Solutes tend to concentrate on surfaces, and thus cells might respond to the higher osmolarity or concentration of particular ions at surfaces. Additionally, bacteria that are situated in biofilms on a surface experience lower oxygen and higher cell density conditions, and might interpret these conditions as location cues. Other modes of surface sensing include responses to physical perturbation of the membrane upon adherence, such as the Cpx two-component system in E. coli , or responding to the increased torque that appendages such as flagella might encounter upon their interaction with surfaces. Thus, it appears that bacteria have a variety of mechanisms with which they can sense surfaces. Different conditions might trigger biosurfactant production in different bacteria, depending on the function of the surfactant to a given species and habitat. However, are there limitations to the tasks a given surfactant can be used for? Although biosurfactant production has been noted for decades, the significance of their different chemical structures is only starting to be appreciated. For instance, it has been found that small changes in peptide components of Bacillus surfactants result in large changes of their anti-fungal and antimicrobial properties. However, as of yet there are no good guidelines on what surfactant structures are appropriate for a given type of bacterial function. This is in contrast to synthetic surfactants, where manufacturers have developed many tools for choosing appropriate surfactant formulations from thousands of synthetic surfactants. One goal of this research is to identify biosurfactants with different physical properties, and determine how these properties affect the biological roles they play to the producing organism. A particularly important property that was focused on in this study is the water solubility of biosurfactants, a proxy for their hydrophilic lipophilic balance HLB. HLB values are a scalar factor that reflects the degree to which a surfactant is hydrophilic or lipophilic, with a value of zero reflecting a completely lipophilic molecule,maceta cuadrada 25 x 25 a value of 10 corresponding to a compound with equivalent hydrophobic and hydrophilic groups, and values over 10 descriptive of predominantly hydrophilic molecules. 

This value is of great significance commercially since it is used to determine appropriate functions of surfactants. For example, common surfactants such as SDS and Tween 20 have high HLB values and are therefore best suited for emulsifying a hydrophobic substance into the water phase. On the other hand, surfactants such as Silwet® L-77 with HLB values near 10 are more suited for wetting, or spreading of a water phase over surfaces such as leaves. At the other end of the spectrum, lipophilic surfactants are best at forming inverseemulsions of water into oil. Although biosurfactants were originally proposed to be used by bacteria to solubilize hydrophobic nutrient sources , by the HLB classification alone it is obvious that only a small subset of biosurfactants would be optimal for this purpose. Biosurfactant producers are common in the environment, with around 10% of culturable bacteria in a given environment readily exhibiting this trait. Given their prevalence, the general field of microbiology will benefit from a better understanding of biosurfactant production. Additionally, in order for humans to best utilize biosurfactants, it should be informative to discover their natural functions which, in turn, might reveal novel applications for these molecules. Biosurfactants have been implicated in a large variety of functions beyond hydrocarbon emulsification. In aqueous environments, bacteria might use surfactants to coat themselves and/or surfaces to alter adherence or deherence. On the other hand, terrestrial surfaces often only harbor thin films of water; bacteria in such habitats often experience water stress and suffer from low diffusional nutrient fluxes. In this circumstance, biosurfactants might prevent evaporation or act as osmotic agents, thus maintaining thicker water films, relieving water stress and increasing microbial access to nutrients. Their ability to lower the surface tension of water has been implicated in promoting aerial hyphal growth , while their emulsification properties might enable delivery of antagonistic compounds. Because biosurfactants are amphiphilic, they can insert into membranes, and some surfactants have thus been noted for their potent membrane disrupting and resultant antimicrobial properties. 

Biosurfactants appear essential for biofilm formation in some bacteria , while they appear to prevent biofilm formation in others. Indeed, the anti-adhesive properties of some biosurfactants make them excellent candidates for coating medical devices. Additionally, some biosurfactants are proposed to act as auto inducers to signal cellular differentiation. Obviously all these traits do not apply to a given biosurfactant, but is inclusive of a rather broad spectrum of diverse molecules. Biosurfactant research would greatly benefit from further categorizations of biosurfactants based on their physical properties and demonstration of functions in which they participate.A classic function of biosurfactant activity is its enhancement of bacterial motility across soft agar plates. This motility, termed swarming motility, is an active form of translocation and is generally reliant on flagellar motility and biosurfactant production. Although biosurfactants are necessary for swarming motility in many bacteria, their production provides no benefit to swimming motility, and it is difficult to imagine a natural environment that would support the large local population sizes necessary for swarming motility. Nonetheless, it is widely assumed that biosurfactant production supports bacterial movement in vivo. How exactly might biosurfactants be beneficial to motility, and under what natural conditions do they aid motility? This question is addressed in chapter 6. Biosurfactant production has been noted in many bacterial species, but few bacterial habitats allow for as easy observation and manipulation of surfactant production as do leaves. Thus, the phyllosphere is an excellent setting in which to test the biological roles of biosurfactant production. Epiphytic bacteria not only survive, but readily flourish on leaves despite the high UV exposure, cycles of desiccation and hydration, rapid temperature fluctuations,macetas de plastico 25 litros and low and heterogeneous nutrient availability found on most leaves. It has been shown that growth of surfactant-producing bacteria on a plant can change the wettability of the leaf. It has previously been postulated that such biosurfactant production might be beneficial to the epiphytic life of bacteria and it is widely assumed that the plant environment is especially enriched with biosurfactant producers for this reason. 

It is already known that once inside the leaf, surfactant production by bacteria such as P. syringae is important for the development of disease symptoms, most likely through the induction of plant cell leakage. However, it remains unclear how biosurfactants specifically aid epiphytic growth of bacteria. Continuous water films may not normally form on such waxy surfaces; by decreasing the interfacial tension between the leaf surface and dispersed water droplets, biosurfactants could increase the wetted surface area of the leaf. Such enlarged water films might increase the distribution of locally abundant nutrients that might be separated by waxy regions of the leaf which would not otherwise be wetted by water. During periods of abundant leaf surface water, it is hypothesized that epiphytes will leave cellular aggregates in which they survive and explore the leaf surface, moving between dispersed nutrient-rich sites ; surfactant-mediated enlarged wetted areas might enable increased regions over which such motility could occur. Furthermore, surfactants might have lubricating properties, and increase bacterial motility on leaves by decreasing potential attractive forces that could immobilize bacteria on surfaces. Besides increasing growth through redistribution of nutrients and bacteria, surfactants might also increase nutrient or water availability in those sites already colonized by bacteria through their plasticizing effect on the cuticle. A number of plant-associated organisms have been studied for biosurfactant production, but few have been directly tested for the role of these compounds in planta. When surfactant-deficient mutants have been tested in planta, the focus is usually on the contributions of the biosurfactants to virulence or to the membrane-disruptive, phytotoxic properties of these molecules. A few studies have attempted to include movement in their assessment of biosurfactant roles, but the results are generally mixed; it is difficult to pinpoint the exact cause of a deficiency of colonization of plant surfaces by a mutant. Thus, although it has been speculated that the decreased fitness of biosurfactant mutants is due to their decreased motility and/or access to nutrients, neither of these factors have been directly proven on plants. Although there is a paucity of research on the role of different types of biosurfactants in the phyllosphere, the widespread use of synthetic surfactants in agriculture has provided a large source of information that might be applied to biosurfactants. Surfactants are capable of solubilizing plant epicuticular wax, thus diminishing the barrier of nutrient diffusion from the leaf onto the surface, although solubilization will only occur at concentrations above the critical micelle concentration. Biosurfactant production could potentially reach high enough local concentrations in bacterial aggregates to solubilize and strip away adjacent waxes if the biosurfactant is suited for solubilizing hydrophobic substances into water.

At lower concentrations, surfactants will have different effects on the cuticle depending on their structures. Hydrophilic surfactants, when adsorbed into the cuticle, will increase the hydration of the cuticle and therefore increase the movement of not only water but also water-soluble molecules. Alternatively, although hydrophobic surfactants readily adsorb into the cuticle, they do not increase the hydration but rather the fluidity of cuticular waxes that, in turn, increases the rate of diffusion of hydrophobic compounds across the cuticle. Additionally, movement of water and bacteria into the apoplast is normally prevented by the high surface tension of water, but can occur spontaneously when the surface tension of the liquid is reduced such as in Zebrina purpusii when the surface tension of liquid is less than 30 dyn/cm. Similarly, during plant invasion, pathogens could be employing a surfactant with high surface tension lowering abilities to facilitate water entry into stomata and other openings. Biosurfactants have been implicated in a wide variety of roles, and all of these roles might prove true in specific situations. However, it is important to start defining what types of surfactants are good at achieving a given result. The goal of this dissertation is to examine biosurfactant production in the phyllosphere with an emphasis on the plant-associated Pseudomonas syringae, in which several surfactants that it produces will be characterized and studed for their specific roles in the phyllosphere, based on clues from their genetic regulation. Biosurfactant-producing organisms have classically been identified by their ability to emulsify and utilize hydrocarbons as a nutrient source. It has only been recently appreciated that biosurfactants are produced by bacteria for many reasons other than access to hydrophobic nutrient sources. Among the numerous functions identified, are their use for swarming motility , biofilm structure and maintenance, and delivery of insoluble signals. Biosurfactants have been identified that can either promote biofilms or disperse them on root and abiotic surfaces. Additionally, some biosurfactants have been noted for their membrane-disrupting and thus zoosporicidal or antimicrobial activity. An unexplored arena where biosurfactants may prove particularly important is the colonization of waxy leaf surfaces. In order to survive on leaf surfaces, epiphytes must be able to access limited and spatially heterogeneous nutrient supplies and endure daily fluctuations in moisture availability in forms such as dew and rainfall. Continuous water films may not normally form on such waxy surfaces, and surfactants might thus aid in diffusion of compounds across the plant. If the bacteria have a pathogenic life phase, they must first have a method to enter plant tissue after which they create a favorable apoplastic environment for growth. It is already known that once inside the leaf, bacteria such as P. syringae use surfactants to cause plant cell leakage and disease symptoms. However, some studies have also implicated biosurfactants in the pre-pathogenic stages of plant-associated bacteria. Pseudomonas syringae pv. syringae B728a, a sequenced model organism with a prominent epiphytic lifestyle, produces biosurfactants. A study of the genetic regulation of biosurfactant production should provide insight into its function in this species. The identification of mutants altered in surfactant production would be an important first step in this process. However, an effective method of identifying such mutants needed to be found. Many studies have compared various screening methods to identify biosurfactant producers from limited collections of environmental isolates. Some of the most commonly used methods for analyzing biosurfactant production are drop-collapse, emulsification, and tensiometric evaluation. However, when many strains need to be assessed for surfactant production, the drop-collapse assay has been the method of choice. 

As DLK2 binds and weakly hydrolyzes 5DS in vitro, we tested whether the compound would inhibit growth of DLK2 OE hypocotyls. DLK2 OE lines were unresponsive to both 5DS and 5DS, indicating that DLK2 does not transduce 5DS signal.To elucidate the spatio-temporal regulation of DLK2 expression induced by dark and SLs, we generated a transcriptional fusion of a 1023 bp DLK2 promoter fragment with the GUS genecoding region. We assayed for GUS expression in at least seven representative T4 homozygous Arabidopsis Col-0 lines. In young control seedlings grown on 0.5 × MS plates, GUS stain was detected first in the cotyledons which progressively intensified with the onset of the cotyledon expansion and subsequently was detected also in the roots. In seedlings grown on plates supplemented with 10 µM racGR24, a specific and strong GUS signal appeared at the basal end of the hypocotyl. In accordance with the real-time PCR data, dark-grown seedlings displayed intensive GUS accumulation , especially in the hypocotyl. In the aerial parts of adult plants, GUS signal was strong in primary and mature leaves and petals. No GUS activity was detected in mature hypocotyl, petiole vasculature and non-elongating, mature stems , while the axillary buds and the vascular bundles of elongating stem segments adjacent to the cauline leaves displayed intensive GUS staining. Interestingly, DLK2 promoter activity was strong in buds and the vascular cells connecting the stipules with the vasculature of the petiole. In the root system of adult plants, GUS activity was strong in the differentiation zone and the GUS signal gradually faded away toward the primary root tip. 

Notably, lateral root primordia displayed no GUS signal,macetas de 10 litros while DLK2 promoter activity was detected in young lateral root tips. These findings indicate that DLK2 expression pattern is tissue specific and regulated by SLs or dark directly. There is compelling evidence that at least two butenolide signaling pathways exist in vascular plants. The ancient KAI2 pathway has an as yet unknown butenolide ligand , which is neither SL nor karrikin. During the course of evolution, KAI2 underwent a gene duplication event which resulted in the D14 clade. The D14 pathway perceives the canonical SL ligand and diverged from the KAI2 clade both evolutionarily and physiologically. The question then emerges, how does DLK2 relate to these MAX2-dependent signaling pathways? We showed that recombinant DLK2 does not hydrolyze 5DS and is not destabilized in the presence of 5DS , indicating that DLK2 is not an SL receptor nor an SL hydrolase that functions in a negative feedback system to remove excess SL. This is further supported by the sensitivity of dlk2 mutants to 5DS and rac-GR24 and DLK2 OE lines do not show a SL-deficient phenotype. On the other hand, compared to AtD14, DLK2 shows weaker stereospecific binding and hydrolysis toward 5DS , a non-natural SL which, along with karrikins, oddly substitutes for the unknown endogenous KAI2 ligand. It is intriguing to consider that DLK2 might be a receptor or hydrolase for the enigmatic KL. The structure of KL is unknown; therefore, it is hard to draw a parallel between DLK2 and KAI2 ligand-binding mechanisms, and SL binding does not necessarily result in physiological effects. The light hyposensitivity of DLK2 over expressing lines might be the consequence of KL metabolism by excess DLK2 and the elongated hypocotyl phenotype of DLK2 OE lines resembles the htl-3hypocotyl phenotype, however, other htl-3-related traits, such as suppressed cotyledon expansion or broad leaves were not observed in these lines.

Furthermore, dlk2 mutants are sensitive to 5DS and to karrikin treatment , suggesting that DLK2 is not involved in KL signaling, although 5DS and karrikin do not necessarily mimic KL action. We propose that DLK2 neither perceives nor hydrolyzes the natural ligand of D14 and KAI2. A remaining question is whether DLK2 should be regarded as a component of a separate signaling pathway, or is its function merely to regulate other MAX2-dependent pathways through the sequestration of the signaling molecules. The known pathways related to the D14 family diverge at the level of SMXL-family proteins. Intuitively, the weakly characterized members of the SMXL/D53 family, SMXL3, -4 and -5 might be co-opted by DLK2. SMXL4, originally referred to as AtHSPR , plays a role in abiotic stress responses and displays a vascular bundle-specific expression , as does DLK2 in elongating stem segments. It was shown recently that smxl4 smxl5 double mutants are defective in carbohydrate accumulation and phloem transport and SMXL3, -4 and -5 are essential for phloem formation. In SMXL3, -4 and -5, the RGKT motif needed for MAX2-mediated protein degradation of D53/SMXL7 is absent , and SMXL5 is not degraded upon rac-GR24 application , suggesting that these proteins may not be degraded through MAX2. Intriguingly, DLK2 lacks the residues required for the physical interaction with MAX2. A recent publication also suggested that DLK2 homologues presumably do not interact with MAX2. The glycine residue in position 158 is required to form a π-turn structure, which is a prerequisite of proper conformational changes of the D14 lid during SL activation. Other substitutions that reportedly do disrupt D14–MAX2 interactions , and are conserved in KAI2, are not present in DLK2. 

Furthermore, DLK2 is not degraded upon rac-GR24 application suggesting that DLK2 does not interact with MAX2; however, its expression regulation is mostly accomplished through MAX2. It was previously shown that upon binding their proposed ligand, AtD14 and KAI2 underwent substrate-induced protein degradation. AtD14 is degraded in a MAX2-dependent manner through the 26S proteasome system , and KAI2 is degraded independently of MAX2 and 26S proteasomes. The immunoblot analysis showed a slight increase in the amount of DLK2:sGFP protein even in 35Spro:DLK2:sGFP plants,medidas maceta 30 litros suggesting a post transcriptional effect. It cannot be ruled out that other but enolides or the proposed KL might promote DLK2 degradation. A potential future direction of DLK2 research could be the elucidation of the relationship between DLK2 and SMXL3, SMXL4, and SMXL5. We demonstrated that KAI2 is a principal promoter of cotyledon expansion in the D14 family, although interactions can be observed. Over expression of DLK2 in wt, dlk2-2 and dlk2-3 d14-1 kai2-2 backgrounds results in more elongated hypocotyls and expanded cotyledons under low light conditions , suggesting that DLK2 is indeed capable of regulating these physiological responses per se. However, dlk2 mutants do not display the opposite phenotypes, and the phenotype of the OE lines does not correlate with the transcript level , so neomorphic or hypermorphic effects of DLK2 over expression cannot be ruled out. We propose that DLK2 can promote hypocotyl elongation under sub-optimal light conditions, although this effect is modulated by other members of the D14 family. This finding is in conflict with the interpretation of an earlier report , where the authors suggested that the shorter mesocotyls of KAI2– RNAi d14 seedlings compared to those of the d3 mutant in rice is due to suppression by DLK2. However, differences between species might also contribute to this effect, and, as the authors noted, this finding should be interpreted with caution as there was residual KAI2 expression in the RNAi lines. We demonstrated that apart from the well documented SL and karrikin responsiveness, DLK2 expression is also down-regulated by light. Dark adaptation promotes DLK2 expression especially in the hypocotyl, and DLK2 upregulation in dark-kept seedlings is accomplished through MAX2 and KAI2. DLK2 expression is suppressed in the pif Q mutant either in light or dark, indicating that light signaling regulates DLK2 transcription via PIFs. It is also noteworthy that the spatial DLK2 expression pattern is regulated by rac-GR24 , suggesting a dynamic adaptation of DLK2 transcription to hormonal and environmental changes. DLK2 activity is strong in root hair and cortex, implying that DLK2 might be involved in the physiological processes linked to these tissues, such as water and nutrient uptake and edaphic stress responses. DLK2 expression was strong in axillary buds and the adjacent vascular bundles might also suggest that DLK2 plays a role in the regulation of nutrient distribution. In summary, the results herein show that although it is structurally similar to its paralog D14 family proteins, DLK2 only weakly binds or hydrolyzes natural and unnatural SL ligands. DLK2 is widely expressed in seedlings and has a role in the promotion of hypocotyl elongation. These data together with the knowledge accumulated so far on DWARF14 family suggest that DLK2 represents a divergent member of the family.

The fine details of DLK2 regulation, signaling and its role in adult plant life are the subject of future investigations.Pesticides are natural or synthetic chemicals used to control pests. In order to support an expanding population there is a continuous need for pesticides. Worldwide, there are thousands of pests including insects, weeds, fungi, bacteria, viruses, mycoplasma and nematodes that destroy crops, transmit diseases and compete for resources. One of the first written records of pesticide use was from around 1000 B.C. when Homer described the use of sulfur to control pests by farmers. Many natural pesticides and botanicals were used since that initial discovery: arsenic, mercury, lead, nicotine, pyrethrum and rotenone. However, insect resistance and safety issues for these inorganics and botanicals led to the production and use of the first synthetic organic insecticide, dichlorodiphenyltrichloroethane discovered in 1939 by Paul Müller. Currently, there are over 40,000 different pesticide products for retail sales with different formulations and control mechanisms. Since the major discovery of DDT, advances have continued with the synthesis and commercialization of hundreds of pesticides including five major neuroactive insecticide classes all with unique toxicity profiles and target sites: chlorinated hydrocarbons , pyrethroids, carbamates, organophosphates and neonicotinoids. Chlorinated hydrocarbons and pyrethroids are insecticidal through their ability to destabilize voltage-gated sodium ion channels receptor for some chlorinated hydrocarbons. DDT has low acute toxicity to mammals, but is persistent in the environment which ultimately led to it being banned in the US in 1972. Other problems from DDT include its potential carcinogenicity, thinning of bird eggshells and fish death. Pyrethroids, modeled from natural pyrethrin compounds from the Chrysanthemum flower, are relatively non-toxic and are less stable in the environment than DDT. Carbamates and organophosphates both inhibit acetylcholinesterase leading to accumulation of acetylcholine and over stimulation of the nervous system. Carbaryl was at one time the most commonly used carbamate with low mammalian toxicity and broad-spectrum use and selectivity. Organophosphates are related to potent nerve agents. Often highly toxic to mammals, they are metabolized and detoxified readily. Neonicotinoids, the most important class of insecticides, have favorable mammalian and environmental toxicology and now account for approximately 25 percent of the worldwide insecticide market value. In an attempt to understand the mechanism of action of nicotine, Izuru Yamamoto discovered that insecticidal activity depends on ionization or basicity of the nitrogen of nicotine and all nicotine-related compounds. Yamamoto and colleagues realized that although ionization prevents penetration of the CNS of insects which decreases insecticidal activity, these insecticides needed to be ionized to interact with the nAChR. The search began for synthetic insecticides with high insecticidal activity, low mammalian toxicity and the ability to penetrate the insect CNS yet basic enough to interact with the nAChR. Nithiazine, a nitromethylene heterocycle, was the first neonicotinoid prototype developed by Shell Development Company in 1978. It had excellent insecticidal activity, good systemic action in plants and low mammalian toxicity. However, nithiazine was highly photolabile. Shinzo Kagabu and colleagues modified the structure of nithiazine and synthesized a series of compounds with varying ring structures and sub-stituents and screened them for insecticidal activity against the major rice pest, the green rice leaf hopper. This led to the discovery of the first highly active neonicotinoid, imidacloprid , in 1985. IMI has 12 times higher insecticidal activity than nicotine, is more systemic and photostable and therefore was commercialized by Bayer in 1991. Other first-generation chloropyridinyl-containing neonicotinoids include nitenpyram , acetamiprid and thiacloprid commercialized in 1995, 1996 and 2000, respectively. Further derivatization and optimization lead to the discovery of the two second-generation neonicotinoids, thiamethoxam and clothianidin by Novartis and Takeda, respectively. Finally, the only tetrahydrofuranyl-containing neonicotinoid, dinotefuran , was commercialized by Mitsui Chemical Company in 2002.

In comparison with the four new fungicides, effectiveness of potassium phosphite in greenhouse studies was high to moderate and was moderate for mefenoxam. In the field study, a significant reduction in disease and soil populations by mefenoxam was only observed after increasing applications to high-label rates. Lower rates were initially used because this fungicide is known to cause phytotoxic effects to young citrus trees as was also observed in preliminary greenhouse studies where a range of rates was evaluated. Thus, the reduced effectiveness of mefenoxam in our study,a treatment that has been used successfully in commercial applications for managing Phytophthora root rot of various tree crops for many years, may have been due to using inadequate rates. Furthermore, trees were inoculated with an isolate of P. nicotianae with an EC50 value for mycelial growth of 0.24 mg/liter that was in the mid-range among 31 isolates from California evaluated previously. Because baseline sensitivities before commercial use of mefenoxam were never established for P. nicotianae from citrus, and the phenylamide class of fungicides has been used since the 1980s in California citriculture, this isolate may be part of a less-sensitive sub-population of the species that cannot be easily managed with mefenoxam applications. Soil populations of untreated control trees in our field and greenhouse studies were often very high considering that >15 propagules/g of soil is considered a threshold level where management is recommended. Still,maceteros fresas disease incidence of feeder roots was mostly low, especially during summer samplings in the field.

We chose ‘Carrizo citrange’ in the field studies because it is commonly used commercially as a rootstock. It is considered of intermediate susceptibility or tolerant to Phytophthora root rot, and this could have accounted for the low disease incidence. In the greenhouse studies, disease incidence may have been increased by pruning feeder roots of seedlings as it was done in studies by others. Root injuries may occur naturally in the field by nematode or root weevil infestations in the soil, and these pests are known to increase the incidence of Phytophthora root rot. Still, although disease incidence was overall low in our studies, fungicide efficacy could be compared and significant differences were observed. The four new Oomycota fungicides are single-site mode of action inhibitors. Their resistance risk currently has not been completely characterized , and resistant field isolates have not yet been detected in Phytophthora species. Resistance, however, has been described for Plasmopara viticola, another Oomycota organism, to mandipropamid. In our previous baseline sensitivity assessments, outliers with higher EC50 values for mycelial growth inhibition of P. syringae by fluopicolide and of P. citrophthora by ethaboxam were identified that were >23-fold less sensitive than the most sensitive isolates of the respective species used in the study, and this was considered to possibly indicate a potential for selecting isolates with reduced sensitivity to these fungicides. Thus, as with any single-site mode of action fungicide, resistance management strategies should be followed from the onset of commercial use. Because two of the new fungicides each have the same registrant in the United States, the commercialization of pre-mixtures will be facilitated. In summary, our study demonstrated that the new Oomycota fungicides ethaboxam, fluopicolide, mandipropamid, and oxathiapiprolin provided highly effective control of Phytophthora root rot of citrus caused by P. nicotianae or P. citrophthora. The efficacy was generally better than for the previously available fungicides mefenoxam and potassium phosphite.

The new compounds promoted the recovery of infected trees andenhanced fruit yield, with fluopicolide and oxathiapiprolin showing the most consistent increases in these measures. Based in part on our studies, fluopicolide recently received a federal and oxathiapiprolin a full registration for use on citrus, whereas registration for ethaboxam and mandipropamid has been requested. Species of Phytophthora cause several diseases on citrus, including root rot, foot rot, brown rot of fruit, and gummosis of tree trunks and larger limbs. Phytophthora root rot is common in orchards in California and other citrus production areas worldwide. The disease can be especially damaging in new citrus plantings where overwatering is conducive for infection, and the limited root system of young trees cannot generate new growth fast enough to replace infected and damaged tissues. This can result in poor tree growth and delayed orchard establishment. In California, the disease is mainly caused by Phytophthora nicotianae Breda de Haan during the warmer months of the year, whereas P. citrophthoraLeonian is active year-round. P. palmivoraE. J. Butler is the major citrus root rot pathogen in Florida. P. cactorumJ. Schröt., P. capsici Leonian, P. cinnamomi Rands, P. drechsleri Tucker, and P. megasperma Drechsler have been occasionally identified in some production areas. Phytophthora root rot is characterized by discoloration and softening of the outer root cortex that becomes water-soaked in appearance and prone to sloughing off, eventually exposing the inner stele. Damage of the root system can lead to tree decline and yield losses from lack of water and nutrient uptake, and if left untreated, to tree death. Phytophthora root rot can be managed by cultural practices such as the use of Phytophthora-tolerant root stocks , irrigation or orchard drainage strategies that avoid overwatering, and fungicide applications. These practices are best used in an integrated approach. Among fungicides,maceta 30l the phenylamides and the phosphonates have been used since the 1980s, and until recently, no alternatives were available.

The limited number of fungicides registered resulted in their over-use, and in subsequent resistance development. Resistance to the phenylamide class of fungicides has been reported in Oomycota pathogens of numerous crops including Phytophthora spp. that are known to be pathogenic to citrus such as P. citricola and P. nicotianae. Phenylamide-resistant populations of P. nicotianae are established in Florida orchards and nurseries. Phosphonate resistance is less common but has been identified in isolates of P. cinnamomi and P. infestans , and more recently in isolates of P. citrophthora, P. syringae, and P. nicotianae from California citrus orchards. With the need for alternative chemical treatments to manage Phytophthora diseases of citrus, new fungicides have recently become available for evaluation. They include the thiazole carboxamide ethaboxam, the benzamide fluopicolide, the carboxylic acid amide mandipropamid, and the piperidinyl thiazole isoxazoline oxathiapiprolin. Each compound has a unique mode of action that is different from those of the previously registered compounds. Among these, oxathiapiprolin was recently registered on citrus for foliar and soil treatments against Phytophthora diseases. This compound was found to be toxic in vitroat very low concentrations against several life stages of the pathogens and was shown to be highly effective in managing root rot and brown rot. Belonging to the Fungicide Resistance Action Committee code 49, its mode of action is the inhibition of an oxysterol binding protein, resulting in the inhibition of multiple cellular processes. Uptake of oxathiapiprolin into citrus plants after soil application is unknown. Previous work has been conducted on annual crops , however, there is currently no information on the mobility and activity of oxathiapiprolin within perennial tree crops. This information may provide a better understanding of its protective and eradicative capabilities in controlling Phytophthora root rot of citrus and have implications on its field use in managing the disease. Therefore, the objectives of this research were to determine if oxathiapiprolin can be detected inside roots and above ground portions of citrus seedlings after soil application as compared to mefenoxam and if concentrations of the fungicides inside the plants can be effective against P. citrophthora. For this, bio-assays and analytical residue analyses were performed at selected time periods after treatment of plants. Sweet orange Osbeck) cv. ‘Madam Vinous’ seedlings in 15 cm x 15 cm x 15 cm pots were grown from seeds in the greenhouse at 24°C to 30°C for 6 to 7 months. At this time, plants were between 25 cm and 30 cm tall. Prior to treatment, plants were moved to an incubator set for a 12-h photoperiod with 34˚C during the light cycle and 26.7˚C during the dark cycle. There were three single-plant replicates for each fungicide treatment and each of the four sample timings. Plants were arranged in a randomized complete block design with all four sampling times in each block. Additionally, three replications of untreated control plants were used.

Solutions of oxathiapiprolin and mefenoxam were prepared in distilled water, and 50 ml was added to each pot, resulting in final applications amounts of 50 mg of oxathiapiprolin and 130 mg of mefenoxam per pot. These amounts are comparable to labeled chemigation rate ranges based on the total basin area for 288 trees/Ha and considering that the treatment area of a potted plant is approximately 1/9 of the basin of a newly planted citrus tree. Solutions were added to each pot without wetting the stem, and distilled water was used for the controls. Each pot was then placed in a plastic bag that was tied around the bottom of the stem to reduce evaporation. Plants were watered once nine days after treatment. Plants were harvested 7, 10, 13, or 16 days after treatment. The root ball was shaken to remove most of the soil, washed using tap water, and allowed to air-dry briefly at ambient temperature. Roots were sampled randomly. The stems were cut 1.5 cm above the soil line to avoid fungicide contamination from the soil application. Another cut was done 10 cm above the first cut, and stem and leaf tissues within this stem segment were separated.One gram of each tissue was placed into glass scintillation vials. The vials were covered with a single layer of cheesecloth and frozen at -80°C for 24 h, lyophilized for 24 h , and then capped and stored at -20°C. A standard procedure was followed for extraction of plant tissues for both fungicides. For this, the lyophilized tissues were transferred to 2-ml impact resistant tubes containing two stainless-steel grinding balls and pulverized for 60 s using the FastPrep-24 set at 6.0 m/s. The contents of each tube were transferred to a 15-ml conical polypropylene plastic tube for a single-phase extraction. For this, 1 ml of sterile ultrapure water was added to each tube and the tube was incubated for 5 min to allow soaking of the sample. An additional 800 µl of sterile ddiH2O, 2.4 ml of acetonitrile, and 20 µl of formic acid were added, and the tubes were placed on an orbital shaker at 300 rpm for 5 min. The tubes were centrifuged at 1,380 g for 10 min. The supernatant was transferred to a 15-ml plastic tube, stored at -20ºC, and used for determining fungicide activity in a bio-assay within 7 days. For analytical residue analyses using HPLC-MS/MS , 500 µl of each tissue extract was transferred into a scintillation glass vial, 2 ml of methanol , and 4.5 ml of 1% formic acid were added, 0.6 ml of the resulting solution was aliquoted into a 2-ml low absorption vial , and vials were stored at -20°C until analyses. The experiment was done twice. Analytical grade oxathiapiprolin and mefenoxam were dissolved in acetonitrile and serially diluted. The samples were analyzed for oxathiapiprolin and mefenoxam using a standard curve method. The concentration of standards used for quantitation were 0.1, 0.5, 1.0, and 10 ng/ml. Each dilution was transferred to a 2-ml low-absorption vial, and aliquots were transferred to auto-sampler vials for analysis that was performed by Environmental Micro Analysis Inc.. The autosampler vials were analyzed using high-pressure liquid chromatography coupled with tandem electrospray mass spectrometer. The chromatographic separation was achieved on a XB-C18 HPLC column. The samples were analyzed with standard concentration levels indicated above. For bio-assays using plant extracts with unknown amounts of fungicides, the dependent variable was the log10-transformed mean inhibition zone; whereas for plant extracts analyzed using HPLC-MS/MS, the dependent variable was the log10-transformed mean amount of fungicide calculated per g of tissue. These data were analyzed using generalized linear mixed models with the GLIMMIX procedure of SAS. For this, root, stem, and leaf extracts or days after treatment were treated as fixed effects, and experiment, replication , and the overall error term were treated as random effects.

Silver uses the Replex replication protocol to address these issues. Driving scale-out distributed software requires more than merely spreading data across clusters and replicating it for fault tolerance; it requires name services to place data and locate it; ownership management, locking and fail over atomicity and isolation of multi-object transactions, in-memory caching, snapshot, checkpoint; and so on. As a result, the software stack of most distributed systems in production today contains a plethora of tools–Cassandra,Redis, ZooKeeper, and others. Each tool comes with its own data-model, proprietary API and query language. In order to make use of any specific tool, a developer needs to cast its own application’s state into the tool’s format, and use the tool’s API or query language in order to extract information about the state and to manipulate it. As an example, consider the life cycle of a typical distributed platform: developers may begin with the need for a distributed database such as Cassandra to store data. As the system grows and scales out, programmers begin to realize they need a way to manage Cassandra itself, so Zoo Keeper is deployed to manage configuration data and provide a mechanism for coordinating clients. Soon, a programmer realizes that funneling everything through ZooKeeper is becoming a bottleneck, so Kafka is bolted on to provide reliable high speed messaging. To further improve performance, Redis is added to implement a distributed cache. Finally, because the programmers still need a way to query data, everything in Kafka is also inserted into Cassandra. Getting different tools to work together and sharing updates across them is a nightmare.

The same information ends up duplicated and translated between multiple tools, resulting in data redundancies,maceta cuadrada plastico inefficiencies, inconsistencies, and difficult maintenance. On boarding new programmers now requires learning multiple tools and picking the correct one for each task.In an on-going joint venture, the NSX team and the VM ware Research Group are contemplating what a Clustered Management PLAT form for driving the control of VM ware’s SDN technology should look like. The design and implementation of Corfu specifically draws motivation from this venture. Figure 6.6 depicts the components of the CMPLAT-Corfu design. The left side of the figure portrays a deployment scenario. Every component in Corfu is built with redundancy and completely automated life-cycle management: Initialization, failure-monitoring, reconfiguration and fail-over. This obviates the operation of CMPLAT as a service with 24/7 availability, driving network control of large, mission critical clusters. The right side portrays the live network model CMPLAT maintains of a real network. Like previous network control planes , examples of items reflected inside CMPLAT are ports, switches, nodes, transport zones, and others. These objects are grouped into maps, e.g., a map of ports, a map of switches. Object and maps may reference one another, e.g., ports and switches belong to zones, and each port resides on some node. CMPLAT exposes an API for admins to manipulate virtual network components, e.g., create a virtual switch containing a certain number of ports, connect ports to virtual machines, and so on.This necessitates back-and-forth translation between the management plane app-servers, which use Java hash-maps to represent the model, and the DBMS. There is a rather complex a data abstraction layer that performs the translation, internally using a SQL-like query-interface for storing and retrieving information from the remote DMBS. In contrast, since Corfu supports arbitrary data-structures, CMPLAT simply uses the most natural data representation, e.g., a hash-map of ports, a linked-list of zones, and so on.

Persisting updates to the data-structure is done transparently and seamlessly, without developer awareness. An example of a NSX logical switch modeled in Corfu is shown in figure 6.7. Since CMPLAT drives the network of entire data centers, it has stringent availability and consistency guarantees. This makes it a catastrophic experience to build over platforms with weaker guarantees. Additionally, there are radically different requirements from different components, for example, live feeds from the network require high-throughput and cannot go through a slow and heavy database service, whereas admin directives must never be lost, and require strong commit guarantees. But building a management platform out of a hybrid system of components is problem-prone. For example, Onix reports anomalous situations in which a node has been updated in a “nodes base”, but the port states this node references have not been updated in the “ports base”. Corfu has the capacity to sustain millions of updates per second, and app-servers efficiently consume updates by selective filtering. This makes it possible to use Corfu as the single data platform for all the information CMPLAT processes. In this way, all of CMPLAT needs are addressed in one place, providing consistency across updates to any part, while avoiding unnecessary duplication and translation of the same information.The era of cloud-scale computing has resulted in the exponential growth of workloads. To cope with the barrage, system designers chose to trade consistency for scalability by partitioning the system and eliminating features which require communication across partitions. As cloud-scale applications became more sophisticated, programmers realized that those features were necessary for building robust, reliable distributed applications. Many of these features were then retrofitted back on, resulting in decreased performance and sometimes serious bugs in an attempt to achieve consistency across a now heavily partitioned system. This dissertation has explored Corfu, a platform for scalable consistency which answers the question: “If we were to build a distributed system from scratch, taking into consideration both the desire for consistency and the need for scalability, what would it look like?”. At the heart of this dissertation is the Corfu distributed log.

The Corfu log achieves strong consistency by presenting the abstraction of a log – clients may read from anywhere in the log but they may only append to the end of the log. The ordering of updates on the log are decided by a high throughput sequencer, which we show can issue millions of tokens per second. The log is scalable as every update to the log is replicated independently, and every append merely needs to acquire a token before beginning replication. This means that we can scale the log by merely adding additional replicas, and our only limit is the number of tokens the sequencer can issue. We have shown that we can build a sequencer using low-level networking interfaces capable of issuing more than half a million tokens per second. We have also built a prototype FPGA storage unit which can interface directly with SSDs and raw flash,maceta 7 litros which can easily saturate a gigabit network a uses a simplified UDP-based protocol. On top of the Corfu distributed log, we have shown how multiple applications may share the same log. By sharing the same log, updates across multiple applications can ordered with respect to one another, which for the basic building block for advanced operations such as transactions. We presented two designs for virtualizing the log: streaming, which divides the log into streams built using log entries which point to one another, and stream materialization, which virtualizes the log by radically changing how data is replicated in the shared log. Materializing streams greatly improves the performance of random reads, and allows applications to exploit locality by placing virtualized logs on a single replica. Efficiently virtualizing the log turns out to be important for implementing distributed objects in Corfu, a convenient and powerful abstraction for interacting with the Corfu distributed log introduced in Chapter 5. Rather than reading and appending entries to a log, distributed objects enable programmers to interact with in-memory objects which resemble traditional data structures such as maps, trees and linked lists. Under the covers, the Corfu runtime, a library which client applications link to, translates accesses and modifications to in-memory objects into operations on the Corfu distributed log. The Corfu runtime provides rich support for objects. An automated translation process converts plain old Java objects directly into Corfu objects through both runtime and compile-time transformation of code. This allows programmers to quickly adapt existing code to run on top of Corfu. The Corfu runtime also provides strong support for transactions, which enable multiple applications to read and modify objects without relaxing consistency guarantees. We show that with stream materialization, Corfu can support storing large amounts of state while supporting strong consistency and transactions. In Chapter 6, we describe our experience in both writing new applications and adapting existing applications to Corfu. We start by building an adapter for Zookeeper clients to run on top of Corfu, then describe the implementation of Silver, a new distributed file system which leverages the power of the vCorfu stream store.

We then conclude the chapter by describing our efforts to retrofit a large and complex application: a software defined network switch controller, and detail how the strong transaction model and rich object interface greatly reduce the burden on distributed system programmers. Overall, Corfu demonstrates a highly scalable yet strongly consistent system, and shows that such a system greatly simplifies development without sacrificing performance. A slow sand filtration system is a filtration process which contaminated water percolates through a sand medium and through various physical, chemical, and biological processes, the contaminants are removed. The first known slow sand filtration system was made in 1804 by John Gibb in Scotland to produce drinking water. Since then, this technique has been widely used not only for drinking water production , but also for improving the quality of wastewater before being reused or discharged into the environment.Bio-filtration generally encompasses any type of filtration of contaminated water through sand, soil, or other various media that contains biomass to aid degradation and removal. Several types of bio-filtration have been extensively studied in literature: bio-swales, trickling filters, constructed wetlands and natural wetlands, treatment ponds, riparian zones, bank filtration, and slow sand filtration. An effective filter is the result of biological degradation and physical/chemical processes such as adsorption and straining of contaminants on the bio-filter media. Both of these processes can be effective as a result of the slow flow rates and long hydraulic residence times that allow the formation of a biological active layer composed of alga, protozoa, bacterium, fungus, actinomycetes, plankton, diatoms, and rotifer population. This layer, called the schmutzdecke, develops within the top centimeters of the filter as a result of the accumulation of the organic matter, microbes, and other particulates that settle from the fluid. Thus, as leachate water is passed through, pathogens and contaminants are trapped and broken down by these microbes as a food source, aiding to the physical and biological processes required for filtration. Depending on the raw and target effluent water quality, a slow sand filtration system can be used by itself or in series to other additional treatments, like pretreatment to protect sensible processes such as reverse osmosis or membrane filtrations , or as a polishing process to eliminate disinfection by-products after ozonation or chlorination. The benefits of SSF combines a high efficiency system in reducing cloudiness and harmful bacteria and viruses along with an economical edge. SSF uses minimal power input and no chemical requirements, does not require close operator supervision, uses locally available materials and labor, and does not produce unwanted by-products. This cost-effective technique that was once used in big cities like London, now has special application in the treatment of water at smaller scales such as isolated households in rural areas, in developing countries, or in small businesses with high water consumption, like plant nurseries.Some other media used in biofiltration are biochar , compost , woodchips , activated carbon , pressmud , anthracite , agricultural wastes , etc. In a study by Nyberg et al. , various substrates were researched as the best effective SSF medium to remove zoospores of P. nicotianae from nursery production effluent. Substrates included sand, crushed brick, calcined clay, Kaldes medium, and polyethylene beads. They discovered that within 21 days, all substrate treatments removed more zoospores than day 0. Of all the substrate treatments evaluated, the columns with 10 cm of sand removed the most zoospores on day 21. By their research, sand was the most effective medium using physical filtration alone at depths of 40 cm and 60 cm.

While our prototype unit is built with an FPGA, we envision that a production device would be built with a low-cost ASIC and a NAND flash array instead of a SSD, offering a better performance, lower price, and lower power than the platform that we are currently using. Inside the FPGA, we use a variant of the Beehive. Beehive is a many-core architecture implemented in a single FPGA. A single Beehive instance can comprise up to 32 conventional RISC cores connected by a fast token ring. Network interfaces, a memory controller, and other devices, such as disk controllers, are implemented as nodes on the ring.Data is returned from reads via a dedicated pipe lined bus. There are additional data paths to enable DMA between high-speed devices and memory. We configure various Beehive cores to take on specific roles, as shown in Figure 3.10. Whereas the memory controller, Ethernet core, and System core are common to all Beehive designs, we use the following special-purpose cores to construct a SLICE.The Beehive architecture enables us to handle requests in parallel stages while running the FPGA at a low frequency , thus reducing device power. Note that new functionality can be easily added to the SLICE design. Additional cores running specialized hardware can enhance the performance of timing-critical tasks. For example, our current design uses a specialized hardware accelerator to speed up packet processing. At the same time, latency-insensitive operations can be coded in a familiar programming language ,vertical garden hydroponic significantly reducing complexity. Table 3.1 shows the percentage of time the various cores are idle under maximal load and number of assembly instructions per core in the SLICE design.

The Comm core has a slightly different architecture than the rest of the cores , thus we did not measure its idle time. If we need more or differently allocated compute resources, we can use different configurations of cores. In an earlier alternative design, we used two Packet Processing Cores running the same code base: one processed even packets and the other processed odd packets. The earlier design used more FPGA resources than the current design, but both designs can run the Ethernet at wire speed. We could also just as easily add a second Comm, Packet Proc, Read or Write core, should the workload require it. We now present our design for using Cuckoo Hashing to efficiently map an SVA to an SPA. Cuckoo Hashing minimizes collisions in the table and provides better worst-case bounds than other methods, like linear scan. Under Cuckoo Hashing, two mapping functions are applied to each inserted key, and such a key can appear at any of the resultant addresses. If, during insertion, all candidate addresses are occupied, the occupant of the first such address is evicted, and a recursive insert is invoked to place it in a different location. The original insertion is placed in the vacated spot. On average, 1.5 index look-ups are required for successful lookups in such a table. Table lookups for entries not in the table always require two lookups, one for each mapping function. In order to save space in each hash table entry, we store only a fraction of the bits of each SVA. The remainder of the bits can be recovered by using hash functions that are also permutations. Such permutations can be reversed, for example during a lookup, to reconstruct the missing bits so as to determine whether the target matches. The end result of hashing an SVA can then be represented by the mapping function F which is the concatenation F1 and F2, computed as described below.

The lower order bits of F are used to index into the mapping hash table and the remainder of F is stored in the table entry for disambiguation, along with a bit indicating which mapping function was used. This ensures that for any given table entry, we can recover all of F from an entry’s position and contents, and thus we can derive X and Y, and finally the original SVA.We evaluated a software implementation of the Cuckoo Hashing page mapping scheme and compared it with Chain Hashing. To do so, we ran sequences of insertion / lookup pairs using a varying number of keys on hash tables of both types, and then compared the elapsed times. Figure 3.12 shows the difference in performance, about 10X, when using the two page mapping schemes. We used a 64,000 entry table for both tests. These tests employed a dense key-space with relatively few hash collisions. The advantage of Cuckoo Hashing should increase with the likelihood of collisions.The stability of SLICE storage depends on the persistence of its mapping table. Building a persistent mapping table for a Corfu software implementation is problematic. Writing separate metadata for every data write is not plausible. The remaining possibilities either involve batching metadata updates, which risks losing state on power failure, or writing metadata and data in the same chunk,vertical farm tower which reduces the space available for data. Fortunately, when custom hardware is in play, a further option becomes available. Using super-capacitors or batteries, we can ensure that the hardware will always operate long enough to flush the mapping table. Our optimized mapping table takes only a few seconds to flush to flash, so this is an attractive option for metadata persistence. We have specified the hardware needed for this capability, but not yet implemented it. Ultimately, solid-state storage with fine write granularity, such as PCM, would provide the best alternative for storing such metadata and modifying it in real time.Our SLICE prototype uses an existing SSD rather than raw flash. Using an SSD, each SPA referenced in our mapping table is a logical SSD page address.

This was an expedient for prototyping, and it eliminates a raft of potential problems. For instance, we don’t need to worry about out-of-order writes, since these are possible on an SSD but problematic on raw flash. Furthermore, we don’t need to worry about bad block detection and management or error correction. But the most significant problem that using an SSD eliminates is the need to handle garbage collection and wear-leveling. With an SSD, allocating a flash page during a write operation is as simple as popping the head of the free list. Similarly, reclaiming a page requires adding it to the free list and issuing a SATA TRIM command to the drive. Wear-leveling is performed by the SSD.The downside of using an SSD is that it duplicates Flash Translation Layer functionality. Specifically, our mapping table requires a extra address translation in addition to that done by the SSD. Since SSDs are fundamentally log-structured, and since we are in practice writing a log, which is significantly simpler than a random-access disk, one might hope that this would result in a less complex FTL. A further downside is that we lose control over the FTL, which might have been useful to facilitate system-wide garbage collection. For example, if there are many SLICEs in a system, it is possible to use the configuration mechanism in Corfu to direct writes away from some units and allow garbage collection and wear-leveling to operate in the absence of write activity. In addition, if we had access to raw flash, our system would be able to store mapping-table metadata in the spare space associated with each flash page and possibly leverage this, ensuring persistence without special hardware, in the manner of Birrell et al.. Fortunately, it seems likely that writing a log over an SSD will in many cases produce optimal behavior. An application that maintains a compact log works actively to move older, but still relevant data from the oldest to the newest part of the log. Doing this allows such applications to trim entire prefixes of the log. This sort of log management is appropriate for applications that maintain fast changing and small datasets, such as ZooKeeper. With this sort of workload, appends to the log march linearly across the address-spaces of all the SLICEs, and prefix trims at the head of the log proceed at the same pace. This should produce optimal wear and capacity balancing across an entire cluster.

Assuming that our firm ware allocates SSD logical pages in a sequential fashion, the regular use of prefix trim should help avoid fragmentation at the SSD block level which is a major contributor to write amplification. In other applications, for example a Corfu virtual disk, it can be too expensive to move all old data to the head of the log. Because offset trim operates at single page granularity, we can support applications that require data to remains at static log positions.For throughput, we evaluate Corfu on a cluster of 32 Intel X25V drives. Our experiment setup consists of two racks; each rack contains 8 servers and 11 clients. Each machine has a 1 Gbps link. Together, the two drives on a server provide around 40,000 4KB read IOPS; accessed over the network, each server bottlenecks on the Gigabit link and gives us around 30,000 4KB read IOPS. Each server runs two processes, one per SSD, which act as individual flash units in the distributed system. Currently, the top-of-rack switches of the two racks are connected to a central 10 Gbps switch; our experiments do not generate more than 8 Gbps of inter-rack traffic. We run two client processes on each of the client machines, for a total of 44 client processes. In all our experiments, we run Corfu with two-way replication, where appends are mirrored on drives in either rack. Reads go from the client to the replica in the local rack. Accordingly, the total read throughput possible on our hardware is equal to 2 GB/sec or 500K/sec 4KB reads. Append throughput is half that number, since appends are mirrored. Unless otherwise mentioned, our throughput numbers are obtained by running all 44 client processes against the entire cluster of 32 drives. We measure throughput at the clients over a 60-second period during each run. We first summarize the end-to-end latency characteristics of Corfu in Figure 3.13. We show the latency for read, append and filloperations issued by clients for four Corfu configurations. The left-most bar for each operation type shows thelatency of the server-attached flash unit where clients access the flash unit over TCP/IP when data is durably stored on the SSD; this represents the configuration of our 32-drive deployment. To illustrate the impact of flash latencies on this number, we then show , in which the flash unit reads and writes to RAM instead of the SSD. Third, presents the impact of the network stack by replacing TCP with UDP between clients and the flash unit. Lastly, shows end-to-end latency for the FPGA+SSD flash unit, with the clients communicating with the unit over UDP. Against these four configurations we evaluate the latency of three operation types. Reads from the client involve a simple request over the network to the flash unit. Appends involve a token acquisition from the sequencer, and then a chained append over two flash unit replicas. Fills involve an initial read on the head of the chain to check for incomplete appends, and then a chained append to two flash unit replicas. In this context, Figure 3.13 makes a number of important points. First, the latency of the FPGA unit is very low for all three operations, providing sub-millisecond appends and fills while satisfying reads within half a millisecond. This justifies our emphasis on a client-centric design; eliminating the server from the critical path appears to have a large impact on latency. Second, the latency to fill a hole in the log is very low; on the FPGA unit, fills complete within 650 microseconds. Corfu’s ability to fill holes rapidly is key to realizing the benefits of a client-centric design, since hole-inducing client crashes can be very frequent in large-scale systems. In addition, the chained replication scheme that allows fast fills in Corfu does not impact append latency drastically; on the FPGA unit, appends complete within 750 microseconds.

In addition, the average fresh weight and diameter of the fruits from the 869T2-inoculated plants were greater than those of the control plants , although the average fruit lengths were similar. These data demonstrate that the okra fruits became heavier and wider after inoculation with strain 869T2. In summary, inoculation of strain 869T2 into hot pepper and okra plants could cause plants to flower at earlier growth stages.The members of the genus Burkholderia belong to the class β-proteobacteria and have a broad distribution, residing universally in soil, water, and in association with plants, fungi, animals, and humans. Some Burkholderia species are plant pathogens in many vegetables and fruits, while others have been reported as opportunistic pathogens of humans and other animals. However, many other Burkholderia species are beneficial to plants, suppressing plant diseases and promoting plant growth by various processes, including the production of antibiotics, secretion of allelochemicals, induction of pathogen resistance in plants, nitrogen fixation, or enhancing nutrient uptake by host plants. These beneficial Burkholderia species are free-living or endophytic and form mutualistic associations with their host plants. Burkholderia species’ high versatility and adaptability to different ecological niches rely on the high genomic plasticity of their large multichromosome genomes and the production of various bacteria secondary metabolites. In this study, we characterized the endophytic bacterium Burkholderia seminalis strain 869T2 isolated from vetiver grass, outdoor vertical plant stands which was recently described and included in the Burkholderia cepacia complex. We have documented the IAA production, siderophore synthesis, and phosphate solubilization abilities of B. seminalis strain 869T2.

Inoculations of strain 869T2 into tested plants demonstrated the plant growth promotion ability of this bacterium in several plant species from the Brassicaceae, Asteraceae, and Amaranthaceae families. Plant endophytic bacteria can increase the nutrient uptake and biomass accumulation of host plants through the production or regulation of various plant hormones, such as auxin, cytokinin, gibberellins, and ethylene. Indole acetic acid is a naturally occurring auxin produced by several endophytic bacterial species through the L-tryptophan metabolism pathway. Tryptophan can exist in the exudates of plants and is utilized by the bacteria to synthesize auxin, which enhances the growth of host plants. Auxin is the major plant hormone that regulates various aspects of plant growth and development, such as root initiation and development, leaf formation, fruit development, floral initiation and patterning, phototropism, and embryogenesis. Several plant-growth promoting bacteria can synthesize IAA, including Bacillus, Burkholderia, and Pseudomonas species. In this study, Burkholderia seminalis strain 869T2 was able to synthesize approximately 2.0 to 2.2 µg mL−1 IAA in the presence of tryptophan and increased both the above ground and below ground biomass of tested plant tissues. Several previous reports also demonstrated that low levels of IAA stimulated primary root growth. Similar to our observations, the Burkholderia sp. SSG that was isolated from boxwood leaves produced 2.9 to 4.5 µg mL−1 of IAA with tryptophan and had plant growth promotion ability in three boxwood varieties. Additionally, Burkholderia phytofirmans strain PsJN, which was isolated from onion roots, showed higher IAA production, around 12 µg mL−1 , with the addition of tryptophan and improved the growth of potato, tomato, maize, and grapevines. Other Burkholderia seminalis strains can also synthesize IAA and have been reported to increase rice and tomato seedling growth.

These previous studies, along with our observations, suggest that B. seminalis strain 869T2 may be similar to other Burkholderia species and other plant-growth-promoting bacteria that utilize IAA to increase root growth, which may assist host plants in taking up nutrients from the surrounding environment and improve aerial tissue growth. Consistent with this hypothesis, we observed that plant size, height, fresh weight, dry weight, and total leaf areas of several tested plant species all significantly increased after inoculation with B. seminalis strain 869T2. It is known that the IAA can positively affect cell division, enlargement, tissue differentiation, root formation, and the control process of nutrition growth. The IAA can also function as a signal molecule to influence the expression of various genes involved in energy metabolism and other plant hormone synthesis, such as gibberellin and ethylene. Interestingly, we observed earlier flowering in the 869T2-inoculated hot pepper and okra plants, suggesting that acceleration of plant growth rates might occur in these plants. In the future, transcriptome analysis of plant hormone response genes and energy-metabolic-related genes in the 869T2-inoculated plants might help us further decipher the possible mechanism of plant growth promotion ability of strain 869T2. From the results of our study, we observed that B. seminalis strain 869T2 had a better IAA yield at a temperature range of 25 ◦C to 37 ◦C and pH of 6 to 9. Similarly, Burkholderia pyrrocinia strain JK-SH007 reached the maximum production of IAA at 37 ◦C and pH 7.0. Several other plant-growth-promoting bacteria, including Bacillus siamensis, Bacillus megaterium, Bacillus subtilis, and Bacillus cereus, had relatively higher IAA yields at temperatures of 2–135 ◦C and pH 7–8. Three different bacteria isolated from therhizosphere of Stevia rebaudiana also exhibited greater production of IAA at a pH range of 6–9 and a temperature of 35 ◦C to 37 ◦C; these bacteria also increased the root and shoot bio-masses of wheat and mung bean.

Various carbon sources are used as an energy source for IAA production and could enhance recycling of cofactors in bacterial cells. Our results revealed that IAA yields of B. seminalis strain 869T2 were slightly better when glucose and fructose were used in media. Several previous publications also indicated that the ability of plant-growth-promoting bacteria to produce IAA was different, depending on the carbon source used in the media. Results from these studies and our study demonstrated that IAA production by different plant-growth promoting bacteria can be influenced by various factors, such as temperature, pH, carbon sources, culture conditions, and bacterial species. In this study, we utilized the colorimetric method to estimate the IAA amounts of B. seminalis strain 869T2 when grown in various in vitro conditions and media. Because the available tryptophan in the rhizosphere and root exudates of plants might be relatively lower than the tryptophan used in the media, the IAA production of B. seminalis strain 869T2 when grown in inoculated plants shall be determined with more sensitive and accurate methods, such as high-performance liquid chromatography or ultra-performance liquid chromatography systems. Apart from the IAA production ability of B. seminalis strain 869T2, this bacterium exhibited siderophore production and phosphate solubilization activities.Most iron in soils is present in the highly insoluble ferric form,vertical plant rack which is unavailable for plant absorption. Endophytic bacteria can yield iron-chelating agents such as siderophores, which bind ferric iron and help transport it into plant cells via root-mediated degradation of organic chelate, ligand exchange, or other mechanisms. Phosphorus is another essential macro-nutrient for numerous metabolism processes in plants, such as biosynthesis of macromolecules, signal transduction, photosynthesis, and respiration. Most of the phosphorus in soil is insoluble and not available for root uptake to support plant growth. In order to increase the bio-availability of phosphorus for plants, certain endophytic bacteria turn insoluble phosphate into soluble forms via the processes of chelation, ion exchange, acidification, or production of organic acids. Previous studies have also correlated siderophore production and phosphate solubilization abilities with the plant growth promotion traits of other Burkholderia species, such as the Burkholderia sp. SSG isolated from boxwood and the Burkholderia sp. MSSP isolated from root nodules of Mimosa pudica. Burkholderia cenocepacia strain CR318, which was isolated from maize roots, significantly enhanced maize plant growth by solubilizing inorganic tricalcium phosphate. Other studies have revealed that additional Burkholderia species also have the ability to solubilize inorganic phosphate to increase available phosphorous in agricultural soils and improve agricultural production. In summary, both previous studies and our results suggest that the IAA synthesis, siderophore production, and phosphate solubilization abilities of B. seminalis strain 869T2 may collectively contribute to the growth enhancement observed in the several plant species tested here.

We successfully inoculated and reisolated B. seminalis strain 869T2, which was originally isolated from the monocot plant vetiver grass, in several eudicot plant species of the Brassicaceae, Asteraceae, Amaranthaceae, Solanaceae, and Malvaceae families. Strain 869T2 can significantly improve the growth of both the roots and aerial parts of Arabidopsis and several leafy vegetables, including ching chiang pak choi, pak choi, loose-leaf lettuce, romaine lettuce, red leaf lettuce, and Chinese amaranth. These results suggest that the endophytic bacterium strain 869T2 may have a wide host range. A similar observation was reported for Burkholderia phytofirmans strain PsJN, first isolated from onion roots, which enhanced the growth of Arabidopsis, switch-grass, potato, tomato, maize, wheat, and grapevines. We did not observe significant growth improvement in hot pepper or okra plants after inoculation with strain 869T2; however, we did observe early flowering and better fruit development in these tested plants. These results suggest that the plant growth promotion abilities of strain 869T2might be more apparent in crops with a shorter life cycle or that the latter two tested host plant species might not be fully compatible with this bacterium. The plant colonization process and growth promotion abilities of endophytic bacteria seem to be active processes that are regulated by different characteristics of both the host plants and bacteria. In conclusion, our study revealed the potential of Burkholderia seminalis strain 869T2 for use as a bio-inoculant in agriculture to improve plant growth and production. The balance between C3 carbon fixation and photorespiration depends on the relative amounts of CO2 and O2 entering the active site of Rubisco and the specificity of the enzyme for each gas. Atmospheric concentrations of CO2 and O2 are currently 0.04% and 20.94%, respectively, yielding a CO2 :O2 ratio of 0.0019. Gaseous CO2 , however, is much more soluble in water than O2 , and so the CO2 :O2 ratio near the chloroplast, the part of a cell where these reactions occur, is about 0.026 at 25°C. Rubisco has about a 50-fold to 100-fold greater specificity for CO2 than O2. Together, because of the relative concentrations of and specificity for CO2 over O2 , Rubisco catalyzes about two to three cycles of C3 carbon fixation for every cycle of photorespiration under current atmospheres. Conditions that inhibit photorespiration—namely, high CO2, or low O2 atmospheric concentrations—stimulate carbon fixation in the short term by about 35%. Temperature influences the balance between C3 carbon fixation and photo respiration in two ways. First, as temperature rises, the solubility of CO2 in water decreases more than the solubility of O2, resulting in a lower CO2:O2 ratio. Second, the enzymatic properties of Rubisco shift with increasing temperature, stimulating the reaction with O2 to a greater degree than the one with CO2. Warmer temperatures, therefore, favor photo respiration over C3 carbon fixation, and photosynthetic conversion of absorbed light into sugars becomes less efficient. Based on the temperature response of Rubisco carboxylation and oxygenation, C4 plants should be more competitive in regions where the mean monthly air temperature exceeds 22°C. Overall, Rubisco seems a vestige of the high CO2 and low O2 atmospheres under which plants first evolved. To compensate for the shortcomings of Rubisco, some plants employ CO2 pumping mechanisms such as C4 carbon fixation that elevate CO2 concentrations at the active site of the enzyme. The C4 pathway is one of the most convergent evolutionary adaptations in life with at least 66 independent origins. Extensive efforts are underway to emulate Mother Nature and transfer the C4 pathway into rice and other C3 crops. Explanations for the decline in plant protein concentrations at elevated CO2 include: plants under elevated CO2 grow larger, diluting the protein within their tissues ; carbohydrates accumulate within leaves, down-regulating the amount of the most prevalent protein Rubisco ; carbon enrichment of the rhizosphere leads to progressively greater limitations in the soil N available to plants ; and elevated CO2 directly inhibits plant N metabolism, especially the assimilation of NO3 – into proteins in shoots of C3 plants. Recently, several independent meta-analyses conclude that this last explanation is the one most consistent with observations from hundreds of studies. Information about the biochemistry of RuBP oxygenation is limited.

Hemicellulose polymers both rigidly associate with cellulose fibrils and extend into the matrix environment where they exhibit significant molecular motion and can interact with lignin polymers in the secondary plant cell wall.Differences across monocot and eudicot plant species have been observed, such as variable substitution patterns on hemicellulose which can dictate cellulose hemicellulose association morphology for arabinose substitutions.The details of lignin structure are particularly challenging to analyze due to high heterogeneity and mobility, so partial extraction of the polymer is often necessary for assessment.Lignin is a polyphenolic network formed from the oxidative cross linking of the monolignols p-coumaryl alcohol , coniferyl alcohol , and sinapyl alcoholas well as Ferulic Acid.Lignin exists within the plant cell matrix, interfacing with both hemicellulose and cellulose.61 Solution-state NMR in combination with MS, which relies on swelling ball-milled plant cell walls with deuterated solvents, provides detailed information on the types, functionalization, and abundance of lignin linkages present.However, due to the necessity for drying, mechanical treatment, dissolution, or solvent extraction in these techniques, previous work does not report on recalcitrance in the intact secondary plant cell wall.NMR is inherently an atomic resolution technique,vertical farming hydroponic as the observed signals derive from nuclear spin magnetic moments located at precise locations in the molecules under study.

In contrast to solution-state NMR, which requires solubilization of the sample, solid-state NMR methods allow for analysis of intact plant tissues.The cost of implementing solid-state NMR limited early studies of the plant cell walls.Access to cost effective 13C labeling has contributed to the feasibility of understanding plant cell walls with solid state NMR.The requirement of NMR-active13C isotopes was a major hurdle for characterizations of native plant cell wall structure.13C has a low natural abundance and the cost of early efforts at isotope incorporation restricted their use.Relatively low13C enrichment enabled early studies on hardwood.The ability to detect the relative populations of rigid polymers was then applied to samples of pure cellulose and heterogeneous assemblies containing cellulose including paper products, cotton, wood chips, and pulp.While early X-ray diffraction studies demonstrated the crystalline nature of cellulose in plant cell walls,solid-state NMR measurements provided more detail, such as the pattern of hydrogen bond interactions responsible for the macroscopic shape of in situ cellulose fibers.A set of 1D cross polarization measurements was successfully applied to crystalline cellulose in birch and spruce biomass and offered the possibility of detecting exterior and interior cellulose components in macroscopic cellulose fibers.These straightforward 1D experiments were also useful for characterizing amorphous cellulose after ionic liquid processing of crystalline cellulose fibrils.The 2D cross polarized refocused Incredible Natural Abundance Double Quantum Transfer Experiment reports on directly bonded carbon atoms within polymers and has been useful for probing rigid structures, for example, resolving carbons and 5 signals of cellulose in Populus euramericana hardwood samples and characterizing the structure of amorphous cellulose.A breakthrough occurred when a highly efficient method of 13C incorporationwas coupled with multi-dimensional solid-state NMR to investigate the primary plant cell wall structure.This series of studies provided both a compositional and architectural description of the primary plant cell wall.

Hemicellulose-cellulose interactions were found to be much less prevalent in the primary plant cell wall than suggested by earlier models based on solvent extracted hemicellulose and enzymatic hemicellulose digestion studies.Furthermore, it was also revealed that the hemicellulose xyloglucan interacts mainly with the flat surfaces of crystalline cellulose fibers,expanding on the idea of xyloglucan associating, cross linking, and embedding into cellulose fibrils.Semiquantitative distance measurements recorded with the Proton Driven Spin Diffusion experiments substantiated the organization of cellulose, xyloglucan, and pectin in primary cell walls of both monocot and eudicot cell species.These advances in 13C enrichment allowed the use of advanced solid-state NMR approaches shaping the primary plant cell wall architecture and how secondary plant cell wall architecture could be approached with solid-state NMR.The strategy of 13C glucose feeding is not suitable to the study of the secondary plant cell wall because the plants need to be grown to relative maturity and complicated by respiration-dependent glucose synthesis.The development of less expensive growth chambers, utilizing 13C enriched carbon dioxide as the sole carbon source, which support the growth of plants throughout their life cycle, enabled the efficient incorporation of 13C isotopesin to plant tissues.Multidimensional solid-state NMR revealed significant differences in the dominant hemicellulose-cellulose contacts in different plant species.For example, in eudicot Arabidopsis thaliana , 2-fold screw conformations of hemicellulose xylan , dictated by even patterns of substitutions, enable a close association with crystalline cellulose.In contrast, in monocot sorghum, the high degree and irregularity of arabinose substitution patterns on xylan dictate a 3-fold screw conformation,enabling association with amorphous cellulose.Additionally, in softwoods, cellulose fibrils can be tethered by both xylan and mannan hemicellulose, increasing the strength of the plant cell wall.

For the sorghum case, limitations in biochemical techniques prevent the analysis of carbohydrate substitutions on xylan and the solid-state NMR measurements which can show the xylan-cellulose interaction that is otherwise unobtainable using other methods.Carbon dioxide 13C labeling and new applications of advanced solid-state NMR techniques have helped elucidate the structure of lignin in the secondary plant cell wall.Signal enhancement by dynamic nuclear polarization demonstrated that lignin directly bridges hemicellulose polymers and interacts strongly with cellulose fibers in uniformly labeled switch grass, highlighting the role of lignin in supporting the 3D organization of hemicellulose and cellulose.However, effective penetration of the DNP reagent into the plant cell wall for this signal enhancement required 15–20 min of milling,which could perturb native lignin structure.Direct polarization experiments utilizing PDSD performed on 13C enriched poplar stems highlight a potential avenue to probe lignin contacts and spatial proximities through selective excitation and magnetization transfer from lignin to other polymers,which provide support for the putative organization of lignin in poplar,switch grass,and Arabidopsis.Further development of selective excitation and other solid-state NMR methods to probe biomass with minimal sample manipulation have the potential to provide a more complete picture of the secondary plant cell wall structure and how established sample preparation methods influence that structure.Although a wide variety of solid-state NMR methods can be applied to highly 13C enriched plant tissues, two methods provide rapid and straightforward characterization of the polymer organization in the secondary plant cell wall.First,vertical planters for vegetables the INADEQUATE approach provides an avenue for the characterization of the polymers present within a secondary cell wall sample at relatively high resolution and can distinguish at least three populations of amorphous and crystalline cellulose, in addition to three populations of xylan.Second, 13C-13C recoupling methods, such as PDSD and Dipolar Assisted Rotational Resonance , report on the spatial proximity of cellulose, hemicellulose, and lignin.

Polymers free, dynamic, and in the plant cell matrix are captured by the refocused Incredible Nuclear Enhancement by Polarization Transfer experiment.Lower power proton decoupling is used in the rINEPT so polymers only with high intrinsic mobilityare detectable.The rINEPT experiment techniques share commonalities with solution state NMR experiments used to evaluate lignin content in deconstruction efforts and marks an upper limit of dynamic polymers which can be captured with solid-state NMR.These experiments provide a more complete picture of the polymers in the plant cell wall than has ever been obtainable before.In plants, cellulose fibrils have genetically and environmentally determined sizes so continuous fibrils change their direction and length resulting in nonuniform fibril orientations in plant tissues.Amorphous cellulose is important in the plant cell wall because they support cellulose fibril junctions so fibrils can change directions and adapt in tissues.For plant cellulose fibrils , only a fraction of the cellulose polymers have perfect hydrogen bonding patterns and order associated with crystalline cellulose.Crystalline cellulose is predicted to be more digestible in deconstruction by hydrolases for chemicals like HMF.Amorphous cellulose polymers in plant cellulose fibrils are associated with indigestible material and treated as a marker for recalcitrance.However there is still ambiguity regarding if the amorphous cellulose is recalcitrant due to being out of register cellulose within the polymer assembly.Considering enzyme digestion, the current consensus correlates the amorphous cellulose content within fibrils with recalcitrance,which can be correlated with a crystallinity index.Hemicellulose, the 1-O-4 linked linear polysaccharides contributing to the structural strength of the plant cell wall, interacts with both lignin and cellulose.The role of hemicellulose as a tethering component within the plant cell wall was first proposed in the primary plant cell wall structure and coheres with mechanical strength of plants provided by the secondary plant cell wall.Past deconstruction methods targeting hemicellulose resulted in higher recalcitrance.Even with ionic liquid digestion, early NMR studies with pulsed sequences show decreased lignin yields and increase in amorphous cellulose.Structural hemicellulose associating with amorphous cellulose fibril surfaces concerns recalcitrance when more amorphous cellulose surfaces form upon mechanical processing as predicted by milled cellulose fibrils in cotton.Structural hemicellulose also cross links with lignin upon plant maturity which greatly complicates digestion of roughly 60% of the secondary plant cell wall.In fact, hemicellulose-first deconstruction methods were largely abandoned due to high observed recalcitrance and supported the switch for deconstruction techniques to focus on lignin first extraction from the secondary plant cell wall.Finally, lignin is critical to the plant and plant development within all species,and high lignin content is associated with recalcitrance.High ratio of G/S lignin is attributed to greater heterogeneity and branching patterns within lignin networks and thus correlated with recalcitrance.Past correlations of recalcitrance outputs to the order in which polymers are digested have directed many deconstruction techniques to a “lignin first” model.Unfortunately, lignin also plays a vital role in plant water transport, pathogenic protection, and maturity; many mutations aimed at eliminating lignin are lethal to the organism.The complexity and insolubility of plant cell wall samples often requires heavy sample manipulation in deconstruction.However, whether recalcitrance is introduced in sample preparation of plant biomass conversion to bio-products is a complicated issue to address given the major discrepancies between lab and industrial processes.An immediate motivation to adopt more systematic approaches is the energy investments differing between the lab and industrial scale.This can become problematic in cases involving massive solvent extraction techniques and other preprocessing techniques as energy does not always scale from laboratorial to industrial settings.One example is the frequently used mechanical preprocessing at the lab scale which often proves to be too energetically expensive at the industrial scale.So, tracking assumptions and changes in the native plant cell wall structure behind the discrepancies is critical so that lab scale optimizations can benefit industrial applications.Mechanical preprocessing is commonly used to reduce biomass particle size to increase solvent accessibility and polymer solubilization.Lab scale vibratory ball-milling achieves this goal by rapidly vibrating a chamber containing lignocellulosic biomass with grinding balls.Importantly, past studies on the plant cell wall structure used mechanical milling to prepare samples for analysis,so the outcomes have been influenced by non-native interactions and contacts between these polymers.However, milling leading to recalcitrance is frequently reported during lignocellulosic biomass conversion efforts, impeding the efficiency of subsequent processing and separation steps.Common preprocessing sample preparations taken before specific deconstruction methods should be under investigation because of the potential for introducing wide spread recalcitrance.Mechanical preprocessing leading to recalcitrance is reported during lignocellulosic deconstruction pathways at the lab scale, which impedes the efficiency of subsequent steps in biomass processing.Milling induced recalcitrance could be due to the production of reactive lignin species promoting aberrant hemicellulose-lign in crosslinks as the lignin self-associates and condenses, resulting in polymers which may be less accessible for digestion.Additionally, increased amorphous cellulose content and exposed cellulose surfaces produced from milling cellulose fibrils5 could induce reorganization of hemicellulose-cellulose contacts due to their multiple modes of interaction in the native plant cell wall.Although the cost of applying milling to biomass as a technique on an industrial scale makes it energetically impractical to apply, the impact of potential recalcitrance induction during lab scale methods development could still influence efforts in developing deconstruction pathways and estimating their effectiveness.One recent study on milling cellulose fibrils offers potential insight into what happens to cellulose fibrils.Cellulose fibrils are nonuniformly oriented in the plant cell wall which results in irregular signal detection making some spectroscopic techniques challenging on intact material.Cellulose fibrils scatter light nonlinearly because crystalline cellulose belongs to a noncentro symmetric crystal group.Milling pure cellulose in cotton allowed for easier sample orientation which is important in the Ling et al.2019 study contrasting 13 different techniques to study crystallinity, including x-ray scattering techniques, vibrational spectroscopy and 1D CP solid-state NMR.In the study, Field-Emission Scanning Electron Microscopywas used to monitor sample morphology for cotton milled between 15–120 minutes at 30 Hz.

Looking back, several research and developmental organizations have contributed significantly to the reclamation and management of salt-affected lands.But they have been mostly working in isolation without interdisciplinary efforts.Considering the magnitude and complexity of the salinity problem, a holistic multidisciplinary and networking approach is required using a systems approach to tailor technologies across scales from the field to the district and the whole ecosystem.Moreover, key policy impediments must be addressed for rapid technology dissemination.These include effective involvement of stakeholders at the community level, provision of incentives such as subsidies and cost sharing, and enacting new laws that enforce reclamation requirements for maintenance and operation of SSD.Web-based platforms should be created to interface among policy planners, researchers, state agricultural departments and development boards, farmer’s associations, self-help groups and NGO’s.These will serve principally to ensure multi-stakeholder input when making decisions on the development and implementation of technologies, thereby accelerating the reclamation rate of saline-sodic soils.The State of Israel was established in 1948 and Israel’s recent history has been heavily influenced by the 1950 Law of Return,danish trolley granting Jewish people the right to immigrate to and settle in the country.Israel’s climate is arid to semi-arid, with two-thirds of its area being desert.

The average annual precipitation ranges from 25 mm in the Negev Desert, to about 300 mm in the coastal plains to 800 mm in the Upper Galilee region, occurring almost exclusively in the winter, between November and March.About two-thirds of the country’s fresh water supply has traditionally come from groundwater pumped from two major aquifers , with the other one-third coming from the Sea of Galilee, fed largely from the upper Jordan river.To ensure equitable distribution and efficient use of the available water resources, already in 1949 Israel enacted a legislative code that made water a public property that is under State control, with water licensing issued by its Water Commission.In order to supply water to Israel’s south, the National Water Carrier was built in the 1960s.About 50–55% of total consumed water is used for irrigation.However, to meet domestic and industrial freshwater demands, the fraction of natural freshwater used for irrigated agriculture has decreased from about two-thirds to currently about one-third.To supplement irrigation water needs, some 60%of the irrigation water supply now comes from treated wastewater and brackish groundwater.Finally, to ensure an adequate future water supply, Israel has embarked on building large-scale seawater desalination plants.In Israel, interest in soils and salts comes mostly from water scarcity and subsequent irrigation-induced salinity.The Israeli experience in salinity management of soils involves three unique intersecting aspects making the lessons learned of interest globally.The three aspects are:early and full adoption of highly efficient irrigation technologies including drip irrigation and knowledge driven scheduling,considerable amounts of relatively high salinity water from brackish groundwater and recycled municipal wastewater utilized for irrigation, and the recent large-scale move to desalination of seawater to insure national municipal water security that has led to reduction of salts in the water system, especially in recycled wastewater.

The lessons learned from Israel’s historical irrigation water policies and practices have been reviewed and discussed by Assouline et al., Tal , Siegel , and Raveh and Ben-Gal.Here we summarize in terms of salinity and soils.Israel is a small country with a relatively solid economic base, but isolated due to geo-political reality, and unique as a water-scarce country with successful agricultural development.Water consumption from all sources and for all sectors in Israel increased tenfold from 230 MCM in 1948 to 2200 MCM in 2018.It is estimated that only 55–65% of the present amount of the country’s water needs is renewed annually in its natural surface and groundwater resources.The remaining water supplied comes from groundwater mining, allocation of reclaimed wastewater, or by seawater desalination.While per capita consumption in the domestic and industrial sectors has remained essentially the same during these last decades, per capita water available for agricultural uses is less than half today than it was in the 1960s.Despite the reduction in water allocation, agricultural production per capita today is more than 150% of that produced 40 years ago.The success can be credited to several central driving principles including:intensification and modernization of agricultural systems;development and adoption of efficient water application technologies and methodologies; and establishment of reliable water sources for irrigation.Intensification and modernization of agriculture were accomplished in Israel by strong research and development programs, knowledge transfer to farmers by means of a solid extension service, and strong government economic support of national strategies.Drip irrigation was developed in Israel where this inherently efficient technology is used at rates higher than anywhere else in the world.Technologies and practices promoting water efficiency have further been encouraged by national water pricing and allocation strategies.

Utilization of low-quality water has been encouraged through a water for irrigation pricing structure where cost to farmers goes down as irrigation water salinity increases.The third principle stimulating success, a reliable source of water for irrigation, has been more difficult to accomplish.The NWC has historically conveyed water from the Sea of Galilee in the north to the south of Israel, seasonally mixing it on the way with various ground and floodwater sources.Average EC of the NWC water has historically ranged from 0.8 to 1.1 dS/m.Freshwater use in agriculture dropped from 950 MCM in 1998 to around 490 MCM today.Total water to agriculture has been maintained via the utilization of brackish and recycled water.Israel’s agriculture directly uses some 80 MCM of brackish groundwater with EC of more than 2 dS/m for irrigation, mainly in arid regions including along the Jordan Valley and the Arava and the Negev Highlands.Wastewater recycling has become a central component of Israel’s water management strategy.A master plan presented in 1956 envisioned the ultimate recycling of 150 MCM of sewage, all of which would go to agriculture.Today four times that level is recycled,vertical aeroponic tower garden representing around 85% of all domestic wastewater produced.Treated effluents today contribute roughly 25–30% of Israel’s total water supply and, depending on annual rainfall, up to 40% of the irrigation supply for agriculture.Salinity of recycled wastewater, depending on its type and origin, can range dramatically, but no matter what, salinity increases as the wastewater stream advances.In Israel, municipal recycled wastewater typically ranges from EC of1 to more than 3 dS/m.Israel’s agriculture directly uses some 80 MCM of brackish groundwater with EC of more than 2 dS/m for irrigation, mainly in arid regions including along the Jordan Valley and the Arava and the Negev Highlands.Wastewater recycling has become a central component of Israel’s water management strategy.A master plan presented in 1956 envisioned the ultimate recycling of 150 MCM of sewage, all of which would go to agriculture.Today four times that level is recycled, representing around 85% of all domestic wastewater produced.Treated effluents today contribute roughly 25–30% of Israel’s total water supply and, depending on annual rainfall, up to 40% of the irrigation supply for agriculture.Salinity of recycled wastewater, depending on its type and origin, can range dramatically, but no matter what, salinity increases as the wastewater stream advances.In Israel, municipal recycled wastewater typically ranges from EC of1 to more than 3 dS/m.Unfortunately, due to the high concentrations of salts in the irrigation water, Israel’s strategy for agricultural success seems to be not sustainable.Long-term application of salts to agricultural soils in a region where seasonal rainfall is low, unpredictable, and often insufficient to systematically mobilize and remove problematic salts, must include application of water designated to leach the accumulating salts out of the root zone.The water applied for leaching and leaving the root zone contains not only the salts that must be leached, but also various other contaminants, found naturally in the water, added in agricultural processes , or mobilized from soil and subsoil.

An example of problematic sustainability stemming from policy and practice of irrigation with water high in salts is found in the Arava desert where brackish groundwater is used to irrigate green and netho use protected vegetables.It is estimated that irrigation to leach salts in the region can be beneficial to yields and profits at rates as high as twice those necessary to satisfy crop evapotranspiration requirements.Regarding continued use of effluents or other salt-rich sources for irrigation water, additional indications of problems are found.These include the long-term increases in sodium adsorption ratio and exchangeable sodium percentage in soils , affecting soil structure and water infiltrability, a trend of increasing sodium and chloride found in irrigated plant tissues, and the tendency for Israeli fresh produce to have higher than international standards of sodium.In addition, there are increasing concerns regarding possible yet undiscovered detrimental long-term repercussions due to trace level contaminants in agricultural systems and the food chain.Despite all this, the latest responses of Israel to insure reliable municipal water supply to its growing population may coincidentally provide opportunity for a more sustainable solution for agriculture.Starting in 2007, Israel has added desalinated seawater to its water distribution stream.Desalination currently provides around 25% of Israel’s total water supply, as more than 40% of the country’s municipal water, often incidentally bringing very good quality water to agricultural areas and consistently reducing the salinity of recycled wastewater.Planned large-scale desalination in The Red Sea, as part of a project to stabilize Dead Sea water level by transporting the brine, would bring a significant amount of good quality water to replace current irrigation with brackish water to Israel.The Red-Dead conduit project, if funded and built, would additionally promote regional strategies for treating water scarcity and salinity together with Jordan and the Palestinian Authority.The turn to desalination as a strategy for water security is a positive opportunity to reverse the maybe dangerous and apparently non-sustainable trends consequential to irrigation with water containing high concentrations of salts.Treatment of brackish groundwater and of water specifically destined for irrigation may in the future benefit from technologies that, contrary to the current popular reverse osmosis based desalination, will selectively remove problematic monovalent ions while leaving agricultural desirable bivalent ions like calcium and magnesium.Israel is projecting that by 2050, two-third of its water supplies will come from treated effluent, desalinized or brackish water.Sustainable, healthy, economical, irrigated agriculture in Israel and other semi-arid and arid regions should be possible if the salts are taken out before application, instead of being allowed to negatively affect soils, crops, produce, and the environment.Latin America is a cultural entity extending from the Rio Grande in North America, to Tierra del Fuego, at the southernmost tip of South America.It is a vast area, spanning for 19.2 million km2 and home for approximately 650 million inhabitants, including countries with diverse availability of natural resources and economies.The Latin languages Spanish and Portuguese are the main tongues in the region, although English, French and Dutch are also spoken.This extensive territory features a huge variety of climates and soils, which lead to a great variability of ecosystems, and support an array of agricultural, livestock and forestry activities.Tropical to temperate/ cold crops are cultivated in it.Globally, the region is a net food exporter of a variety of primary products like grains , coffee, vegetables, and fruits, etc., and industrialized derivatives as sugar, vegetable oil, and wine.Unfortunately, estimations of the extension and distribution of salt-affected soils in Latin America are neither updated nor very precise, and partially based on expert judgment.Soil salinity and alkalinity are found in diverse environments throughout the region and include both primary and secondary salinity.Some estimations indicate that an area of about 7 105 km2 is affected by salinity and 6 105 km2 by sodicity, for a total salinized area of 1.3 suggest a total area of 1.7 106 km2 , however, other area estimations 106 km2.The total irrigated area is around 25–30 Mha.It is estimated that 25–50% of that area is affected by human-induced secondary salinization and sodification, adding approximately 4–5 Mha of recent human-induced salinization processes in non-irrigated areas.Primary salinization processes occur in the humid and sub-humid regions where natural saline, but mainly sodic soils are found.They are found in large plains with shallow saline or sodic ground-waters like the Chaco-Pampas regions, which are among the flattest sedimentary plains of the planet and a major grain exporter of the continent.

The new breeding lines are then tested in different soil types in different climatic zones within the regions of release, to ensure no yield penalty of the salt-tolerance gene.This approach of crossing and selection is usually done using molecular markers: DNA fragments that are associated with the trait.Selection for the trait itself is more laborious and expensive.Conventional breeding—For centuries, farmers in countries with extensive soil salinity have long been selecting best yielding crops for their land, as have the more recent commercial breeding companies.If their soil contains salt, they have selected salt-tolerant material without specifically intending to do so.An example is the salt-tolerant bread wheat Kharchia, which forms the basis of most of the salt-tolerant bread wheat germplasm released in India and Pakistan.Kharchia 65 is a land race developed from selections in farmers’ fields in the sodic-saline soils of the Kharchi-Pali area of Rajasthan.We do not yet know the physiological or molecular basis of the salt tolerance of Kharchia.For bread wheat a summary by Naeem et al.listed 14 varieties or land races under commercial production in India, Pakistan, Egypt and China.All of these were produced by conventional breeding.For rice, derivatives of the land races Pokkali or Nona Bokra which occur in the coastal regions of southern India have formed the basis of salt-tolerant rice cultivars.Ismail and Horielist 27 cultivars that have been released for salt tolerance between 2007 and 2014 for Bangladesh, the Philippines and India.These have been developed by conventional selection and breeding.The two most significant cultivars are CSR 36 for salt-affected soils in India, and BRRI Dhan 10 for soils inundated by seawater in coastal Bangladesh.We know the molecular basis of some of this salt tolerance: the presence of specific alleles of the Na+ transporter OsHKT1;5 that enhance Na+ exclusion.

These were identified in Nona Bokra as the QTL SKC1 and identified in Pokkali as the genomic region Saltol which encompasses OsHKT1;5.Molecular markers are now being used to accelerate breeding and to pyramid salt tolerance with other traits relevant to saline soils such as water logging tolerance.Trait-based breeding—A lack of fast and reliable screening methods has been the major limitation to exploring large germplasm collections,round plastic pots selecting genotypes with greater salt tolerance than the current cultivars, and introducing the salt tolerance into breeders’ advanced breeding lines for release of a new salt-tolerant cultivar.Munns and James summarized the various methods used in the laboratory or glasshouse to select for salt tolerance, along with their advantages and disadvantages.The simplest method is that of screening at germination as it is such a quick and easy test for large numbers of genotypes.However, for most species there is little or no correlation between genotypic differences in germination and genotypic differences in later growth or yield.The most reliable and useful method has been to measure rates of Na+ or Cl
accumulation in leaves, selecting individuals with low rates of accumulation.Ideally, biomass or grain yield should be the ultimate criterion for salt tolerance.Selections of various genotypes of pasture species like clover or alfalfa can conveniently be done in hydroponics or sand cultures with added salt, as cuts can be made every 6–8 weeks for replications.Cereals are more difficult to assess as grain yield needs to be measured in saline soil in the field, as does the yield of perennial horticultural species like citrus and grapevine.However, field experiments are plagued by heterogeneities in soil texture and surface elevation and its associated effect on soil salinity and compaction over short distances by influencing soil water deficits or water logging.This heterogeneity makes validation of breeding trials difficult as soil salinity varies greatly over area and depth.Soil salinity under each of a thousand or so breeding plots needs to be measured by electromagnetic induction with a simple-to-use meter such as Geonics EM38 after calibration.Incorporation of plot EC as a co-variant in the statistical analysis was essential to finding durum wheat genotypes and bread wheat and barley genotypes with higher yield in saline soil.

Over the last 20 years, selection of new salt-tolerant germplasm and its use in subsequent breeding has depended on traits and molecular markers for traits, which can be obtained from genetic analysis as Quantitative Trait Loci or by Genome Wide Association Studies.For many crop species, genetic variation in ion exclusion correlates highly with salt tolerance, and screening based on the measurement of ion accumulation in leaves is the most precise and effective form of selection, being quantitative and non-destructive.Examples include Na+ exclusion from leaves of durum wheat and rice.As an example, we describe a successful project on introduction of genes for salt tolerance from a wheat relative into a durum wheat cultivar, using molecular markers for the trait of Na+ exclusion.Durum wheat lacks the gene for Na+ exclusion found in bread wheat.Using the screening method of Na+ exclusion from leaves among 60 durum wheat relatives, Na+ exclusion equal to bread wheat was found in an unusual durum genotype named Line 149.Line 149 was crossed with the durum cultivar Tamaroi which had five times the leaf Na+ concentration and subsequent genetic analysis showed that Na+ exclusion was due to two genes that were named Nax1 and Nax2.Further crossing enabled separation of the two genes, which were identified as HKT1 transporters.Field trials in multiple sites showed that Nax2 increased yield on highly saline soil by 25% without affecting yield on better soils.However, Nax1 had a yield penalty that outweighed its advantage as a Na+ excluder.This yield penalty had not been obvious in glasshouse trials but became significant in the field.Phenomics—For crop species where a trait is multi-genic and covering different chromosome regions, molecular markers have limited value and selection is driven by phenomics.High-throughput phenotyping methods, now employed in the field as well as in the laboratory, allow large numbers of plants to be screened efficiently with limited handling and labor.Screening for salt tolerance in species which do not have a selectable salt-specific trait is only feasible using non-destructive methods.Such methods include biomass growth as assessed by photosynthesis, stomatal conductance, chlorophyll fluorescence and spectral reflectance.

Using color imaging along with nondestructive measurements of the leaf area and growth rate of each plant, it is possible to separate the effects of salinity on new leaf production from the acceleration of senescence and death of old leaves.Imaging allows the short-term osmotic effects on plant growth to be distinguished from the longer-term ionic effects.Infrared thermography is a widely used phenomic tool to detect differences between genotypes in soilless culture, pots, and field plots.In addition, hyperspectral imaging is used to quantify differences in water status and photosynthetic capacity and to detect genotypic differences in salinity tolerance, for example,hydroponic bucket among wheat cultivars after anthesis.Most candidate genes so far discovered and proven to be part of the mechanism of salt tolerance are membrane transporters for Na+, K+ or Cl.Few transcription factors have a known function, either in the downstream target genes, or the cells or tissues in which they operate.Genes involved in signaling pathways are not known to be specific for salinity but have commonalities with other abiotic stresses that reduce growth rate like drought, heat and cold.Transgenics—Use of the Arabidopsis genome has greatly accelerated the sequencing and functional analysis of candidate genes.In total there have been about 7300 papers on salt tolerance involving Arabidopsis.For the six main crop plants there are 9200.How much of this work has led to improving salt tolerance of crops in the field? A summary of 27 genes that have been over expressed in various crop species with “reported plant transgenic performance during salt stress” is listed by Roy et al.in their table 1, but with three exceptions, these transgenics have not been tested in the field or handed over to commercial plant breeders.In a review of genetic engineering for salinity tolerance in wheat , a list of 45 publications on wheat transformed with genes from other species, or other species transformed with genes from wheat, showed only one that included performance in the field; over expression of AtNHX1 improved grain yield of bread wheat.A notable success story is with barley: over expression of AVP1 increased biomass and yield in both non-saline and saline soil.Over expression of genes for accumulation of organic molecules that act as osmolytes such as proline have been studied for decades, but no cultivar has been released with enhanced proline accumulation that improves yield on saline soils.To date, QTL continues to be the main tool of genetic analysis for breeders, yet very few pre-breeding efforts have led to production of salt-tolerant cultivars.Similarly, the early optimism for GWAS to discover new loci for salinity tolerance and their subsequent utilization in varietal development is still not realized.

Success in has been hampered by lack of quantitative and repeatable measurements of the value of the trait to plant growth and yield in saline soil and selection of the best parents for QTL analysis or genotype array.Further research into selection techniques and germplasm diversity is needed.Key genes for Na+ transporters presented in Section 10.2 should be studied using species other than Arabidopsis.Crop species that are amenable to transformation and do not have complex genomes should be used.Omics methodologies should use relevant treatments, such as a gradual and moderate salt stress, not a severe and sudden one.Osmotic shocks cause plasmolysis and induce the synthesis of enzymes that repair the trauma caused to cells by their sudden shrinkage which may take at least 24 h to repair.Gene expression patterns are very different when the stress is imposed gradually compared to a salt shock.Cell-specific and tissue-specific expression is critical for the function of transporters and transcription factors, so studies should consider this should, for example, separately analyze growing from mature tissues.As take-up of genes for salt tolerance by commercial crop breeders has been so slow, and few studies arising with model plants such as Arabidopsis have been validated in the field, there is a high priority to engage plant breeders at an early stage of the project, working along with physiologists, molecular biologists and agronomists.Only then will molecular biology translate to the field and reach crop production targets.There are clear opportunities to make substantial yield gains by targeting basic strategic research, especially by utilizing pre-breeding results of undomesticated varieties, to improve abiotic stress tolerance of crops.Additional recommendations for future research include to use pre-breeding approaches seeking salt tolerance traits, rather than focus on model plants such as Arabidopsis.Also, while research at the cell level is likely to advance our physiological understanding of salt tolerance mechanisms, in parallel significant investments should be made at the field-level, employing the latest in phenotyping methodology.Summary: Unexplored and under-utilized biodiversity exists within crop species and their close relatives, which could be used to improve germplasm for crop production on salt-affected land, without resorting to GM methods that are at present unaccepted in many countries.Ongoing advances in rapid generation turnover, improved phenotyping, envirotyping and analytical methods can increase the rate of genetic gain in breeding.Further understanding of mechanisms at the molecular and physiological level will complement these new technologies and provide farmers with alternatives to increasing crop production on saline land.While genetic improvements cannot provide a permanent solution to increasing soil salinity, and salt-tolerant crops cannot de-salinize the land, a 10% increase in yield may double the famer’s profits, where the profit margin is small.In most of the salt-affected regions with dominance of sodium salts, salinity and sodicity are related, but they are different in terms of their effects on soil environments.“Salinity,” usually measured as total soluble salt concentration, affects plant growth and productivity through osmotic effects and ion toxicity or deficient effects on plant physiological processes.“Sodicity,” generally defined by soil ESPor SARof soil solution, causes constraints to plant growth through its effects on soil physical properties.Natural climatic and soil processes can lead to the formation of sodic soils from saline soils.In irrigated agriculture, the use of sodium containing waters leads to sodic soils by the adsorption of sodium by soils.Sodic soils with low salt concentration undergo structural degradation when wet because of swelling and clay dispersion, causing reduced water and air transport in near-surface soils and to limitations in soil aeration and infiltration.The effects of sodicity on soil physical properties are modified by soil salinity levels.

The soil salinity map derived from this updated Soils database is presented in Fig.5and is available on the FAO website.This updated information was largely needed to plan for land use changes that came about because of rising urban cities and growing rural populations, and to curb associated land degradation by erosion, pollution, salinity, as well as biodiversity losses.More recently, FAO through the Intergovernmental Technical Panel on Soils published the Status of the World’s Soil Resources report , intended to serve as a reference document on the status of global soil resources to support studies of regional assessment of soil change.It also contains a synthesis report for policy makers that summarizes its findings, conclusions, and recommendations.The SWSR report identifies the likely rapid increase of salt-affected soils globally and estimates that currently each year some 0.3–1.5Mha of farmland is taken out of production because of soil salinity problems.The SWSR report also states that about half of the total currently salt-affected soils are further decreasing their production potential.Annual economic costs were estimated to be about US $440 per ha of salt-induced agricultural land.Currently available maps continue to be out-of-date and too coarse for predicting trends on soil salinization.Global estimates of salinization combine different regional estimates that are not necessarily compatible.It is already noted that percentages vary widely between various literature sources.Across the world,fodder growing system countries and regions typically apply different soil classification systems, and as a result the definition of saline or sodic soils varies, thus changing the acreage of salt-affected lands.

A harmonized soil salinity classification system is needed that is universally applied.Gathering accurate, up-to-date information is critical for developing policies to halt the trend of increasing soil salinity across the world and regionally.Efforts to develop an updated and harmonized global soil salinity map were recently initiated by FAO through the Global Soil Partnership or GSP , through mapping of soil EC, SAR, and pH using existing country-level data.Soil salinity and the increase in areal extent is a serious global threat to agricultural production as soil degradation jeopardizes reaching a food-secure world.The only database that currently provides soil salinity data with global coverage is the Harmonized World Soil Database, but it is outdated and has several limitations when assessing changes in soil salinity and its areal extent.Except for a few country-focused reports, there is limited information on the world’s changing extent of salinized soils.Therefore, we recommend taking steps toward a new assessment.There are various reasons to suggest that the areal extent of soil salinization is increasing as well as becoming more severe.Information on such trends is extremely relevant as global and national policies on land use are being developed to advance Sustainable Development Goalsand to mitigate and/or adapt to climate change.Moreover, areas of salt-affected irrigated lands are inconclusive and vary between 25% and 50%depending on the data source.Soil salinization may be accelerating for several reasons including the changing climate.Rising temperatures increase soil evaporation and crop water requirements, enhancing soil salinization in areas already prone for salinity.Especially, coastal regions will be subjected to increasing risk of salinization by rising seawater levels, thereby pushing more saltwater into coastal aquifers, and increasing groundwater salinity.In addition, the likelihood of extreme storms and tsunamis can cause flooding of seawater, resulting in saltwater infiltration into soils and contaminating groundwater resources.

In his analysis of climate change impacts on soil salinization processes, Corwin states that the consequences of climate change have been overlooked and that changes in soil salinity extent will need to be monitored and mapped.He suggests that both proximal and remote sensors are the best methods to achieve this in a timely manner.Another reason that the area of saline soils is expanding relates to the increased use of marginal waters for irrigation, as decreased freshwater availability encourages application of treated wastewater or low salinity water for irrigation.Also, changing land uses from prime agricultural land to residential development promotes cultivation of more marginal lands, thereby enhancing the potential for land degradation.Furthermore, the decreasing availability of freshwater promotes more efficient irrigation methods such as drip and sprinkler irrigation, leading to reduced leaching of accumulated soil salts in regions with limited winter rains.Yet, to meet the world’s demand for nutritious food with the rising population, one may expect a further increase in irrigated area, especially in regions where freshwater availability is adequate.Lastly, salts accumulate over extended periods of continuous irrigation, thus further causing more salinity-prone areas over time.A universal global soil salinity map can be achieved using satellite imagery, soil properties maps, other land surface information, and advanced data analysis methods such as machine learning techniques.A recent example of such an approach was taken by Ivushkin et al., supported by the International Soil Reference and Information Centre.In their work, a total of six soil salinity maps were produced for 1986, 2000, 2002, 2005, 2009, 2016, using thermal IR imagery data from Landsat satellites.Their analysis presented a clear trend over this 20-year period, indicating that the global area of salt-affected soils increased from about 900 to 1000Mha, at an annual rate of about 2–5Mha/year.Various limitations of their methodology were given, including the need for higher spatial resolution, more ground truth data for regions with sparse data, uncertainty associated with temperature response due to plant variations in salt tolerance, and potential improvement using machine learning techniques.Salt-affected soils have significant impacts on the environment, freshwater availability, and agricultural production.Updated maps are needed to quantify soil salinization rates and to inform country level and new international policies and strategies to protect soils from further salinization.We urge prioritizing development of remote sensing instruments for future satellite missions that focus on observing spatial and temporal changes in land degradation, including soil erosion and salinity, at a global scale.

Detecting and monitoring soil salinity across agricultural regions is needed for inventorying soil resources; for identifying trends and drivers in salinization; and for judging the effectiveness of reclamation and conservation programs.Due to the impracticality of directly measuring root zone ECex over large areas , most regional-scale salinity assessment research has focused on alternative measures of salinity obtained through aerial photography and satellite remote sensing.Despite being developed many decades ago, remote detection of salinity has not been widely used in salinity monitoring programs and has achieved only limited success to date.However, methodological and technological advances made over the last 20 years suggest the routine use of remote sensing for monitoring agricultural salinity may be possible.Two approaches to remote salinity detection have been used: indirect and direct.With indirect methods, the level of root zone salinity is inferred based on crop growth and health,chicken fodder system usually as indicated by canopy spectral reflectance or thermographic data.The reflectance of certain visible or infrared spectra generally differs for healthy and stressed leaves.Thus, if a correlation between root zone ECex and spectral response can be established, regression or classifier models can be developed to quantify or label soil salinity levels in a remote sensing image.Direct methods detect salinity in bare soils based on the reflectance properties of surface salts and crusts.Sections of landscapes with and without surface salts can be distinguished due to the high reflectance of salt covered areas in the visible part of the spectrum.Within salt covered areas, salinity levels and salt types may be differentiated because of the effects that salt abundance, mineralogy, moisture, color, and surface crusting and roughness all have on reflectance.The direct approach is useful for assessing salt marshes and other highly saline, non-agricultural landscapes, as well as for tracking encroachment or appearance of barren, high salinity areas in dryland pastures and range lands.However, it has less utility for agricultural regions because of the presence of extensive vegetation.Therefore, we focus on indirect RS methods for soil salinity monitoring.By the middle of the 20th century, aerial photography and image analysis were touted as a means of inventorying crops and detecting disease.Portable or airborne spectral reflectance instruments did not exist, but laboratory measurements made on tissues from leaves in varying states of distress could reveal, for a given crop and development stage, the portion of the spectrum most sensitive to variations in leaf health.Aerial photographs sensitive to the identified spectral range could then be made using an appropriate combination of film and lens filter.

Through analysis of the aerial images, it was proposed that areas with healthy and diseased plants could be distinguished.Myers et al.were the first to connect aerial images of crops with root zone salinity.Working in Texas cotton fields, Myers et al.found that the salinity level in the 0.3–1.2m soil layer could be correlated with the spectral reflectance of cotton leaves, determined from aerial photographs using infrared film and a dark red filter that was sensitive at 675–900μm wavelengths.In a subsequent paper, Myers et al.reported it was possible to distinguish five levels of salinity and to estimate with reasonable accuracy the degree of salinity in the soil profile.It was also found that soil salinity could be predicted with reasonable accuracy from leaf temperatures measured with an infrared radiometer.Thomas et al.examined in greater detail the spectral reflectance of salt-affected cotton leaves and found that they changed during the growing season.At most wavelengths, percent reflectance from individual leaves was negatively correlated with salinity early in the year and positively correlated later.Multiple regression analyses of aerial image density indicated that under field conditions reflectance was influenced by soil salinity and percentage ground cover.The Landsat program and launch of the first operational Landsat satellite in 1972 spurred interest in using multi-spectral satellite imagery for natural resource management.Notable early examples of using space borne aircraft to detect salinity include identifying salt flats in Imperial Valley, California from photo images taken aboard Apollo 9and distinguishing saline from non-saline rangelands in South Texas using Skylab satellite imagery.The review of Metternicht and Zinck covers advances made during this period with respect to direct observation of visible surface salts.With the growing availability of multi-spectral reflectance data from satellites and other platforms, it became common from the 1970s onward to quantify multi-band canopy reflectance using vegetation indices such as the Normalized Difference Vegetation Index, NDVI¼/ , where R and NIR are spectral reflectance in the visible red and near-infrared bands, respectively.Wiegand et al.used imaging data from the SPOT-I satellite to evaluate the relationship of NDVI and the Greenness Vegetation Index to plant growth and yield in a single salt-affected, irrigated cotton field in Texas.Later, Wiegand et al.determined NDVI and GVI for four cotton fields in San Joaquin Valley , California using airborne photographic imagery made with multiple lens filters.Regression equations with NDVI and GVI as predictor variables were used to estimate salinity at about 100,000 pixels per field.The last 2 decades have seen a steady increase in the availability of remote sensing data, in the capabilities of various sensors and platforms, and in remote sensing applications.Even with improved technologies, a major problem with indirect salinity detection methods is that a single image generally cannot differentiate salinity-induced crop stress from stress caused by other factors such as weather, pests, and water management.Lobell et al.addressed this difficulty by evaluating multi-year data, hypothesizing that soil salinity is relatively constant compared to other more transient stressors.Lobell et al.found that using 6 years of reflectance data greatly improved the correlation between salinity and wheat yield, whereas Lobell et al.successfully evaluated regional-scale salinity using a 7-year average enhanced vegetation index derived from satellite MODIS data.Multi-temporal data was also used by Caccettaand Furby et al.for improved soil salinity classifications.Along the same lines, Zhang et al.used interpolated and integrated vegetation index time-series data as an explanatory variable rather than analyzing single-date data.Whitney et al.later applied the same integrated index method to the SJV and concluded that multi-year data further enhanced correlations with soil salinity.The use of environmental covariates as additional predictor variables in regression equations and classifiers has also improved accuracy.Scudiero et al.developed a linear regression equation for estimating soil salinity using spatial precipitation and temperature data, croptype data, and multi-temporal Landsat 7 ETM+ canopy reflectance data.They calibrated their model using data for thousands of Landsat 7 pixels at 30m resolution across 22 fields for which ground truth salinity data were available.For each 30 30m Landsat pixel, average root zone ECe for a 6-year period was modeled using the Canopy Response Salinity Index, CRSI, which combines spectral reflectance in the green, blue, red, and near-infrared bands.