agroecological food systems are to be taken seriously. Mendéz and co-authors discussed transformative agroecology and stated that agroecology is explicitly committed to a more just and sustainable future by reshaping power relations from farm to table. In our contextualiza tion of agroecological food systems, we see the need to explore how the food system can be connected in whole cycles, that is, from table to farm as well. As mentioned above, Gliessman discusses what “our food system” would look like, if transformed so that it follows the basic thinking of agroecology. This is envisioned as the unfolding across five potential levels of transformation, where the first three address agroecosystem changes, and levels four and five target formation of more local and global food systems, respectively. Level four targets the local level food systems and creation of the above mentioned “food citizenship,” where food is grounded in a direct relationship between eaters and growers. Level 5, however, targets a wider change: “… build a new global food system, based on equity, participation, democracy, and justice, that is not only sustainable, but helps restore and protects earth’s life support systems upon which we all depend”. This vision for integrating webs of different food systems – whilst emphasizing the importance of fairness throughout the systems – becomes of high relevance in complex and multifunctional city-region food systems.There is much evidence of severe negative long-term environmental and social effects of our current globalized food system, for example, the feed and livestock production as one example. The ideas of agroecological food systems present alternatives to this, among others by contributing to local economic and resource circulation and inclusive, equitable food systems. Such systems should perhaps be described as “socio-agroecological food systems,” emphasizing the closely woven social, agroecological, and ecological interactions, for example, in terms of networks involving both farmers and non-farmers and between actors in the regions, no matter whether we talk ecological or political zones.

Based on this finding, and on the conclusions drawn from the data presented in Figures 3.1-3.3, it is likely that removal of these compounds was not markedly influenced by seasonal fluctuations in temperature or weather patterns and was more dependent on availability of sediment bindings sites, degradation in the sediment compartment, and, in the case of fipronil, rate of plant uptake. Sediment microorganisms responsible for biotic degradation likely appeared to be unaffected by seasonal temperature variations because temperatures are relatively high year-round in Southern California. In addition, the emergent macrophytes present in the PCW experience rampant growth due to the constant availability of nutrients in the Santa Ana River water. Therefore, aquatic macrophytes were always available for plant uptake and subsequent transformation of fipronil. In addition to concentration removal, another important metric for ascertaining the efficacy of the PCW is the mass flux of fiproles and pyrethroids. In particular, mass influx, mass efflux,nft hydroponic and change in mass flux were calculated from the chemical concentrations and water flow rates.

Fipronil, bifenthrin, and cyfluthrin were imported into the PCW at the highest rates, with mean mass influxes of 115-12700 mg d- 1 , 2.37-701 mg d-1, and 100-6090 mg d-1, respectively. Fipronil desulfinyl ,fipronil sulfide , and fipronil sulfone exhibited much lower import rates into the wetland. Changes in mass flux, which represents the net import or export of chemicals to or from the PCW, were also the highest for fipronil , bifenthrin , and cyfluthrin. The majority of changes in mass flux for these three compounds were statistically significant. In contrast, only one of the changes in mass flux values was statistically significant for fipronil desulfinyl , fipronil sulfide , and fipronil sulfone since the difference between the mass influxes and effluxes for these compounds was much smaller. Negative changes in mass flux values were found for fipronil and cyfluthrin in the months of November and December 2018, though only two of these four measurements were statistically significant. However, the export of these compounds during this time corresponded to higher outflow than inflow for the PCW , which likely resulted in resuspension of sediment particles as evidenced by the negative sedimentation rates observed during these two months. The flow of water through the entire Prado wetlands is regulated to optimize water quality and quantity, which leads to occasional net outflow from certain wetland cells, as was the case for the PCW in November and December 2018. Therefore, although net mass export of fipronil and cyfluthrin occurred during this time, it was compensated for by the high volume of water exiting the PCW, as indicated by the positive concentration removal values. 

Although no outflow, mass efflux, or change in mass flux values could be calculated for January 2019, it is important to mention that the rainfall that occurred during this month resulted in spikes of chemical mass influx and possibly additional resuspension of contaminated sediment particles. However, positive removal values again showed that dilution prevented an increase in outlet concentrations. To further highlight the importance of adsorption in the removal of fiproles and pyrethroids by the PCW, the relative presence of each compound on TSS obtained from water samples was calculated. With two exceptions, the % of each chemical on TSS at the wetland inlet was statistically similar to the outlet value. In August 2018, an average of 87.7% of the bifenthrin in the whole water sample was associated with TSS at the inlet, as compared to 100% at the outlet. In contrast, values decreased from 92.1% at the inlet to 71.9% at the outlet for cyfluthrin in December 2018. In addition, inlet, midpoint, and outlet values were anomalously low for fipronil and cyfluthrin in July 2018. It is likely that some cyfluthrin was associated with dissolved organic matter and included in the aqueous phase concentration. The lower values for fiproles may be attributed to their moderate hydrophobicity as compared to the pyrethroids. The overall results suggested that the fractions of these compounds on TSS were similar throughout the PCW and were also similar over time, with inlet and outlet values ranging from 60-100%.

Combined with the evidence for the importance of sediment binding in the removal of pyrethroids and fiproles, it may be concluded that adsorption to suspended particles and subsequent sedimentation was likely a dominant process governing the fate and transport of these contaminants in CW systems. Linear regression was carried out to identify additional factors contributing to the removal of fiproles and pyrethroids in the PCW. Two dependent variables, concentration-based removal and change in mass flux, and three independent variables, sedimentation rate, water pH, and water temperature, were considered. Statistically significant linear relationships were observed between fipronil removal and water pH , between change in fipronil mass flux and sedimentation rate ,nft system and between change in cyfluthrin mass flux and sedimentation rate. These results demonstrate that water pH and water temperature had minimal impact on the removal of fiproles and pyrethroids in the PCW, with the exception of the influence of water pH on the concentration-based removal of fipronil. This finding may emphasize the importance of pH in determining the ionization state of fipronil and hence its adsorption onto sediment particles under field conditions. In addition, the effect of sedimentation rate on the changes in mass flux for fipronil and cyfluthrin—the analytes detected at the highest concentrations and mass influxes— further supports the notion that settling of insecticide-laden particles played a major role in the removal of fiproles and pyrethroids. The evidence provided by this study therefore highlights that settling of contaminated particles and partition into the wetland sediment are crucial in achieving removal of these urban-use insecticides, which is in agreement with findings from an agricultural drainage wetland. Calculated TUs based on the concentrations measured at the PCW inlet and outlet are given in Table 3.4. Sublethal and lethal toxicity values for the amphipod Hyalella azteca were used to determine the change in potential pyrethroid toxicity between inlet and outlet measurements since previous research has demonstrated this organism’s sensitivity to pyrethroids. Mean sublethal bifenthrin TUs decreased from 0.704-19.4 at the inlet to 0-4.91 at the outlet, while mean lethal TUs decreased from 0.302-8.30 to 0- 2.10 at the inlet and outlet, respectively. All decreases were statistically significant except for the month of November 2018 when inlet TUs were relatively low with high variability and outlet TUs were 0 since no bifenthrin was detected. Cyfluthrin mean sublethal TUs were 26.0-240 at the inlet, and decreased to 7.27-68.0 at the outlet. The corresponding mean lethal TUs were 21.5-198 and 6.01-56.1 at the inlet and outlet, respectively. All decreases in cyfluthrin TUs were statistically significant. The midge Chironomus dilutus was selected for the calculation of fiprole TUs since it has been shown to be extremely sensitive to these chemicals. Mean sublethal TUs for fipronil sulfide decreased from 0-0.414 at the inlet to 0-0.00131 at the outlet in a statistically significant manner. Similarly, mean lethal fipronil sulfide TUs underwent statistically significant decreases from 0-0.0592 at the inlet to 0-1.88 x 10-4 at the outlet. Fipronil mean sublethal TUs decreased from 0.984- 11.4 at the inlet to 0.416-2.72 at the outlet, while mean lethal TUs decreased from 0.392- 4.53 at the inlet to 0.166-1.08 at the outlet.

All inlet-outlet comparisons for fipronil were statistically significant except for TUs corresponding to the month of January 2019 when variability in concentrations at the inlet was high. Mean sublethal fipronil sulfone TUs were 0-4.22 at the inlet, decreasing to 0-1.03 at the outlet. Mean lethal TUs for fipronil sulfone were 0-0.312 and 0-0.0761 at the inlet and outlet, respectively. Statistically significant differences for fipronil sulfone were only observed in the months of October 2018, December 2018, and January 2019, but TU values for the other months were all <1 at the inlet and 0 at the outlet. These results showed that removal of fiproles and pyrethroids by the PCW resulted in toxicity reductions for all urban-use insecticides, and the reductions were statistically significant in most instances. The TU values reported in this study represent hypothetical worst-case single chemical exposure scenarios for the most sensitive aquatic invertebrates. Furthermore, the TU values were derived from whole water concentrations and did not take into account bio-available concentrations. For pyrethroids, studies have shown that bio-availability in whole water and sediment is inhibited by DOM or organic matter. Therefore, it is likely that the TU values in this study overestimated the actual toxicity and would serve as a conservative assessment. The influence of bio-availability on fiproles should be less significant given their moderate hydrophobicity. Moreover, the TUs calculated from PCW data do not represent the Prado Wetlands as a whole, since it is composed of many interconnected ponds operating in series. The effluent from the PCW undergoes dilution as it recombines with additional treated water emanating from adjacent wetland cells, is subjected to further treatment, and is ultimately deposited into Chino Creek. As a result, the TU values for the entire treatment chain would very likely be further reduced. Constructed wetlands are a promising option for the treatment of water containing hydrophobic organic contaminants such as fiproles and pyrethroids. There is a great deal of evidence in the literature demonstrating the efficacy of CWs in the removal of nitrogen species, phosphorous species, metals, antibiotic resistance genes, total suspended solids , biological oxygen demand, and chemical oxygen demand. CWs of various designs have been studied, and it is clear that treatment is typically facilitated by some combination of abiotic degradation, microbial degradation, sorption, and phytoremediation, depending on the treatment endpoint. Existing data regarding select organic contaminants have demonstrated that CWs are effective in their removal , but detailed mechanistic information is largely lacking for many important classes of organic pollutants. There is evidence that sediment sorption and subsequent degradation is vital for removal of HOCs , and plant uptake appears to play a role as well. However, differences in HOC removal efficiency and the mechanisms responsible among CW types and configurations is not well understood, which prevents comprehension of the optimal conditions for their treatment. Unit process CWs are designed to facilitate treatment of a particular endpoint or set of endpoints by encouraging specific physical, chemical, and/or biological processes. Unit processes include open water cells, macrophyte-dominated wetland cells, and bivalve filtration wetland cells. These unit processes encourage degradation of their target contaminants via the following mechanisms: direct photolysis, indirect photolysis, sorption, and biotransformation in open water cells; denitrification, metal sulfide precipitation, plant-derived carbon biotransformation, and peat sorption in macrophyte-dominated wetland cells; and pathogen ingestion, particle-associated contaminant ingestion, and inactivation or transformation of ingested contaminants in bivalve filtration wetland cells. Some water treatment initiatives seek to leverage the unit process concept by installing distinct unit process cells in series to remove several classes of contaminants, allowing for optimization of CW size and isolation of necessary physical and chemical conditions. Previous work has demonstrated that unit process open water cells are effective for the removal of pharmaceuticals via photolysis and microbial biodegradation. It is unknown if UPOW cells are similarly effective for removal of HOCs such as fiproles and pyrethroids. To investigate the efficacy of UPOW cells in the removal of HOCs and begin to understand the mechanisms underlying said removal, water and sediment samples were collected from the Prado Wetlands from June 2018-January 2019 and analyzed for fipronil desulfinyl, fipronil sulfide, fipronil, and fipronil sulfone as well as the pyrethroids bifenthrin and cyfluthrin. The primary objectives of this study were to examine the spatial and temporal trends of fiproles and pyrethroids in the water and sediment compartments of a UPOW wetland cell, to calculate the percent removal of each analyte by the wetland as well as their mass fluxes through it, and to measure changes in invertebrate toxic units caused by UPOW treatment. It was hypothesized that sedimentation of contaminated particles and sediment binding would play a major role in the removal of fiproles and pyrethroids by the UPOW cell, causing significant reductions in sensitive aquatic invertebrate toxicity.